libSBML
5.16.0
A B C D E F G H I K L M N O P Q R S T U V W X Y Z 

A

add(String) - Method in class org.sbml.libsbml.XMLNamespaces
Appends an XML namespace prefix and URI pair to this list of namespace declarations.
add(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Adds an attribute to this list of attributes.
add(String, String) - Method in class org.sbml.libsbml.XMLNamespaces
Appends an XML namespace prefix and URI pair to this list of namespace declarations.
add(String, String, String) - Method in class org.sbml.libsbml.XMLAttributes
Adds an attribute to this list of attributes.
add(String, String, String, String) - Method in class org.sbml.libsbml.XMLAttributes
Adds an attribute to this list of attributes.
add(ASTNode) - Method in class org.sbml.libsbml.ASTNodeList
 
add(CVTerm) - Method in class org.sbml.libsbml.CVTermList
 
add(Date) - Method in class org.sbml.libsbml.DateList
 
add(ModelCreator) - Method in class org.sbml.libsbml.ModelCreatorList
 
add(SBase) - Method in class org.sbml.libsbml.SBaseList
 
add(SBMLNamespaces) - Method in class org.sbml.libsbml.SBMLNamespacesList
 
add(XMLTriple, String) - Method in class org.sbml.libsbml.XMLAttributes
Adds an attribute to this list of attributes.
addAdditionalDir(String) - Method in class org.sbml.libsbml.SBMLFileResolver
Adds a directory to the list of directories to search for files to resolve.
addAdditionalGraphicalObject(GraphicalObject) - Method in class org.sbml.libsbml.Layout
Adds a new additional graphical object glyph.
addAssociation(Association) - Method in class org.sbml.libsbml.Association
Adds a child Association to this Association object.
addAssociation(FbcAssociation) - Method in class org.sbml.libsbml.FbcAnd
Adds a copy the given FbcAssociation to this FbcAnd.
addAssociation(FbcAssociation) - Method in class org.sbml.libsbml.FbcOr
Adds a copy the given FbcAssociation to this FbcOr.
addAttr(String, String) - Method in class org.sbml.libsbml.XMLToken
Adds an attribute to the XML element represented by this token.
addAttr(String, String, String) - Method in class org.sbml.libsbml.XMLToken
Adds an attribute to the XML element represented by this token.
addAttr(String, String, String, String) - Method in class org.sbml.libsbml.XMLToken
Adds an attribute to the XML element represented by this token.
addAttr(XMLTriple, String) - Method in class org.sbml.libsbml.XMLToken
Adds an attribute to the XML element represented by this token.
addChild(ASTNode) - Method in class org.sbml.libsbml.ASTNode
Adds the given node as a child of this ASTNode.
addChild(XMLNode) - Method in class org.sbml.libsbml.XMLNode
Adds a copy of node as a child of this XMLNode.
addChildElement(Transformation2D) - Method in class org.sbml.libsbml.RenderGroup
Adds a copy of the given element to the end of the list of children elements.
addColorDefinition(ColorDefinition) - Method in class org.sbml.libsbml.RenderInformationBase
Adds a copy of the given color definition to the end of the list of color definitions.
addCompartment(Compartment) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Compartment object to this Model.
addCompartmentGlyph(CompartmentGlyph) - Method in class org.sbml.libsbml.Layout
Adds a new compartment glyph.
addCompartmentType(CompartmentType) - Method in class org.sbml.libsbml.Model
Adds a copy of the given CompartmentType object to this Model.
addConstraint(Constraint) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Constraint object to this Model.
addConverter(SBMLConverter) - Method in class org.sbml.libsbml.SBMLConverterRegistry
Adds the given converter to the registry of SBML converters.
addCreator(ModelCreator) - Method in class org.sbml.libsbml.ModelHistory
Adds a copy of a ModelCreator object to the list of 'model creator' values stored in this ModelHistory object.
addCurveSegment(LineSegment) - Method in class org.sbml.libsbml.Curve
Adds a copy of the given LineSegment to the end of the ListOfLineSegments.
addCVTerm(CVTerm) - Method in class org.sbml.libsbml.SBase
Adds a copy of the given CVTerm object to this SBML object.
addCVTerm(CVTerm, boolean) - Method in class org.sbml.libsbml.SBase
Adds a copy of the given CVTerm object to this SBML object.
addDash(long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Adds a dash at the end of the current list
addDeletion(Deletion) - Method in class org.sbml.libsbml.Submodel
Adds a copy of the given Deletion object to the list of deletions.
addElement(RenderPoint) - Method in class org.sbml.libsbml.Polygon
Adds a copy of the given segment to the end of the list of segments.
addElement(RenderPoint) - Method in class org.sbml.libsbml.RenderCurve
Adds a copy of the given curve segment to the end of the list of curve segments.
addEvent(Event) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Event object to this Model.
addEventAssignment(EventAssignment) - Method in class org.sbml.libsbml.Event
Appends a copy of the given EventAssignment to this Event.
addExpectedAttributes(SWIGTYPE_p_ExpectedAttributes) - Method in class org.sbml.libsbml.Transition
Get the list of expected attributes for this element.
addExtension(SBMLExtension) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Add the given SBMLExtension object to this SBMLExtensionRegistry.
addExternalModelDefinition(ExternalModelDefinition) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Adds a copy of the given ExternalModelDefinition object to the ListOfExternalModelDefinitions.
addFbcAssociation(FbcAssociation) - Method in class org.sbml.libsbml.ListOfFbcAssociations
Adds a copy the given FbcAssociation object to this ListOfFbcAssociations.
addFluxBound(FluxBound) - Method in class org.sbml.libsbml.FbcModelPlugin
Adds a copy of the given FluxBound object to the list of FluxBounds.
addFluxObjective(FluxObjective) - Method in class org.sbml.libsbml.ListOfFluxObjectives
Adds a copy the given FluxObjective to this ListOfFluxObjectives.
addFluxObjective(FluxObjective) - Method in class org.sbml.libsbml.Objective
Adds a copy the given FluxObjective to this Objective.
addFunctionDefinition(FunctionDefinition) - Method in class org.sbml.libsbml.Model
Adds a copy of the given FunctionDefinition object to this Model.
addFunctionTerm(FunctionTerm) - Method in class org.sbml.libsbml.Transition
Adds a copy the given FunctionTerm to this Transition.
addGene(String) - Method in class org.sbml.libsbml.Association
Adds a gene with the given id to the association.
addGeneAssociation(GeneAssociation) - Method in class org.sbml.libsbml.FbcModelPlugin
Adds a copy of the given GeneAssociation annotation object to the list of GeneAssociations.
addGeneProduct(GeneProduct) - Method in class org.sbml.libsbml.FbcModelPlugin
Adds a copy the given GeneProduct to this FbcModelPlugin.
addGeneProduct(GeneProduct) - Method in class org.sbml.libsbml.ListOfGeneProducts
Adds a copy the given GeneProduct to this ListOfGeneProducts.
addGeneralGlyph(GeneralGlyph) - Method in class org.sbml.libsbml.Layout
Adds a new general glyph.
addGlobalRenderInformation(GlobalRenderInformation) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Adds a copy of the given local render information object to the list of local render information objects.
addGradientDefinition(GradientBase) - Method in class org.sbml.libsbml.RenderInformationBase
Adds a copy of the given gradient definition to the end of the list of gradient definitions.
addGradientStop(GradientStop) - Method in class org.sbml.libsbml.GradientBase
Adds a copy of the given GradientStop object to the end of the list of gradient stops.
addGroup(Group) - Method in class org.sbml.libsbml.GroupsModelPlugin
Adds a copy of the given Group to this GroupsModelPlugin.
addGroup(Group) - Method in class org.sbml.libsbml.ListOfGroups
Adds a copy of the given Group to this ListOfGroups.
addId(String) - Method in class org.sbml.libsbml.LocalStyle
Adds another id to the set.
addInitialAssignment(InitialAssignment) - Method in class org.sbml.libsbml.Model
Adds a copy of the given InitialAssignment object to this Model.
addInput(Input) - Method in class org.sbml.libsbml.Transition
Adds a copy the given Input to this Transition.
addL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.LayoutExtension
adds all L2 Extension namespaces to the namespace list.
addL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.RenderExtension
adds all L2 Extension namespaces to the namespace list.
addL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Adds SBML Level 2 namespaces to the namespace list.
addLayout(Layout) - Method in class org.sbml.libsbml.LayoutModelPlugin
Adds a copy of the layout object to the list of layouts.
addLineEnding(LineEnding) - Method in class org.sbml.libsbml.RenderInformationBase
Adds a copy of the given line ending to the end of the list of line endings.
addLocalParameter(LocalParameter) - Method in class org.sbml.libsbml.KineticLaw
Adds a copy of the given LocalParameter object to the list of local parameters in this KineticLaw.
addLocalRenderInformation(LocalRenderInformation) - Method in class org.sbml.libsbml.RenderLayoutPlugin
Adds a copy of the given local render information object to the list of local render information objects.
addMember(Member) - Method in class org.sbml.libsbml.Group
Adds a copy of the given Member to this Group.
addMember(Member) - Method in class org.sbml.libsbml.ListOfMembers
Adds a copy of the given Member to this ListOfMembers.
addModelDefinition(ModelDefinition) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Adds a copy of the given ModelDefinition object to the ListOfModelDefinitions.
addModifiedDate(Date) - Method in class org.sbml.libsbml.ModelHistory
Adds a copy of a Date object to the list of 'modified date' values stored in this ModelHistory object.
addModifier(ModifierSpeciesReference) - Method in class org.sbml.libsbml.Reaction
Adds a given ModifierSpeciesReference object as a product in this Reaction.
addModifier(Species) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a modifier to this reaction
addModifier(Species, String) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a modifier to this reaction
addNamespace(String) - Method in class org.sbml.libsbml.XMLToken
Appends an XML namespace declaration to this token.
addNamespace(String, String) - Method in class org.sbml.libsbml.SBMLNamespaces
Add an XML namespace (a pair of URI and prefix) to the set of namespaces within this SBMLNamespaces object.
addNamespace(String, String) - Method in class org.sbml.libsbml.XMLToken
Appends an XML namespace declaration to this token.
addNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLNamespaces
Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object.
addNestedCVTerm(CVTerm) - Method in class org.sbml.libsbml.CVTerm
Adds a copy of the given CVTerm object to the list of nested CVTerm objects within this CVTerm object.
addObjective(Objective) - Method in class org.sbml.libsbml.FbcModelPlugin
Adds a copy the given Objective to this FbcModelPlugin.
addObjective(Objective) - Method in class org.sbml.libsbml.ListOfObjectives
Adds a copy the given Objective to this ListOfObjectives.
addOption(String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, boolean) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, boolean, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, double) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, double, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, float) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, float, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, int) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, int, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, String, int) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, String, int, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(String, String, String) - Method in class org.sbml.libsbml.ConversionProperties
Adds a new ConversionOption object with the given parameters.
addOption(ConversionOption) - Method in class org.sbml.libsbml.ConversionProperties
Adds a copy of the given option to this properties object.
addOutput(Output) - Method in class org.sbml.libsbml.Transition
Adds a copy the given Output to this Transition.
addOwnedSBMLDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLResolverRegistry
Adds the given SBMLDocument to the registry of SBML documents that will need to be deleted.
addPackageNamespace(String, long) - Method in class org.sbml.libsbml.SBMLNamespaces
Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object.
addPackageNamespace(String, long, String) - Method in class org.sbml.libsbml.SBMLNamespaces
Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object.
addPackageNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLNamespaces
Add the XML namespaces of package extensions in the given XMLNamespace object to the set of namespaces within this SBMLNamespaces object (Non-package XML namespaces are not added by this function).
addParameter(Parameter) - Method in class org.sbml.libsbml.KineticLaw
Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.
addParameter(Parameter) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Parameter object to this Model.
addPort(Port) - Method in class org.sbml.libsbml.CompModelPlugin
Adds a copy of the given Port object to the list of ports.
addProduct(Species) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a product with the given stoichiometry
addProduct(Species, double) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a product with the given stoichiometry
addProduct(Species, double, String) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a product with the given stoichiometry
addProduct(Species, double, String, boolean) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a product with the given stoichiometry
addProduct(SpeciesReference) - Method in class org.sbml.libsbml.Reaction
Adds a given SpeciesReference object as a product in this Reaction.
addQualitativeSpecies(QualitativeSpecies) - Method in class org.sbml.libsbml.QualModelPlugin
Adds a copy of the given QualitativeSpecies object to the list of qual.
addReactant(Species) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a reactant with the given stoichiometry
addReactant(Species, double) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a reactant with the given stoichiometry
addReactant(Species, double, String) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a reactant with the given stoichiometry
addReactant(Species, double, String, boolean) - Method in class org.sbml.libsbml.Reaction
Adds the given species as a reactant with the given stoichiometry
addReactant(SpeciesReference) - Method in class org.sbml.libsbml.Reaction
Adds a given SpeciesReference object as a reactant in this Reaction.
addReaction(Reaction) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Reaction object to this Model.
addReactionGlyph(ReactionGlyph) - Method in class org.sbml.libsbml.Layout
Adds a new reaction glyph.
addReferenceGlyph(ReferenceGlyph) - Method in class org.sbml.libsbml.GeneralGlyph
Adds a new reference glyph to the list.
addReplacedElement(ReplacedElement) - Method in class org.sbml.libsbml.CompSBasePlugin
Adds a copy of the given ReplacedElement object to the list of ReplacedElements.
addResolver(SBMLResolver) - Method in class org.sbml.libsbml.SBMLResolverRegistry
Adds the given resolver to the registry of SBML resolvers.
addResource(String) - Method in class org.sbml.libsbml.CVTerm
Adds a resource reference to this CVTerm object.
addRole(String) - Method in class org.sbml.libsbml.Style
Adds an id to the role list.
addRule(Rule) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Rule object to this Model.
addSemanticsAnnotation(XMLNode) - Method in class org.sbml.libsbml.ASTNode
Adds the given XMLNode as a MathML <semantics> element to this ASTNode.
addSpecies(Species) - Method in class org.sbml.libsbml.Model
Adds a copy of the given Species object to this Model.
addSpeciesGlyph(SpeciesGlyph) - Method in class org.sbml.libsbml.Layout
Adds a new species glyph.
addSpeciesReferenceGlyph(SpeciesReferenceGlyph) - Method in class org.sbml.libsbml.ReactionGlyph
Adds a new species reference glyph to the list.
addSpeciesType(SpeciesType) - Method in class org.sbml.libsbml.Model
Adds a copy of the given SpeciesType object to this Model.
addStyle(GlobalStyle) - Method in class org.sbml.libsbml.GlobalRenderInformation
Adds a copy of a GlobalStyle to the GlobalRenderInformation object.
addStyle(LocalStyle) - Method in class org.sbml.libsbml.LocalRenderInformation
Adds a copy of a LocalStyle to the GlobalRenderInformation object.
addSubGlyph(GraphicalObject) - Method in class org.sbml.libsbml.GeneralGlyph
Adds a new subglyph to the list.
addSubmodel(Submodel) - Method in class org.sbml.libsbml.CompModelPlugin
Adds a copy of the given Submodel object to the list of submodels.
addTextGlyph(TextGlyph) - Method in class org.sbml.libsbml.Layout
Adds a new text glyph.
addTransition(Transition) - Method in class org.sbml.libsbml.QualModelPlugin
Adds a copy of the given Transition object to the list of qual.
addType(String) - Method in class org.sbml.libsbml.Style
Adds a type string to the type list.
addUnit(Unit) - Method in class org.sbml.libsbml.UnitDefinition
Adds a copy of the given Unit to this UnitDefinition.
addUnitDefinition(UnitDefinition) - Method in class org.sbml.libsbml.Model
Adds a copy of the given UnitDefinition object to this Model.
AlgebraicRule - Class in org.sbml.libsbml
An SBML algebraic rule representing 0 = f(W).
AlgebraicRule(long, long) - Constructor for class org.sbml.libsbml.AlgebraicRule
Creates a new AlgebraicRule object using the given SBML level and version values.
AlgebraicRule(SBMLNamespaces) - Constructor for class org.sbml.libsbml.AlgebraicRule
Creates a new AlgebraicRule object using the given SBMLNamespaces object sbmlns.
AllChecksON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnAlgRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnAssignRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnDelay - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnEventAssignment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnFunc - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnInitialAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfComps - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfConstraints - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfEventAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfEvents - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfFuncs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfInitAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfLocalParam - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfMods - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfParams - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfReactions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfRules - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfSpeciesRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfUnitDefs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnListOfUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnLocalParameter - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnModifier - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnParameter - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnPriority - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnRateRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnSBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnSpeciesReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnTrigger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnUnit - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AllowedAttributesOnUnitDefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ANCHOR_BASELINE - Static variable in class org.sbml.libsbml.Text
 
ANCHOR_BOTTOM - Static variable in class org.sbml.libsbml.Text
 
ANCHOR_END - Static variable in class org.sbml.libsbml.Text
 
ANCHOR_INVALID - Static variable in class org.sbml.libsbml.Text
 
ANCHOR_MIDDLE - Static variable in class org.sbml.libsbml.Text
 
ANCHOR_START - Static variable in class org.sbml.libsbml.Text
 
ANCHOR_TOP - Static variable in class org.sbml.libsbml.Text
 
ANCHOR_UNSET - Static variable in class org.sbml.libsbml.Text
 
AND_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AnnotationNotElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AnnotationNotesNotAllowedLevel1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
append(String) - Method in class org.sbml.libsbml.XMLToken
Appends characters to the text content of token.
append(SBase) - Method in class org.sbml.libsbml.ListOf
Adds an item to the end of this ListOf's list of items.
appendAndOwn(SBase) - Method in class org.sbml.libsbml.ListOf
Adds an item to the end of this ListOf's list of items.
appendAnnotation(String) - Method in class org.sbml.libsbml.Model
Appends annotation content to any existing content in the 'annotation' subelement of this object.
appendAnnotation(String) - Method in class org.sbml.libsbml.SBase
Appends the given annotation to the 'annotation' subelement of this object.
appendAnnotation(String) - Method in class org.sbml.libsbml.SpeciesReference
Appends annotation content to any existing content in the 'annotation' subelement of this object.
appendAnnotation(XMLNode) - Method in class org.sbml.libsbml.Model
Appends annotation content to any existing content in the 'annotation' subelement of this object.
appendAnnotation(XMLNode) - Method in class org.sbml.libsbml.SBase
Appends the given annotation to the 'annotation' subelement of this object.
appendAnnotation(XMLNode) - Method in class org.sbml.libsbml.SpeciesReference
Appends annotation content to any existing content in the 'annotation' subelement of this object.
appendFrom(ListOf) - Method in class org.sbml.libsbml.ListOf
Adds a clone of a list of items to this ListOf's list.
appendFrom(ListOf) - Method in class org.sbml.libsbml.ListOfObjectives
Adds a clone of all items in the provided ListOf to this object.
appendFrom(Model) - Method in class org.sbml.libsbml.Model
Copies a given Model object's subcomponents and appends the copies to the appropriate places in this Model.
appendNotes(String) - Method in class org.sbml.libsbml.SBase
Appends the given notes to the 'notes' subelement of this object.
appendNotes(XMLNode) - Method in class org.sbml.libsbml.SBase
Appends the given notes to the 'notes' subelement of this object.
ApplyCiMustBeModelComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ApplyCiMustBeUserFunction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
areEquivalent(UnitDefinition, UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if two UnitDefinition objects are equivalent.
areEquivalent(Unit, Unit) - Static method in class org.sbml.libsbml.Unit
Predicate returning true if Unit objects are equivalent.
areIdentical(UnitDefinition, UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if two UnitDefinition objects are identical.
areIdentical(Unit, Unit) - Static method in class org.sbml.libsbml.Unit
Predicate returning true if two Unit objects are identical.
ArgsToEqNeedSameType - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignmentRule - Class in org.sbml.libsbml
An SBML assignment rule representing x = f(Y).
AssignmentRule(long, long) - Constructor for class org.sbml.libsbml.AssignmentRule
Creates a new AssignmentRule using the given SBML level and version values.
AssignmentRule(SBMLNamespaces) - Constructor for class org.sbml.libsbml.AssignmentRule
Creates a new AssignmentRule using the given SBMLNamespaces object sbmlns.
AssignmentToConstantEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignRuleCompartmentMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignRuleParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignRuleSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AssignRuleStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Association - Class in org.sbml.libsbml
fbc Annotation helper class for “fbc” Version 1.
Association() - Constructor for class org.sbml.libsbml.Association
Creates a new Association objet with the given SBML Level, Version, and “fbc” package version.
Association(long) - Constructor for class org.sbml.libsbml.Association
Creates a new Association objet with the given SBML Level, Version, and “fbc” package version.
Association(long, long) - Constructor for class org.sbml.libsbml.Association
Creates a new Association objet with the given SBML Level, Version, and “fbc” package version.
Association(long, long, long) - Constructor for class org.sbml.libsbml.Association
Creates a new Association objet with the given SBML Level, Version, and “fbc” package version.
Association(Association) - Constructor for class org.sbml.libsbml.Association
Copy constructor.
Association(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.Association
Creates a new Association with the given FbcPkgNamespaces object.
Association(XMLNode, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.Association
Creates a new Association with the given FbcPkgNamespaces object, and constructed to mimic the XMLNode: a '<gene>' node argument will result in a GENE_ASSOCIATION node; an <and> node argument will result in a AND_ASSOCIATION node; an <or> node argument will result in a OR_ASSOCIATION node.
AST_CONSTANT_E - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CONSTANT_FALSE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CONSTANT_PI - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CONSTANT_TRUE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CONSTRUCTOR_OTHERWISE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CONSTRUCTOR_PIECE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_CSYMBOL_FUNCTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_DIVIDE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ABS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCOS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCOSH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCOT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCOTH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCSC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCCSCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCSEC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCSECH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCSIN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCSINH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCTAN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ARCTANH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_CEILING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_COS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_COSH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_COT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_COTH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_CSC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_CSCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_DELAY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_EXP - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_FACTORIAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_FLOOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_LN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_LOG - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_MAX - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_MIN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_PIECEWISE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_POWER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_QUOTIENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_RATE_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_REM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_ROOT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_SEC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_SECH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_SIN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_SINH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_TAN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_FUNCTION_TANH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_INTEGER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LAMBDA - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_AND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_IMPLIES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_NOT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_OR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_LOGICAL_XOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_MINUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_NAME - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_NAME_AVOGADRO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_NAME_TIME - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_ORIGINATES_IN_PACKAGE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_PLUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_POWER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_QUALIFIER_BVAR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_QUALIFIER_DEGREE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_QUALIFIER_LOGBASE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RATIONAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_REAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_REAL_E - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_EQ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_GEQ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_GT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_LEQ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_LT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_RELATIONAL_NEQ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_SEMANTICS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TIMES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_ASTNODE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_BASE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CI_NUMBER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CN_BASE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CN_EXPONENTIAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CN_INTEGER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CN_RATIONAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CN_REAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CONSTANT_NUMBER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CSYMBOL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CSYMBOL_AVOGADRO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CSYMBOL_DELAY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CSYMBOL_RATE_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_CSYMBOL_TIME - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_BASE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_BINARY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_CI - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_LAMBDA - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_NARY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_PIECEWISE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_QUALIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_SEMANTIC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_FUNCTION_UNARY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_TYPECODE_NUMBER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
AST_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ASTNode - Class in org.sbml.libsbml
Abstract Syntax Trees for mathematical expressions.
ASTNode(ASTNode) - Constructor for class org.sbml.libsbml.ASTNode
Copy constructor; creates a deep copy of the given ASTNode.
ASTNodeList - Class in org.sbml.libsbml
 
ASTNodeList() - Constructor for class org.sbml.libsbml.ASTNodeList
 
AvogadroNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

B

BadCsymbolDefinitionURLValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadlyFormedXML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadMathML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadMathMLNodeType - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadProcessingInstruction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLAttributeValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLComment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLDecl - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLDeclLocation - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLDOCTYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLDocumentStructure - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLIDRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLIDValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLPrefix - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BadXMLPrefixValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
basePoint1_X() - Method in class org.sbml.libsbml.RenderCubicBezier
Returns the x value of the first base point of the curve (the one closer to the starting point) as a reference.
basePoint1_Y() - Method in class org.sbml.libsbml.RenderCubicBezier
Returns the y value of the first base point of the curve (the one closer to the starting point) as a reference.
basePoint1_Z() - Method in class org.sbml.libsbml.RenderCubicBezier
Returns the z value of the first base point of the curve (the one closer to the starting point) as a reference.
basePoint2_X() - Method in class org.sbml.libsbml.RenderCubicBezier
Returns the x value of the second base point of the curve (the one further from the starting point) as a reference.
basePoint2_Y() - Method in class org.sbml.libsbml.RenderCubicBezier
Returns the y value of the second base point of the curve (the one further from the starting point) as a reference.
basePoint2_Z() - Method in class org.sbml.libsbml.RenderCubicBezier
Returns the z value of the second base point of the curve (the one further from the starting point) as a reference.
BIOLOGICAL_QUALIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BiolQualifierType_fromString(String) - Static method in class org.sbml.libsbml.libsbml
This method takes a string and returns a biol qualifier representing the string.
BiolQualifierType_toString(int) - Static method in class org.sbml.libsbml.libsbml
This method takes a biol qualifier type code and returns a string representing the code.
BooleanNumericDiscrepancy - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BooleanOpsNeedBooleanArgs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BothAmountAndConcentrationSet - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BothStoichiometryAndMath - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BoundingBox - Class in org.sbml.libsbml
layout A bounding box for an item in a diagram.
BoundingBox() - Constructor for class org.sbml.libsbml.BoundingBox
Default Constructor.
BoundingBox(long) - Constructor for class org.sbml.libsbml.BoundingBox
Default Constructor.
BoundingBox(long, long) - Constructor for class org.sbml.libsbml.BoundingBox
Default Constructor.
BoundingBox(long, long, long) - Constructor for class org.sbml.libsbml.BoundingBox
Default Constructor.
BoundingBox(BoundingBox) - Constructor for class org.sbml.libsbml.BoundingBox
Copy constructor.
BoundingBox(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.BoundingBox
Creates a new BoundingBox object with the given LayoutPkgNamespaces object.
BoundingBox(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.BoundingBox
Constructor.
BoundingBox(LayoutPkgNamespaces, String, double, double, double, double) - Constructor for class org.sbml.libsbml.BoundingBox
Constructor which sets the id, the coordinates and the dimensions to the given 2D values.
BoundingBox(LayoutPkgNamespaces, String, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.BoundingBox
Constructor which sets the id, the coordinates and the dimensions to the given 3D values.
BoundingBox(LayoutPkgNamespaces, String, Point, Dimensions) - Constructor for class org.sbml.libsbml.BoundingBox
Constructor which sets the id, the coordinates and the dimensions to the given values.
BoundingBox(XMLNode) - Constructor for class org.sbml.libsbml.BoundingBox
Creates a new BoundingBox from the given XMLNode
BoundingBox(XMLNode, long) - Constructor for class org.sbml.libsbml.BoundingBox
Creates a new BoundingBox from the given XMLNode
BQB_ENCODES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_HAS_PART - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_HAS_PROPERTY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_HAS_TAXON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_HAS_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_DESCRIBED_BY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_ENCODED_BY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_HOMOLOG_TO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_PART_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_PROPERTY_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_IS_VERSION_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_OCCURS_IN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQB_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_HAS_INSTANCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_IS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_IS_DERIVED_FROM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_IS_DESCRIBED_BY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_IS_INSTANCE_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
BQM_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

C

CannotConvertToL1V1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CannotVerifyUnitsObjectNoMath - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
canonicalize() - Method in class org.sbml.libsbml.ASTNode
Converts this ASTNode to a canonical form.
cast() - Method in class org.sbml.libsbml.double_array
 
cast() - Method in class org.sbml.libsbml.int_array
 
CelsiusNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
cerr - Static variable in class org.sbml.libsbml.libsbml
Stream handle for low-level C++ standard error stream.
CERR - Static variable in class org.sbml.libsbml.OStream
 
changeErrorSeverity(int, int) - Method in class org.sbml.libsbml.XMLErrorLog
Changes the severity override for errors in the log that have a given severity.
changeErrorSeverity(int, int, String) - Method in class org.sbml.libsbml.XMLErrorLog
Changes the severity override for errors in the log that have a given severity.
checkCompatibility() - Method in class org.sbml.libsbml.CobraToFbcConverter
Returns true if the option property to check Level and Version of the source document ('checkCompatibility') is true.
checkConsistency() - Method in class org.sbml.libsbml.SBMLDocument
Performs consistency checking and validation on this SBML document.
checkConsistencyWithStrictUnits() - Method in class org.sbml.libsbml.SBMLDocument
Performs consistency checking and validation on this SBML document using the ultra strict units validator that assumes that there are no hidden numerical conversion factors.
checkInternalConsistency() - Method in class org.sbml.libsbml.SBMLDocument
Performs consistency checking on libSBML's internal representation of an SBML Model.
checkL1Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 1 and can be converted to Level 1.
checkL1Compatibility(boolean) - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 1 and can be converted to Level 1.
checkL2v1Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 1 and can be converted to Level 2 Version 1.
checkL2v1Compatibility(boolean) - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 1 and can be converted to Level 2 Version 1.
checkL2v2Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 2 and can be converted to Level 2 Version 2.
checkL2v2Compatibility(boolean) - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 2 and can be converted to Level 2 Version 2.
checkL2v3Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 3 and can be converted to Level 2 Version 3.
checkL2v3Compatibility(boolean) - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 3 and can be converted to Level 2 Version 3.
checkL2v4Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 4 and can be converted to Level 2 Version 4.
checkL2v5Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 5 and can be converted to Level 2 Version 5.
checkL3v1Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 3 Version 1 and can be converted to Level 3 Version 1.
checkL3v2Compatibility() - Method in class org.sbml.libsbml.SBMLDocument
Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 3 Version 2 and can be converted to Level 3 Version 2.
checkTerm(int) - Static method in class org.sbml.libsbml.SBO
Checks the format of the given SBO identifier, given in the form of the integer portion alone.
checkTerm(String) - Static method in class org.sbml.libsbml.SBO
Checks the format of the given SBO identifier string.
CiCannotReference0DCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CircularDependencyRateOf - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CircularRuleDependency - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
clear() - Method in class org.sbml.libsbml.ListOf
Removes all items in this ListOf object.
clear() - Method in class org.sbml.libsbml.StringSet
 
clear() - Method in class org.sbml.libsbml.XMLAttributes
Removes all attributes in this XMLAttributes object.
clear() - Method in class org.sbml.libsbml.XMLNamespaces
Clears (deletes) all XML namespace declarations in this XMLNamespaces object.
clear(boolean) - Method in class org.sbml.libsbml.ListOf
Removes all items in this ListOf object.
clearAdditionalDirs() - Method in class org.sbml.libsbml.SBMLFileResolver
Removes the list of directories to search for files to resolve.
clearAllElementIdList() - Method in class org.sbml.libsbml.Model
Clears the internal list of the identifiers of all elements within this Model object.
clearAllElementMetaIdList() - Method in class org.sbml.libsbml.Model
Clears the internal list of the metaids of all elements within this Model object.
clearAssociations() - Method in class org.sbml.libsbml.Association
Removes all children of this Association object.
clearAttributes() - Method in class org.sbml.libsbml.XMLToken
Removes all attributes of this XMLToken object.
clearDashes() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Clears all defined dashes.
clearFailures() - Method in class org.sbml.libsbml.SBMLValidator
Clears this validator's list of failures.
clearInstantiation() - Method in class org.sbml.libsbml.Submodel
Delete the instantiated Model, if it exists.
clearLog() - Method in class org.sbml.libsbml.XMLErrorLog
Deletes all errors from this log.
clearNamespaces() - Method in class org.sbml.libsbml.XMLToken
Removes all XML namespace declarations from this token.
clearReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
Removes the saved referenced element, if it had been saved earlier.
clearReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
Remove all ReplacedElements, if any exist.
clog - Static variable in class org.sbml.libsbml.libsbml
Stream handle for low-level C++ standard logging stream.
CLOG - Static variable in class org.sbml.libsbml.OStream
 
cloneObject() - Method in class org.sbml.libsbml.AlgebraicRule
Creates and returns a deep copy of this AlgebraicRule object.
cloneObject() - Method in class org.sbml.libsbml.AssignmentRule
Creates and returns a deep copy of this AssignmentRule object.
cloneObject() - Method in class org.sbml.libsbml.Association
Creates and returns a deep copy of this Association object.
cloneObject() - Method in class org.sbml.libsbml.BoundingBox
Creates and returns a deep copy of this BoundingBox.
cloneObject() - Method in class org.sbml.libsbml.CobraToFbcConverter
Creates and returns a deep copy of this CobraToFbcConverter object.
cloneObject() - Method in class org.sbml.libsbml.ColorDefinition
Creates and returns a deep copy of this ColorDefinition object.
cloneObject() - Method in class org.sbml.libsbml.Compartment
Creates and returns a deep copy of this Compartment object.
cloneObject() - Method in class org.sbml.libsbml.CompartmentGlyph
Creates and returns a deep copy of this CompartmentGlyph.
cloneObject() - Method in class org.sbml.libsbml.CompartmentType
Creates and returns a deep copy of this CompartmentType object.
cloneObject() - Method in class org.sbml.libsbml.CompExtension
Creates and returns a deep copy of this CompExtension object.
cloneObject() - Method in class org.sbml.libsbml.CompFlatteningConverter
Creates and returns a deep copy of this CompFlatteningConverter.
cloneObject() - Method in class org.sbml.libsbml.CompModelPlugin
Creates and returns a deep copy of this CompModelPlugin object.
cloneObject() - Method in class org.sbml.libsbml.CompPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces object.
cloneObject() - Method in class org.sbml.libsbml.CompSBasePlugin
Creates and returns a deep copy of this CompSBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Creates and returns a deep copy of this CompSBMLDocumentPlugin object.
cloneObject() - Method in class org.sbml.libsbml.Constraint
Creates and returns a deep copy of this Constraint object.
cloneObject() - Method in class org.sbml.libsbml.ConversionOption
Creates and returns a deep copy of this ConversionOption object.
cloneObject() - Method in class org.sbml.libsbml.ConversionProperties
Creates and returns a deep copy of this ConversionProperties object.
cloneObject() - Method in class org.sbml.libsbml.CubicBezier
Creates and returns a deep copy of this CubicBezier.
cloneObject() - Method in class org.sbml.libsbml.Curve
Creates and returns a deep copy of this Curve.
cloneObject() - Method in class org.sbml.libsbml.CVTerm
Creates and returns a deep copy of this CVTerm object.
cloneObject() - Method in class org.sbml.libsbml.Date
Creates and returns a deep copy of this Date object.
cloneObject() - Method in class org.sbml.libsbml.DefaultTerm
Creates and returns a deep copy of this DefaultTerm object.
cloneObject() - Method in class org.sbml.libsbml.DefaultValues
Creates and returns a deep copy of this DefaultValues object.
cloneObject() - Method in class org.sbml.libsbml.Delay
Creates and returns a deep copy of this Delay object.
cloneObject() - Method in class org.sbml.libsbml.Deletion
Creates and returns a deep copy of this Deletion object.
cloneObject() - Method in class org.sbml.libsbml.Dimensions
Creates and returns a deep copy of this Dimensions.
cloneObject() - Method in class org.sbml.libsbml.Ellipse
Creates and returns a deep copy of this Ellipse object.
cloneObject() - Method in class org.sbml.libsbml.Event
Creates and returns a deep copy of this Event object.
cloneObject() - Method in class org.sbml.libsbml.EventAssignment
Creates and returns a deep copy of this EventAssignment object.
cloneObject() - Method in class org.sbml.libsbml.ExternalModelDefinition
Creates and returns a deep copy of this ExternalModelDefinition object.
cloneObject() - Method in class org.sbml.libsbml.FbcAnd
Creates and returns a deep copy of this FbcAnd object.
cloneObject() - Method in class org.sbml.libsbml.FbcAssociation
Creates and returns a deep copy of this FbcAssociation object.
cloneObject() - Method in class org.sbml.libsbml.FbcExtension
Creates and returns a deep copy of this FbcExtension object.
cloneObject() - Method in class org.sbml.libsbml.FbcModelPlugin
Creates and returns a deep copy of this FbcModelPlugin object.
cloneObject() - Method in class org.sbml.libsbml.FbcOr
Creates and returns a deep copy of this FbcOr object.
cloneObject() - Method in class org.sbml.libsbml.FbcPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces object.
cloneObject() - Method in class org.sbml.libsbml.FbcReactionPlugin
Creates and returns a deep copy of this FbcReactionPlugin object.
cloneObject() - Method in class org.sbml.libsbml.FbcSBMLDocumentPlugin
Creates and returns a deep copy of this FbcSBMLDocumentPlugin object.
cloneObject() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Creates and returns a deep copy of this FbcSpeciesPlugin object.
cloneObject() - Method in class org.sbml.libsbml.FbcToCobraConverter
Creates and returns a deep copy of this FbcToCobraConverter object.
cloneObject() - Method in class org.sbml.libsbml.FbcV1ToV2Converter
Creates and returns a deep copy of this FbcV1ToV2Converter.
cloneObject() - Method in class org.sbml.libsbml.FbcV2ToV1Converter
Creates and returns a deep copy of this FbcV2ToV1Converter object.
cloneObject() - Method in class org.sbml.libsbml.FluxBound
Creates and returns a deep copy of this FluxBound object.
cloneObject() - Method in class org.sbml.libsbml.FluxObjective
Creates and returns a deep copy of this FluxObjective object.
cloneObject() - Method in class org.sbml.libsbml.FunctionDefinition
Creates and returns a deep copy of this FunctionDefinition object.
cloneObject() - Method in class org.sbml.libsbml.FunctionTerm
Creates and returns a deep copy of this FunctionTerm object.
cloneObject() - Method in class org.sbml.libsbml.GeneAssociation
Creates and returns a deep copy of this GeneAssociation.
cloneObject() - Method in class org.sbml.libsbml.GeneProduct
Creates and returns a deep copy of this GeneProduct object.
cloneObject() - Method in class org.sbml.libsbml.GeneProductAssociation
Creates and returns a deep copy of this GeneProductAssociation object.
cloneObject() - Method in class org.sbml.libsbml.GeneProductRef
Creates and returns a deep copy of this GeneProductRef object.
cloneObject() - Method in class org.sbml.libsbml.GeneralGlyph
Creates and returns a deep copy of this GeneralGlyph.
cloneObject() - Method in class org.sbml.libsbml.GlobalRenderInformation
Creates and returns a deep copy of this GlobalRenderInformation object.
cloneObject() - Method in class org.sbml.libsbml.GlobalStyle
Creates and returns a deep copy of this GlobalStyle object.
cloneObject() - Method in class org.sbml.libsbml.GradientBase
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.GradientStop
Creates and returns a deep copy of this GradientStop object.
cloneObject() - Method in class org.sbml.libsbml.GraphicalObject
Creates and returns a deep copy of this GraphicalObject.
cloneObject() - Method in class org.sbml.libsbml.Group
Creates and returns a deep copy of this Group object.
cloneObject() - Method in class org.sbml.libsbml.GroupsExtension
Creates and returns a deep copy of this GroupsExtension object.
cloneObject() - Method in class org.sbml.libsbml.GroupsModelPlugin
Creates and returns a deep copy of this GroupsModelPlugin object.
cloneObject() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces object.
cloneObject() - Method in class org.sbml.libsbml.Image
Creates and returns a deep copy of this Image object.
cloneObject() - Method in class org.sbml.libsbml.InitialAssignment
Creates and returns a deep copy of this InitialAssignment object.
cloneObject() - Method in class org.sbml.libsbml.Input
Creates and returns a deep copy of this Input object.
cloneObject() - Method in class org.sbml.libsbml.KineticLaw
Creates and returns a deep copy of this KineticLaw object.
cloneObject() - Method in class org.sbml.libsbml.Layout
Creates and returns a deep copy of this Layout.
cloneObject() - Method in class org.sbml.libsbml.LayoutExtension
Creates and returns a deep copy of this LayoutExtension object.
cloneObject() - Method in class org.sbml.libsbml.LayoutModelPlugin
Creates and returns a deep copy of this LayoutModelPlugin object.
cloneObject() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces object.
cloneObject() - Method in class org.sbml.libsbml.LayoutSpeciesReferencePlugin
Creates and returns a deep copy of this LayoutSpeciesReferencePlugin object.
cloneObject() - Method in class org.sbml.libsbml.LinearGradient
Creates and returns a deep copy of this LinearGradient object.
cloneObject() - Method in class org.sbml.libsbml.LineEnding
Creates and returns a deep copy of this LineEnding object.
cloneObject() - Method in class org.sbml.libsbml.LineSegment
Creates and returns a deep copy of this LineSegment.
cloneObject() - Method in class org.sbml.libsbml.ListOf
Creates and returns a deep copy of this ListOf object.
cloneObject() - Method in class org.sbml.libsbml.ListOfColorDefinitions
Creates and returns a deep copy of the ListOfColorDefinitions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Creates and returns a deep copy of this ListOfCompartmentGlyphs.
cloneObject() - Method in class org.sbml.libsbml.ListOfCompartments
Creates and returns a deep copy of this ListOfCompartments object.
cloneObject() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Creates and returns a deep copy of this ListOfCompartmentTypes object.
cloneObject() - Method in class org.sbml.libsbml.ListOfConstraints
Creates and returns a deep copy of this ListOfConstraints object.
cloneObject() - Method in class org.sbml.libsbml.ListOfCurveElements
Creates and returns a deep copy of the ListOfCurveElements object.
cloneObject() - Method in class org.sbml.libsbml.ListOfDeletions
Creates and returns a deep copy of this ListOfDeletions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfDrawables
Creates and returns a deep copy of the ListOfDrawables object.
cloneObject() - Method in class org.sbml.libsbml.ListOfEventAssignments
Creates and returns a deep copy of this ListOfEventAssignments object.
cloneObject() - Method in class org.sbml.libsbml.ListOfEvents
Creates and returns a deep copy of this ListOfEvents object.
cloneObject() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Creates and returns a deep copy of this ListOfExternalModelDefinitions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Creates and returns a deep copy of this ListOfFbcAssociations object.
cloneObject() - Method in class org.sbml.libsbml.ListOfFluxBounds
Creates and returns a deep copy of this ListOfFluxBounds.
cloneObject() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Creates and returns a deep copy of this ListOfFluxObjectives object.
cloneObject() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Creates and returns a deep copy of this ListOfFunctionDefinitions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfFunctionTerms
Creates and returns a deep copy of this ListOfFunctionTerms object.
cloneObject() - Method in class org.sbml.libsbml.ListOfGeneAssociations
Creates and returns a deep copy of this ListOfGeneAssociations.
cloneObject() - Method in class org.sbml.libsbml.ListOfGeneProducts
Creates and returns a deep copy of this ListOfGeneProducts object.
cloneObject() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Creates and returns a deep copy of the ListOfGlobalRenderInformation object.
cloneObject() - Method in class org.sbml.libsbml.ListOfGlobalStyles
Creates and returns a deep copy of the ListOfGlobalStyles object.
cloneObject() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Creates and returns a deep copy of the ListOfGradientDefinitions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfGradientStops
Creates a deep copy of the ListOfGradientStops object.
cloneObject() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Creates and returns a deep copy of this ListOfGraphicalObjects.
cloneObject() - Method in class org.sbml.libsbml.ListOfGroups
Creates and returns a deep copy of this ListOfGroups object.
cloneObject() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Creates and returns a deep copy of this ListOfInitialAssignments object.
cloneObject() - Method in class org.sbml.libsbml.ListOfInputs
Creates and returns a deep copy of this ListOfInputs object.
cloneObject() - Method in class org.sbml.libsbml.ListOfLayouts
Creates and returns a deep copy of this ListOfLayouts.
cloneObject() - Method in class org.sbml.libsbml.ListOfLineEndings
Creates and returns a deep copy of the ListOfLineEndings object.
cloneObject() - Method in class org.sbml.libsbml.ListOfLineSegments
Creates and returns a deep copy of this ListOfLineSegments.
cloneObject() - Method in class org.sbml.libsbml.ListOfLocalParameters
Creates and returns a deep copy of this ListOfLocalParameters object.
cloneObject() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Creates and returns a deep copy of the ListOfLocalRenderInformation object.
cloneObject() - Method in class org.sbml.libsbml.ListOfLocalStyles
Creates and returns a deep copy of the ListOfLocalStyles object.
cloneObject() - Method in class org.sbml.libsbml.ListOfMembers
Creates and returns a deep copy of this ListOfMembers object.
cloneObject() - Method in class org.sbml.libsbml.ListOfModelDefinitions
Creates and returns a deep copy of this ListOfModelDefinitions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfObjectives
Creates and returns a deep copy of this ListOfObjectives object.
cloneObject() - Method in class org.sbml.libsbml.ListOfOutputs
Creates and returns a deep copy of this ListOfOutputs object.
cloneObject() - Method in class org.sbml.libsbml.ListOfParameters
Creates and returns a deep copy of this ListOfParameters object.
cloneObject() - Method in class org.sbml.libsbml.ListOfPorts
Creates and returns a deep copy of this ListOfPorts object.
cloneObject() - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
Creates and returns a deep copy of this ListOfQualitativeSpecies object.
cloneObject() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Creates and returns a deep copy of this ListOfReactionGlyphs.
cloneObject() - Method in class org.sbml.libsbml.ListOfReactions
Creates and returns a deep copy of this ListOfReactions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Creates and returns a deep copy of this ListOfReferenceGlyphs.
cloneObject() - Method in class org.sbml.libsbml.ListOfReplacedElements
Creates and returns a deep copy of this ListOfReplacedElements object.
cloneObject() - Method in class org.sbml.libsbml.ListOfRules
Creates and returns a deep copy of this ListOfRules object.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpecies
Creates and returns a deep copy of this ListOfSpecies object.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Creates and returns a deep copy of this ListOfSpeciesGlyphs.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Creates and returns a deep copy of this ListOfSpeciesReferenceGlyphs.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Creates and returns a deep copy of this ListOfSpeciesReferences object.
cloneObject() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Creates and returns a deep copy of this ListOfSpeciesTypes object.
cloneObject() - Method in class org.sbml.libsbml.ListOfSubmodels
Creates and returns a deep copy of this ListOfSubmodels object.
cloneObject() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Creates and returns a deep copy of this ListOfTextGlyphs.
cloneObject() - Method in class org.sbml.libsbml.ListOfTransitions
Creates and returns a deep copy of this ListOfTransitions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Creates and returns a deep copy of this ListOfUnitDefinitions object.
cloneObject() - Method in class org.sbml.libsbml.ListOfUnits
Creates and returns a deep copy of this ListOfUnits object.
cloneObject() - Method in class org.sbml.libsbml.LocalParameter
Creates and returns a deep copy of this LocalParameter object.
cloneObject() - Method in class org.sbml.libsbml.LocalRenderInformation
Creates and returns a deep copy of this LocalRenderInformation object.
cloneObject() - Method in class org.sbml.libsbml.LocalStyle
Creates and returns a deep copy of this LocalStyle object.
cloneObject() - Method in class org.sbml.libsbml.Member
Creates and returns a deep copy of this Member object.
cloneObject() - Method in class org.sbml.libsbml.Model
Creates and returns a deep copy of this Model object.
cloneObject() - Method in class org.sbml.libsbml.ModelCreator
Creates and returns a deep copy of this ModelCreator object.
cloneObject() - Method in class org.sbml.libsbml.ModelDefinition
Creates and returns a deep copy of this ModelDefinition object.
cloneObject() - Method in class org.sbml.libsbml.ModelHistory
Creates and returns a deep copy of this ModelHistory object.
cloneObject() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Creates and returns a deep copy of this ModifierSpeciesReference object.
cloneObject() - Method in class org.sbml.libsbml.Objective
Creates and returns a deep copy of this Objective object.
cloneObject() - Method in class org.sbml.libsbml.Output
Creates and returns a deep copy of this Output object.
cloneObject() - Method in class org.sbml.libsbml.Parameter
Creates and returns a deep copy of this Parameter object.
cloneObject() - Method in class org.sbml.libsbml.Point
Creates and returns a deep copy of this Point.
cloneObject() - Method in class org.sbml.libsbml.Polygon
Creates and returns a deep copy of the Polygon object.
cloneObject() - Method in class org.sbml.libsbml.Port
Creates and returns a deep copy of this Port object.
cloneObject() - Method in class org.sbml.libsbml.Priority
Creates and returns a deep copy of this Priority object.
cloneObject() - Method in class org.sbml.libsbml.QualExtension
Creates and returns a deep copy of this QualExtension object.
cloneObject() - Method in class org.sbml.libsbml.QualitativeSpecies
Creates and returns a deep copy of this QualitativeSpecies object.
cloneObject() - Method in class org.sbml.libsbml.QualModelPlugin
Creates and returns a deep copy of this QualModelPlugin object.
cloneObject() - Method in class org.sbml.libsbml.QualPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces object.
cloneObject() - Method in class org.sbml.libsbml.RadialGradient
Creates and returns a deep copy of this RadialGradient object.
cloneObject() - Method in class org.sbml.libsbml.RateRule
Creates and returns a deep copy of this RateRule object.
cloneObject() - Method in class org.sbml.libsbml.Reaction
Creates and returns a deep copy of this Reaction object.
cloneObject() - Method in class org.sbml.libsbml.ReactionGlyph
Creates and returns a deep copy of this ReactionGlyph object.
cloneObject() - Method in class org.sbml.libsbml.Rectangle
Creates and returns a deep copy of this Rectangle object.
cloneObject() - Method in class org.sbml.libsbml.ReferenceGlyph
Creates and returns a deep copy of this ReferenceGlyph.
cloneObject() - Method in class org.sbml.libsbml.RenderCubicBezier
Creates and returns a deep copy of the RenderCubicBezier object.
cloneObject() - Method in class org.sbml.libsbml.RenderCurve
Creates and returns a deep copy of the RenderCurve object.
cloneObject() - Method in class org.sbml.libsbml.RenderExtension
Creates and returns a deep copy of this RenderExtension object.
cloneObject() - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
Creates and returns a deep copy of this RenderGraphicalObjectPlugin object.
cloneObject() - Method in class org.sbml.libsbml.RenderGroup
Creates and returns a deep copy of this RenderGroup object.
cloneObject() - Method in class org.sbml.libsbml.RenderLayoutPlugin
Creates and returns a deep copy of this RenderLayoutPlugin object.
cloneObject() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Creates and returns a deep copy of this RenderListOfLayoutsPlugin object.
cloneObject() - Method in class org.sbml.libsbml.RenderPkgNamespaces
Creates and returns a deep copy of this SBMLNamespaces object.
cloneObject() - Method in class org.sbml.libsbml.RenderPoint
Creates and returns a deep copy of this RenderPoint object.
cloneObject() - Method in class org.sbml.libsbml.ReplacedBy
Creates and returns a deep copy of this ReplacedBy object.
cloneObject() - Method in class org.sbml.libsbml.ReplacedElement
Creates and returns a deep copy of this ReplacedElement object.
cloneObject() - Method in class org.sbml.libsbml.Rule
Creates and returns a deep copy of this Rule object.
cloneObject() - Method in class org.sbml.libsbml.SBase
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.SBasePlugin
Creates and returns a deep copy of this SBasePlugin object.
cloneObject() - Method in class org.sbml.libsbml.SBaseRef
Creates and returns a deep copy of this SBaseRef object.
cloneObject() - Method in class org.sbml.libsbml.SBMLConverter
Creates and returns a deep copy of this SBMLConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLDocument
Creates and returns a deep copy of this SBMLDocument object.
cloneObject() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Creates and returns a deep copy of this SBMLDocumentPlugin object.
cloneObject() - Method in class org.sbml.libsbml.SBMLExtension
Creates and returns a deep copy of this SBMLExtension object.
cloneObject() - Method in class org.sbml.libsbml.SBMLFileResolver
Creates and returns a deep copy of this SBMLFileResolver object.
cloneObject() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Creates and returns a deep copy of this SBMLFunctionDefinitionConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLIdConverter
Creates and returns a deep copy of this SBMLIdConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLInferUnitsConverter
Creates and returns a deep copy of this SBMLInferUnitsConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Creates and returns a deep copy of this SBMLInitialAssignmentConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLLevel1Version1Converter
Creates and returns a deep copy of this SBMLLevel1Version1Converter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Creates and returns a deep copy of this SBMLLevelVersionConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLLocalParameterConverter
Creates and returns a deep copy of this SBMLLocalParameterConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLNamespaces
Creates and returns a deep copy of this SBMLNamespaces object.
cloneObject() - Method in class org.sbml.libsbml.SBMLReactionConverter
Creates and returns a deep copy of this SBMLReactionConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLResolver
Creates and returns a deep copy of this SBMLResolver object.
cloneObject() - Method in class org.sbml.libsbml.SBMLRuleConverter
Creates and returns a deep copy of this SBMLLevelVersionConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Creates and returns a deep copy of this SBMLStripPackageConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLUnitsConverter
Creates and returns a deep copy of this SBMLUnitsConverter object.
cloneObject() - Method in class org.sbml.libsbml.SBMLUri
Creates and returns a deep copy of this SBMLUri object.
cloneObject() - Method in class org.sbml.libsbml.SBMLValidator
Creates and returns a deep copy of this SBMLValidator object.
cloneObject() - Method in class org.sbml.libsbml.Species
Creates and returns a deep copy of this Species object.
cloneObject() - Method in class org.sbml.libsbml.SpeciesGlyph
Creates and returns a deep copy of this SpeciesGlyph.
cloneObject() - Method in class org.sbml.libsbml.SpeciesReference
Creates and returns a deep copy of this SpeciesReference object.
cloneObject() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Creates and returns a deep copy of this SpeciesReferenceGlyph.
cloneObject() - Method in class org.sbml.libsbml.SpeciesType
Creates and returns a deep copy of this SpeciesType object.
cloneObject() - Method in class org.sbml.libsbml.StoichiometryMath
Creates and returns a deep copy of this StoichiometryMath object.
cloneObject() - Method in class org.sbml.libsbml.Style
Creates and returns a deep copy of this Style object.
cloneObject() - Method in class org.sbml.libsbml.Submodel
Creates and returns a deep copy of this Submodel object.
cloneObject() - Method in class org.sbml.libsbml.Text
Creates and returns a deep copy of this SBase object.
cloneObject() - Method in class org.sbml.libsbml.TextGlyph
Creates and returns a deep copy of this TextGlyph.
cloneObject() - Method in class org.sbml.libsbml.Transition
Creates and returns a deep copy of this Transition object.
cloneObject() - Method in class org.sbml.libsbml.Trigger
Creates and returns a deep copy of this Trigger object.
cloneObject() - Method in class org.sbml.libsbml.Unit
Creates and returns a deep copy of this Unit object.
cloneObject() - Method in class org.sbml.libsbml.UnitDefinition
Creates and returns a deep copy of this UnitDefinition object.
cloneObject() - Method in class org.sbml.libsbml.XMLAttributes
Creates and returns a deep copy of this XMLAttributes object.
cloneObject() - Method in class org.sbml.libsbml.XMLNamespaces
Creates and returns a deep copy of this XMLNamespaces object.
cloneObject() - Method in class org.sbml.libsbml.XMLNode
Creates and returns a deep copy of this XMLNode object.
cloneObject() - Method in class org.sbml.libsbml.XMLToken
Creates and returns a deep copy of this XMLToken object.
cloneObject() - Method in class org.sbml.libsbml.XMLTriple
Creates and returns a deep copy of this XMLTriple object.
close() - Method in class org.sbml.libsbml.OFStream
 
CNV_TYPE_BOOL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CNV_TYPE_DOUBLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CNV_TYPE_INT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CNV_TYPE_SINGLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CNV_TYPE_STRING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CobraToFbcConverter - Class in org.sbml.libsbml
fbc COBRA to SBML Level 3 “fbc” converter.
CobraToFbcConverter() - Constructor for class org.sbml.libsbml.CobraToFbcConverter
Creates a new CobraToFbcConverter object.
CobraToFbcConverter(CobraToFbcConverter) - Constructor for class org.sbml.libsbml.CobraToFbcConverter
Copy constructor; creates a copy of an CobraToFbcConverter object.
ColorDefinition - Class in org.sbml.libsbml
LibSBML implementation for the ColorDefinition construct from the SBML render extension.
ColorDefinition() - Constructor for class org.sbml.libsbml.ColorDefinition
Creates a new ColorDefinition object with the given SBML level and SBML version.
ColorDefinition(long) - Constructor for class org.sbml.libsbml.ColorDefinition
Creates a new ColorDefinition object with the given SBML level and SBML version.
ColorDefinition(long, long) - Constructor for class org.sbml.libsbml.ColorDefinition
Creates a new ColorDefinition object with the given SBML level and SBML version.
ColorDefinition(long, long, long) - Constructor for class org.sbml.libsbml.ColorDefinition
Creates a new ColorDefinition object with the given SBML level and SBML version.
ColorDefinition(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ColorDefinition
Creates a new ColorDefinition object with the given SBMLNamespaces.
ColorDefinition(RenderPkgNamespaces, short, short, short) - Constructor for class org.sbml.libsbml.ColorDefinition
Constructor which sets the ColorDefinition to the given RGBA values.
ColorDefinition(RenderPkgNamespaces, short, short, short, short) - Constructor for class org.sbml.libsbml.ColorDefinition
Constructor which sets the ColorDefinition to the given RGBA values.
ColorDefinition(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.ColorDefinition
Constructor which sets the ColorDefinition to completely opaque black and sets the id to the given string.
ColorDefinition(RenderPkgNamespaces, String, short, short, short) - Constructor for class org.sbml.libsbml.ColorDefinition
Constructor which sets the ColorDefinition to the given RGBA values and sets the id.
ColorDefinition(RenderPkgNamespaces, String, short, short, short, short) - Constructor for class org.sbml.libsbml.ColorDefinition
Constructor which sets the ColorDefinition to the given RGBA values and sets the id.
ColorDefinition(XMLNode) - Constructor for class org.sbml.libsbml.ColorDefinition
Creates a new ColorDefinition object from the given XMLNode object.
ColorDefinition(XMLNode, long) - Constructor for class org.sbml.libsbml.ColorDefinition
Creates a new ColorDefinition object from the given XMLNode object.
combine(UnitDefinition, UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Combines two UnitDefinition objects into a single UnitDefinition.
Compartment - Class in org.sbml.libsbml
An SBML compartment, where species are located.
Compartment(long, long) - Constructor for class org.sbml.libsbml.Compartment
Creates a new Compartment object using the given SBML level and version values.
Compartment(Compartment) - Constructor for class org.sbml.libsbml.Compartment
Copy constructor.
Compartment(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Compartment
Creates a new Compartment object using the given SBMLNamespaces object sbmlns.
CompartmentGlyph - Class in org.sbml.libsbml
layout A glyph for an SBML compartment.
CompartmentGlyph() - Constructor for class org.sbml.libsbml.CompartmentGlyph
Default Constructor which creates a new CompartmentGlyph.
CompartmentGlyph(long) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Default Constructor which creates a new CompartmentGlyph.
CompartmentGlyph(long, long) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Default Constructor which creates a new CompartmentGlyph.
CompartmentGlyph(long, long, long) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Default Constructor which creates a new CompartmentGlyph.
CompartmentGlyph(CompartmentGlyph) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Copy constructor.
CompartmentGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Constructor.
CompartmentGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Constructor which creates a new CompartmentGlyph with the given id.
CompartmentGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Constructor which creates a new CompartmentGlyph.
CompartmentGlyph(XMLNode) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Creates a new CompartmentGlyph from the given XMLNode
CompartmentGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.CompartmentGlyph
Creates a new CompartmentGlyph from the given XMLNode
CompartmentNotOnL1Reaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompartmentOnReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompartmentShouldHaveSize - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompartmentType - Class in org.sbml.libsbml
A compartment type in SBML Level 2.
CompartmentType(long, long) - Constructor for class org.sbml.libsbml.CompartmentType
Creates a new CompartmentType object using the given SBML level and version values.
CompartmentType(CompartmentType) - Constructor for class org.sbml.libsbml.CompartmentType
Copy constructor; creates a copy of this CompartmentType object.
CompartmentType(SBMLNamespaces) - Constructor for class org.sbml.libsbml.CompartmentType
Creates a new CompartmentType object using the given SBMLNamespaces object sbmlns.
CompartmentTypeNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompartmentTypeNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompAttributeRequiredMissing - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompAttributeRequiredMustBeBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompAttributeRequiredMustBeTrue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompBase - Class in org.sbml.libsbml
comp Convenience class for SBase-derived classes.
CompCircularExternalModelReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompDeletedReplacement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompDeletionAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompDeletionMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompDeletionMustReferOnlyOneObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompDeprecatedDeleteFunction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompDeprecatedReplaceFunction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompDeprecatedSBaseRefSpelling - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompDuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompElementNotInNs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompEmptyLOModelDefs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompEmptyLOReplacedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompExtension - Class in org.sbml.libsbml
comp Base extension class for the package.
CompExtension() - Constructor for class org.sbml.libsbml.CompExtension
Creates a new CompExtension instance.
CompExtension(CompExtension) - Constructor for class org.sbml.libsbml.CompExtension
Copy constructor.
CompExtentConversionMustBeParameter - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompExtModDefAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompExtModDefAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompExtModDefAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompExtModDefBad - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompExtModMd5DoesNotMatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompFlatModelNotValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompFlatteningConverter - Class in org.sbml.libsbml
comp 'Flattens' a model, removing composition.
CompFlatteningConverter() - Constructor for class org.sbml.libsbml.CompFlatteningConverter
Creates a new CompFlatteningConverter object.
CompFlatteningConverter(CompFlatteningConverter) - Constructor for class org.sbml.libsbml.CompFlatteningConverter
Copy constructor.
CompFlatteningNotImplementedNotReqd - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompFlatteningNotImplementedReqd - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompFlatteningNotRecognisedNotReqd - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompFlatteningNotRecognisedReqd - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompFlatteningWarning - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompIdRefMayReferenceUnknownPackage - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidConversionFactorSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidDeletionSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidExtentConvFactorSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidIdRefSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidMD5Syntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidMetaIdRefSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidModelRefSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidNameSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidPortRefSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidSIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidSourceSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidSubmodelRefSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidTimeConvFactorSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompInvalidUnitRefSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLineNumbersUnreliable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLODeletionAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLODeletionsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOExtModDefsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOExtModelDefsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOModelDefsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOModelDefsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOPortsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOPortsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOReplacedElementsAllowedAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOReplaceElementsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOSubmodelsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompLOSubmodelsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompMetaIdRefMayReferenceUnknownPkg - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompModCannotCircularlyReferenceSelf - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompModelFlatteningFailed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompModelPlugin - Class in org.sbml.libsbml
comp Extension of Model.
CompModelPlugin(String, String, CompPkgNamespaces) - Constructor for class org.sbml.libsbml.CompModelPlugin
Creates a new CompModelPlugin object using the given parameters.
CompModelPlugin(CompModelPlugin) - Constructor for class org.sbml.libsbml.CompModelPlugin
Copy constructor.
CompModReferenceMustIdOfModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompModReferenceSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompMustReplaceIDs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompMustReplaceMetaIDs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompMustReplacePackageIDs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompMustReplaceSameClass - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompNoEmptyListOfOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompNoModelInReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompNoMultipleReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompNSUndeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompOneListOfDeletionOnSubmodel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompOneListOfExtModelDefinitions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompOneListOfModelDefinitions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompOneListOfOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompOneListOfReplacedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompOneReplacedByElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompOneSBaseRefOnly - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompParentOfSBRefChildMustBeSubmodel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompPkgNamespaces - Class in org.sbml.libsbml
Set of SBML Level + Version + namespace triples.
CompPkgNamespaces() - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(long) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPkgNamespaces(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.CompPkgNamespaces
 
CompPortAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompPortMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompPortMustReferenceOnlyOneObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompPortReferencesUnique - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompPortRefMustReferencePort - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReferenceMustBeL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedByAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedByMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedByMustRefOnlyOne - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedBySubModelRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedElementAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedElementConvFactorRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedElementDeletionRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedElementMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedElementMustRefOnlyOne - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedElementNoDelAndConvFact - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedElementSameReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedElementSubModelRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompReplacedUnitsShouldMatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompRequiredFalseIfAllElementsReplaced - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompRequiredTrueIfElementsRemain - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompSBasePlugin - Class in org.sbml.libsbml
comp Extension of SBase.
CompSBasePlugin(String, String, CompPkgNamespaces) - Constructor for class org.sbml.libsbml.CompSBasePlugin
Creates a new CompSBasePlugin object using the given parameters.
CompSBasePlugin(CompSBasePlugin) - Constructor for class org.sbml.libsbml.CompSBasePlugin
Copy constructor.
CompSBaseRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompSBaseRefMustReferenceOnlyOneObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompSBMLDocumentPlugin - Class in org.sbml.libsbml
comp Extension of SBMLDocument.
CompSBMLDocumentPlugin(String, String, CompPkgNamespaces) - Constructor for class org.sbml.libsbml.CompSBMLDocumentPlugin
Creates a new CompSBMLDocumentPlugin object using the given parameters.
CompSBMLDocumentPlugin(CompSBMLDocumentPlugin) - Constructor for class org.sbml.libsbml.CompSBMLDocumentPlugin
Copy constructor.
CompSubmodelAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompSubmodelAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompSubmodelAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompSubmodelCannotReferenceSelf - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompSubmodelMustReferenceModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompSubmodelNoEmptyLODeletions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompTimeConversionMustBeParameter - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompUniqueModelIds - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompUniquePortIds - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompUnitRefMustReferenceUnitDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompUnknown - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
CompUnresolvedReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
connectToChild() - Method in class org.sbml.libsbml.BoundingBox
 
connectToChild() - Method in class org.sbml.libsbml.CubicBezier
 
connectToChild() - Method in class org.sbml.libsbml.Curve
 
connectToChild() - Method in class org.sbml.libsbml.Event
 
connectToChild() - Method in class org.sbml.libsbml.GeneralGlyph
 
connectToChild() - Method in class org.sbml.libsbml.GlobalRenderInformation
 
connectToChild() - Method in class org.sbml.libsbml.GradientBase
 
connectToChild() - Method in class org.sbml.libsbml.GraphicalObject
 
connectToChild() - Method in class org.sbml.libsbml.KineticLaw
 
connectToChild() - Method in class org.sbml.libsbml.Layout
 
connectToChild() - Method in class org.sbml.libsbml.LineEnding
 
connectToChild() - Method in class org.sbml.libsbml.LineSegment
 
connectToChild() - Method in class org.sbml.libsbml.ListOf
 
connectToChild() - Method in class org.sbml.libsbml.LocalRenderInformation
 
connectToChild() - Method in class org.sbml.libsbml.Model
 
connectToChild() - Method in class org.sbml.libsbml.Polygon
 
connectToChild() - Method in class org.sbml.libsbml.Reaction
 
connectToChild() - Method in class org.sbml.libsbml.ReactionGlyph
 
connectToChild() - Method in class org.sbml.libsbml.ReferenceGlyph
 
connectToChild() - Method in class org.sbml.libsbml.RenderCurve
 
connectToChild() - Method in class org.sbml.libsbml.RenderGroup
 
connectToChild() - Method in class org.sbml.libsbml.RenderInformationBase
 
connectToChild() - Method in class org.sbml.libsbml.SBase
 
connectToChild() - Method in class org.sbml.libsbml.SBaseRef
 
connectToChild() - Method in class org.sbml.libsbml.SBMLDocument
 
connectToChild() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
connectToChild() - Method in class org.sbml.libsbml.Style
 
connectToChild() - Method in class org.sbml.libsbml.Submodel
 
connectToChild() - Method in class org.sbml.libsbml.UnitDefinition
 
ConstantNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstantSpeciesNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Constraint - Class in org.sbml.libsbml
An SBML constraint, for stating validity assumptions.
Constraint(long, long) - Constructor for class org.sbml.libsbml.Constraint
Creates a new Constraint using the given SBML level and version values.
Constraint(Constraint) - Constructor for class org.sbml.libsbml.Constraint
Copy constructor; creates a copy of this Constraint.
Constraint(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Constraint
Creates a new Constraint using the given SBMLNamespaces object sbmlns.
ConstraintContainsDOCTYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstraintContainsXMLDecl - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstraintMathNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstraintNotInXHTMLNamespace - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConstraintNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
contains(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Returns true if SBMLErrorLog contains an errorId
contains(long) - Method in class org.sbml.libsbml.XMLErrorLog
Returns true if XMLErrorLog contains an errorId
containsChild(String, String) - Method in class org.sbml.libsbml.XMLInputStream
Predicate returning true if a child token of the specified type occurs within a given container element.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.Delay
Predicate returning true if the 'math' expression in this Delay instance contains parameters with undeclared units or literal numbers.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.EventAssignment
Predicate returning true if the math expression of this EventAssignment contains literal numbers or parameters with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if the math expression of this InitialAssignment contains parameters/numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.Rule
Predicate returning true if the math expression of this Rule contains parameters/numbers with undeclared units.
containsUndeclaredUnits() - Method in class org.sbml.libsbml.StoichiometryMath
Predicate returning true if the math expression of this StoichiometryMath object contains literal numbers or parameters with undeclared units.
containsUri(String) - Method in class org.sbml.libsbml.XMLNamespaces
Tests whether the given uri is contained in this set of namespaces.
ConversionFactorMustConstant - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConversionFactorNotInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConversionFactorOnSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ConversionOption - Class in org.sbml.libsbml
A single configuration setting for an SBML converter.
ConversionOption(String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption.
ConversionOption(String, boolean) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for Boolean-type options.
ConversionOption(String, boolean, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for Boolean-type options.
ConversionOption(String, double) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for double-type options.
ConversionOption(String, double, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for double-type options.
ConversionOption(String, float) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for float-type options.
ConversionOption(String, float, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for float-type options.
ConversionOption(String, int) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for integer-type options.
ConversionOption(String, int, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for integer-type options.
ConversionOption(String, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption.
ConversionOption(String, String, int) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption.
ConversionOption(String, String, int, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption.
ConversionOption(String, String, String) - Constructor for class org.sbml.libsbml.ConversionOption
Creates a new ConversionOption specialized for string-type options.
ConversionOption(ConversionOption) - Constructor for class org.sbml.libsbml.ConversionOption
Copy constructor; creates a copy of an ConversionOption object.
ConversionProperties - Class in org.sbml.libsbml
Set of configuration option values for a converter.
ConversionProperties() - Constructor for class org.sbml.libsbml.ConversionProperties
Constructor that initializes the conversion properties with a specific SBML target namespace.
ConversionProperties(ConversionProperties) - Constructor for class org.sbml.libsbml.ConversionProperties
Copy constructor.
ConversionProperties(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ConversionProperties
Constructor that initializes the conversion properties with a specific SBML target namespace.
convert() - Method in class org.sbml.libsbml.CobraToFbcConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.CompFlatteningConverter
Performs the conversion.
convert() - Method in class org.sbml.libsbml.FbcToCobraConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.FbcV1ToV2Converter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.FbcV2ToV1Converter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLIdConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLInferUnitsConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLLevel1Version1Converter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLLocalParameterConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLReactionConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLRuleConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Perform the conversion.
convert() - Method in class org.sbml.libsbml.SBMLUnitsConverter
Perform the conversion.
convert(ConversionProperties) - Method in class org.sbml.libsbml.SBMLDocument
Converts this document using the converter that best matches the given conversion properties.
ConvertibleMathInitialAssignment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
convertStringToXMLNode(String) - Static method in class org.sbml.libsbml.XMLNode
Returns an XMLNode which is derived from a string containing XML content.
convertStringToXMLNode(String, XMLNamespaces) - Static method in class org.sbml.libsbml.XMLNode
Returns an XMLNode which is derived from a string containing XML content.
convertTimeAndExtent() - Method in class org.sbml.libsbml.Submodel
Convert all references to time and extent in the instantiated Model, according to the timeConversionFactor and extentConversionFactor attributes.
convertToSI(Unit) - Static method in class org.sbml.libsbml.Unit
Returns a UnitDefinition object containing the given unit converted to the appropriate SI unit.
convertToSI(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Convert a given UnitDefinition into a new UnitDefinition object that uses SI units.
convertXMLNodeToString(XMLNode) - Static method in class org.sbml.libsbml.XMLNode
Returns a string representation of a given XMLNode.
copyInformationToNestedLists() - Method in class org.sbml.libsbml.GroupsModelPlugin
For nested groups (Member objects that reference a ListOfMembers object), SBO terms, Notes, and Annotation from the parent ListOfMembers applies to the child.
cout - Static variable in class org.sbml.libsbml.libsbml
Stream handle for low-level C++ standard output stream.
COUT - Static variable in class org.sbml.libsbml.OStream
 
createAdditionalGraphicalObject() - Method in class org.sbml.libsbml.Layout
Creates a GraphicalObject object, adds it to the end of the additional graphical objects list and returns a pointer to the newly created object.
createAlgebraicRule() - Method in class org.sbml.libsbml.Model
Creates a new AlgebraicRule inside this Model and returns it.
createAnd() - Method in class org.sbml.libsbml.Association
Creates a new Association of type 'and'.
createAnd() - Method in class org.sbml.libsbml.FbcAnd
Creates a new FbcAnd object, adds it to this FbcAnd's ListOfFbcAssociations and returns the FbcAnd object created.
createAnd() - Method in class org.sbml.libsbml.FbcOr
Creates a new FbcAnd object, adds it to this FbcOr's ListOfFbcAssociations and returns the FbcAnd object created.
createAnd() - Method in class org.sbml.libsbml.GeneProductAssociation
Creates a new 'association' and sets it for this GeneProductAssociation.
createAnd() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Creates a new FbcAnd object.
createAnnotation() - Static method in class org.sbml.libsbml.RDFAnnotationParser
Creates a blank annotation and returns its root XMLNode object.
createAssignmentRule() - Method in class org.sbml.libsbml.Model
Creates a new AssignmentRule inside this Model and returns it.
createAssociation() - Method in class org.sbml.libsbml.GeneAssociation
Creates a new association, sets it to this element and returns it.
createColorDefinition() - Method in class org.sbml.libsbml.RenderInformationBase
Creates a new color definition object without an id.
createCompartment() - Method in class org.sbml.libsbml.Model
Creates a new Compartment inside this Model and returns it.
createCompartmentGlyph() - Method in class org.sbml.libsbml.Layout
Creates a CompartmentGlyph object, adds it to the end of the compartment glyph objects list and returns a pointer to the newly created object.
createCompartmentType() - Method in class org.sbml.libsbml.Model
Creates a new CompartmentType inside this Model and returns it.
createConstraint() - Method in class org.sbml.libsbml.Model
Creates a new Constraint inside this Model and returns it.
createCubicBezier() - Method in class org.sbml.libsbml.Curve
Creates a new CubicBezier and adds it to the end of the list.
createCubicBezier() - Method in class org.sbml.libsbml.GeneralGlyph
Creates a new CubicBezier object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
createCubicBezier() - Method in class org.sbml.libsbml.Layout
Creates a new CubicBezier for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.
createCubicBezier() - Method in class org.sbml.libsbml.Polygon
Creates a new bezier element.
createCubicBezier() - Method in class org.sbml.libsbml.ReactionGlyph
Creates a new CubicBezier object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
createCubicBezier() - Method in class org.sbml.libsbml.ReferenceGlyph
Creates a new CubicBezier object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
createCubicBezier() - Method in class org.sbml.libsbml.RenderCurve
Creates a new bezier element.
createCubicBezier() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new CubicBezier object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
createCurve() - Method in class org.sbml.libsbml.RenderGroup
Creates a curve object and adds it to the end of the list of child elements The new element is owned by the group..
createCVTerms(SBase) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Takes a list of CVTerm objects and creates a the RDF 'Description' element.
createDefaultTerm() - Method in class org.sbml.libsbml.ListOfFunctionTerms
Creates a new DefaultTerm object, adds it to this ListOfFunctionTerms and returns the DefaultTerm object created.
createDefaultTerm() - Method in class org.sbml.libsbml.Transition
Creates a new DefaultTerm object, adds it to this Transition's ListOfFunctionTerms and returns the DefaultTerm object created.
createDefaultValues() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Creates a new DefaultValues object, adds it to this ListOfGlobalRenderInformation object and returns the DefaultValues object created.
createDefaultValues() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Creates a new DefaultValues object, adds it to this ListOfLocalRenderInformation object and returns the DefaultValues object created.
createDelay() - Method in class org.sbml.libsbml.Event
Creates a new, empty Delay, adds it to this Event and returns the Delay.
createDelay() - Method in class org.sbml.libsbml.Model
Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.
createDeletion() - Method in class org.sbml.libsbml.Submodel
Creates a Deletion object, adds it to the end of the deletion objects list and returns a pointer to the newly created object.
createEllipse() - Method in class org.sbml.libsbml.RenderGroup
Creates an ellipse object and adds it to the end of the list of child elements The new element is owned by the group..
createEvent() - Method in class org.sbml.libsbml.Model
Creates a new Event inside this Model and returns it.
createEventAssignment() - Method in class org.sbml.libsbml.Event
Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment.
createEventAssignment() - Method in class org.sbml.libsbml.Model
Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.
createExternalModelDefinition() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Creates a ExternalModelDefinition object, adds it to the end of the ExternalModelDefinition objects list and returns a pointer to the newly created object.
createFluxBound() - Method in class org.sbml.libsbml.FbcModelPlugin
Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.
createFluxObjective() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Creates a new FluxObjective object, adds it to the ListOfFluxObjectives and returns the FluxObjective object created.
createFluxObjective() - Method in class org.sbml.libsbml.Objective
Creates a new FluxObjective object.
createFunctionDefinition() - Method in class org.sbml.libsbml.Model
Creates a new FunctionDefinition inside this Model and returns it.
createFunctionTerm() - Method in class org.sbml.libsbml.Transition
Creates a new FunctionTerm object, adds it to this Transition's ListOfFunctionTerms and returns the FunctionTerm object created.
createGene() - Method in class org.sbml.libsbml.Association
Creates a new Association of type 'and' with a given gene reference.
createGene(String) - Method in class org.sbml.libsbml.Association
Creates a new Association of type 'and' with a given gene reference.
createGeneAssociation() - Method in class org.sbml.libsbml.FbcModelPlugin
Creates a new GeneAssociation annotation object and adds it to the list of GeneAssociation objects and returns it.
createGeneProduct() - Method in class org.sbml.libsbml.FbcModelPlugin
Creates a new GeneProduct object, adds it to this FbcModelPlugin's ListOfGeneProducts and returns the GeneProduct object created.
createGeneProduct() - Method in class org.sbml.libsbml.ListOfGeneProducts
Creates a new GeneProduct object, adds it to the ListOfGeneProducts and returns the GeneProduct object created.
createGeneProductAssociation() - Method in class org.sbml.libsbml.FbcReactionPlugin
Creates a new GeneProductAssociation object and adds it to the FbcReactionPlugin object.
createGeneProductRef() - Method in class org.sbml.libsbml.FbcAnd
Creates a new GeneProductRef object, adds it to this FbcAnd's ListOfFbcAssociations and returns the GeneProductRef object created.
createGeneProductRef() - Method in class org.sbml.libsbml.FbcOr
Creates a new GeneProductRef object, adds it to this FbcOr's ListOfFbcAssociations and returns the GeneProductRef object created.
createGeneProductRef() - Method in class org.sbml.libsbml.GeneProductAssociation
Creates a new 'association' and sets it for this GeneProductAssociation.
createGeneProductRef() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Creates a new GeneProductRef object.
createGeneralGlyph() - Method in class org.sbml.libsbml.Layout
Creates a GeneralGlyph object, adds it to the end of the additional objects list and returns a reference to the newly created object.
createGlobalRenderInformation() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Creates a new local render information object and adds it to the list.
createGradientStop() - Method in class org.sbml.libsbml.GradientBase
Creates a new GradientStop.
createGroup() - Method in class org.sbml.libsbml.GroupsModelPlugin
Creates a new Group object, adds it to this GroupsModelPlugin object and returns the Group object created.
createGroup() - Method in class org.sbml.libsbml.ListOfGroups
Creates a new Group object, adds it to this ListOfGroups object and returns the Group object created.
createGroup() - Method in class org.sbml.libsbml.RenderGroup
Creates an group object and adds it to the end of the list of child elements The new element is owned by the group..
createIdString() - Method in class org.sbml.libsbml.LocalStyle
 
createImage() - Method in class org.sbml.libsbml.RenderGroup
Creates an image object and adds it to the end of the list of child elements.
createInitialAssignment() - Method in class org.sbml.libsbml.Model
Creates a new InitialAssignment inside this Model and returns it.
createInput() - Method in class org.sbml.libsbml.Transition
Creates a new Input object, adds it to this Transition's ListOfInputs and returns the Input object created.
createKineticLaw() - Method in class org.sbml.libsbml.Model
Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.
createKineticLaw() - Method in class org.sbml.libsbml.Reaction
Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' subelement, and returns it.
createKineticLawLocalParameter() - Method in class org.sbml.libsbml.Model
Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
createKineticLawParameter() - Method in class org.sbml.libsbml.Model
Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
createLayout() - Method in class org.sbml.libsbml.LayoutModelPlugin
Creates a new layout object and adds it to the list of layout objects and returns it.
createLinearGradientDefinition() - Method in class org.sbml.libsbml.RenderInformationBase
Creates a new linear gradient definition.
createLineEnding() - Method in class org.sbml.libsbml.RenderInformationBase
Creates a new line ending.
createLineSegment() - Method in class org.sbml.libsbml.Curve
Creates a new LineSegment and adds it to the end of the list.
createLineSegment() - Method in class org.sbml.libsbml.GeneralGlyph
Creates a new LineSegment object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
createLineSegment() - Method in class org.sbml.libsbml.Layout
Creates a new LineSegment for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.
createLineSegment() - Method in class org.sbml.libsbml.ReactionGlyph
Creates a new LineSegment object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
createLineSegment() - Method in class org.sbml.libsbml.ReferenceGlyph
Creates a new LineSegment object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
createLineSegment() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new LineSegment object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
createLocalParameter() - Method in class org.sbml.libsbml.KineticLaw
Creates a new LocalParameter object, adds it to this KineticLaw's list of local parameters, and returns the LocalParameter object created.
createLocalRenderInformation() - Method in class org.sbml.libsbml.RenderLayoutPlugin
Creates a new local render information object and adds it to the list.
createMember() - Method in class org.sbml.libsbml.Group
Creates a new Member object, adds it to this Group object and returns the Member object created.
createMember() - Method in class org.sbml.libsbml.ListOfMembers
Creates a new Member object, adds it to this ListOfMembers object and returns the Member object created.
createModel() - Method in class org.sbml.libsbml.SBMLDocument
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
createModel(String) - Method in class org.sbml.libsbml.SBMLDocument
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
createModelDefinition() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns a pointer to the newly created object.
createModifier() - Method in class org.sbml.libsbml.Model
Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.
createModifier() - Method in class org.sbml.libsbml.Reaction
Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.
createObject(XMLInputStream) - Method in class org.sbml.libsbml.Transition
Create and return an SBML object of this class, if present.
createObjective() - Method in class org.sbml.libsbml.FbcModelPlugin
Creates a new Objective object, adds it to this FbcModelPlugin's ListOfObjectives and returns the Objective object created.
createObjective() - Method in class org.sbml.libsbml.ListOfObjectives
Creates a new Objective object, adds it to the ListOfObjectives and returns the Objective object created.
createOr() - Method in class org.sbml.libsbml.Association
Creates a new Association of type 'or'.
createOr() - Method in class org.sbml.libsbml.FbcAnd
Creates a new FbcOr object, adds it to this FbcAnd's ListOfFbcAssociations and returns the FbcOr object created.
createOr() - Method in class org.sbml.libsbml.FbcOr
Creates a new FbcOr object, adds it to this FbcOr's ListOfFbcAssociations and returns the FbcOr object created.
createOr() - Method in class org.sbml.libsbml.GeneProductAssociation
Creates a new 'association' and sets it for this GeneProductAssociation.
createOr() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Creates a new FbcOr object.
createOutput() - Method in class org.sbml.libsbml.Transition
Creates a new Output object, adds it to this Transition's ListOfOutputs and returns the Output object created.
createParameter() - Method in class org.sbml.libsbml.KineticLaw
Creates a new Parameter object, adds it to this KineticLaw's list of parameters, and returns the Parameter object created.
createParameter() - Method in class org.sbml.libsbml.Model
Creates a new Parameter inside this Model and returns it.
createPoint() - Method in class org.sbml.libsbml.Polygon
Creates a new point element.
createPoint() - Method in class org.sbml.libsbml.RenderCurve
Creates a new point element.
createPolygon() - Method in class org.sbml.libsbml.RenderGroup
Creates a polygon object and adds it to the end of the list of child elements The new element is owned by the group..
createPort() - Method in class org.sbml.libsbml.CompModelPlugin
Creates a Port object, adds it to the end of the port objects list and returns a pointer to the newly created object.
createPriority() - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Creates a new, empty Priority, adds it to this Event and returns the Priority.
createProduct() - Method in class org.sbml.libsbml.Model
Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.
createProduct() - Method in class org.sbml.libsbml.Reaction
Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.
createQualitativeSpecies() - Method in class org.sbml.libsbml.QualModelPlugin
Creates a new qual object and adds it to the list of qual objects and returns it.
createRadialGradientDefinition() - Method in class org.sbml.libsbml.RenderInformationBase
Creates a new radial gradient definition.
createRateRule() - Method in class org.sbml.libsbml.Model
Creates a new RateRule inside this Model and returns it.
createRDFAnnotation() - Static method in class org.sbml.libsbml.RDFAnnotationParser
Creates a blank RDF element suitable for use in SBML annotations.
createRDFAnnotation(long) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Creates a blank RDF element suitable for use in SBML annotations.
createRDFAnnotation(long, long) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Creates a blank RDF element suitable for use in SBML annotations.
createReactant() - Method in class org.sbml.libsbml.Model
Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
createReactant() - Method in class org.sbml.libsbml.Reaction
Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.
createReaction() - Method in class org.sbml.libsbml.Model
Creates a new Reaction inside this Model and returns it.
createReactionGlyph() - Method in class org.sbml.libsbml.Layout
Creates a ReactionGlyph object, adds it to the end of the reaction glyph objects list and returns a pointer to the newly created object.
createRectangle() - Method in class org.sbml.libsbml.RenderGroup
Creates a rectangle object and adds it to the end of the list of child elements The new element is owned by the group..
createReferenceGlyph() - Method in class org.sbml.libsbml.GeneralGlyph
Creates a new ReferenceGlyph object, adds it to the end of the list of reference objects and returns a reference to the newly created object.
createReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy.
createReplacedElement() - Method in class org.sbml.libsbml.CompSBasePlugin
Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object.
createRoleString() - Method in class org.sbml.libsbml.Style
 
createSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef.
createSpecies() - Method in class org.sbml.libsbml.Model
Creates a new Species inside this Model and returns it.
createSpeciesGlyph() - Method in class org.sbml.libsbml.Layout
Creates a SpeciesGlyph object, adds it to the end of the species glyph objects list and returns a pointer to the newly created object.
createSpeciesReferenceGlyph() - Method in class org.sbml.libsbml.Layout
Creates a new SpeciesReferenceGlyph for the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.
createSpeciesReferenceGlyph() - Method in class org.sbml.libsbml.ReactionGlyph
Creates a new SpeciesReferenceGlyph object, adds it to the end of the list of species reference objects and returns a reference to the newly created object.
createSpeciesType() - Method in class org.sbml.libsbml.Model
Creates a new SpeciesType inside this Model and returns it.
createStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
Creates a new, empty StoichiometryMath object, adds it to this SpeciesReference, and returns it.
createStyle(String) - Method in class org.sbml.libsbml.GlobalRenderInformation
Creates a new GlobalStyle object.
createStyle(String) - Method in class org.sbml.libsbml.LocalRenderInformation
Creates a new LocalStyle object.
createSubmodel() - Method in class org.sbml.libsbml.CompModelPlugin
Creates a Submodel object, adds it to the end of the submodel objects list and returns a pointer to the newly created object.
createText() - Method in class org.sbml.libsbml.RenderGroup
Creates a text object and adds it to the end of the list of child elements The new element is owned by the group..
createTextGlyph() - Method in class org.sbml.libsbml.Layout
Creates a TextGlyph object, adds it to the end of the text glyph objects list and returns a pointer to the newly created object.
createTransition() - Method in class org.sbml.libsbml.QualModelPlugin
Creates a new qual object and adds it to the list of qual objects and returns it.
createTrigger() - Method in class org.sbml.libsbml.Event
Creates a new, empty Trigger, adds it to this Event and returns the Trigger.
createTrigger() - Method in class org.sbml.libsbml.Model
Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.
createTypeString() - Method in class org.sbml.libsbml.Style
 
createUnit() - Method in class org.sbml.libsbml.Model
Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
createUnit() - Method in class org.sbml.libsbml.UnitDefinition
Creates a new and empty Unit, adds it to this UnitDefinition's list of units, and returns it.
createUnitDefinition() - Method in class org.sbml.libsbml.Model
Creates a new UnitDefinition inside this Model and returns it.
createValueString() - Method in class org.sbml.libsbml.ColorDefinition
Creates a string the represents the current color value.
CubicBezier - Class in org.sbml.libsbml
layout A Cubic Bézier smooth curve.
CubicBezier() - Constructor for class org.sbml.libsbml.CubicBezier
Creates a CubicBezier and returns the pointer.
CubicBezier(long) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a CubicBezier and returns the pointer.
CubicBezier(long, long) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a CubicBezier and returns the pointer.
CubicBezier(long, long, long) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a CubicBezier and returns the pointer.
CubicBezier(CubicBezier) - Constructor for class org.sbml.libsbml.CubicBezier
Copy constructor.
CubicBezier(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.CubicBezier
Constructor.
CubicBezier(LayoutPkgNamespaces, double, double, double, double) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a CubicBezier with the given 2D coordinates and returns the pointer.
CubicBezier(LayoutPkgNamespaces, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a CubicBezier with the given 3D coordinates and returns the pointer.
CubicBezier(LayoutPkgNamespaces, Point, Point) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a CubicBezier with the given points and returns the pointer.
CubicBezier(LayoutPkgNamespaces, Point, Point, Point, Point) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a CubicBezier with the given points and returns the pointer.
CubicBezier(XMLNode) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a new Layout from the given XMLNode
CubicBezier(XMLNode, long) - Constructor for class org.sbml.libsbml.CubicBezier
Creates a new Layout from the given XMLNode
Curve - Class in org.sbml.libsbml
layout A curve connecting elements in a diagram.
Curve() - Constructor for class org.sbml.libsbml.Curve
Creates a curve with an empty list of segments.
Curve(long) - Constructor for class org.sbml.libsbml.Curve
Creates a curve with an empty list of segments.
Curve(long, long) - Constructor for class org.sbml.libsbml.Curve
Creates a curve with an empty list of segments.
Curve(long, long, long) - Constructor for class org.sbml.libsbml.Curve
Creates a curve with an empty list of segments.
Curve(Curve) - Constructor for class org.sbml.libsbml.Curve
Copy constructor.
Curve(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Curve
Creates a new Curve with the given LayoutPkgNamespaces object.
Curve(XMLNode) - Constructor for class org.sbml.libsbml.Curve
Creates a new Curve from the given XMLNode
Curve(XMLNode, long) - Constructor for class org.sbml.libsbml.Curve
Creates a new Curve from the given XMLNode
CVTerm - Class in org.sbml.libsbml
A MIRIAM-compliant controlled vocabulary term.
CVTerm() - Constructor for class org.sbml.libsbml.CVTerm
Creates an empty CVTerm, optionally with the given qualifier type .
CVTerm(int) - Constructor for class org.sbml.libsbml.CVTerm
Creates an empty CVTerm, optionally with the given qualifier type .
CVTerm(CVTerm) - Constructor for class org.sbml.libsbml.CVTerm
Copy constructor; creates a copy of a CVTerm object.
CVTerm(XMLNode) - Constructor for class org.sbml.libsbml.CVTerm
Creates a new CVTerm from the given XMLNode.
CVTermList - Class in org.sbml.libsbml
 
CVTermList() - Constructor for class org.sbml.libsbml.CVTermList
 

D

DanglingUnitReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DanglingUnitSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Date - Class in org.sbml.libsbml
A MIRIAM-compliant date representation.
Date() - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(long, long, long, long, long, long, long, long, long) - Constructor for class org.sbml.libsbml.Date
Creates a time and date representation for use in model annotations and elsewhere.
Date(String) - Constructor for class org.sbml.libsbml.Date
Creates a Date object from a string expressing a date and time value.
Date(Date) - Constructor for class org.sbml.libsbml.Date
Copy constructor; creates a copy of this Date.
DateList - Class in org.sbml.libsbml
 
DateList() - Constructor for class org.sbml.libsbml.DateList
 
deepCopy() - Method in class org.sbml.libsbml.ASTNode
Creates a recursive copy of this node and all its children.
DefaultTerm - Class in org.sbml.libsbml
qual The default result of a Transition.
DefaultTerm() - Constructor for class org.sbml.libsbml.DefaultTerm
Creates a new DefaultTerm with the given level, version, and package version.
DefaultTerm(long) - Constructor for class org.sbml.libsbml.DefaultTerm
Creates a new DefaultTerm with the given level, version, and package version.
DefaultTerm(long, long) - Constructor for class org.sbml.libsbml.DefaultTerm
Creates a new DefaultTerm with the given level, version, and package version.
DefaultTerm(long, long, long) - Constructor for class org.sbml.libsbml.DefaultTerm
Creates a new DefaultTerm with the given level, version, and package version.
DefaultTerm(DefaultTerm) - Constructor for class org.sbml.libsbml.DefaultTerm
Copy constructor for DefaultTerm.
DefaultTerm(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.DefaultTerm
Creates a new DefaultTerm with the given QualPkgNamespaces object.
DefaultValues - Class in org.sbml.libsbml
TODO:Definition of the DefaultValues class.
DefaultValues() - Constructor for class org.sbml.libsbml.DefaultValues
Creates a new DefaultValues using the given SBML Level, Version and “render” package version.
DefaultValues(long) - Constructor for class org.sbml.libsbml.DefaultValues
Creates a new DefaultValues using the given SBML Level, Version and “render” package version.
DefaultValues(long, long) - Constructor for class org.sbml.libsbml.DefaultValues
Creates a new DefaultValues using the given SBML Level, Version and “render” package version.
DefaultValues(long, long, long) - Constructor for class org.sbml.libsbml.DefaultValues
Creates a new DefaultValues using the given SBML Level, Version and “render” package version.
DefaultValues(DefaultValues) - Constructor for class org.sbml.libsbml.DefaultValues
Copy constructor for DefaultValues.
DefaultValues(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.DefaultValues
Creates a new DefaultValues using the given RenderPkgNamespaces object.
del(String) - Method in class org.sbml.libsbml.StringSet
 
Delay - Class in org.sbml.libsbml
A delay on the time of execution of an SBML event.
Delay(long, long) - Constructor for class org.sbml.libsbml.Delay
Creates a new Delay using the given SBML level and version values.
Delay(Delay) - Constructor for class org.sbml.libsbml.Delay
Copy constructor; creates a copy of this Delay.
Delay(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Delay
Creates a new Delay using the given SBMLNamespaces object sbmlns.
DelayNeedsValuesFromTriggerTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DelayUnitsNotTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
delete() - Method in class org.sbml.libsbml.AlgebraicRule
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.AssignmentRule
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Association
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ASTNode
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ASTNodeList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.BoundingBox
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CobraToFbcConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ColorDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Compartment
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompartmentGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompartmentType
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompBase
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompFlatteningConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompModelPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompSBasePlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Constraint
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ConversionOption
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ConversionProperties
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CubicBezier
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Curve
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CVTerm
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.CVTermList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Date
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.DateList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.DefaultTerm
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.DefaultValues
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Delay
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Deletion
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Dimensions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.double_array
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ElementFilter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Ellipse
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Event
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.EventAssignment
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ExternalModelDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcAnd
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcAssociation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcModelPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcOr
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcReactionPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcSBMLDocumentPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcToCobraConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcV1ToV2Converter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FbcV2ToV1Converter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FluxBound
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FluxObjective
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FunctionDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.FunctionTerm
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GeneAssociation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GeneProduct
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GeneProductAssociation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GeneProductRef
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GeneralGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GlobalRenderInformation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GlobalStyle
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GradientBase
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GradientStop
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GraphicalObject
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Group
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GroupsExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GroupsModelPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Image
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.InitialAssignment
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Input
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.int_array
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.KineticLaw
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.L3ParserSettings
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Layout
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LayoutExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LayoutModelPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LayoutSpeciesReferencePlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LinearGradient
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LineEnding
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LineSegment
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOf
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfColorDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfCompartments
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfConstraints
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfCurveElements
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfDeletions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfDrawables
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfEventAssignments
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfEvents
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfFluxBounds
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfFunctionTerms
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGeneAssociations
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGeneProducts
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGlobalStyles
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGradientStops
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfGroups
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfInputs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLayouts
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLineEndings
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLineSegments
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLocalParameters
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfLocalStyles
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfMembers
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfModelDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfObjectives
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfOutputs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfParameters
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfPorts
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfReactions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfReplacedElements
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfRules
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpecies
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfSubmodels
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfTransitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ListOfUnits
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LocalParameter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LocalRenderInformation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.LocalStyle
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.MathFilter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.MathML
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Member
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Model
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModelCreator
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModelCreatorList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModelDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModelHistory
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Objective
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.OFStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.OStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.OStringStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Output
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Parameter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Point
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Polygon
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Port
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Priority
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.QualExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.QualitativeSpecies
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.QualModelPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.QualPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RadialGradient
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RateRule
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RDFAnnotationParser
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Reaction
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ReactionGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Rectangle
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ReferenceGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RelAbsVector
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderCubicBezier
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderCurve
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderGroup
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderInformationBase
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderLayoutPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderPkgNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.RenderPoint
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ReplacedBy
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.ReplacedElement
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Replacing
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Rule
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBase
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBaseList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBasePlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBaseRef
Explicitly deletes the underlying native object.
delete() - Method in exception org.sbml.libsbml.SBMLConstructorException
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLConverterRegistry
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLDocument
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLError
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLErrorLog
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLExtension
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLExtensionException
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLFileResolver
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLIdConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLInferUnitsConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLLevel1Version1Converter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLLocalParameterConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLNamespacesList
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLReactionConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLReader
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLResolver
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLResolverRegistry
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLRuleConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLUnitsConverter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLUri
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLValidator
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBMLWriter
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SBO
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Species
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SpeciesGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SpeciesReference
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SpeciesType
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.StoichiometryMath
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.StringSet
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Style
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Submodel
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.SyntaxChecker
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Text
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.TextGlyph
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Transformation
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Transformation2D
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Transition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Trigger
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.Unit
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.UnitDefinition
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLAttributes
Explicitly deletes the underlying native object.
delete() - Method in exception org.sbml.libsbml.XMLConstructorException
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLError
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLErrorLog
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLInputStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLNamespaces
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLNode
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLOutputStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLOwningOutputFileStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLOwningOutputStringStream
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLToken
Explicitly deletes the underlying native object.
delete() - Method in class org.sbml.libsbml.XMLTriple
Explicitly deletes the underlying native object.
deleteDisabledPlugins() - Method in class org.sbml.libsbml.SBase
Deletes all information stored in disabled plugins.
deleteDisabledPlugins(boolean) - Method in class org.sbml.libsbml.SBase
Deletes all information stored in disabled plugins.
deleteLayoutAnnotation(XMLNode) - Static method in class org.sbml.libsbml.libsbml
Takes an XMLNode and tries to find the layout annotation node and deletes it if it was found.
deleteLayoutIdAnnotation(XMLNode) - Static method in class org.sbml.libsbml.libsbml
Takes an XMLNode and tries to find the layoutId annotation node and deletes it if it was found.
deleteRDFAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Deletes any SBML MIRIAM RDF annotation found in the given XMLNode tree and returns any remaining annotation content.
deleteRDFCVTermAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Deletes any SBML MIRIAM RDF 'CVTerm' annotation found in the given XMLNode tree and returns any remaining annotation content.
deleteRDFHistoryAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Deletes any SBML MIRIAM RDF 'History' annotation found in the given XMLNode tree and returns any remaining annotation content.
deleteResolerRegistryInstance() - Static method in class org.sbml.libsbml.SBMLResolverRegistry
deletes the static resolver registry instance
Deletion - Class in org.sbml.libsbml
comp Deletion of an object from a submodel.
Deletion() - Constructor for class org.sbml.libsbml.Deletion
Creates a new Deletion with the given level, version, and package version.
Deletion(long) - Constructor for class org.sbml.libsbml.Deletion
Creates a new Deletion with the given level, version, and package version.
Deletion(long, long) - Constructor for class org.sbml.libsbml.Deletion
Creates a new Deletion with the given level, version, and package version.
Deletion(long, long, long) - Constructor for class org.sbml.libsbml.Deletion
Creates a new Deletion with the given level, version, and package version.
Deletion(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Deletion
Creates a new Deletion with the given CompPkgNamespaces object.
Deletion(Deletion) - Constructor for class org.sbml.libsbml.Deletion
Copy constructor.
depth() - Method in class org.sbml.libsbml.BoundingBox
Get the depth of the bounding box.
depth() - Method in class org.sbml.libsbml.Dimensions
Returns the depth.
determineNumberChildren() - Method in class org.sbml.libsbml.XMLInputStream
Returns the number of child tokens of the given element in this stream.
determineNumberChildren(String) - Method in class org.sbml.libsbml.XMLInputStream
Returns the number of child tokens of the given element in this stream.
determineNumSpecificChildren(String, String) - Method in class org.sbml.libsbml.XMLInputStream
Returns the number of child tokens of the specified type within a given container element.
Dimensions - Class in org.sbml.libsbml
layout Spatial dimensions of a 2D or 3D shape.
Dimensions() - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object with the given level, version, and package version and with all sizes set to 0.0.
Dimensions(long) - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object with the given level, version, and package version and with all sizes set to 0.0.
Dimensions(long, long) - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object with the given level, version, and package version and with all sizes set to 0.0.
Dimensions(long, long, long) - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object with the given level, version, and package version and with all sizes set to 0.0.
Dimensions(Dimensions) - Constructor for class org.sbml.libsbml.Dimensions
Copy constructor.
Dimensions(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object with the given LayoutPkgNamespaces object and with all sizes set to 0.0.
Dimensions(LayoutPkgNamespaces, double, double) - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object with the given sizes.
Dimensions(LayoutPkgNamespaces, double, double, double) - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object with the given sizes.
Dimensions(XMLNode) - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object from the given XMLNode
Dimensions(XMLNode, long) - Constructor for class org.sbml.libsbml.Dimensions
Creates a new Dimensions object from the given XMLNode
disablePackage(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Disables the package with the given URI or name.
disablePackage(String, String) - Method in class org.sbml.libsbml.SBase
Disables the given SBML Level 3 package on this object.
disableUnusedPackages(SBMLDocument) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Disables unused packages.
DisallowedDefinitionURLUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathMLEncodingUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathMLSymbol - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathTypeAttributeUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathTypeAttributeValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DisallowedMathUnitsUse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
divide(UnitDefinition, UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Combines two UnitDefinition objects into a single UnitDefinition as a division.
double_array - Class in org.sbml.libsbml
 
double_array(int) - Constructor for class org.sbml.libsbml.double_array
 
DoubleExponentNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DowncastASTBasePlugin(long, boolean) - Static method in class org.sbml.libsbml.libsbml
 
DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.GroupsExtension
 
DowncastSBase(long, boolean) - Method in class org.sbml.libsbml.RenderExtension
 
DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.GroupsExtension
 
DowncastSBasePlugin(long, boolean) - Method in class org.sbml.libsbml.RenderExtension
 
downIndent() - Method in class org.sbml.libsbml.XMLOutputStream
Decreases the indentation level for this XMLOutputStream.
DuplicateAnnotationInvalidInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateAnnotationInvalidInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateAnnotationInvalidInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateAnnotationInvalidInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateAnnotationNamespaces - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateLocalParameterId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateMetaId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateUnitDefinitionId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
DuplicateXMLAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

E

ElementFilter - Class in org.sbml.libsbml
Base class for filter functions.
ElementFilter() - Constructor for class org.sbml.libsbml.ElementFilter
Creates a new ElementFilter object.
Ellipse - Class in org.sbml.libsbml
graphical representation of an ellipse from the SBML render extension
Ellipse() - Constructor for class org.sbml.libsbml.Ellipse
Creates a new Ellipse object with the given SBML level and SBML version.
Ellipse(long) - Constructor for class org.sbml.libsbml.Ellipse
Creates a new Ellipse object with the given SBML level and SBML version.
Ellipse(long, long) - Constructor for class org.sbml.libsbml.Ellipse
Creates a new Ellipse object with the given SBML level and SBML version.
Ellipse(long, long, long) - Constructor for class org.sbml.libsbml.Ellipse
Creates a new Ellipse object with the given SBML level and SBML version.
Ellipse(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.Ellipse
Creates a new Ellipse object with the given SBMLNamespaces.
Ellipse(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.Ellipse
Instantiates a new ellipse object with the center set to 0,0,0 and the radii also set to 0.
Ellipse(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Ellipse
Constructor with id, 2D center and radius.
Ellipse(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Ellipse
Constructor with id, 2D center and radii.
Ellipse(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Ellipse
Constructor with id, 3D center and radii.
Ellipse(RenderPkgNamespaces, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Ellipse
Constructor with 2D center and radius.
Ellipse(RenderPkgNamespaces, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Ellipse
Constructor with 2D center and radii.
Ellipse(RenderPkgNamespaces, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Ellipse
Constructor with 3D center and radii.
Ellipse(XMLNode) - Constructor for class org.sbml.libsbml.Ellipse
Creates a new RadialGradient object from the given XMLNode object.
Ellipse(XMLNode, long) - Constructor for class org.sbml.libsbml.Ellipse
Creates a new RadialGradient object from the given XMLNode object.
empty() - Method in class org.sbml.libsbml.RelAbsVector
 
empty() - Method in class org.sbml.libsbml.StringSet
 
EmptyListElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyListInKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyListInReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyListOfElementNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyListOfUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EmptyUnitListElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
enableDefaultNS(String, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Set/unset default namespace to each top-level element defined in the given package extension.
enableL2NamespaceForDocument(SBMLDocument) - Method in class org.sbml.libsbml.LayoutExtension
Adds the L2 Namespace to the document and enables the extension.
enableL2NamespaceForDocument(SBMLDocument) - Method in class org.sbml.libsbml.RenderExtension
Adds the L2 Namespace to the document and enables the extension.
enableL2NamespaceForDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Enables package extensions that support serialization to SBML annotations.
enablePackage(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Enables the package with the given URI / name.
enablePackage(String, String, boolean) - Method in class org.sbml.libsbml.SBase
Enables or disables the given SBML Level 3 package on this object.
endElement(String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given XML end element name to this XMLOutputStream.
endElement(String, String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given XML end element name to this XMLOutputStream.
endElement(XMLTriple) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given element to the stream.
endElement(XMLTriple, boolean) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given element to the stream.
endl() - Method in class org.sbml.libsbml.OStream
 
equals(Object) - Method in class org.sbml.libsbml.ASTNode
Equality comparison method for ASTNode.
equals(Object) - Method in class org.sbml.libsbml.CVTerm
Equality comparison method for CVTerm.
equals(Object) - Method in class org.sbml.libsbml.Date
Equality comparison method for Date.
equals(Object) - Method in class org.sbml.libsbml.ModelCreator
Equality comparison method for ModelCreator.
equals(Object) - Method in class org.sbml.libsbml.ModelHistory
Equality comparison method for ModelHistory.
equals(Object) - Method in class org.sbml.libsbml.SBase
Equality comparison method for SBase.
equals(Object) - Method in class org.sbml.libsbml.SBMLNamespaces
Equality comparison method for SBMLNamespaces.
equals(Object) - Method in class org.sbml.libsbml.SBMLReader
Equality comparison method for SBMLReader.
equals(Object) - Method in class org.sbml.libsbml.SBMLWriter
Equality comparison method for SBMLWriter.
equals(Object) - Method in class org.sbml.libsbml.XMLAttributes
Equality comparison method for XMLAttributes.
equals(Object) - Method in class org.sbml.libsbml.XMLError
Equality comparison method for XMLError.
equals(Object) - Method in class org.sbml.libsbml.XMLErrorLog
Equality comparison method for XMLErrorLog.
equals(Object) - Method in class org.sbml.libsbml.XMLNamespaces
Equality comparison method for XMLNamespaces.
equals(Object) - Method in class org.sbml.libsbml.XMLNode
Equality comparison method for XMLNode.
equals(Object) - Method in class org.sbml.libsbml.XMLOutputStream
Equality comparison method for XMLOutputStream.
equals(Object) - Method in class org.sbml.libsbml.XMLToken
Equality comparison method for XMLToken.
equals(Object) - Method in class org.sbml.libsbml.XMLTriple
Equality comparison method for XMLTriple.
erase() - Method in class org.sbml.libsbml.RelAbsVector
resets this element by setting its component to 0
EVENODD - Static variable in class org.sbml.libsbml.GraphicalPrimitive2D
 
Event - Class in org.sbml.libsbml
A discontinuous SBML event.
Event(long, long) - Constructor for class org.sbml.libsbml.Event
Creates a new Event using the given SBML level and version values.
Event(Event) - Constructor for class org.sbml.libsbml.Event
Copy constructor; creates a copy of this Event.
Event(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Event
Creates a new Event using the given SBMLNamespaces object sbmlns.
EventAndAssignmentRuleForId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignCompartmentMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignment - Class in org.sbml.libsbml
An assignment to a variable by an SBML event.
EventAssignment(long, long) - Constructor for class org.sbml.libsbml.EventAssignment
Creates a new EventAssignment using the given SBML level and version values.
EventAssignment(EventAssignment) - Constructor for class org.sbml.libsbml.EventAssignment
Copy constructor; creates a copy of this EventAssignment.
EventAssignment(SBMLNamespaces) - Constructor for class org.sbml.libsbml.EventAssignment
Creates a new EventAssignment using the given SBMLNamespaces object sbmlns.
EventAssignmentForConstantEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventAssignStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
EventNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
expandFunctionDefinitions() - Method in class org.sbml.libsbml.SBMLDocument
Removes FunctionDefinition constructs from the document and expands any instances of their use within <math> elements.
expandInitialAssignments() - Method in class org.sbml.libsbml.SBMLDocument
Removes InitialAssignment constructs from the document and replaces them with appropriate values.
ExtentUnitsNotSubstance - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ExternalModelDefinition - Class in org.sbml.libsbml
comp A reference to an externally-defined model.
ExternalModelDefinition() - Constructor for class org.sbml.libsbml.ExternalModelDefinition
Creates a new ExternalModelDefinition with the given level, version, and package version.
ExternalModelDefinition(long) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
Creates a new ExternalModelDefinition with the given level, version, and package version.
ExternalModelDefinition(long, long) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
Creates a new ExternalModelDefinition with the given level, version, and package version.
ExternalModelDefinition(long, long, long) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
Creates a new ExternalModelDefinition with the given level, version, and package version.
ExternalModelDefinition(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
Creates a new ExternalModelDefinition with the given CompPkgNamespaces object.
ExternalModelDefinition(ExternalModelDefinition) - Constructor for class org.sbml.libsbml.ExternalModelDefinition
Copy constructor.

F

FailedMathMLReadOfDouble - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FailedMathMLReadOfExponential - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FailedMathMLReadOfInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FailedMathMLReadOfRational - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FastReactionsNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcActiveObjectiveRefersObjective - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcActiveObjectiveSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcAnd - Class in org.sbml.libsbml
fbc An “and” relationship for gene products
FbcAnd() - Constructor for class org.sbml.libsbml.FbcAnd
Creates a new FbcAnd with the given SBML Level, Version, and “fbc”package version.
FbcAnd(long) - Constructor for class org.sbml.libsbml.FbcAnd
Creates a new FbcAnd with the given SBML Level, Version, and “fbc”package version.
FbcAnd(long, long) - Constructor for class org.sbml.libsbml.FbcAnd
Creates a new FbcAnd with the given SBML Level, Version, and “fbc”package version.
FbcAnd(long, long, long) - Constructor for class org.sbml.libsbml.FbcAnd
Creates a new FbcAnd with the given SBML Level, Version, and “fbc”package version.
FbcAnd(FbcAnd) - Constructor for class org.sbml.libsbml.FbcAnd
Copy constructor for FbcAnd.
FbcAnd(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcAnd
Creates a new FbcAnd with the given FbcPkgNamespaces object.
FbcAndAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcAndAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcAndTwoChildren - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcAssociation - Class in org.sbml.libsbml
fbc Base class for FbcAnd, FbcOr, and GeneProductRef
FbcAssociation() - Constructor for class org.sbml.libsbml.FbcAssociation
Creates a new FbcAssociation with the given SBML Level, Version, and “fbc”package version.
FbcAssociation(long) - Constructor for class org.sbml.libsbml.FbcAssociation
Creates a new FbcAssociation with the given SBML Level, Version, and “fbc”package version.
FbcAssociation(long, long) - Constructor for class org.sbml.libsbml.FbcAssociation
Creates a new FbcAssociation with the given SBML Level, Version, and “fbc”package version.
FbcAssociation(long, long, long) - Constructor for class org.sbml.libsbml.FbcAssociation
Creates a new FbcAssociation with the given SBML Level, Version, and “fbc”package version.
FbcAssociation(FbcAssociation) - Constructor for class org.sbml.libsbml.FbcAssociation
Copy constructor for FbcAssociation.
FbcAssociation(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcAssociation
Creates a new FbcAssociation with the given FbcPkgNamespaces object.
FbcAttributeRequiredMissing - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcAttributeRequiredMustBeBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcDuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcElementNotInNs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcExtension - Class in org.sbml.libsbml
fbc Base extension class for the “fbc” package.
FbcExtension() - Constructor for class org.sbml.libsbml.FbcExtension
Creates a new FbcExtension instance.
FbcExtension(FbcExtension) - Constructor for class org.sbml.libsbml.FbcExtension
Copy constructor for FbcExtension.
FbcFluxBoundAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxBoundAllowedL3Attributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxBoundNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxBoundOperationMustBeEnum - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxBoundReactionMustExist - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxBoundRectionMustBeSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxBoundRequiredAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxBoundsForReactionConflict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxBoundValueMustBeDouble - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxObjectAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxObjectAllowedL3Attributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxObjectCoefficientMustBeDouble - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxObjectCoefficientWhenStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxObjectNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxObjectReactionMustBeSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxObjectReactionMustExist - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcFluxObjectRequiredAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdAssocAllowedAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdAssocAllowedCoreAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdAssocAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdAssocContainsOneElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdAssocIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdAssocNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdRefAllowedAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdRefAllowedCoreAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdRefAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdRefGeneProductExists - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProdRefGeneProductSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProductAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProductAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProductAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProductAssocSpeciesMustExist - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProductLabelMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProductLabelMustBeUnique - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcGeneProductNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcLOFluxBoundsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcLOFluxBoundsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcLOGeneProductsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcLOGeneProductsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcLOObjectivesAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcLOObjectivesAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcModelMustHaveStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcModelPlugin - Class in org.sbml.libsbml
fbc Extension of Model.
FbcModelPlugin(String, String, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcModelPlugin
Creates a new FbcModelPlugin object using the given parameters.
FbcModelPlugin(FbcModelPlugin) - Constructor for class org.sbml.libsbml.FbcModelPlugin
Copy constructor for FbcModelPlugin.
FbcModelStrictMustBeBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcNoEmptyListOfs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcNSUndeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveAllowedL3Attributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveLOFluxObjAllowedAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveLOFluxObjMustNotBeEmpty - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveLOFluxObjOnlyFluxObj - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveOneListOfObjectives - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveRequiredAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcObjectiveTypeMustBeEnum - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcOnlyOneEachListOf - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcOr - Class in org.sbml.libsbml
fbc An “or” relationship for gene products
FbcOr() - Constructor for class org.sbml.libsbml.FbcOr
Creates a new FbcOr with the given SBML Level, Version, and “fbc”package version.
FbcOr(long) - Constructor for class org.sbml.libsbml.FbcOr
Creates a new FbcOr with the given SBML Level, Version, and “fbc”package version.
FbcOr(long, long) - Constructor for class org.sbml.libsbml.FbcOr
Creates a new FbcOr with the given SBML Level, Version, and “fbc”package version.
FbcOr(long, long, long) - Constructor for class org.sbml.libsbml.FbcOr
Creates a new FbcOr with the given SBML Level, Version, and “fbc”package version.
FbcOr(FbcOr) - Constructor for class org.sbml.libsbml.FbcOr
Copy constructor for FbcOr.
FbcOr(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcOr
Creates a new FbcOr with the given FbcPkgNamespaces object.
FbcOrAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcOrAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcOrTwoChildren - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcPkgNamespaces - Class in org.sbml.libsbml
Set of SBML Level + Version + namespace triples.
FbcPkgNamespaces() - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(long) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcPkgNamespaces(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcPkgNamespaces
 
FbcReactionAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionBoundsMustHaveValuesStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionBoundsNotAssignedStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionConstantBoundsStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionLwrBoundNotInfStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionLwrBoundRefExists - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionLwrBoundSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionLwrLessThanUpStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionMustHaveBoundsStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionOnlyOneGeneProdAss - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionPlugin - Class in org.sbml.libsbml
fbc Extension of Reaction by the “fbc” package.
FbcReactionPlugin(String, String, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcReactionPlugin
Creates a new FbcReactionPlugin object using the given parameters.
FbcReactionPlugin(FbcReactionPlugin) - Constructor for class org.sbml.libsbml.FbcReactionPlugin
Copy constructor for FbcReactionPlugin.
FbcReactionUpBoundNotNegInfStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionUpBoundRefExists - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcReactionUpBoundSIdRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcRequiredFalse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcSBMLDocumentPlugin - Class in org.sbml.libsbml
fbc Extension of SBMLDocument for the “fbc” package.
FbcSBMLDocumentPlugin(String, String, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcSBMLDocumentPlugin
Creates a new FbcSBMLDocumentPlugin object using the given parameters.
FbcSBMLDocumentPlugin(FbcSBMLDocumentPlugin) - Constructor for class org.sbml.libsbml.FbcSBMLDocumentPlugin
Copy constructor for FbcSBMLDocumentPlugin.
FbcSBMLSIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcSpeciesAllowedL3Attributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcSpeciesChargeMustBeInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcSpeciesFormulaMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcSpeciesPlugin - Class in org.sbml.libsbml
fbc Extension of Species.
FbcSpeciesPlugin(String, String, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FbcSpeciesPlugin
Creates a new FbcSpeciesPlugin
FbcSpeciesPlugin(FbcSpeciesPlugin) - Constructor for class org.sbml.libsbml.FbcSpeciesPlugin
Copy constructor for FbcSpeciesPlugin.
FbcSpeciesReferenceConstantStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcSpeciesRefNotAssignedStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcSpeciesRefsStoichMustBeRealStrict - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcToCobraConverter - Class in org.sbml.libsbml
fbc SBML Level 3 “fbc” to COBRA converter.
FbcToCobraConverter() - Constructor for class org.sbml.libsbml.FbcToCobraConverter
Creates a new FbcToCobraConverter object.
FbcToCobraConverter(FbcToCobraConverter) - Constructor for class org.sbml.libsbml.FbcToCobraConverter
Copy constructor; creates a copy of an FbcToCobraConverter object.
FbcUnknown - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FbcV1ToV2Converter - Class in org.sbml.libsbml
fbc Convert “fbc” Version 1 models to Version 2
FbcV1ToV2Converter() - Constructor for class org.sbml.libsbml.FbcV1ToV2Converter
Creates a new FbcV1ToV2Converter object.
FbcV1ToV2Converter(FbcV1ToV2Converter) - Constructor for class org.sbml.libsbml.FbcV1ToV2Converter
Copy constructor; creates a copy of an FbcV1ToV2Converter object.
FbcV2ToV1Converter - Class in org.sbml.libsbml
fbc Convert “fbc” Version 2 models to Version 1
FbcV2ToV1Converter() - Constructor for class org.sbml.libsbml.FbcV2ToV1Converter
Creates a new FbcV2ToV1Converter object.
FbcV2ToV1Converter(FbcV2ToV1Converter) - Constructor for class org.sbml.libsbml.FbcV2ToV1Converter
Copy constructor; creates a copy of an FbcV2ToV1Converter object.
FillRule_fromString(String) - Static method in class org.sbml.libsbml.libsbml
 
FillRule_toString(int) - Static method in class org.sbml.libsbml.libsbml
 
filter(SBase) - Method in class org.sbml.libsbml.ElementFilter
Predicate to test elements.
FluxBound - Class in org.sbml.libsbml
fbc Max or min value for a reaction flux.
FluxBound() - Constructor for class org.sbml.libsbml.FluxBound
Creates a new FbcAssociation with the given SBML Level, Version, and “fbc”package version.
FluxBound(long) - Constructor for class org.sbml.libsbml.FluxBound
Creates a new FbcAssociation with the given SBML Level, Version, and “fbc”package version.
FluxBound(long, long) - Constructor for class org.sbml.libsbml.FluxBound
Creates a new FbcAssociation with the given SBML Level, Version, and “fbc”package version.
FluxBound(long, long, long) - Constructor for class org.sbml.libsbml.FluxBound
Creates a new FbcAssociation with the given SBML Level, Version, and “fbc”package version.
FluxBound(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FluxBound
Creates a new FluxBound with the given FbcPkgNamespaces object.
FluxBound(FluxBound) - Constructor for class org.sbml.libsbml.FluxBound
Copy constructor.
FLUXBOUND_OPERATION_EQUAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_GREATER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_GREATER_EQUAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_LESS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_LESS_EQUAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FLUXBOUND_OPERATION_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FluxObjective - Class in org.sbml.libsbml
fbc An objective function for a flux.
FluxObjective() - Constructor for class org.sbml.libsbml.FluxObjective
Creates a new FluxObjective with the given SBML Level, Version, and “fbc”package version.
FluxObjective(long) - Constructor for class org.sbml.libsbml.FluxObjective
Creates a new FluxObjective with the given SBML Level, Version, and “fbc”package version.
FluxObjective(long, long) - Constructor for class org.sbml.libsbml.FluxObjective
Creates a new FluxObjective with the given SBML Level, Version, and “fbc”package version.
FluxObjective(long, long, long) - Constructor for class org.sbml.libsbml.FluxObjective
Creates a new FluxObjective with the given SBML Level, Version, and “fbc”package version.
FluxObjective(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.FluxObjective
Creates a new FluxObjective with the given FbcPkgNamespaces object.
FluxObjective(FluxObjective) - Constructor for class org.sbml.libsbml.FluxObjective
Copy constructor for FluxObjective.
FontStyle_fromString(String) - Static method in class org.sbml.libsbml.libsbml
 
FontStyle_toString(int) - Static method in class org.sbml.libsbml.libsbml
 
FontWeight_fromString(String) - Static method in class org.sbml.libsbml.libsbml
 
FontWeight_toString(int) - Static method in class org.sbml.libsbml.libsbml
 
FormulaInLevel1KL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
formulaToL3String(ASTNode) - Static method in class org.sbml.libsbml.libsbml
Converts an AST to a text string representation of a formula using an extended syntax.
formulaToL3StringWithSettings(ASTNode, L3ParserSettings) - Static method in class org.sbml.libsbml.libsbml
Converts an AST to a text string representation of a formula, using specific formatter settings.
formulaToString(ASTNode) - Static method in class org.sbml.libsbml.libsbml
Converts an AST to a text string representation of a formula using a basic syntax derived from SBML Level 1.
freeName() - Method in class org.sbml.libsbml.ASTNode
Frees the name of this ASTNode and sets it to null.
freeSBMLNamespaces(SWIGTYPE_p_List) - Static method in class org.sbml.libsbml.SBMLNamespaces
Frees the list of supported namespaces as generated by getSupportedNamespaces().
frompointer(SWIGTYPE_p_double) - Static method in class org.sbml.libsbml.double_array
 
frompointer(SWIGTYPE_p_int) - Static method in class org.sbml.libsbml.int_array
 
FuncDefNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FunctionDefinition - Class in org.sbml.libsbml
A user-defined function in an SBML model.
FunctionDefinition(long, long) - Constructor for class org.sbml.libsbml.FunctionDefinition
Creates a new FunctionDefinition using the given SBML level and version values.
FunctionDefinition(FunctionDefinition) - Constructor for class org.sbml.libsbml.FunctionDefinition
Copy constructor; creates a copy of this FunctionDefinition.
FunctionDefinition(SBMLNamespaces) - Constructor for class org.sbml.libsbml.FunctionDefinition
Creates a new FunctionDefinition using the given SBMLNamespaces object sbmlns.
FunctionDefMathNotLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
FunctionTerm - Class in org.sbml.libsbml
qual A function term.
FunctionTerm() - Constructor for class org.sbml.libsbml.FunctionTerm
Creates a new FunctionTerm with the given level, version, and package version.
FunctionTerm(long) - Constructor for class org.sbml.libsbml.FunctionTerm
Creates a new FunctionTerm with the given level, version, and package version.
FunctionTerm(long, long) - Constructor for class org.sbml.libsbml.FunctionTerm
Creates a new FunctionTerm with the given level, version, and package version.
FunctionTerm(long, long, long) - Constructor for class org.sbml.libsbml.FunctionTerm
Creates a new FunctionTerm with the given level, version, and package version.
FunctionTerm(FunctionTerm) - Constructor for class org.sbml.libsbml.FunctionTerm
Copy constructor for FunctionTerm.
FunctionTerm(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.FunctionTerm
Creates a new FunctionTerm with the given QualPkgNamespaces object.

G

GENE_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GeneAssociation - Class in org.sbml.libsbml
fbc Annotation helper class for “fbc” Version 1.
GeneAssociation() - Constructor for class org.sbml.libsbml.GeneAssociation
Creates a new GeneAssociation with the given level, version, and pkgVersion.
GeneAssociation(long) - Constructor for class org.sbml.libsbml.GeneAssociation
Creates a new GeneAssociation with the given level, version, and pkgVersion.
GeneAssociation(long, long) - Constructor for class org.sbml.libsbml.GeneAssociation
Creates a new GeneAssociation with the given level, version, and pkgVersion.
GeneAssociation(long, long, long) - Constructor for class org.sbml.libsbml.GeneAssociation
Creates a new GeneAssociation with the given level, version, and pkgVersion.
GeneAssociation(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneAssociation
Creates a new GeneAssociation with the given FbcPkgNamespaces object.
GeneAssociation(GeneAssociation) - Constructor for class org.sbml.libsbml.GeneAssociation
Copy constructor.
GeneAssociation(XMLNode, FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneAssociation
Creates a new GeneAssociation with the given node and FbcPkgNamespaces fbcns.
GeneProduct - Class in org.sbml.libsbml
fbc Association of a gene product with a Reaction
GeneProduct() - Constructor for class org.sbml.libsbml.GeneProduct
Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
GeneProduct(long) - Constructor for class org.sbml.libsbml.GeneProduct
Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
GeneProduct(long, long) - Constructor for class org.sbml.libsbml.GeneProduct
Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
GeneProduct(long, long, long) - Constructor for class org.sbml.libsbml.GeneProduct
Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
GeneProduct(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneProduct
Creates a new GeneProduct with the given FbcPkgNamespaces object.
GeneProduct(GeneProduct) - Constructor for class org.sbml.libsbml.GeneProduct
Copy constructor for GeneProduct.
GeneProductAssociation - Class in org.sbml.libsbml
fbc Association between gene products and reactions
GeneProductAssociation() - Constructor for class org.sbml.libsbml.GeneProductAssociation
Creates a new GeneProductAssociation with the given SBML Level, Version, and “fbc” package version.
GeneProductAssociation(long) - Constructor for class org.sbml.libsbml.GeneProductAssociation
Creates a new GeneProductAssociation with the given SBML Level, Version, and “fbc” package version.
GeneProductAssociation(long, long) - Constructor for class org.sbml.libsbml.GeneProductAssociation
Creates a new GeneProductAssociation with the given SBML Level, Version, and “fbc” package version.
GeneProductAssociation(long, long, long) - Constructor for class org.sbml.libsbml.GeneProductAssociation
Creates a new GeneProductAssociation with the given SBML Level, Version, and “fbc” package version.
GeneProductAssociation(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneProductAssociation
Creates a new GeneProductAssociation with the given FbcPkgNamespaces object.
GeneProductAssociation(GeneProductAssociation) - Constructor for class org.sbml.libsbml.GeneProductAssociation
Copy constructor for GeneProductAssociation.
GeneProductRef - Class in org.sbml.libsbml
fbc Reference to a gene product of a reaction
GeneProductRef() - Constructor for class org.sbml.libsbml.GeneProductRef
Creates a new GeneProductRef with the given SBML Level, Version, and “fbc”package version.
GeneProductRef(long) - Constructor for class org.sbml.libsbml.GeneProductRef
Creates a new GeneProductRef with the given SBML Level, Version, and “fbc”package version.
GeneProductRef(long, long) - Constructor for class org.sbml.libsbml.GeneProductRef
Creates a new GeneProductRef with the given SBML Level, Version, and “fbc”package version.
GeneProductRef(long, long, long) - Constructor for class org.sbml.libsbml.GeneProductRef
Creates a new GeneProductRef with the given SBML Level, Version, and “fbc”package version.
GeneProductRef(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneProductRef
Creates a new GeneProductRef with the given FbcPkgNamespaces object.
GeneProductRef(GeneProductRef) - Constructor for class org.sbml.libsbml.GeneProductRef
Copy constructor for GeneProductRef.
GeneralGlyph - Class in org.sbml.libsbml
layout A glyph for miscellaneous items.
GeneralGlyph() - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a new GeneralGlyph.
GeneralGlyph(long) - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a new GeneralGlyph.
GeneralGlyph(long, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a new GeneralGlyph.
GeneralGlyph(long, long, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a new GeneralGlyph.
GeneralGlyph(GeneralGlyph) - Constructor for class org.sbml.libsbml.GeneralGlyph
Copy constructor.
GeneralGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a new GeneralGlyph with the given LayoutPkgNamespaces object.
GeneralGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a glyph with the given LayoutPkgNamespaces and id.
GeneralGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a glyph with the given LayoutPkgNamespaces, id and set the id of the associated element to the second argument.
GeneralGlyph(XMLNode) - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a new GeneralGlyph from the given XMLNode
GeneralGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.GeneralGlyph
Creates a new GeneralGlyph from the given XMLNode
GeneralWarningNotSpecified - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
get(long) - Method in class org.sbml.libsbml.ASTNodeList
 
get(long) - Method in class org.sbml.libsbml.CVTermList
 
get(long) - Method in class org.sbml.libsbml.DateList
 
get(long) - Method in class org.sbml.libsbml.ListOf
Get an item from the list.
get(long) - Method in class org.sbml.libsbml.ListOfColorDefinitions
Returns a pointer to the ColorDefinition with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
get(long) - Method in class org.sbml.libsbml.ListOfCompartments
Get a Compartment object from the ListOfCompartments.
get(long) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
get(long) - Method in class org.sbml.libsbml.ListOfConstraints
get(long) - Method in class org.sbml.libsbml.ListOfCurveElements
Returns a pointer to the RenderPoint with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfDeletions
Get a Deletion from the ListOfDeletions.
get(long) - Method in class org.sbml.libsbml.ListOfDrawables
Returns a pointer to the Transformation2D with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfEventAssignments
get(long) - Method in class org.sbml.libsbml.ListOfEvents
Get an Event from the ListOfEvents.
get(long) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
get(long) - Method in class org.sbml.libsbml.ListOfFbcAssociations
get(long) - Method in class org.sbml.libsbml.ListOfFluxBounds
Get a FluxBound from the ListOfFluxBounds.
get(long) - Method in class org.sbml.libsbml.ListOfFluxObjectives
get(long) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
get(long) - Method in class org.sbml.libsbml.ListOfFunctionTerms
get(long) - Method in class org.sbml.libsbml.ListOfGeneAssociations
get(long) - Method in class org.sbml.libsbml.ListOfGeneProducts
get(long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Returns a pointer to the GlobalRenderInformation with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfGlobalStyles
Returns a pointer to the GlobalStyle with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Returns a pointer to the GradientBase with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfGradientStops
Returns a pointer to the GradientStop with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
get(long) - Method in class org.sbml.libsbml.ListOfGroups
Get a Group from the ListOfGroups.
get(long) - Method in class org.sbml.libsbml.ListOfInitialAssignments
get(long) - Method in class org.sbml.libsbml.ListOfInputs
Get a Input from the ListOfInputs.
get(long) - Method in class org.sbml.libsbml.ListOfLayouts
Get a Layout from the ListOfLayouts.
get(long) - Method in class org.sbml.libsbml.ListOfLineEndings
Returns a pointer to the LineEnding with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfLineSegments
get(long) - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the LocalParameter object located at position n within this ListOfLocalParameters instance.
get(long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Returns a pointer to the LocalRenderInformation with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfLocalStyles
Returns a pointer to the LocalStyle with the given index or null if the index is invalid.
get(long) - Method in class org.sbml.libsbml.ListOfMembers
Get a Member from the ListOfMembers.
get(long) - Method in class org.sbml.libsbml.ListOfModelDefinitions
get(long) - Method in class org.sbml.libsbml.ListOfObjectives
Get an Objective from the ListOfObjectives.
get(long) - Method in class org.sbml.libsbml.ListOfOutputs
Get a Output from the ListOfOutputs.
get(long) - Method in class org.sbml.libsbml.ListOfParameters
Returns the Parameter object located at position n within this ListOfParameters instance.
get(long) - Method in class org.sbml.libsbml.ListOfPorts
Get a Port from the ListOfPorts.
get(long) - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
get(long) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
get(long) - Method in class org.sbml.libsbml.ListOfReactions
Get a Reaction from the ListOfReactions.
get(long) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
get(long) - Method in class org.sbml.libsbml.ListOfReplacedElements
get(long) - Method in class org.sbml.libsbml.ListOfRules
Get a Rule from the ListOfRules.
get(long) - Method in class org.sbml.libsbml.ListOfSpecies
Get a Species from the ListOfSpecies.
get(long) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
get(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
get(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
get(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
get(long) - Method in class org.sbml.libsbml.ListOfSubmodels
Get a Submodel from the ListOfSubmodels.
get(long) - Method in class org.sbml.libsbml.ListOfTextGlyphs
Get a TextGlyph from the ListOfTextGlyphs.
get(long) - Method in class org.sbml.libsbml.ListOfTransitions
get(long) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
get(long) - Method in class org.sbml.libsbml.ListOfUnits
Get a Unit from the ListOfUnits.
get(long) - Method in class org.sbml.libsbml.ModelCreatorList
 
get(long) - Method in class org.sbml.libsbml.SBaseList
 
get(long) - Method in class org.sbml.libsbml.SBMLNamespacesList
 
get(String) - Method in class org.sbml.libsbml.ListOfColorDefinitions
Returns a pointer to the ColorDefinition with the given id or null if the id is invalid.
get(String) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Get a CompartmentGlyph from the ListOfCompartmentGlyphs based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfCompartments
Get a Compartment object from the ListOfCompartments based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Get a CompartmentType object from the ListOfCompartmentTypes based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfDeletions
Get a Deletion from the ListOfDeletions based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfDrawables
Returns a pointer to the Transformation2D with the given id or null if the id is invalid.
get(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
Get a EventAssignment from the ListOfEventAssignments based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfEvents
Get an Event from the ListOfEvents based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Get a Model from the ListOfExternalModelDefinitions based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfFbcAssociations
Get a FbcAssociation from the ListOfFbcAssociations based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfFluxBounds
Get a FluxBound from the ListOfFluxBounds based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfFluxObjectives
Get a FluxObjective from the ListOfFluxObjectives based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Get a FunctionDefinition from the ListOfFunctionDefinitions based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfFunctionTerms
Get a FunctionTerm from the ListOfFunctionTerms based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfGeneAssociations
Get a GeneAssociation from the ListOfGeneAssociations based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfGeneProducts
Get a GeneProduct from the ListOfGeneProducts based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Returns a pointer to the GlobalRenderInformation with the given id or null if the id is invalid.
get(String) - Method in class org.sbml.libsbml.ListOfGlobalStyles
Returns a pointer to the GlobalStyle with the given id or null if the id is invalid.
get(String) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Returns a pointer to the GradientBase with the given id or null if the id is invalid.
get(String) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Get a GraphicalObject from the ListOfGraphicalObjects based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfGroups
Get a Group from the ListOfGroups based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
Get a InitialAssignment from the ListOfInitialAssignments based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfInputs
Get a Input from the ListOfInputs based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfLayouts
Get a Layout from the ListOfLayouts based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfLineEndings
Returns a pointer to the LineEnding with the given id or null if the id is invalid.
get(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the first LocalParameter object matching the given identifier.
get(String) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Returns a pointer to the LocalRenderInformation with the given id or null if the id is invalid.
get(String) - Method in class org.sbml.libsbml.ListOfLocalStyles
Returns a pointer to the LocalStyle with the given id or null if the id is invalid.
get(String) - Method in class org.sbml.libsbml.ListOfMembers
Get a Member from the ListOfMembers based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfModelDefinitions
Get a Model from the ListOfModelDefinitions based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfObjectives
Get an Objective from the ListOfObjectives based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfOutputs
Get a Output from the ListOfOutputs based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfParameters
Returns the first Parameter object matching the given identifier.
get(String) - Method in class org.sbml.libsbml.ListOfPorts
Get a Port from the ListOfPorts based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
Get a QualitativeSpecies from the ListOfQualitativeSpecies based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Get a ReactionGlyph from the ListOfReactionGlyphs based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfReactions
Get a Reaction from the ListOfReactions based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Get a ReferenceGlyph from the ListOfReferenceGlyphs based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfRules
Get a Rule from the ListOfRules based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfSpecies
Get a Species from the ListOfSpecies based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Get a SpeciesGlyph from the ListOfSpeciesGlyphs based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Get a SpeciesReferenceGlyph from the ListOfSpeciesReferenceGlyphs based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Get a SpeciesReference from the ListOfSpeciesReferences based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Get a SpeciesType from the ListOfSpeciesTypes based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfSubmodels
Get a Model from the ListOfSubmodels based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfTextGlyphs
Get a TextGlyph from the ListOfTextGlyphs based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfTransitions
Get a Transition from the ListOfTransitions based on its identifier.
get(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Get a UnitDefinition from the ListOfUnitDefinitions based on its identifier.
get(String) - Method in class org.sbml.libsbml.StringSet
 
get_ostream() - Method in class org.sbml.libsbml.OStream
 
getAbsoluteValue() - Method in class org.sbml.libsbml.RelAbsVector
Returns the absolute coordinate value.
getActiveObjective() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the current active objective.
getActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
Returns the value of the 'activeObjective' attribute of this ListOfObjectives.
getActiveObjectiveId() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the id of the current active objective.
getAddDefaultUnits() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the flag indicating whether default units should be added when converting to L3 or not.
getAdditionalGraphicalObject(long) - Method in class org.sbml.libsbml.Layout
Returns the additional graphical object with the given index.
getAdditionalGraphicalObject(String) - Method in class org.sbml.libsbml.Layout
Returns the additional graphical object that has the given id, or null if no graphical object has the id.
getAllElementIdList() - Method in class org.sbml.libsbml.Model
Returns the internal list of the identifiers of all elements within this Model object.
getAllElementMetaIdList() - Method in class org.sbml.libsbml.Model
Returns the internal list of the metaids of all elements within this Model object.
getAllRegisteredPackageNames() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns a list of registered packages.
getAlpha() - Method in class org.sbml.libsbml.ColorDefinition
Returns the alpha color component.
getAncestorOfType(int) - Method in class org.sbml.libsbml.SBase
Returns the first ancestor object that has the given SBML type code from the given package.
getAncestorOfType(int, String) - Method in class org.sbml.libsbml.SBase
Returns the first ancestor object that has the given SBML type code from the given package.
getAnnotation() - Method in class org.sbml.libsbml.SBase
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
getAnnotationString() - Method in class org.sbml.libsbml.SBase
Returns the content of the 'annotation' subelement of this object as a character string.
getAreaUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'areaUnits' attribute of this Model.
getArgument(long) - Method in class org.sbml.libsbml.FunctionDefinition
Get the nth argument to this function.
getArgument(String) - Method in class org.sbml.libsbml.FunctionDefinition
Get the argument named name to this FunctionDefinition.
getAssignmentRule(String) - Method in class org.sbml.libsbml.Model
Get a Rule object based on the variable to which it assigns a value.
getAssignmentRuleByVariable(String) - Method in class org.sbml.libsbml.Model
Get a Rule object based on the variable to which it assigns a value.
getAssociatedSpecies() - Method in class org.sbml.libsbml.GeneProduct
Returns the value of the 'associatedSpecies' attribute of this GeneProduct.
getAssociation() - Method in class org.sbml.libsbml.GeneAssociation
Returns Association object of this GeneAssociation.
getAssociation() - Method in class org.sbml.libsbml.GeneProductAssociation
Returns the 'association' element of this GeneProductAssociation.
getAssociation(long) - Method in class org.sbml.libsbml.FbcAnd
Get the nth object from the ListOfFbcAssociations.
getAssociation(long) - Method in class org.sbml.libsbml.FbcOr
getAssociation(String) - Method in class org.sbml.libsbml.FbcAnd
Get an FbcAssociation from the ListOfFbcAssociations based on its identifier.
getAssociation(String) - Method in class org.sbml.libsbml.FbcOr
Get a Association from the ListOfFbcAssociations based on its identifier.
getAttributes() - Method in class org.sbml.libsbml.XMLToken
Returns the attributes of the XML element represented by this token.
getAttributesLength() - Method in class org.sbml.libsbml.XMLToken
Returns the number of attributes on this XMLToken object.
getAttrIndex(String) - Method in class org.sbml.libsbml.XMLToken
Returns the index of the attribute with the given name and namespace URI.
getAttrIndex(String, String) - Method in class org.sbml.libsbml.XMLToken
Returns the index of the attribute with the given name and namespace URI.
getAttrIndex(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Returns the index of the attribute defined by the given XMLTriple object.
getAttrName(int) - Method in class org.sbml.libsbml.XMLToken
Returns the name of the nth attribute in this token's list of attributes.
getAttrPrefix(int) - Method in class org.sbml.libsbml.XMLToken
Returns the prefix of the nth attribute in this token's list of attributes.
getAttrPrefixedName(int) - Method in class org.sbml.libsbml.XMLToken
Returns the prefixed name of the nth attribute in this token's list of attributes.
getAttrURI(int) - Method in class org.sbml.libsbml.XMLToken
Returns the XML namespace URI of the nth attribute in this token's list of attributes.
getAttrValue(int) - Method in class org.sbml.libsbml.XMLToken
Returns the value of the nth attribute in this token's list of attributes.
getAttrValue(String) - Method in class org.sbml.libsbml.XMLToken
Returns the value of the attribute with a given name and XML namespace URI.
getAttrValue(String, String) - Method in class org.sbml.libsbml.XMLToken
Returns the value of the attribute with a given name and XML namespace URI.
getAttrValue(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Returns the value of the attribute specified by a given XMLTriple object.
getBackgroundColor() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'backgroundColor' attribute of this DefaultValues.
getBackgroundColor() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the background color which is either the id of a color in the list of color definitions, or a color value.
getBasePoint1() - Method in class org.sbml.libsbml.CubicBezier
Returns the first base point of the curve (the one closer to the starting point).
getBasePoint2() - Method in class org.sbml.libsbml.CubicBezier
Returns the second base point of the curve (the one closer to the end point).
getBiologicalQualifierType() - Method in class org.sbml.libsbml.CVTerm
Returns the biological qualifier type of this CVTerm object.
getBlue() - Method in class org.sbml.libsbml.ColorDefinition
Returns the blue color component.
getBody() - Method in class org.sbml.libsbml.FunctionDefinition
Get the mathematical expression that is the body of this FunctionDefinition object.
getBoolValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option as a Boolean.
getBoolValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as a Boolean.
getBoundaryCondition() - Method in class org.sbml.libsbml.Species
Get the value of the 'boundaryCondition' attribute.
getBoundingBox() - Method in class org.sbml.libsbml.GraphicalObject
Returns the bounding box for the GraphicalObject.
getBoundingBox() - Method in class org.sbml.libsbml.LineEnding
Returns a pointer to the viewport bounding box.
getBoundingBoxExplicitlySet() - Method in class org.sbml.libsbml.GraphicalObject
 
getByIdRef(String) - Method in class org.sbml.libsbml.ListOfMembers
Get a Member from the ListOfMembers based on the element to which it refers.
getBySpecies(String) - Method in class org.sbml.libsbml.ListOfInputs
Get a Input from the ListOfInputs based on the qualitativeSpecies to which it refers.
getBySpecies(String) - Method in class org.sbml.libsbml.ListOfOutputs
Get a Output from the ListOfOutputs based on the qualitativeSpecies to which it refers.
getCategory() - Method in class org.sbml.libsbml.XMLError
Returns the category of this error.
getCategoryAsString() - Method in class org.sbml.libsbml.XMLError
Returns a string describing the category of this error.
getCenterX() - Method in class org.sbml.libsbml.RadialGradient
Returns the x coordinate for the center point as a reference.
getCenterY() - Method in class org.sbml.libsbml.RadialGradient
Returns the y coordinate for the center point as a reference.
getCenterZ() - Method in class org.sbml.libsbml.RadialGradient
Returns the z coordinate for the center point as a reference.
getCharacter() - Method in class org.sbml.libsbml.ASTNode
Returns the value of this node as a single character.
getCharacters() - Method in class org.sbml.libsbml.XMLToken
Returns the character text of token.
getCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Returns the value of the 'charge' attribute of this FbcSpeciesPlugin.
getCharge() - Method in class org.sbml.libsbml.Species
Get the value of the 'charge' attribute.
getChemicalFormula() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Returns the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.
getChild(long) - Method in class org.sbml.libsbml.ASTNode
Returns the child at index n of this node.
getChild(long) - Method in class org.sbml.libsbml.XMLNode
Returns the nth child of this XMLNode.
getChild(String) - Method in class org.sbml.libsbml.XMLNode
Returns the first child of this XMLNode with the corresponding name.
getClassName() - Method in class org.sbml.libsbml.ASTNode
Returns the MathML class attribute value of this ASTNode.
getCoefficient() - Method in class org.sbml.libsbml.FluxObjective
Returns the value of the 'coefficient' attribute of this FluxObjective.
getColorDefinition(long) - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the color definition with the given index, or null if the index is invalid.
getColorDefinition(String) - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the color definition with the given id, or null if there is no color definition with that id.
getColumn() - Method in class org.sbml.libsbml.SBase
Returns the column number where this object first appears in the XML representation of the SBML document.
getColumn() - Method in class org.sbml.libsbml.XMLError
Returns the column number in the XML input near where the error, warning or other diagnostic occurred.
getColumn() - Method in class org.sbml.libsbml.XMLToken
Returns the column number at which this token occurs in the input.
getComparisonCaseSensitivity() - Method in class org.sbml.libsbml.L3ParserSettings
Returns true if the parser is configured to match built-in symbols in a case-insensitive way.
getCompartment() - Method in class org.sbml.libsbml.QualitativeSpecies
Returns the value of the 'compartment' attribute of this QualitativeSpecies.
getCompartment() - Method in class org.sbml.libsbml.Reaction
(SBML Level 3 only) Returns the value of the 'compartment' attribute on the Reaction.
getCompartment() - Method in class org.sbml.libsbml.Species
Get the compartment in which this species is located.
getCompartment(long) - Method in class org.sbml.libsbml.Model
Get the nth Compartment object in this Model.
getCompartment(String) - Method in class org.sbml.libsbml.Model
Get a Compartment object based on its identifier.
getCompartmentGlyph(long) - Method in class org.sbml.libsbml.Layout
Returns the compartment glyph with the given index.
getCompartmentGlyph(String) - Method in class org.sbml.libsbml.Layout
Returns the compartment glyph that has the given id, or null if no compartment glyph has the id.
getCompartmentId() - Method in class org.sbml.libsbml.CompartmentGlyph
Returns the id of the associated compartment.
getCompartmentType() - Method in class org.sbml.libsbml.Compartment
Get the value of the 'compartmentType' attribute of this Compartment object.
getCompartmentType(long) - Method in class org.sbml.libsbml.Model
Get the nth CompartmentType object in this Model.
getCompartmentType(String) - Method in class org.sbml.libsbml.Model
Get a CompartmentType object based on its identifier.
getConstant() - Method in class org.sbml.libsbml.Compartment
Get the value of the 'constant' attribute of this Compartment object.
getConstant() - Method in class org.sbml.libsbml.Parameter
Gets the value of the 'constant' attribute of this Parameter instance.
getConstant() - Method in class org.sbml.libsbml.QualitativeSpecies
Returns the value of the 'constant' attribute of this QualitativeSpecies.
getConstant() - Method in class org.sbml.libsbml.Species
Get the value of the 'constant' attribute.
getConstant() - Method in class org.sbml.libsbml.SpeciesReference
Get the value of the 'constant' attribute.
getConstraint(long) - Method in class org.sbml.libsbml.Model
Get the nth Constraint object in this Model.
getConversionFactor() - Method in class org.sbml.libsbml.Model
Returns the value of the 'conversionFactor' attribute of this Model.
getConversionFactor() - Method in class org.sbml.libsbml.ReplacedElement
Returns the value of the 'conversionFactor' attribute of this ReplacedElement.
getConversionFactor() - Method in class org.sbml.libsbml.Species
Get the value of the 'conversionFactor' attribute.
getConverterByIndex(int) - Method in class org.sbml.libsbml.SBMLConverterRegistry
Returns the converter with the given index number.
getConverterFor(ConversionProperties) - Method in class org.sbml.libsbml.SBMLConverterRegistry
Returns the converter that best matches the given configuration properties.
getCreatedDate() - Method in class org.sbml.libsbml.ModelHistory
Returns the 'creation date' portion of this ModelHistory object.
getCreator(long) - Method in class org.sbml.libsbml.ModelHistory
Get the nth ModelCreator object stored in this ModelHistory object.
getCurve() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the curve object for the reaction glyph
getCurve() - Method in class org.sbml.libsbml.ReactionGlyph
Returns the curve object for the reaction glyph
getCurve() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns the curve object for the reference glyph
getCurve() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns the curve object for the species reference glyph
getCurveElement(long) - Method in class org.sbml.libsbml.RenderCurve
Returns a pointer to the curve segment with the given index or null if the id is invalid.
getCurveExplicitlySet() - Method in class org.sbml.libsbml.GeneralGlyph
 
getCurveExplicitlySet() - Method in class org.sbml.libsbml.ReactionGlyph
 
getCurveExplicitlySet() - Method in class org.sbml.libsbml.ReferenceGlyph
 
getCurveExplicitlySet() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
 
getCurveSegment(long) - Method in class org.sbml.libsbml.Curve
Returns a pointer to the curve segment with the given index.
getCVTerm(long) - Method in class org.sbml.libsbml.SBase
Returns the nth CVTerm in the list of CVTerms of this SBML object.
getCVTerms() - Method in class org.sbml.libsbml.SBase
Returns a list of CVTerm objects in the annotations of this SBML object.
getCX() - Method in class org.sbml.libsbml.Ellipse
Returns the x coordinate for the center point as a reference.
getCY() - Method in class org.sbml.libsbml.Ellipse
Returns the y coordinate for the center point as a reference.
getCZ() - Method in class org.sbml.libsbml.Ellipse
Returns the z coordinate for the center point as a reference.
getDashByIndex(long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Returns the dash at the given index.
getDateAsString() - Method in class org.sbml.libsbml.Date
Returns the current Date value in text-string form.
getDay() - Method in class org.sbml.libsbml.Date
Returns the day from this Date.
getDefault_z() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'default_z' attribute of this DefaultValues.
getDefaultL3ParserSettings() - Static method in class org.sbml.libsbml.libsbml
Returns a copy of the default Level 3 ('L3') formula parser settings.
getDefaultLevel() - Static method in class org.sbml.libsbml.CompExtension
Returns the default SBML Level used by this libSBML package extension.
getDefaultLevel() - Static method in class org.sbml.libsbml.FbcExtension
Returns the default SBML Level used by this libSBML package extension.
getDefaultLevel() - Static method in class org.sbml.libsbml.GroupsExtension
Returns the default SBML Level implemented by this libSBML extension.
getDefaultLevel() - Static method in class org.sbml.libsbml.LayoutExtension
Returns the default SBML Level used by this libSBML package extension.
getDefaultLevel() - Static method in class org.sbml.libsbml.QualExtension
Returns the default SBML Level used by this libSBML package extension.
getDefaultLevel() - Static method in class org.sbml.libsbml.RenderExtension
Returns the default SBML Level this extension.
getDefaultLevel() - Static method in class org.sbml.libsbml.SBMLDocument
The default SBML Level of new SBMLDocument objects.
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.CompExtension
Returns the default version of the SBML Level 3 package implemented by this libSBML extension.
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.FbcExtension
Returns the default version of the SBML Level 3 package implemented by this libSBML extension.
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.GroupsExtension
Returns the default version of the SBML Level 3 package implemented by this libSBML extension.
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.LayoutExtension
Returns the default version of the SBML Level 3 package implemented by this libSBML extension.
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.QualExtension
Returns the default version of the SBML Level 3 package implemented by this libSBML extension.
getDefaultPackageVersion() - Static method in class org.sbml.libsbml.RenderExtension
Returns the default SBML version this extension.
getDefaultProperties() - Method in class org.sbml.libsbml.CobraToFbcConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.CompFlatteningConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.FbcToCobraConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.FbcV1ToV2Converter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.FbcV2ToV1Converter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLIdConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLInferUnitsConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLLevel1Version1Converter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLLocalParameterConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLReactionConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLRuleConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Returns the default properties of this converter.
getDefaultProperties() - Method in class org.sbml.libsbml.SBMLUnitsConverter
Returns the default properties of this converter.
getDefaultTerm() - Method in class org.sbml.libsbml.ListOfFunctionTerms
Get the DefaultTerm from this ListOfFunctionTerms.
getDefaultTerm() - Method in class org.sbml.libsbml.Transition
getDefaultValues() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Returns the value of the 'defaultValues' element of this ListOfGlobalRenderInformation.
getDefaultValues() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Returns the value of the 'defaultValues' element of this ListOfLocalRenderInformation.
getDefaultVersion() - Static method in class org.sbml.libsbml.CompExtension
Returns the default SBML Version used by this libSBML package extension.
getDefaultVersion() - Static method in class org.sbml.libsbml.FbcExtension
Returns the default SBML Version used by this libSBML package extension.
getDefaultVersion() - Static method in class org.sbml.libsbml.GroupsExtension
Returns the default SBML Version implemented by this libSBML extension.
getDefaultVersion() - Static method in class org.sbml.libsbml.LayoutExtension
Returns the default SBML Version used by this libSBML package extension.
getDefaultVersion() - Static method in class org.sbml.libsbml.QualExtension
Returns the default SBML Version used by this libSBML package extension.
getDefaultVersion() - Static method in class org.sbml.libsbml.RenderExtension
Returns the default SBML Version this extension.
getDefaultVersion() - Static method in class org.sbml.libsbml.SBMLDocument
The default Version of new SBMLDocument objects.
getDefinitionURL() - Method in class org.sbml.libsbml.ASTNode
Returns the MathML definitionURL attribute value.
getDefinitionURLString() - Method in class org.sbml.libsbml.ASTNode
Returns the MathML definitionURL attribute value as a string.
getDelay() - Method in class org.sbml.libsbml.Event
Get the assignment delay portion of this Event, if there is one.
getDeletion() - Method in class org.sbml.libsbml.ReplacedElement
Returns the value of the 'deletion' attribute of this ReplacedElement.
getDeletion(long) - Method in class org.sbml.libsbml.Submodel
Returns the deletion with the given index.
getDeletion(String) - Method in class org.sbml.libsbml.Submodel
Returns the deletion with the given id.
getDenominator() - Method in class org.sbml.libsbml.ASTNode
Returns the value of the denominator of this node.
getDenominator() - Method in class org.sbml.libsbml.SpeciesReference
Get the value of the 'denominator' attribute, for the case of a rational-numbered stoichiometry or a model in SBML Level 1.
getDepth() - Method in class org.sbml.libsbml.Dimensions
Returns the depth.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Compartment
Constructs and returns a UnitDefinition that corresponds to the units of this Compartment object's designated size.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Delay
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this Delay.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.EventAssignment
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this EventAssignment.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.InitialAssignment
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this InitialAssignment.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.KineticLaw
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this KineticLaw.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.LocalParameter
Constructs and returns a UnitDefinition that corresponds to the units of this LocalParameter's value.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Parameter
Constructs and returns a UnitDefinition that corresponds to the units of this Parameter's value.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Rule
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this Rule.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.Species
Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or concentration.
getDerivedUnitDefinition() - Method in class org.sbml.libsbml.StoichiometryMath
Calculates and returns a UnitDefinition object that expresses the units returned by the math expression in this StoichiometryMath object.
getDescription() - Method in class org.sbml.libsbml.ConversionOption
Returns the description string for this option.
getDescription(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the description string for a given option in this properties object.
getDExplicitlySet() - Method in class org.sbml.libsbml.Dimensions
Checks whether the depth has been explicitly set.
getDimensions() - Method in class org.sbml.libsbml.BoundingBox
Returns the dimensions of the BoundingBox as reference to a Dimensions object.
getDimensions() - Method in class org.sbml.libsbml.Layout
Returns the dimensions of the layout.
getDimensionsExplicitlySet() - Method in class org.sbml.libsbml.BoundingBox
Return true or false based on whether Dimensions have been set.
getDimensionsExplicitlySet() - Method in class org.sbml.libsbml.Layout
Predicate returning true if the dimensions has been set
getDisabledPlugin(long) - Method in class org.sbml.libsbml.SBase
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
getDivider() - Method in class org.sbml.libsbml.CompModelPlugin
Get the string used as the divider between names when renaming and flattening models.
getDocument() - Method in class org.sbml.libsbml.SBMLConverter
Returns the SBML document that is the subject of the conversions.
getDocument() - Method in class org.sbml.libsbml.SBMLValidator
Returns the current SBML document in use by this validator.
getDoubleValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option as a double.
getDoubleValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as a double.
getElement(long) - Method in class org.sbml.libsbml.Polygon
Returns a pointer to the segment with the given index or null if the id is invalid.
getElement(long) - Method in class org.sbml.libsbml.RenderCurve
Returns a pointer to the curve segment with the given index or null if the id is invalid.
getElement(long) - Method in class org.sbml.libsbml.RenderGroup
Returns pointer to the element with index n.
getElement(String) - Method in class org.sbml.libsbml.RenderGroup
Returns pointer to the element with the given id.
getElementByMetaId(String) - Method in class org.sbml.libsbml.CompModelPlugin
Returns the first child element it can find with the given meta identifier, or itself if it has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.CompSBasePlugin
Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Event
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Group
Returns the first child element that has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.GroupsModelPlugin
Returns the first child element that has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.KineticLaw
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.ListOf
Returns the first child element found with the given meta-identifier.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Model
Returns the first child element it can find with the given metaid.
getElementByMetaId(String) - Method in class org.sbml.libsbml.QualModelPlugin
Returns the first child element that has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Reaction
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.SBase
Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.SBasePlugin
Return the first child object found with a given meta identifier.
getElementByMetaId(String) - Method in class org.sbml.libsbml.SBaseRef
Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Submodel
Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.Transition
Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
getElementByMetaId(String) - Method in class org.sbml.libsbml.UnitDefinition
Returns the first child element it can find with the given metaid, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.CompModelPlugin
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.CompSBasePlugin
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Event
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Group
Returns the first child element that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.GroupsModelPlugin
Returns the first child element that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.KineticLaw
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOf
Returns the first child element found that has the given identifier.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfPorts
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfRules
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Model
Returns the first child element found that has the given id.
getElementBySId(String) - Method in class org.sbml.libsbml.QualModelPlugin
Returns the first child element that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Reaction
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.SBase
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.SBasePlugin
Return the first child object found with a given identifier.
getElementBySId(String) - Method in class org.sbml.libsbml.SBaseRef
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Submodel
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.Transition
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementBySId(String) - Method in class org.sbml.libsbml.UnitDefinition
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
getElementName() - Method in class org.sbml.libsbml.Association
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.BoundingBox
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ColorDefinition
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Compartment
Returns the XML element name of this object
getElementName() - Method in class org.sbml.libsbml.CompartmentGlyph
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.CompartmentType
Returns the XML element name of this object
getElementName() - Method in class org.sbml.libsbml.Constraint
Returns the XML element name of this object, which for Constraint, is always 'constraint'.
getElementName() - Method in class org.sbml.libsbml.CubicBezier
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Curve
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.DefaultTerm
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.DefaultValues
Returns the XML element name of this DefaultValues object.
getElementName() - Method in class org.sbml.libsbml.Delay
Returns the XML element name of this object, which for Delay, is always 'delay'.
getElementName() - Method in class org.sbml.libsbml.Deletion
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Dimensions
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Ellipse
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Event
Returns the XML element name of this object, which for Event, is always 'event'.
getElementName() - Method in class org.sbml.libsbml.EventAssignment
Returns the XML element name of this object, which for EventAssignment, is always 'eventAssignment'.
getElementName() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.FbcAnd
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.FbcAssociation
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.FbcOr
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.FluxBound
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.FluxObjective
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.FunctionDefinition
Returns the XML element name of this object, which for FunctionDefinition, is always 'functionDefinition'.
getElementName() - Method in class org.sbml.libsbml.FunctionTerm
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.GeneAssociation
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.GeneProduct
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.GeneProductAssociation
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.GeneProductRef
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.GlobalRenderInformation
Returns the XML element name of this object, which for GlobalRenderInformation, is always 'renderInformation'.
getElementName() - Method in class org.sbml.libsbml.GlobalStyle
Returns the XML element name of this object, which for GlobalStyle, is always 'renderInformation'.
getElementName() - Method in class org.sbml.libsbml.GradientBase
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.GradientStop
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.GraphicalObject
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Group
Returns the XML element name of this Group object.
getElementName() - Method in class org.sbml.libsbml.Image
Returns the XML element name of this object, which for Image, is always 'image'.
getElementName() - Method in class org.sbml.libsbml.InitialAssignment
Returns the XML element name of this object, which for InitialAssignment, is always 'initialAssignment'.
getElementName() - Method in class org.sbml.libsbml.Input
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.KineticLaw
Returns the XML element name of this object, which for Species, is always 'kineticLaw'.
getElementName() - Method in class org.sbml.libsbml.Layout
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.LinearGradient
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.LineEnding
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.LineSegment
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOf
Returns the XML element name of this object, which for ListOf, is always 'listOf'.
getElementName() - Method in class org.sbml.libsbml.ListOfColorDefinitions
Returns the XML element name of this object, which for ListOfColorDefinitions, is always 'listOfColorDefinitions'.
getElementName() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfCompartments
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfConstraints
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfCurveElements
Returns the XML element name of this object, which for ListOfCurveElements, is always 'listOfCurveElements'.
getElementName() - Method in class org.sbml.libsbml.ListOfDeletions
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfDrawables
Returns the name of this element.
getElementName() - Method in class org.sbml.libsbml.ListOfEventAssignments
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfEvents
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfFluxBounds
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfFunctionTerms
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfGeneAssociations
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfGeneProducts
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Returns the XML element name of this object, which for ListOfGlobalRenderInformation, is always 'listOfGlobalRenderInformation'.
getElementName() - Method in class org.sbml.libsbml.ListOfGlobalStyles
Returns the XML element name of this object, which for ListOfGlobalStyles, is always 'listOfStyles'.
getElementName() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Returns the XML element name of this object, which for ListOfGradientDefinitions, is always 'listOfGradientDefinitions'.
getElementName() - Method in class org.sbml.libsbml.ListOfGradientStops
Returns the XML element name of this object, which for ListOfGradientStops, is always 'listOfGradientStops'.
getElementName() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfGroups
Returns the XML element name of this ListOfGroups object.
getElementName() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfInputs
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfLayouts
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfLineEndings
Returns the XML element name of this object, which for ListOfLineEndings, is always 'listOfLineEndings'.
getElementName() - Method in class org.sbml.libsbml.ListOfLineSegments
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Returns the XML element name of this object, which for ListOfLocalRenderInformation, is always 'listOfRenderInformation'.
getElementName() - Method in class org.sbml.libsbml.ListOfLocalStyles
Returns the XML element name of this object, which for ListOfLocalStyles, is always 'listOfLocalStyles'.
getElementName() - Method in class org.sbml.libsbml.ListOfMembers
Returns the XML element name of this ListOfMembers object.
getElementName() - Method in class org.sbml.libsbml.ListOfModelDefinitions
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfObjectives
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfOutputs
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfParameters
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfPorts
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfReactions
Returns the XML element name of this object
getElementName() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfReplacedElements
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfRules
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfSpecies
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfSubmodels
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ListOfTransitions
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ListOfUnits
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.LocalParameter
Returns the XML element name of this object, which for LocalParameter, is always 'localParameter'.
getElementName() - Method in class org.sbml.libsbml.LocalRenderInformation
Returns the XML element name of this object, which for LocalRenderInformation, is always 'renderInformation'.
getElementName() - Method in class org.sbml.libsbml.LocalStyle
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Member
Returns the XML element name of this Member object.
getElementName() - Method in class org.sbml.libsbml.Model
Returns the XML element name of this object, which for Model, is always 'model'.
getElementName() - Method in class org.sbml.libsbml.ModelDefinition
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Returns the XML element name of this object, which for Species, is always 'modifierSpeciesReference'.
getElementName() - Method in class org.sbml.libsbml.Objective
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Output
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.Parameter
Returns the XML element name of this object, which for Parameter, is always 'parameter'.
getElementName() - Method in class org.sbml.libsbml.Point
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Polygon
Returns the XML element name of this object, which for Polygon, is always 'polygon'.
getElementName() - Method in class org.sbml.libsbml.Port
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Priority
Returns the XML element name of this object, which for Priority, is always 'priority'.
getElementName() - Method in class org.sbml.libsbml.QualitativeSpecies
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.RadialGradient
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Reaction
Returns the XML element name of this object, which for Reaction, is always 'reaction'.
getElementName() - Method in class org.sbml.libsbml.ReactionGlyph
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Rectangle
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.RenderCubicBezier
Returns the XML element name of this object, which for RenderCubicBezier, is always 'element'.
getElementName() - Method in class org.sbml.libsbml.RenderCurve
Returns the XML element name of this object, which for RenderCurve, is always 'curve'.
getElementName() - Method in class org.sbml.libsbml.RenderGroup
Returns the XML element name of this object, which for RenderGroup, is always 'g'.
getElementName() - Method in class org.sbml.libsbml.RenderPoint
Returns the XML element name of this object, which for RenderPoint, depends on the context.
getElementName() - Method in class org.sbml.libsbml.ReplacedBy
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.ReplacedElement
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Rule
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.SBase
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.SBaseRef
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.SBMLDocument
Returns the XML element name of this object, which for SBMLDocument, is always 'sbml'.
getElementName() - Method in class org.sbml.libsbml.Species
Returns the XML element name of this object, which for Species, is always 'species'.
getElementName() - Method in class org.sbml.libsbml.SpeciesGlyph
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.SpeciesReference
Returns the XML element name of this object, which for SpeciesReference, is always 'speciesReference'.
getElementName() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.SpeciesType
Returns the XML element name of this object, which for SpeciesType, is always 'compartmentType'.
getElementName() - Method in class org.sbml.libsbml.StoichiometryMath
Returns the XML element name of this object, which for StoichiometryMath, is always 'stoichiometryMath'.
getElementName() - Method in class org.sbml.libsbml.Style
Returns the XML element name of this object.
getElementName() - Method in class org.sbml.libsbml.Submodel
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.TextGlyph
Returns the XML element name of this SBML object.
getElementName() - Method in class org.sbml.libsbml.Transition
Returns the XML name of this object.
getElementName() - Method in class org.sbml.libsbml.Trigger
Returns the XML element name of this object, which for Trigger, is always 'trigger'.
getElementName() - Method in class org.sbml.libsbml.Unit
Returns the XML element name of this object, which for Unit, is always 'unit'.
getElementName() - Method in class org.sbml.libsbml.UnitDefinition
Returns the XML element name of this object, which for UnitDefinition, is always 'unitDefinition'.
getElementNamespace() - Method in class org.sbml.libsbml.SBasePlugin
Returns the namespace URI of the package to which this plugin object belongs.
getEmail() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'email' stored in this ModelCreator object.
getEnableRotationalMapping() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'enableRotationalMapping' attribute of this DefaultValues.
getEncoding() - Method in class org.sbml.libsbml.XMLInputStream
Returns the encoding of the XML stream.
getEnd() - Method in class org.sbml.libsbml.LineSegment
Returns the end point of the line.
getEndHead() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'endHead' attribute of this DefaultValues.
getEndHead() - Method in class org.sbml.libsbml.RenderCurve
Returns the id of the LineEnding object to be applied to the end of the curve.
getEndHead() - Method in class org.sbml.libsbml.RenderGroup
Returns the id of the LineEnding object to be applied to the end of the curve.
getError(long) - Method in class org.sbml.libsbml.SBMLDocument
Returns the nth error or warning encountered during parsing, consistency checking, or attempted translation of this model.
getError(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Returns the nth SBMLError object in this log.
getError(long) - Method in class org.sbml.libsbml.XMLErrorLog
Returns the nth XMLError object in this log.
getErrorId() - Method in class org.sbml.libsbml.XMLError
Returns the identifier of this error.
getErrorIdOffset() - Method in class org.sbml.libsbml.XMLError
Returns libSBML's internal numerical offset for the error code associated with this error.
getErrorLog() - Method in class org.sbml.libsbml.SBMLDocument
Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.
getErrorLog() - Method in class org.sbml.libsbml.SBMLValidator
Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.
getErrorLog() - Method in class org.sbml.libsbml.XMLInputStream
Returns the XMLErrorLog used to log parsing problems.
getErrorWithSeverity(long, long) - Method in class org.sbml.libsbml.SBMLDocument
Returns the nth error or warning with the given severity encountered during parsing, consistency checking, or attempted translation of this model.
getErrorWithSeverity(long, long) - Method in class org.sbml.libsbml.SBMLErrorLog
Returns the nth SBMLError object with given severity in this log.
getEvent(long) - Method in class org.sbml.libsbml.Model
Get the nth Event object in this Model.
getEvent(String) - Method in class org.sbml.libsbml.Model
Get an Event object based on its identifier.
getEventAssignment(long) - Method in class org.sbml.libsbml.Event
Return a specific EventAssignment object of this Event.
getEventAssignment(String) - Method in class org.sbml.libsbml.Event
Return the event assignment indicated by the given variable.
getExponent() - Method in class org.sbml.libsbml.ASTNode
Returns the exponent value of this ASTNode.
getExponent() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'exponent' attribute of this unit.
getExponentAsDouble() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'exponent' attribute of this unit.
getExtendedType() - Method in class org.sbml.libsbml.ASTNode
Returns the extended type of this ASTNode.
getExtension(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns an SBMLExtension object with the given package URI or package name.
getExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
Returns the value of the 'extentConversionFactor' attribute of this Submodel.
getExtentUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'extentUnits' attribute of this Model.
getExternalModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the ExternalModelDefinition with the given index.
getExternalModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the model definition object based on its identifier.
getFailure(long) - Method in class org.sbml.libsbml.SBMLValidator
Returns the failure object at index n in this validator's list of failures logged during the last run.
getFamilyName() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'family name' stored in this ModelCreator object.
getFast() - Method in class org.sbml.libsbml.Reaction
Returns the value of the 'fast' attribute of this Reaction.
getFill() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fill' attribute of this DefaultValues.
getFillColor() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
Returns the fill color.
getFillRule() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fillRule' attribute of this DefaultValues.
getFillRule() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
Returns the fill rule.
getFillRuleAsString() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fillRule' attribute of this DefaultValues.
getFloatValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option as a float.
getFloatValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as a float.
getFluxBound(long) - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the FluxBound object that belongs to the given index.
getFluxBound(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the FluxBound object based on its identifier.
getFluxBoundOperation() - Method in class org.sbml.libsbml.FluxBound
Returns the value of the 'operation' attribute of this FluxBound object.
getFluxBoundsForReaction(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Creates a new ListOfFluxBounds object that contains only the FluxBound objects associated with the given Reaction.
getFluxObjective(long) - Method in class org.sbml.libsbml.Objective
getFluxObjective(String) - Method in class org.sbml.libsbml.Objective
Get a FluxObjective from the ListOfFluxObjectives based on its identifier.
getFocalPointX() - Method in class org.sbml.libsbml.RadialGradient
Returns the x coordinate for the focal point as a reference.
getFocalPointY() - Method in class org.sbml.libsbml.RadialGradient
Returns the y coordinate for the focal point as a reference.
getFocalPointZ() - Method in class org.sbml.libsbml.RadialGradient
Returns the z coordinate for the focal point as a reference.
getFontFamily() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fontFamily' attribute of this DefaultValues.
getFontFamily() - Method in class org.sbml.libsbml.RenderGroup
Returns the font family.
getFontFamily() - Method in class org.sbml.libsbml.Text
Returns the font family.
getFontSize() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fontSize' attribute of this DefaultValues.
getFontSize() - Method in class org.sbml.libsbml.RenderGroup
Returns the font size as a reference.
getFontSize() - Method in class org.sbml.libsbml.Text
Returns the font size as a reference.
getFontStyle() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fontStyle' attribute of this DefaultValues.
getFontStyle() - Method in class org.sbml.libsbml.RenderGroup
Returns the font style.
getFontStyle() - Method in class org.sbml.libsbml.Text
Returns the font style.
getFontStyleAsString() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fontStyle' attribute of this DefaultValues.
getFontWeight() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fontWeight' attribute of this DefaultValues.
getFontWeight() - Method in class org.sbml.libsbml.RenderGroup
Returns the font weight.
getFontWeight() - Method in class org.sbml.libsbml.Text
Returns the font weight.
getFontWeightAsString() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'fontWeight' attribute of this DefaultValues.
getFormula() - Method in class org.sbml.libsbml.KineticLaw
Returns the mathematical formula for this KineticLaw object and return it as as a text string.
getFormula() - Method in class org.sbml.libsbml.Rule
Returns the mathematical expression of this Rule in text-string form.
getFunctionDefinition(long) - Method in class org.sbml.libsbml.Model
Get the nth FunctionDefinitions object in this Model.
getFunctionDefinition(String) - Method in class org.sbml.libsbml.Model
Get a FunctionDefinition object based on its identifier.
getFunctionTerm(long) - Method in class org.sbml.libsbml.Transition
getFunctionTerm(String) - Method in class org.sbml.libsbml.Transition
Get a FunctionTerm from the ListOfFunctionTerms based on its identifier.
getGeneAssociation(long) - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the GeneAssociation annotation object that belongs to the given index.
getGeneAssociation(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the GeneAssociation annotation object based on its identifier.
getGeneProduct() - Method in class org.sbml.libsbml.GeneProductRef
Returns the value of the 'geneProduct' attribute of this GeneProductRef.
getGeneProduct(long) - Method in class org.sbml.libsbml.FbcModelPlugin
getGeneProduct(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Get a GeneProduct from the ListOfGeneProducts based on its identifier.
getGeneProductAssociation() - Method in class org.sbml.libsbml.FbcReactionPlugin
Returns the GeneProductAssociation from this FbcReactionPlugin object.
getGeneProductByLabel(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Get a GeneProduct from the ListOfGeneProducts based on its label.
getGeneralGlyph(long) - Method in class org.sbml.libsbml.Layout
Returns the general glyph with the given index.
getGeneralGlyph(String) - Method in class org.sbml.libsbml.Layout
Returns the general glyph that has the given id, or null if no graphical object has the id.
getGivenName() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'given name' stored in this ModelCreator object.
getGlyphId() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns the id of the associated glyph.
getGradientDefinition(long) - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the gradient definition with the given index, or null if the index is invalid.
getGradientDefinition(String) - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the gradient definition with the given id, or null if there is no gradient definition with that id.
getGradientStop(long) - Method in class org.sbml.libsbml.GradientBase
Returns a pointer to the gradient stop with the given index or null if the index is invalid.
getGraphicalObjectId() - Method in class org.sbml.libsbml.TextGlyph
Returns the id of the associated graphical object.
getGreen() - Method in class org.sbml.libsbml.ColorDefinition
Returns the green color component.
getGroup() - Method in class org.sbml.libsbml.LineEnding
Returns a pointer to the group object.
getGroup() - Method in class org.sbml.libsbml.Style
Returns a pointer to the group of the Style.
getGroup(long) - Method in class org.sbml.libsbml.GroupsModelPlugin
Get a Group from the GroupsModelPlugin.
getGroup(String) - Method in class org.sbml.libsbml.GroupsModelPlugin
Get a Group from the GroupsModelPlugin based on its identifier.
getHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
Get the value of the 'hasOnlySubstanceUnits' attribute.
getHeight() - Method in class org.sbml.libsbml.Dimensions
Returns the height.
getHeight() - Method in class org.sbml.libsbml.Image
Returns a reference to the height of the image.
getHeight() - Method in class org.sbml.libsbml.Rectangle
Returns the height of the rectangle
getHost() - Method in class org.sbml.libsbml.SBMLUri
Returns the host portion of the stored URI.
getHour() - Method in class org.sbml.libsbml.Date
Returns the hour from this Date.
getHoursOffset() - Method in class org.sbml.libsbml.Date
Returns the hours of the time zone offset from this Date.
getId() - Method in class org.sbml.libsbml.ASTNode
Returns the MathML id attribute value of this ASTNode.
getId() - Method in class org.sbml.libsbml.BoundingBox
Returns the value of the 'id' attribute of this BoundingBox.
getId() - Method in class org.sbml.libsbml.ColorDefinition
Returns the value of the 'id' attribute of this ColorDefinition.
getId() - Method in class org.sbml.libsbml.Compartment
Returns the value of the 'id' attribute of this Compartment.
getId() - Method in class org.sbml.libsbml.CompartmentType
Returns the value of the 'id' attribute of this CompartmentType.
getId() - Method in class org.sbml.libsbml.Deletion
Returns the value of the 'id' attribute of this Deletion.
getId() - Method in class org.sbml.libsbml.Dimensions
Returns the value of the 'id' attribute of this Dimensions.
getId() - Method in class org.sbml.libsbml.Event
Returns the value of the 'id' attribute of this Event.
getId() - Method in class org.sbml.libsbml.EventAssignment
Returns the value of the 'variable' attribute of this EventAssignment (NOT the 'id').
getId() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the value of the 'id' attribute of this ExternalModelDefinition.
getId() - Method in class org.sbml.libsbml.FluxBound
Returns the value of the 'id' attribute of this FluxBound.
getId() - Method in class org.sbml.libsbml.FluxObjective
Returns the value of the 'id' attribute of this FluxObjective.
getId() - Method in class org.sbml.libsbml.FunctionDefinition
Returns the value of the 'id' attribute of this FunctionDefinition.
getId() - Method in class org.sbml.libsbml.GeneAssociation
Returns the value of the 'id' attribute of this GeneAssociation.
getId() - Method in class org.sbml.libsbml.GeneProduct
Returns the value of the 'id' attribute of this GeneProduct.
getId() - Method in class org.sbml.libsbml.GeneProductAssociation
Returns the value of the 'id' attribute of this GeneProductAssociation.
getId() - Method in class org.sbml.libsbml.GeneProductRef
Returns the value of the 'id' attribute of this GeneProductRef.
getId() - Method in class org.sbml.libsbml.GradientBase
Returns the value of the 'id' attribute of this SBML object, if it has one, or the 'variable' attribute of a Rule, or the 'symbol' attribute of an InitialAssignment.
getId() - Method in class org.sbml.libsbml.GraphicalObject
Returns the value of the 'id' attribute of this GraphicalObject.
getId() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Returns the value of the 'id' attribute of this GraphicalPrimitive.
getId() - Method in class org.sbml.libsbml.Group
Returns the value of the 'id' attribute of this Group.
getId() - Method in class org.sbml.libsbml.Image
Returns the value of the 'id' attribute of this Image.
getId() - Method in class org.sbml.libsbml.InitialAssignment
Returns the value of the 'symbol' attribute of this InitialAssignment (NOT the 'id').
getId() - Method in class org.sbml.libsbml.Input
Returns the value of the 'id' attribute of this Input.
getId() - Method in class org.sbml.libsbml.Layout
Returns the value of the 'id' attribute of this Layout.
getId() - Method in class org.sbml.libsbml.LineEnding
Returns the value of the 'id' attribute of this GraphicalPrimitive.
getId() - Method in class org.sbml.libsbml.ListOfMembers
Returns the value of the 'id' attribute of this ListOfMembers.
getId() - Method in class org.sbml.libsbml.Member
Returns the value of the 'id' attribute of this Member.
getId() - Method in class org.sbml.libsbml.Model
Returns the value of the 'id' attribute of this Model.
getId() - Method in class org.sbml.libsbml.Objective
Returns the value of the 'id' attribute of this Objective.
getId() - Method in class org.sbml.libsbml.Output
Returns the value of the 'id' attribute of this Output.
getId() - Method in class org.sbml.libsbml.Parameter
Returns the value of the 'id' attribute of this Parameter.
getId() - Method in class org.sbml.libsbml.Point
Returns the value of the 'id' attribute of this Point.
getId() - Method in class org.sbml.libsbml.Port
Returns the value of the 'id' attribute of this Port.
getId() - Method in class org.sbml.libsbml.QualitativeSpecies
Returns the value of the 'id' attribute of this QualitativeSpecies.
getId() - Method in class org.sbml.libsbml.Reaction
Returns the value of the 'id' attribute of this Reaction.
getId() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the value of the 'id' attribute of this RenderInformationBase.
getId() - Method in class org.sbml.libsbml.Rule
Returns the value of the 'variable' attribute of this Rule (NOT the 'id').
getId() - Method in class org.sbml.libsbml.SBase
Returns the value of the 'id' attribute of this SBML object, if it has one, or the 'variable' attribute of a Rule, or the 'symbol' attribute of an InitialAssignment.
getId() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Returns the value of the 'id' attribute of this SimpleSpeciesReference.
getId() - Method in class org.sbml.libsbml.Species
Returns the value of the 'id' attribute of this Species.
getId() - Method in class org.sbml.libsbml.SpeciesType
Returns the value of the 'id' attribute of this SpeciesType.
getId() - Method in class org.sbml.libsbml.Style
Returns the value of the 'id' attribute of this Style.
getId() - Method in class org.sbml.libsbml.Submodel
Returns the value of the 'id' attribute of this Submodel.
getId() - Method in class org.sbml.libsbml.Transition
Returns the value of the 'id' attribute of this Transition.
getId() - Method in class org.sbml.libsbml.UnitDefinition
Returns the value of the 'id' attribute of this UnitDefinition.
getIdAttribute() - Method in class org.sbml.libsbml.SBase
Returns the value of the 'id' attribute of this SBML object.
getIdentityMatrix() - Static method in class org.sbml.libsbml.Transformation
Returns a 3D identity matrix.
getIdentityMatrix2D() - Static method in class org.sbml.libsbml.Transformation2D
Returns a 2D identity matrix.
getIdList() - Method in class org.sbml.libsbml.LocalStyle
Returns the id list.
getIdRef() - Method in class org.sbml.libsbml.Member
Returns the value of the 'idRef' attribute of this Member.
getIdRef() - Method in class org.sbml.libsbml.SBaseRef
Returns the value of the 'idRef' attribute of this SBaseRef.
getImageReference() - Method in class org.sbml.libsbml.Image
Returns the image reference URL string.
getIndex(String) - Method in class org.sbml.libsbml.XMLAttributes
Returns the index of an attribute having a given name.
getIndex(String) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the index of an XML namespace declaration by URI.
getIndex(String) - Method in class org.sbml.libsbml.XMLNode
Return the index of the first child of this XMLNode with the given name.
getIndex(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Returns the index of the attribute having a given name and XML namespace URI.
getIndex(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
Returns the index of the attribute defined by the given XMLTriple object.
getIndexByPrefix(String) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the index of an XML namespace declaration by prefix.
getIndexForReferenceGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
Returns the index of the reference glyph with the given id.
getIndexForSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.ReactionGlyph
Returns the index of the species reference glyph with the given id.
getIndexForSubGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
Returns the index of the subglyph with the given id.
getInitialAmount() - Method in class org.sbml.libsbml.Species
Get the value of the 'initialAmount' attribute.
getInitialAssignment(long) - Method in class org.sbml.libsbml.Model
Get the nth InitialAssignment object in this Model.
getInitialAssignment(String) - Method in class org.sbml.libsbml.Model
Get an InitialAssignment object based on the symbol to which it assigns a value.
getInitialAssignmentBySymbol(String) - Method in class org.sbml.libsbml.Model
Get an InitialAssignment object based on the symbol to which it assigns a value.
getInitialConcentration() - Method in class org.sbml.libsbml.Species
Get the value of the 'initialConcentration' attribute.
getInitialLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
Returns the value of the 'initialLevel' attribute of this QualitativeSpecies.
getInitialValue() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Get the value of the 'initialValue' attribute of this Trigger.
getInput(long) - Method in class org.sbml.libsbml.Transition
Get a Input from the ListOfInputs.
getInput(String) - Method in class org.sbml.libsbml.Transition
Get a Input from the ListOfInputs based on its identifier.
getInputBySpecies(String) - Method in class org.sbml.libsbml.Transition
Get a Input from the ListOfInputs based on its qualitativeSpecies attribute.
getInstance() - Static method in class org.sbml.libsbml.SBMLConverterRegistry
Returns the singleton instance for the converter registry.
getInstance() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns a singleton instance of the registry.
getInstance() - Static method in class org.sbml.libsbml.SBMLResolverRegistry
Returns the singleton instance for the resolver registry.
getInstantiation() - Method in class org.sbml.libsbml.Submodel
Get the instantiated Model this Submodel contains rules to create.
getInteger() - Method in class org.sbml.libsbml.ASTNode
Returns the value of this node as an integer.
getIntValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option as an integer.
getIntValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as an integer.
getIsEnabledRotationalMapping() - Method in class org.sbml.libsbml.LineEnding
Returns whether rotational mapping is enabled or not.
getitem(int) - Method in class org.sbml.libsbml.double_array
 
getitem(int) - Method in class org.sbml.libsbml.int_array
 
getItemTypeCode() - Method in class org.sbml.libsbml.ListOf
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfColorDefinitions
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartments
Returns the libSBML type code for the objects contained in this ListOf (i.e., Compartment objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Returns the libSBML type code for the objects contained in this ListOf (i.e., CompartmentType objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfConstraints
Returns the libSBML type code for the objects contained in this ListOf (i.e., Constraint objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfCurveElements
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfDeletions
Returns the libSBML type code for the objects contained in this ListOf (i.e., Deletion objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfDrawables
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfEventAssignments
Returns the libSBML type code for the objects contained in this ListOf (i.e., EventAssignment objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfEvents
Returns the libSBML type code for the objects contained in this ListOf (i.e., Event objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Returns the libSBML type code for the objects contained in this ListOf (i.e., Model objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Returns the libSBML type code for the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFluxBounds
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Returns the libSBML type code for the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Returns the libSBML type code for the objects contained in this ListOf (i.e., FunctionDefinition objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfFunctionTerms
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGeneAssociations
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGeneProducts
Returns the libSBML type code for the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGlobalStyles
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGradientStops
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfGroups
Returns the libSBML type code for the SBML objects contained in this ListOfGroups object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfInitialAssignments
Returns the libSBML type code for the objects contained in this ListOf (i.e., InitialAssignment objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfInputs
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLayouts
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLineEndings
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLineSegments
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLocalParameters
Returns the libSBML type code for the objects contained in this ListOf (i.e., LocalParameter objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Get the type code of the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfLocalStyles
Returns the libSBML type code for this SBML object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfMembers
Returns the libSBML type code for the SBML objects contained in this ListOfMembers object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfModelDefinitions
Returns the libSBML type code for the objects contained in this ListOf (i.e., ModelDefinition objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfObjectives
Returns the libSBML type code for the objects contained in this ListOf.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfOutputs
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfParameters
Returns the libSBML type code for the objects contained in this ListOf (i.e., Parameter objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfPorts
Returns the libSBML type code for the objects contained in this ListOf (i.e., Port objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReactions
Returns the libSBML type code for the objects contained in this ListOf (i.e., Reaction objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfReplacedElements
Returns the libSBML type code for the objects contained in this ListOf (i.e., ReplacedElements objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfRules
Returns the libSBML type code for the objects contained in this ListOf (i.e., Rule objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpecies
Returns the libSBML type code for the objects contained in this ListOf (i.e., Species objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Returns the libSBML type code for the objects contained in this ListOf (i.e., SpeciesReference objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Returns the libSBML type code for the objects contained in this ListOf (i.e., SpeciesType objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfSubmodels
Returns the libSBML type code for the objects contained in this ListOf (i.e., Submodel objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfTransitions
Returns the libSBML type code for the SBML objects contained in this ListOf object.
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Returns the libSBML type code for the objects contained in this ListOf (i.e., UnitDefinition objects, if the list is non-empty).
getItemTypeCode() - Method in class org.sbml.libsbml.ListOfUnits
Returns the libSBML type code for the objects contained in this ListOf (i.e., Unit objects, if the list is non-empty).
getKey() - Method in class org.sbml.libsbml.ConversionOption
Returns the key for this option.
getKind() - Method in class org.sbml.libsbml.Group
Returns the value of the 'kind' attribute of this Group.
getKind() - Method in class org.sbml.libsbml.Unit
Returns the 'kind' of Unit this is.
getKindAsString() - Method in class org.sbml.libsbml.Group
Returns the value of the 'kind' attribute of this Group.
getKineticLaw() - Method in class org.sbml.libsbml.Reaction
Returns the KineticLaw object contained in this Reaction.
getL1TypeCode() - Method in class org.sbml.libsbml.Rule
Returns the SBML Level 1 type code for this Rule object.
getLabel() - Method in class org.sbml.libsbml.GeneProduct
Returns the value of the 'label' attribute of this GeneProduct.
getLastParseL3Error() - Static method in class org.sbml.libsbml.libsbml
Returns the last error reported by the 'L3' mathematical formula parser.
getLayout(long) - Method in class org.sbml.libsbml.LayoutModelPlugin
Returns the layout object that belongs to the given index.
getLayout(String) - Method in class org.sbml.libsbml.LayoutModelPlugin
Returns the layout object with the given sid attribute.
getLeftChild() - Method in class org.sbml.libsbml.ASTNode
Returns the left child of this node.
getLength() - Method in class org.sbml.libsbml.XMLAttributes
Returns the number of attributes in this list of attributes.
getLength() - Method in class org.sbml.libsbml.XMLNamespaces
Returns the total number of URI-and-prefix pairs stored in this particular XMLNamespaces instance.
getLengthUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'lengthUnits' attribute of this Model.
getLevel() - Method in class org.sbml.libsbml.SBase
Returns the SBML Level of the SBMLDocument object containing this object.
getLevel() - Method in class org.sbml.libsbml.SBasePlugin
Returns the SBML Level of the package extension of this plugin object.
getLevel() - Method in class org.sbml.libsbml.SBMLNamespaces
Get the SBML Level of this SBMLNamespaces object.
getLevel(String) - Method in class org.sbml.libsbml.CompExtension
Returns the SBML Level for the given URI of this package.
getLevel(String) - Method in class org.sbml.libsbml.FbcExtension
Returns the SBML Level for the given URI of this package.
getLevel(String) - Method in class org.sbml.libsbml.GroupsExtension
Returns the SBML Level for the given URI of this package.
getLevel(String) - Method in class org.sbml.libsbml.LayoutExtension
Returns the SBML Level for the given URI of this package.
getLevel(String) - Method in class org.sbml.libsbml.QualExtension
Returns the SBML Level for the given URI of this package.
getLevel(String) - Method in class org.sbml.libsbml.RenderExtension
Returns the SBML level with the given URI of this package.
getLevel(String) - Method in class org.sbml.libsbml.SBMLExtension
Returns the SBML Level associated with the given XML namespace URI.
getLibraryName() - Static method in class org.sbml.libsbml.XMLOutputStream
 
getLibraryVersion() - Static method in class org.sbml.libsbml.XMLOutputStream
 
getLibSBMLDependencyVersionOf(String) - Static method in class org.sbml.libsbml.libsbml
Returns the version string for the dependency library used.
getLibSBMLDottedVersion() - Static method in class org.sbml.libsbml.libsbml
Returns the version number of this copy of libSBML as a string.
getLibSBMLVersion() - Static method in class org.sbml.libsbml.libsbml
Returns the version number of this copy of libSBML as an integer.
getLibSBMLVersionString() - Static method in class org.sbml.libsbml.libsbml
Returns the version number of this copy of libSBML as a string without periods.
getLine() - Method in class org.sbml.libsbml.SBase
Returns the line number where this object first appears in the XML representation of the SBML document.
getLine() - Method in class org.sbml.libsbml.XMLError
Returns the line number in the XML input near where the error, warning or other diagnostic occurred.
getLine() - Method in class org.sbml.libsbml.XMLToken
Returns the line number at which this token occurs in the input.
getLinearGradient_x1() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'linearGradient_x1' attribute of this DefaultValues.
getLinearGradient_x2() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'linearGradient_x2' attribute of this DefaultValues.
getLinearGradient_y1() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'linearGradient_y1' attribute of this DefaultValues.
getLinearGradient_y2() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'linearGradient_y2' attribute of this DefaultValues.
getLinearGradient_z1() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'linearGradient_z1' attribute of this DefaultValues.
getLinearGradient_z2() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'linearGradient_z2' attribute of this DefaultValues.
getLineEnding(long) - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the line ending with the given index, or null if the index is invalid.
getLineEnding(String) - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the line ending with the given id, or null if there is no line ending with that id.
getListCreators() - Method in class org.sbml.libsbml.ModelHistory
Returns the list of ModelCreator objects stored in this ModelHistory object.
getListModifiedDates() - Method in class org.sbml.libsbml.ModelHistory
Returns the list of 'modified date' values (as Date objects) stored in this ModelHistory object.
getListNestedCVTerms() - Method in class org.sbml.libsbml.CVTerm
Returns a list of CVTerm objects contained within this CVTerm object.
getListOfAdditionalGraphicalObjects() - Method in class org.sbml.libsbml.Layout
Returns the ListOf object that holds all additional graphical objects.
getListOfAllElements() - Method in class org.sbml.libsbml.SBase
 
getListOfAllElements() - Method in class org.sbml.libsbml.SBasePlugin
 
getListOfAllElements(ElementFilter) - Method in class org.sbml.libsbml.SBase
 
getListOfAllElements(ElementFilter) - Method in class org.sbml.libsbml.SBasePlugin
 
getListOfAllElementsFromPlugins() - Method in class org.sbml.libsbml.SBase
 
getListOfAllElementsFromPlugins(ElementFilter) - Method in class org.sbml.libsbml.SBase
 
getListOfAllInstantiatedElements() - Method in class org.sbml.libsbml.Submodel
 
getListOfAssociations() - Method in class org.sbml.libsbml.FbcAnd
Returns the ListOfFbcAssociations in this FbcAnd object.
getListOfAssociations() - Method in class org.sbml.libsbml.FbcOr
Returns the ListOfFbcAssociations in this FbcOr object.
getListOfColorDefinitions() - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the list of color definitions.
getListOfCompartmentGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the ListOf object that holds all compartment glyphs.
getListOfCompartments() - Method in class org.sbml.libsbml.Model
Get the ListOfCompartments object in this Model.
getListOfCompartmentTypes() - Method in class org.sbml.libsbml.Model
Get the ListOfCompartmentTypes object in this Model.
getListOfConstraints() - Method in class org.sbml.libsbml.Model
Get the ListOfConstraints object in this Model.
getListOfCurveSegments() - Method in class org.sbml.libsbml.Curve
Returns a refernce to the ListOf object That holds all the curve segments.
getListOfDeletions() - Method in class org.sbml.libsbml.Submodel
Returns the ListOf object that holds all deletions.
getListOfElements() - Method in class org.sbml.libsbml.Polygon
Returns a pointer to the list of segments.
getListOfElements() - Method in class org.sbml.libsbml.RenderCurve
Returns a pointer to the list of curve segments.
getListOfElements() - Method in class org.sbml.libsbml.RenderGroup
Returns a pointer to the list of elements.
getListOfEventAssignments() - Method in class org.sbml.libsbml.Event
Returns the list of event assignments for this Event.
getListOfEvents() - Method in class org.sbml.libsbml.Model
Get the ListOfEvents object in this Model.
getListOfExternalModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the ListOf object that holds each ExternalModelDefinition.
getListOfFluxBounds() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the ListOfFluxBounds in this plugin object.
getListOfFluxObjectives() - Method in class org.sbml.libsbml.Objective
Returns the ListOfFluxObjectives in this Objective object.
getListOfFunctionDefinitions() - Method in class org.sbml.libsbml.Model
Get the ListOfFunctionDefinitions object in this Model.
getListOfFunctionTerms() - Method in class org.sbml.libsbml.Transition
Returns the ListOfFunctionTerms in this Transition object.
getListOfGeneAssociations() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object.
getListOfGeneProducts() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the ListOfGeneProducts in this FbcModelPlugin object.
getListOfGlobalRenderInformation() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Returns a pointer to the list object that contains local render information.
getListOfGradientDefinitions() - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the list of gradient definitions.
getListOfGradientStops() - Method in class org.sbml.libsbml.GradientBase
Returns a pointer to the gradient stop vector.
getListOfGroups() - Method in class org.sbml.libsbml.GroupsModelPlugin
Returns the ListOfGroups from this GroupsModelPlugin.
getListOfInitialAssignments() - Method in class org.sbml.libsbml.Model
Get the ListOfInitialAssignments object in this Model.
getListOfInputs() - Method in class org.sbml.libsbml.Transition
Returns the ListOfInputs in this Transition object.
getListOfLayouts() - Method in class org.sbml.libsbml.LayoutModelPlugin
Returns the ListOfLayouts object for this Model.
getListOfLineEndings() - Method in class org.sbml.libsbml.RenderInformationBase
Returns a pointer to the list of line endings.
getListOfLocalParameters() - Method in class org.sbml.libsbml.KineticLaw
Returns the list of local parameters in this KineticLaw object.
getListOfLocalRenderInformation() - Method in class org.sbml.libsbml.RenderLayoutPlugin
Returns a pointer to the list object that contains local render information.
getListOfMembers() - Method in class org.sbml.libsbml.Group
Returns the ListOfMembers from this Group.
getListOfModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the ListOf object that holds each ModelDefinition.
getListOfModifiers() - Method in class org.sbml.libsbml.Reaction
Returns the list of modifiers in this Reaction object.
getListOfNodes() - Method in class org.sbml.libsbml.ASTNode
 
getListOfObjectives() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the ListOfObjectives in this FbcModelPlugin object.
getListOfOutputs() - Method in class org.sbml.libsbml.Transition
Returns the ListOfOutputs in this Transition object.
getListOfParameters() - Method in class org.sbml.libsbml.KineticLaw
Returns the list of parameters in this KineticLaw object.
getListOfParameters() - Method in class org.sbml.libsbml.Model
Get the ListOfParameters object in this Model.
getListOfPorts() - Method in class org.sbml.libsbml.CompModelPlugin
Returns the ListOfPorts from this CompModelPlugin.
getListOfProducts() - Method in class org.sbml.libsbml.Reaction
Returns the list of products in this Reaction object.
getListOfQualitativeSpecies() - Method in class org.sbml.libsbml.QualModelPlugin
Returns the ListOfQualitativeSpecies in this plugin object.
getListOfReactants() - Method in class org.sbml.libsbml.Reaction
Returns the list of reactants in this Reaction object.
getListOfReactionGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the ListOf object that holds all reaction glyphs.
getListOfReactions() - Method in class org.sbml.libsbml.Model
Get the ListOfReactions object in this Model.
getListOfReferenceGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the ListOf object that hold the reference glyphs.
getListOfReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
Returns the ListOf object that holds all replacedElements.
getListOfRules() - Method in class org.sbml.libsbml.Model
Get the ListOfRules object in this Model.
getListOfSpecies() - Method in class org.sbml.libsbml.Model
Get the ListOfSpecies object in this Model.
getListOfSpeciesGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the ListOf object that holds all species glyphs.
getListOfSpeciesReferenceGlyphs() - Method in class org.sbml.libsbml.ReactionGlyph
Returns the ListOf object that hold the species reference glyphs.
getListOfSpeciesTypes() - Method in class org.sbml.libsbml.Model
Get the ListOfSpeciesTypes object in this Model.
getListOfStyles() - Method in class org.sbml.libsbml.GlobalRenderInformation
Returns a pointer to the ListOfGlobalStyles object.
getListOfStyles() - Method in class org.sbml.libsbml.LocalRenderInformation
Returns a pointer to the ListOfLocalStyles object.
getListOfSubGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the ListOf object that hold the sub glyphs.
getListOfSubmodels() - Method in class org.sbml.libsbml.CompModelPlugin
Returns the ListOfSubmodels from this CompModelPlugin.
getListOfTextGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the ListOf object that holds all text glyphs.
getListOfTransitions() - Method in class org.sbml.libsbml.QualModelPlugin
Returns the ListOfTransitions in this plugin object.
getListOfUnitDefinitions() - Method in class org.sbml.libsbml.Model
Get the ListOfUnitDefinitions object in this Model.
getListOfUnits() - Method in class org.sbml.libsbml.UnitDefinition
Returns the list of Units for this UnitDefinition instance.
getLocalParameter(long) - Method in class org.sbml.libsbml.KineticLaw
Returns the nth LocalParameter object in the list of local parameters in this KineticLaw instance.
getLocalParameter(String) - Method in class org.sbml.libsbml.KineticLaw
Returns a local parameter based on its identifier.
getLocationURI() - Method in class org.sbml.libsbml.SBMLDocument
Get the location of this SBMLDocument.
getLowerFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
Returns the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.
getMajorVersion() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Returns the major version of the render information list.
getMajorVersion() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Returns the major version of the render information list.
getMantissa() - Method in class org.sbml.libsbml.ASTNode
Returns the mantissa value of this node.
getMath() - Method in class org.sbml.libsbml.Constraint
Get the mathematical expression of this Constraint
getMath() - Method in class org.sbml.libsbml.Delay
Get the mathematical formula for the delay and return it as an AST.
getMath() - Method in class org.sbml.libsbml.EventAssignment
Get the mathematical expression in this EventAssignment's 'math' subelement.
getMath() - Method in class org.sbml.libsbml.FunctionDefinition
Get the mathematical formula of this FunctionDefinition.
getMath() - Method in class org.sbml.libsbml.FunctionTerm
Returns the 'math' element of this FunctionTerm.
getMath() - Method in class org.sbml.libsbml.InitialAssignment
Get the mathematical formula of this InitialAssignment.
getMath() - Method in class org.sbml.libsbml.KineticLaw
Returns the mathematical formula for this KineticLaw object and return it as as an AST.
getMath() - Method in class org.sbml.libsbml.Priority
Get the mathematical formula for the priority and return it as an AST.
getMath() - Method in class org.sbml.libsbml.Rule
Get the mathematical formula of this Rule as an ASTNode tree.
getMath() - Method in class org.sbml.libsbml.StoichiometryMath
Retrieves the mathematical formula within this StoichiometryMath and return it as an AST.
getMath() - Method in class org.sbml.libsbml.Trigger
Get the mathematical formula for the trigger and return it as an AST.
getMatrix() - Method in class org.sbml.libsbml.Transformation
Returns the matrix which is an array of double values of length 12.
getMatrix2D() - Method in class org.sbml.libsbml.Transformation2D
Returns the 2D matrix which is an array of double values of length 6.
getMaxLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
Returns the value of the 'maxLevel' attribute of this QualitativeSpecies.
getMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the value of the 'md5' attribute of this ExternalModelDefinition.
getMember(long) - Method in class org.sbml.libsbml.Group
Get a Member from the Group.
getMember(String) - Method in class org.sbml.libsbml.Group
Get a Member from the Group based on its identifier.
getMemberByIdRef(String) - Method in class org.sbml.libsbml.Group
Get a Member from the Group based on the element to which it refers.
getMessage() - Method in class org.sbml.libsbml.Constraint
Get the message, if any, associated with this Constraint
getMessage() - Method in class org.sbml.libsbml.XMLError
Returns the message text of this error.
getMessageString() - Method in class org.sbml.libsbml.Constraint
Get the message string, if any, associated with this Constraint
getMetaId() - Method in class org.sbml.libsbml.SBase
Returns the value of the 'metaid' attribute of this SBML object.
getMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
Returns the value of the 'metaidRef' attribute of this GraphicalObject.
getMetaIdRef() - Method in class org.sbml.libsbml.Member
Returns the value of the 'metaIdRef' attribute of this Member.
getMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
Returns the value of the 'metaIdRef' attribute of this SBaseRef.
getMinorVersion() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Returns the minor version of the render information list.
getMinorVersion() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Returns the minor version of the render information list.
getMinute() - Method in class org.sbml.libsbml.Date
Returns the minute from this Date.
getMinutesOffset() - Method in class org.sbml.libsbml.Date
Returns the minutes of the time zone offset from this Date.
getModel() - Method in class org.sbml.libsbml.L3ParserSettings
Returns the Model object referenced by this L3ParserSettings object.
getModel() - Method in class org.sbml.libsbml.SBase
Returns the Model object for the SBML Document in which the current object is located.
getModel() - Method in class org.sbml.libsbml.SBMLDocument
Returns the Model object stored in this SBMLDocument.
getModel() - Method in class org.sbml.libsbml.SBMLValidator
Returns the Model object stored in the SBMLDocument.
getModel(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier.
getModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the ModelDefinition with the given index.
getModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the model definition object based on its identifier.
getModelHistory() - Method in class org.sbml.libsbml.SBase
Returns the ModelHistory object, if any, attached to this object.
getModelQualifierType() - Method in class org.sbml.libsbml.CVTerm
Returns the model qualifier type of this CVTerm object.
getModelRef() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the value of the 'modelRef' attribute of this ExternalModelDefinition.
getModelRef() - Method in class org.sbml.libsbml.Submodel
Returns the value of the 'modelRef' attribute of this Submodel.
getModifiedDate() - Method in class org.sbml.libsbml.ModelHistory
Returns the 'modified date' portion of this ModelHistory object.
getModifiedDate(long) - Method in class org.sbml.libsbml.ModelHistory
Get the nth Date object in the list of 'modified date' values stored in this ModelHistory object.
getModifier(long) - Method in class org.sbml.libsbml.Reaction
Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction.
getModifier(String) - Method in class org.sbml.libsbml.Reaction
Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction.
getModifierSpeciesReference(String) - Method in class org.sbml.libsbml.Model
Get a ModifierSpeciesReference object based on its identifier.
getMonth() - Method in class org.sbml.libsbml.Date
Returns the month from this Date.
getMultiplier() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'multiplier' attribute of this Unit.
getName() - Method in class org.sbml.libsbml.ASTNode
Returns the value of this node as a string.
getName() - Method in class org.sbml.libsbml.ColorDefinition
Returns the value of the 'name' attribute of this ColorDefinition.
getName() - Method in class org.sbml.libsbml.Compartment
Returns the value of the 'name' attribute of this Compartment object.
getName() - Method in class org.sbml.libsbml.CompartmentType
Returns the value of the 'name' attribute of this CompartmentType object.
getName() - Method in class org.sbml.libsbml.CompExtension
Returns the name of this package as a short-form label ("comp").
getName() - Method in class org.sbml.libsbml.Deletion
Returns the value of the 'name' attribute of this Deletion object.
getName() - Method in class org.sbml.libsbml.Event
Returns the value of the 'name' attribute of this Event.
getName() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the value of the 'name' attribute of this ExternalModelDefinition object.
getName() - Method in class org.sbml.libsbml.FbcExtension
Returns the name of this SBML Level 3 package ('fbc').
getName() - Method in class org.sbml.libsbml.FluxBound
Returns the value of the 'name' attribute of this FluxBound object.
getName() - Method in class org.sbml.libsbml.FluxObjective
Returns the value of the 'name' attribute of this FluxObjective object.
getName() - Method in class org.sbml.libsbml.FunctionDefinition
Returns the value of the 'name' attribute of this FunctionDefinition object.
getName() - Method in class org.sbml.libsbml.GeneProduct
Returns the value of the 'name' attribute of this GeneProduct object.
getName() - Method in class org.sbml.libsbml.GeneProductAssociation
Returns the value of the 'name' attribute of this GeneProductAssociation object.
getName() - Method in class org.sbml.libsbml.GeneProductRef
Returns the value of the 'name' attribute of this GeneProductRef object.
getName() - Method in class org.sbml.libsbml.GradientBase
Returns the value of the 'name' attribute of this SBML object.
getName() - Method in class org.sbml.libsbml.Group
Returns the value of the 'name' attribute of this Group.
getName() - Method in class org.sbml.libsbml.GroupsExtension
Returns the name of this SBML Level 3 package ('groups').
getName() - Method in class org.sbml.libsbml.Input
Returns the value of the 'name' attribute of this Input object.
getName() - Method in class org.sbml.libsbml.Layout
Returns the value of the 'name' attribute of this Layout object.
getName() - Method in class org.sbml.libsbml.LayoutExtension
Returns the name of this package ('layout')
getName() - Method in class org.sbml.libsbml.ListOfMembers
Returns the value of the 'name' attribute of this ListOfMembers.
getName() - Method in class org.sbml.libsbml.Member
Returns the value of the 'name' attribute of this Member.
getName() - Method in class org.sbml.libsbml.Model
Returns the value of the 'name' attribute of this Model object.
getName() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'fn' stored in this ModelCreator object when using vCard4.
getName() - Method in class org.sbml.libsbml.Objective
Returns the value of the 'name' attribute of this Objective object.
getName() - Method in class org.sbml.libsbml.Output
Returns the value of the 'name' attribute of this Output object.
getName() - Method in class org.sbml.libsbml.Parameter
Returns the value of the 'name' attribute of this Parameter object.
getName() - Method in class org.sbml.libsbml.Port
Returns the value of the 'name' attribute of this Port object.
getName() - Method in class org.sbml.libsbml.QualExtension
Returns the name of this package ('qual')
getName() - Method in class org.sbml.libsbml.QualitativeSpecies
Returns the value of the 'name' attribute of this QualitativeSpecies object.
getName() - Method in class org.sbml.libsbml.Reaction
Returns the value of the 'name' attribute of this Reaction object.
getName() - Method in class org.sbml.libsbml.RenderExtension
Returns the name of this package ('fbc')
getName() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the value of the 'name' attribute of this RenderInformationBase.
getName() - Method in class org.sbml.libsbml.SBase
Returns the value of the 'name' attribute of this SBML object.
getName() - Method in class org.sbml.libsbml.SBMLConverter
Returns the name of this converter.
getName() - Method in class org.sbml.libsbml.SBMLExtension
Returns the nickname of this package.
getName() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Returns the value of the 'name' attribute of this SimpleSpeciesReference object.
getName() - Method in class org.sbml.libsbml.Species
Returns the value of the 'name' attribute of this Species object.
getName() - Method in class org.sbml.libsbml.SpeciesType
Returns the value of the 'name' attribute of this SpeciesType object.
getName() - Method in class org.sbml.libsbml.Style
Returns the value of the 'name' attribute of this Style.
getName() - Method in class org.sbml.libsbml.Submodel
Returns the value of the 'name' attribute of this Submodel object.
getName() - Method in class org.sbml.libsbml.Transformation
Returns the value of the 'name' attribute of this Transformation.
getName() - Method in class org.sbml.libsbml.Transition
getName() - Method in class org.sbml.libsbml.UnitDefinition
Returns the value of the 'name' attribute of this UnitDefinition object.
getName() - Method in class org.sbml.libsbml.XMLToken
Returns the (unqualified) name of token.
getName() - Method in class org.sbml.libsbml.XMLTriple
Returns the name portion of this XMLTriple object.
getName(int) - Method in class org.sbml.libsbml.XMLAttributes
Returns the name of the nth attribute in this list of attributes.
getNamespaceIndex(String) - Method in class org.sbml.libsbml.XMLToken
Returns the index of an XML namespace declaration based on its URI.
getNamespaceIndexByPrefix(String) - Method in class org.sbml.libsbml.XMLToken
Returns the index of an XML namespace declaration based on its prefix.
getNamespacePrefix(int) - Method in class org.sbml.libsbml.XMLToken
Returns the prefix of the nth XML namespace declaration.
getNamespacePrefix(String) - Method in class org.sbml.libsbml.XMLToken
Returns the prefix associated with a given XML namespace URI on this token.
getNamespaces() - Method in class org.sbml.libsbml.SBase
Returns a list of the XML Namespaces declared on the SBML document owning this object.
getNamespaces() - Method in class org.sbml.libsbml.SBMLDocument
Returns a list of XML Namespaces associated with the XML content of this SBML document.
getNamespaces() - Method in class org.sbml.libsbml.SBMLNamespaces
Get the XML namespaces list for this SBMLNamespaces object.
getNamespaces() - Method in class org.sbml.libsbml.XMLToken
Returns the XML namespaces declared for this token.
getNamespacesLength() - Method in class org.sbml.libsbml.XMLToken
Returns the number of XML namespaces declared on this token.
getNamespaceURI() - Method in class org.sbml.libsbml.XMLToken
Returns the URI of an XML namespace with a given prefix.
getNamespaceURI(int) - Method in class org.sbml.libsbml.XMLToken
Returns the URI of the nth XML namespace declared on this token.
getNamespaceURI(String) - Method in class org.sbml.libsbml.XMLToken
Returns the URI of an XML namespace with a given prefix.
getNestedCVTerm(long) - Method in class org.sbml.libsbml.CVTerm
Returns the nth CVTerm in the list of CVTerms of this CVTerm object.
getNotes() - Method in class org.sbml.libsbml.SBase
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
getNotesString() - Method in class org.sbml.libsbml.SBase
Returns the content of the 'notes' subelement of this object as a string.
getNumAdditionalGraphicalObjects() - Method in class org.sbml.libsbml.Layout
Returns the number of additional graphical objects for the layout.
getNumArguments() - Method in class org.sbml.libsbml.FunctionDefinition
Get the number of arguments (bound variables) taken by this FunctionDefinition.
getNumAssociations() - Method in class org.sbml.libsbml.Association
Returns the number of child Associations of this Association object.
getNumAssociations() - Method in class org.sbml.libsbml.FbcAnd
Get the number of FbcAssociation objects in this FbcAnd.
getNumAssociations() - Method in class org.sbml.libsbml.FbcOr
Get the number of FbcAssociation objects in this FbcOr.
getNumAttributes() - Method in class org.sbml.libsbml.XMLAttributes
Returns the number of attributes in this list of attributes.
getNumChildren() - Method in class org.sbml.libsbml.ASTNode
Returns the number of children of this node.
getNumChildren() - Method in class org.sbml.libsbml.XMLNode
Returns the number of children for this XMLNode.
getNumColorDefinitions() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the number of color definitions.
getNumCompartmentGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the number of compartment glyphs for the layout.
getNumCompartments() - Method in class org.sbml.libsbml.Model
Get the number of Compartment objects in this Model.
getNumCompartmentTypes() - Method in class org.sbml.libsbml.Model
Get the number of CompartmentType objects in this Model.
getNumConstraints() - Method in class org.sbml.libsbml.Model
Get the number of Constraint objects in this Model.
getNumConverters() - Method in class org.sbml.libsbml.SBMLConverterRegistry
Returns the number of converters known by the registry.
getNumCreators() - Method in class org.sbml.libsbml.ModelHistory
Get the number of ModelCreator objects stored in this ModelHistory object.
getNumCurveSegments() - Method in class org.sbml.libsbml.Curve
Returns the number of curve segments.
getNumCVTerms() - Method in class org.sbml.libsbml.SBase
Returns the number of CVTerm objects in the annotations of this SBML object.
getNumDashes() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Returns the number of defined dashes.
getNumDeletions() - Method in class org.sbml.libsbml.Submodel
Returns the number of deletions for this Submodel.
getNumDisabledPlugins() - Method in class org.sbml.libsbml.SBase
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.
getNumElements() - Method in class org.sbml.libsbml.Polygon
Returns the number of segments.
getNumElements() - Method in class org.sbml.libsbml.RenderCurve
Returns the number of curve segments.
getNumElements() - Method in class org.sbml.libsbml.RenderGroup
Returns the number of children in the group.
getNumerator() - Method in class org.sbml.libsbml.ASTNode
Returns the value of the numerator of this node if of type AST_RATIONAL, or the numerical value of the node if of type AST_INTEGER; 0 (false) otherwise.
getNumErrors() - Method in class org.sbml.libsbml.SBMLDocument
Returns the number of errors or warnings encountered during parsing, consistency checking, or attempted translation of this model.
getNumErrors() - Method in class org.sbml.libsbml.XMLErrorLog
Returns the number of errors that have been logged.
getNumErrors(long) - Method in class org.sbml.libsbml.SBMLDocument
Returns the number of errors or warnings encountered with the given severity during parsing, consistency checking, or attempted translation of this model.
getNumEventAssignments() - Method in class org.sbml.libsbml.Event
Returns the number of EventAssignment objects attached to this Event.
getNumEvents() - Method in class org.sbml.libsbml.Model
Get the number of Event objects in this Model.
getNumExtension(SBaseExtensionPoint) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns the number of extensions that have a given extension point.
getNumExternalModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the number of ExternalModelDefinition objects for this SBMLDocumentPlugin.
getNumFailsWithSeverity(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Returns the number of errors that have been logged with the given severity code.
getNumFailures() - Method in class org.sbml.libsbml.SBMLValidator
Returns the number of failures encountered in the last validation run.
getNumFbcAssociations() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Get the number of FbcAssociation objects in this ListOfFbcAssociations.
getNumFluxBounds() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the number of FluxBound object in this plugin object.
getNumFluxObjectives() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Get the number of FluxObjective objects in this ListOfFluxObjectives.
getNumFluxObjectives() - Method in class org.sbml.libsbml.Objective
Get the number of FluxObjective objects in this Objective.
getNumFunctionDefinitions() - Method in class org.sbml.libsbml.Model
Get the number of FunctionDefinition objects in this Model.
getNumFunctionTerms() - Method in class org.sbml.libsbml.Transition
Get the number of FunctionTerm objects in this Transition.
getNumGeneAssociations() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the number of GeneAssociation annotation object in this plugin object.
getNumGeneProducts() - Method in class org.sbml.libsbml.FbcModelPlugin
Get the number of GeneProduct objects in this FbcModelPlugin.
getNumGeneProducts() - Method in class org.sbml.libsbml.ListOfGeneProducts
Get the number of GeneProduct objects in this ListOfGeneProducts.
getNumGeneralGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the number of general glyphs for the layout.
getNumGlobalRenderInformationObjects() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Returns the number of local render information objects.
getNumGradientDefinitions() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the number of gradient definitions in the render information.
getNumGradientStops() - Method in class org.sbml.libsbml.GradientBase
Returns the number of gradient stops.
getNumGroups() - Method in class org.sbml.libsbml.GroupsModelPlugin
Get the number of Group objects in this GroupsModelPlugin.
getNumGroups() - Method in class org.sbml.libsbml.ListOfGroups
Get the number of Group objects in this ListOfGroups.
getNumIds() - Method in class org.sbml.libsbml.LocalStyle
Returns the number of ids in the id set.
getNumInitialAssignments() - Method in class org.sbml.libsbml.Model
Get the number of InitialAssignment objects in this Model.
getNumInputs() - Method in class org.sbml.libsbml.Transition
Get the number of Input objects in this Transition.
getNumLayouts() - Method in class org.sbml.libsbml.LayoutModelPlugin
Returns the number of layout objects.
getNumLineEndings() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the number of line endings for the render information.
getNumLocalParameters() - Method in class org.sbml.libsbml.KineticLaw
Returns the number of local parameters in this KineticLaw instance.
getNumLocalRenderInformationObjects() - Method in class org.sbml.libsbml.RenderLayoutPlugin
Returns the number of local render information objects.
getNumMembers() - Method in class org.sbml.libsbml.Group
Get the number of Member objects in this Group.
getNumMembers() - Method in class org.sbml.libsbml.ListOfMembers
Get the number of Member objects in this ListOfMembers.
getNumModelDefinitions() - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Returns the number of ModelDefinition objects for this SBMLDocumentPlugin.
getNumModifiedDates() - Method in class org.sbml.libsbml.ModelHistory
Get the number of Date objects in this ModelHistory object's list of 'modified dates'.
getNumModifiers() - Method in class org.sbml.libsbml.Reaction
Returns the number of modifier species in this Reaction.
getNumNamespaces() - Method in class org.sbml.libsbml.XMLNamespaces
Returns the total number of URI-and-prefix pairs stored in this particular XMLNamespaces instance.
getNumNestedCVTerms() - Method in class org.sbml.libsbml.CVTerm
Returns the number of CVTerm objects nested within this CVTerm object.
getNumObjectives() - Method in class org.sbml.libsbml.FbcModelPlugin
Get the number of Objective objects in this FbcModelPlugin.
getNumObjectives() - Method in class org.sbml.libsbml.ListOfObjectives
Get the number of Objective objects in this ListOfObjectives.
getNumOfSBasePlugins() - Method in class org.sbml.libsbml.SBMLExtension
Returns the number of SBasePluginCreatorBase objects stored in this object.
getNumOfSupportedPackageURI() - Method in class org.sbml.libsbml.SBMLExtension
Returns the number of supported package namespace URIs.
getNumOptions() - Method in class org.sbml.libsbml.ConversionProperties
Returns the number of options in this Conversion Properties object
getNumOutputs() - Method in class org.sbml.libsbml.Transition
Get the number of Output objects in this Transition.
getNumParameters() - Method in class org.sbml.libsbml.KineticLaw
Returns the number of parameters in this KineticLaw instance.
getNumParameters() - Method in class org.sbml.libsbml.Model
Get the number of Parameter objects in this Model.
getNumPlugins() - Method in class org.sbml.libsbml.SBase
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumPorts() - Method in class org.sbml.libsbml.CompModelPlugin
Returns the number of ports for this CompModelPlugin.
getNumProducts() - Method in class org.sbml.libsbml.Reaction
Returns the number of product species in this Reaction.
getNumQualitativeSpecies() - Method in class org.sbml.libsbml.QualModelPlugin
Returns the number of QualitativeSpecies object in this plugin object.
getNumReactants() - Method in class org.sbml.libsbml.Reaction
Returns the number of reactant species in this Reaction.
getNumReactionGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the number of reaction glyphs for the layout.
getNumReactions() - Method in class org.sbml.libsbml.Model
Get the number of Reaction objects in this Model.
getNumReferenceGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the number of reference glyph objects.
getNumReferents() - Method in class org.sbml.libsbml.ReplacedElement
Returns how many elements are being referred to by this ReplacedElement.
getNumReferents() - Method in class org.sbml.libsbml.SBaseRef
Returns how many elements are being referred to by this SBaseRef.
getNumRegisteredPackages() - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns the number of registered packages.
getNumReplacedElements() - Method in class org.sbml.libsbml.CompSBasePlugin
Returns the number of ReplacedElements for this CompSBasePlugin.
getNumResolvers() - Method in class org.sbml.libsbml.SBMLResolverRegistry
Returns the number of resolvers known by the registry.
getNumResources() - Method in class org.sbml.libsbml.CVTerm
Returns the number of resources for this CVTerm object.
getNumRoles() - Method in class org.sbml.libsbml.Style
Returns the number of ids in the role list.
getNumRules() - Method in class org.sbml.libsbml.Model
Get the number of Rule objects in this Model.
getNumSemanticsAnnotations() - Method in class org.sbml.libsbml.ASTNode
Returns the number of MathML <semantics> element elements on this node.
getNumSpecies() - Method in class org.sbml.libsbml.Model
Get the number of Species objects in this Model.
getNumSpeciesGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the number of species glyphs for the layout.
getNumSpeciesReferenceGlyphs() - Method in class org.sbml.libsbml.ReactionGlyph
Returns the number of species reference glyph objects.
getNumSpeciesTypes() - Method in class org.sbml.libsbml.Model
Get the number of SpeciesType objects in this Model.
getNumSpeciesWithBoundaryCondition() - Method in class org.sbml.libsbml.Model
Get the number of Species in this Model having their 'boundaryCondition' attribute value set to true.
getNumStyles() - Method in class org.sbml.libsbml.GlobalRenderInformation
Returns the number of styles.
getNumStyles() - Method in class org.sbml.libsbml.LocalRenderInformation
Returns the number of styles.
getNumSubGlyphs() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the number of subglyph objects.
getNumSubmodels() - Method in class org.sbml.libsbml.CompModelPlugin
Returns the number of submodels for this CompModelPlugin.
getNumTextGlyphs() - Method in class org.sbml.libsbml.Layout
Returns the number of text glyphs for the layout.
getNumTransitions() - Method in class org.sbml.libsbml.QualModelPlugin
Returns the number of Transition object in this plugin object.
getNumTypes() - Method in class org.sbml.libsbml.Style
Returns the number of types in the type list.
getNumUnitDefinitions() - Method in class org.sbml.libsbml.Model
Get the number of UnitDefinition objects in this Model.
getNumUnits() - Method in class org.sbml.libsbml.UnitDefinition
Returns the number of Unit objects contained within this UnitDefinition.
getObjective(long) - Method in class org.sbml.libsbml.FbcModelPlugin
Get an Objective from the ListOfObjectives.
getObjective(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Get an Objective from the ListOfObjectives based on its identifier.
getObjectiveType() - Method in class org.sbml.libsbml.Objective
Returns the enumeration value of the 'type' attribute of this Objective.
getObjectRole() - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
Returns the object role string for the object.
getOffset() - Method in class org.sbml.libsbml.GradientStop
Returns the offset of the gradient.
getOffset() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'offset' attribute of this Unit.
getOperation() - Method in class org.sbml.libsbml.FluxBound
Returns the value of the 'operation' attribute of this FluxBound object.
getOperatorName() - Method in class org.sbml.libsbml.ASTNode
Returns the value of this operator node as a string.
getOption(int) - Method in class org.sbml.libsbml.ConversionProperties
Returns the ConversionOption object for the given index.
getOption(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the ConversionOption object for a given key.
getOrder() - Method in class org.sbml.libsbml.CompartmentGlyph
Returns the compartment order.
getOrganisation() - Method in class org.sbml.libsbml.ModelCreator
(Alternate spelling) Returns the 'organization' stored in this ModelCreator object.
getOrganization() - Method in class org.sbml.libsbml.ModelCreator
Returns the 'organization' stored in this ModelCreator object.
getOriginOfTextId() - Method in class org.sbml.libsbml.TextGlyph
Returns the id of the origin of text.
getOutput(long) - Method in class org.sbml.libsbml.Transition
Get a Output from the ListOfOutputs.
getOutput(String) - Method in class org.sbml.libsbml.Transition
Get a Output from the ListOfOutputs based on its identifier.
getOutputBySpecies(String) - Method in class org.sbml.libsbml.Transition
Get a Output from the ListOfOutputs based on its qualitativeSpecies attribute.
getOutputLevel() - Method in class org.sbml.libsbml.Output
Returns the value of the 'outputLevel' attribute of this Output.
getOutside() - Method in class org.sbml.libsbml.Compartment
Get the identifier, if any, of the Compartment object that is designated as being outside of this one.
getPackage() - Method in class org.sbml.libsbml.XMLError
Returns the SBML Level 3 package extension (if any) that logged this error.
getPackageCoreVersion() - Method in class org.sbml.libsbml.SBase
Returns the SBML Core Version within the SBML Level of the actual object.
getPackageName() - Method in class org.sbml.libsbml.CompBase
Returns the package name of this plugin object.
getPackageName() - Static method in class org.sbml.libsbml.CompExtension
Returns the nickname of the SBML Level 3 package implemented by this libSBML extension.
getPackageName() - Method in class org.sbml.libsbml.CompPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Static method in class org.sbml.libsbml.FbcExtension
Returns the nickname of the SBML Level 3 package implemented by this libSBML extension.
getPackageName() - Method in class org.sbml.libsbml.FbcPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Static method in class org.sbml.libsbml.GroupsExtension
Returns the nickname of the SBML Level 3 package implemented by this libSBML extension.
getPackageName() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Static method in class org.sbml.libsbml.LayoutExtension
Returns the nickname of the SBML Level 3 package implemented by this libSBML extension.
getPackageName() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Static method in class org.sbml.libsbml.QualExtension
Returns the nickname of the SBML Level 3 package implemented by this libSBML extension.
getPackageName() - Method in class org.sbml.libsbml.QualPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Static method in class org.sbml.libsbml.RenderExtension
Returns the package name of this extension.
getPackageName() - Method in class org.sbml.libsbml.RenderPkgNamespaces
Returns the name of the main package for this namespace.
getPackageName() - Method in class org.sbml.libsbml.SBase
Returns the name of the SBML Level 3 package in which this element is defined.
getPackageName() - Method in class org.sbml.libsbml.SBasePlugin
Returns the short-form name of the package to which this plugin object belongs.
getPackageName() - Method in class org.sbml.libsbml.SBMLNamespaces
Returns the name of the main package for this namespace.
getPackageRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns the required attribute of the given package extension.
getPackageToStrip() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
 
getPackageURI() - Method in class org.sbml.libsbml.CompBase
Returns the XML namespace (URI) of the package extension of this object.
getPackageVersion() - Method in class org.sbml.libsbml.CompBase
Returns the package version of the package extension of this plugin object.
getPackageVersion() - Method in class org.sbml.libsbml.CompPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.FbcPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.QualPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.RenderPkgNamespaces
 
getPackageVersion() - Method in class org.sbml.libsbml.SBase
Returns the Version of the SBML Level 3 package to which this element belongs to.
getPackageVersion() - Method in class org.sbml.libsbml.SBasePlugin
Returns the package version of the package extension of this plugin object.
getPackageVersion(String) - Method in class org.sbml.libsbml.CompExtension
Returns the SBML Level 3 package version for the given URI of this package.
getPackageVersion(String) - Method in class org.sbml.libsbml.FbcExtension
Returns the SBML Level 3 package version for the given URI of this package.
getPackageVersion(String) - Method in class org.sbml.libsbml.GroupsExtension
Returns the SBML Level 3 package version for the given URI of this package.
getPackageVersion(String) - Method in class org.sbml.libsbml.LayoutExtension
Returns the SBML Level 3 package version for the given URI of this package.
getPackageVersion(String) - Method in class org.sbml.libsbml.QualExtension
Returns the SBML Level 3 package version for the given URI of this package.
getPackageVersion(String) - Method in class org.sbml.libsbml.RenderExtension
Returns the package version with the given URI of this package.
getPackageVersion(String) - Method in class org.sbml.libsbml.SBMLExtension
Returns the package version associated with the given XML namespace URI.
getParameter(long) - Method in class org.sbml.libsbml.KineticLaw
Returns the nth Parameter object in the list of parameters in this KineticLaw instance.
getParameter(long) - Method in class org.sbml.libsbml.Model
Get the nth Parameter object in this Model.
getParameter(String) - Method in class org.sbml.libsbml.KineticLaw
Returns a parameter based on its identifier.
getParameter(String) - Method in class org.sbml.libsbml.Model
Get a Parameter object based on its identifier.
getParentModel(SBase) - Static method in class org.sbml.libsbml.CompBase
Returns the Model object to which the referenced child object belongs.
getParentSBMLObject() - Method in class org.sbml.libsbml.ASTNode
Returns the parent SBML object.
getParentSBMLObject() - Method in class org.sbml.libsbml.SBase
Returns the parent SBML object containing this object.
getParentSBMLObject() - Method in class org.sbml.libsbml.SBasePlugin
Returns the parent object to which this plugin object is connected.
getParseAvogadroCsymbol() - Method in class org.sbml.libsbml.L3ParserSettings
Indicates the current behavior set for handling avogadro for SBML Level 3.
getParseCollapseMinus() - Method in class org.sbml.libsbml.L3ParserSettings
Indicates the current behavior set for handling multiple unary minuses in formulas.
getParseL3v2Functions() - Method in class org.sbml.libsbml.L3ParserSettings
Indicates the current behavior set for handling the @% symbol in mathematical formulas.
getParseLog() - Method in class org.sbml.libsbml.L3ParserSettings
Indicates the current behavior set for handling the function log with one argument.
getParseModuloL3v2() - Method in class org.sbml.libsbml.L3ParserSettings
Indicates the current behavior set for handling the @% symbol in mathematical formulas.
getParseUnits() - Method in class org.sbml.libsbml.L3ParserSettings
Indicates the current behavior set for handling units in text-string mathematical formulas.
getPath() - Method in class org.sbml.libsbml.SBMLUri
Returns the path and filename portion of the stored URI.
getPersistent() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Get the value of the 'persistent' attribute of this Trigger.
getPkgRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
Deprecated.
Replaced in libSBML 5.2.0 by getPackageRequired(String)
getPlugin(long) - Method in class org.sbml.libsbml.SBase
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
getPlugin(String) - Method in class org.sbml.libsbml.SBase
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
getPort(long) - Method in class org.sbml.libsbml.CompModelPlugin
Returns the port with the given index.
getPort(String) - Method in class org.sbml.libsbml.CompModelPlugin
Returns the port with the given identifier.
getPortRef() - Method in class org.sbml.libsbml.SBaseRef
Returns the value of the 'portRef' attribute of this SBaseRef.
getPosition() - Method in class org.sbml.libsbml.BoundingBox
Returns the position of the BoundingBox as reference to a Point object.
getPositionExplicitlySet() - Method in class org.sbml.libsbml.BoundingBox
Return true or false based on whether Position has been set.
getPrecedence() - Method in class org.sbml.libsbml.ASTNode
Returns the precedence of this node in the infix math syntax of SBML Level 1.
getPrefix() - Method in class org.sbml.libsbml.SBase
Returns the XML namespace prefix of this element.
getPrefix() - Method in class org.sbml.libsbml.SBasePlugin
Returns the XML namespace prefix of the package to which this plugin object belongs.
getPrefix() - Method in class org.sbml.libsbml.XMLToken
Returns the XML namespace prefix of token.
getPrefix() - Method in class org.sbml.libsbml.XMLTriple
Returns the prefix portion of this XMLTriple object.
getPrefix(int) - Method in class org.sbml.libsbml.XMLAttributes
Returns the namespace prefix of the nth attribute in this attribute set.
getPrefix(int) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the prefix of an XML namespace declaration by its position.
getPrefix(String) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the prefix of an XML namespace declaration by its URI.
getPrefixedName() - Method in class org.sbml.libsbml.XMLTriple
Returns the prefixed name from this XMLTriple.
getPrefixedName(int) - Method in class org.sbml.libsbml.XMLAttributes
Returns the prefix name of the nth attribute in this attribute set.
getPriority() - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Get the event priority portion of this Event.
getProduct(long) - Method in class org.sbml.libsbml.Reaction
Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction.
getProduct(String) - Method in class org.sbml.libsbml.Reaction
Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction.
getProgramName() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the program name that created the render information.
getProgramVersion() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the version of the program that created the render information.
getProperties() - Method in class org.sbml.libsbml.SBMLConverter
Returns the current properties in effect for this converter.
getQualifierType() - Method in class org.sbml.libsbml.CVTerm
Returns the qualifier type of this CVTerm object.
getQualitativeSpecies() - Method in class org.sbml.libsbml.Input
Returns the value of the 'qualitativeSpecies' attribute of this Input.
getQualitativeSpecies() - Method in class org.sbml.libsbml.Output
Returns the value of the 'qualitativeSpecies' attribute of this Output.
getQualitativeSpecies(long) - Method in class org.sbml.libsbml.QualModelPlugin
Returns the QualitativeSpecies object that belongs to the given index.
getQualitativeSpecies(String) - Method in class org.sbml.libsbml.QualModelPlugin
Returns the qualitativeSpecies object based on its identifier.
getQuery() - Method in class org.sbml.libsbml.SBMLUri
Returns the query portion of the stored URI.
getRadialGradient_cx() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'radialGradient_cx' attribute of this DefaultValues.
getRadialGradient_cy() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'radialGradient_cy' attribute of this DefaultValues.
getRadialGradient_cz() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'radialGradient_cz' attribute of this DefaultValues.
getRadialGradient_fx() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'radialGradient_fx' attribute of this DefaultValues.
getRadialGradient_fy() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'radialGradient_fy' attribute of this DefaultValues.
getRadialGradient_fz() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'radialGradient_fz' attribute of this DefaultValues.
getRadialGradient_r() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'radialGradient_r' attribute of this DefaultValues.
getRadius() - Method in class org.sbml.libsbml.RadialGradient
Returns the radius as a reference.
getRadiusX() - Method in class org.sbml.libsbml.Rectangle
Returns the corner radius along the x axis
getRadiusY() - Method in class org.sbml.libsbml.Rectangle
Returns the corner radius along the y axis
getRateRule(String) - Method in class org.sbml.libsbml.Model
Get a Rule object based on the variable to which it assigns a value.
getRateRuleByVariable(String) - Method in class org.sbml.libsbml.Model
Get a Rule object based on the variable to which it assigns a value.
getRatio() - Method in class org.sbml.libsbml.Ellipse
Returns the value of the 'ratio' attribute of this Ellipse.
getRatio() - Method in class org.sbml.libsbml.Rectangle
Returns the value of the 'ratio' attribute of this Rectangle.
getReactant(long) - Method in class org.sbml.libsbml.Reaction
Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction.
getReactant(String) - Method in class org.sbml.libsbml.Reaction
Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction.
getReaction() - Method in class org.sbml.libsbml.FluxBound
Returns the value of the 'reaction' attribute of this FluxBound object.
getReaction() - Method in class org.sbml.libsbml.FluxObjective
Returns the value of the 'reaction' attribute of this FluxObjective.
getReaction() - Method in class org.sbml.libsbml.GeneAssociation
Returns the string of the 'reaction' attribute of this GeneAssociation.
getReaction(long) - Method in class org.sbml.libsbml.Model
Get the nth Reaction object in this Model.
getReaction(String) - Method in class org.sbml.libsbml.Model
Get a Reaction object based on its identifier.
getReactionGlyph(long) - Method in class org.sbml.libsbml.Layout
Returns the reaction glyph with the given index.
getReactionGlyph(String) - Method in class org.sbml.libsbml.Layout
Returns the reaction glyph that has the given id, or null if no reaction glyph has the id.
getReactionId() - Method in class org.sbml.libsbml.ReactionGlyph
Returns the id of the associated reaction.
getReal() - Method in class org.sbml.libsbml.ASTNode
Returns the real-numbered value of this node.
getRed() - Method in class org.sbml.libsbml.ColorDefinition
Returns the red color component.
getReference() - Method in class org.sbml.libsbml.Association
Returns the string of the 'reference' attribute of this Association object.
getReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
Returns the object pointed to by this element.
getReferencedElementFrom(Model) - Method in class org.sbml.libsbml.ReplacedElement
Finds the SBase object this ReplacedElement object points to, if any.
getReferencedElementFrom(Model) - Method in class org.sbml.libsbml.SBaseRef
Examines the referenced Model for the referenced object, and returns it, if found.
getReferencedModel() - Method in class org.sbml.libsbml.ExternalModelDefinition
Resolves and returns the referenced Model object of this ExternalModelDefinition.
getReferenceGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
Returns the reference glyph with the given index.
getReferenceId() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the id of the associated element.
getReferenceId() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns the id of the associated sbml reference.
getReferenceRenderInformationId() - Method in class org.sbml.libsbml.RenderInformationBase
Returns the id of the referenced render information object.
getRegisteredPackageName(long) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns the nth registered package.
getRelativeValue() - Method in class org.sbml.libsbml.RelAbsVector
Returns the relative coordinate value.
getRenderInformation(long) - Method in class org.sbml.libsbml.RenderLayoutPlugin
Returns a pointer to the local render information object with the given index.
getRenderInformation(long) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Returns a pointer to the local render information object with the given index.
getRenderInformation(String) - Method in class org.sbml.libsbml.RenderLayoutPlugin
Returns a pointer to the local render information object with the given id.
getRenderInformation(String) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Returns a pointer to the local render information object with the given id.
getReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
Get the child ReplacedBy of this SBase.
getReplacedElement(long) - Method in class org.sbml.libsbml.CompSBasePlugin
Returns the ReplacedElement with the given index.
getRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Returns the value of the 'required' attribute.
getResolverByIndex(int) - Method in class org.sbml.libsbml.SBMLResolverRegistry
Returns the resolver with the given index number.
getResourceBiologicalQualifier(String) - Method in class org.sbml.libsbml.SBase
Returns the MIRIAM biological qualifier associated with the given resource.
getResourceModelQualifier(String) - Method in class org.sbml.libsbml.SBase
Returns the MIRIAM model qualifier associated with the given resource.
getResources() - Method in class org.sbml.libsbml.CVTerm
Returns the resource references for this CVTerm object.
getResourceURI(long) - Method in class org.sbml.libsbml.CVTerm
Returns the value of the nth resource for this CVTerm object.
getResultLevel() - Method in class org.sbml.libsbml.DefaultTerm
Returns the value of the 'resultLevel' attribute of this DefaultTerm.
getResultLevel() - Method in class org.sbml.libsbml.FunctionTerm
Returns the value of the 'resultLevel' attribute of this FunctionTerm.
getReversible() - Method in class org.sbml.libsbml.Reaction
Returns the value of the 'reversible' attribute on the Reaction as a boolean value.
getRightChild() - Method in class org.sbml.libsbml.ASTNode
Returns the right child of this node.
getRole() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns a string representation of the role.
getRole() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns the role.
getRoleList() - Method in class org.sbml.libsbml.Style
Returns a reference to the role list.
getRoleString() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns a string representation of the role.
getRule(long) - Method in class org.sbml.libsbml.Model
Get the nth Rule object in this Model.
getRule(String) - Method in class org.sbml.libsbml.Model
Get a Rule object based on the variable to which it assigns a value.
getRuleByVariable(String) - Method in class org.sbml.libsbml.Model
Get a Rule object based on the variable to which it assigns a value.
getRX() - Method in class org.sbml.libsbml.Ellipse
Returns the radius along the x axis as a reference.
getRY() - Method in class org.sbml.libsbml.Ellipse
Returns the radius along the y axis as a reference.
getSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
Get the child sBaseRef of this sBaseRef.
getSBMLDocument() - Method in class org.sbml.libsbml.SBase
Returns the SBMLDocument object containing this object instance.
getSBMLDocument() - Method in class org.sbml.libsbml.SBasePlugin
Returns the SBMLDocument object containing this object instance.
getSBMLErrMsg() - Method in exception org.sbml.libsbml.SBMLConstructorException
Returns the message associated with this SBML exception.
getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.CompExtension
Returns an CompPkgNamespaces object.
getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.FbcExtension
Returns an FbcPkgNamespaces object.
getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.GroupsExtension
Returns a GroupsPkgNamespaces object.
getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.LayoutExtension
Returns an LayoutPkgNamespaces object.
getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.QualExtension
Returns an QualPkgNamespaces object.
getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.RenderExtension
Returns an SBMLExtensionNamespaces object whose alias type is LayoutPkgNamespace.
getSBMLExtensionNamespaces(String) - Method in class org.sbml.libsbml.SBMLExtension
Returns a specialized SBMLNamespaces object corresponding to a given namespace URI.
getSBMLNamespaces() - Method in class org.sbml.libsbml.XMLInputStream
Returns the SBMLNamespaces object attached to this XMLInputStream.
getSBMLNamespaces() - Method in class org.sbml.libsbml.XMLOutputStream
Returns the SBMLNamespaces object attached to this output stream.
getSBMLNamespaceURI(long, long) - Static method in class org.sbml.libsbml.SBMLNamespaces
Returns a string representing the SBML XML namespace for the given level and version of SBML.
getSBOTerm() - Method in class org.sbml.libsbml.SBase
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
getSBOTermAsURL() - Method in class org.sbml.libsbml.SBase
Returns the URL representation of the 'sboTerm' attribute of this object.
getSBOTermID() - Method in class org.sbml.libsbml.SBase
Returns the string representation of the 'sboTerm' attribute of this object.
getScale() - Method in class org.sbml.libsbml.Unit
Returns the value of the 'scale' attribute of this unit.
getScheme() - Method in class org.sbml.libsbml.SBMLUri
Returns the scheme of the stored URI.
getSecond() - Method in class org.sbml.libsbml.Date
Returns the seconds from this Date.
getSemanticsAnnotation(long) - Method in class org.sbml.libsbml.ASTNode
Returns the nth MathML <semantics> element on this ASTNode.
getSeverity() - Method in class org.sbml.libsbml.XMLError
Returns the severity of this error.
getSeverityAsString() - Method in class org.sbml.libsbml.XMLError
Returns a string describing the severity level of this error.
getSeverityOverride() - Method in class org.sbml.libsbml.XMLErrorLog
Returns the current override.
getShortMessage() - Method in class org.sbml.libsbml.XMLError
Returns a brief message for this error.
getSign() - Method in class org.sbml.libsbml.Input
Returns the value of the 'sign' attribute of this Input.
getSignOffset() - Method in class org.sbml.libsbml.Date
Returns the sign of the time zone offset from this Date.
getSize() - Method in class org.sbml.libsbml.ASTNodeList
 
getSize() - Method in class org.sbml.libsbml.Compartment
Get the size of this Compartment object.
getSize() - Method in class org.sbml.libsbml.CVTermList
 
getSize() - Method in class org.sbml.libsbml.DateList
 
getSize() - Method in class org.sbml.libsbml.ModelCreatorList
 
getSize() - Method in class org.sbml.libsbml.SBaseList
 
getSize() - Method in class org.sbml.libsbml.SBMLNamespacesList
 
getSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the value of the 'source' attribute of this ExternalModelDefinition.
getSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
Get the number of spatial dimensions of this Compartment object.
getSpatialDimensionsAsDouble() - Method in class org.sbml.libsbml.Compartment
Get the number of spatial dimensions of this Compartment object, as a double.
getSpatialSizeUnits() - Method in class org.sbml.libsbml.Species
Get the value of the 'spatialSizeUnits' attribute.
getSpecies() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Get the value of the 'species' attribute.
getSpecies(long) - Method in class org.sbml.libsbml.Model
Get the nth Species object in this Model.
getSpecies(String) - Method in class org.sbml.libsbml.Model
Get a Species object based on its identifier.
getSpeciesGlyph(long) - Method in class org.sbml.libsbml.Layout
Returns the species glyph with the given index.
getSpeciesGlyph(String) - Method in class org.sbml.libsbml.Layout
Returns the species glyph that has the given id, or null if no species glyph has the id.
getSpeciesGlyphId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns the id of the associated SpeciesGlyph.
getSpeciesId() - Method in class org.sbml.libsbml.SpeciesGlyph
Returns the id of the associated species object.
getSpeciesReference(String) - Method in class org.sbml.libsbml.Model
Get a SpeciesReference object based on its identifier.
getSpeciesReferenceGlyph(long) - Method in class org.sbml.libsbml.ReactionGlyph
Returns the species reference glyph with the given index.
getSpeciesReferenceId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns the id of the associated species reference.
getSpeciesType() - Method in class org.sbml.libsbml.Species
Get the type of this Species object object.
getSpeciesType(long) - Method in class org.sbml.libsbml.Model
Get the nth SpeciesType object in this Model.
getSpeciesType(String) - Method in class org.sbml.libsbml.Model
Get a SpeciesType object based on its identifier.
getSpreadMethod() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'spreadMethod' attribute of this DefaultValues.
getSpreadMethod() - Method in class org.sbml.libsbml.GradientBase
Returns the spreadmethod of the gradient.
getSpreadMethodAsString() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'spreadMethod' attribute of this DefaultValues.
getStandardMessage(int) - Static method in class org.sbml.libsbml.XMLError
Returns a copy of the message string associated with the given predefined XMLError code.
getStart() - Method in class org.sbml.libsbml.LineSegment
Returns the start point of the line.
getStartHead() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'startHead' attribute of this DefaultValues.
getStartHead() - Method in class org.sbml.libsbml.RenderCurve
Returns the id of the LineEnding object to be applied to the start of the curve.
getStartHead() - Method in class org.sbml.libsbml.RenderGroup
Returns the id of the LineEnding object to be applied to the start of the curve.
getStoichiometry() - Method in class org.sbml.libsbml.SpeciesReference
Get the value of the 'stoichiometry' attribute.
getStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
Get the content of the 'stoichiometryMath' subelement as an ASTNode tree.
getStopColor() - Method in class org.sbml.libsbml.GradientStop
Returns the stop color id or the value string.
getStrict() - Method in class org.sbml.libsbml.FbcModelPlugin
Returns the value of the 'strict' attribute of this FbcModelPlugin.
getStrict() - Method in class org.sbml.libsbml.FbcV1ToV2Converter
 
getStringFromTypeCode(int) - Method in class org.sbml.libsbml.CompExtension
Takes a type code of the “comp” package and returns a string describing the code.
getStringFromTypeCode(int) - Method in class org.sbml.libsbml.FbcExtension
Takes a type code of the “fbc” package and returns a string describing the code.
getStringFromTypeCode(int) - Method in class org.sbml.libsbml.GroupsExtension
Takes a type code of the “groups” package and returns a string describing the code.
getStringFromTypeCode(int) - Method in class org.sbml.libsbml.LayoutExtension
Takes a type code of the “layout” package and returns a string describing the code.
getStringFromTypeCode(int) - Method in class org.sbml.libsbml.QualExtension
Takes a type code of the “qual” package and returns a string describing the code.
getStringFromTypeCode(int) - Method in class org.sbml.libsbml.RenderExtension
This method takes a type code of groups package and returns a string representing the code.
getStringFromTypeCode(int) - Method in class org.sbml.libsbml.SBMLExtension
Returns a string representation of a type code.
getStroke() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'stroke' attribute of this DefaultValues.
getStroke() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Returns the stroke color.
getStrokeWidth() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'strokeWidth' attribute of this DefaultValues.
getStrokeWidth() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Returns the stroke width.
getStyle() - Method in class org.sbml.libsbml.ASTNode
Returns the MathML style attribute value of this ASTNode.
getStyle(long) - Method in class org.sbml.libsbml.GlobalRenderInformation
Returns a pointer to the style with the given index.
getStyle(long) - Method in class org.sbml.libsbml.LocalRenderInformation
Returns a pointer to the style with the given index.
getStyle(String) - Method in class org.sbml.libsbml.GlobalRenderInformation
Returns a pointer to the style with the given id.
getStyle(String) - Method in class org.sbml.libsbml.LocalRenderInformation
Returns a pointer to the style with the given id.
getSubGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
Returns the sub glyph with the given index.
getSubmodel(long) - Method in class org.sbml.libsbml.CompModelPlugin
Returns the submodel with the given index.
getSubmodel(String) - Method in class org.sbml.libsbml.CompModelPlugin
Returns the submodel with the given identifier.
getSubmodelRef() - Method in class org.sbml.libsbml.Replacing
Returns the value of the 'submodelRef' attribute of this SBaseRef.
getSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
Returns an empty string, since 'substanceConversionFactor' is not a part of the comp spec.
getSubstanceUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Returns the value of the 'substanceUnits' attribute of this KineticLaw object.
getSubstanceUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'substanceUnits' attribute of this Model.
getSubstanceUnits() - Method in class org.sbml.libsbml.Species
Get the value of the 'substanceUnits' attribute.
getSupportedNamespaces() - Static method in class org.sbml.libsbml.SBMLNamespaces
Returns a list of all supported SBMLNamespaces in this version of libsbml.
getSupportedPackageURI(long) - Method in class org.sbml.libsbml.SBMLExtension
Returns the nth XML namespace URI.
getSymbol() - Method in class org.sbml.libsbml.InitialAssignment
Get the value of the 'symbol' attribute of this InitialAssignment.
getTargetLevel() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the target SBML Level for the conversion.
getTargetNamespaces() - Method in class org.sbml.libsbml.ConversionProperties
Returns the current target SBML namespace.
getTargetNamespaces() - Method in class org.sbml.libsbml.SBMLConverter
Returns the target SBML namespaces of the currently set properties.
getTargetVersion() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the target SBML Version for the conversion.
getText() - Method in class org.sbml.libsbml.Text
Returns the text for the Text object.
getText() - Method in class org.sbml.libsbml.TextGlyph
Returns the text to be displayed by the text glyph.
getTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'textAnchor' attribute of this DefaultValues.
getTextAnchor() - Method in class org.sbml.libsbml.RenderGroup
Returns the text anchor.
getTextAnchor() - Method in class org.sbml.libsbml.Text
Returns the text anchor.
getTextAnchorAsString() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'textAnchor' attribute of this DefaultValues.
getTextGlyph(long) - Method in class org.sbml.libsbml.Layout
Returns the text glyph with the given index.
getTextGlyph(String) - Method in class org.sbml.libsbml.Layout
Returns the text glyph that has the given id, or null if no text glyph has the id.
getThresholdLevel() - Method in class org.sbml.libsbml.Input
Returns the value of the 'thresholdLevel' attribute of this Input.
getTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
Returns the value of the 'timeConversionFactor' attribute of this Submodel.
getTimeUnits() - Method in class org.sbml.libsbml.Event
Get the value of the 'timeUnits' attribute of this Event, if it has one.
getTimeUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Returns the value of the 'timeUnits' attribute of this KineticLaw object.
getTimeUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'timeUnits' attribute of this Model.
getTransformer() - Method in class org.sbml.libsbml.CompModelPlugin
 
getTransition(long) - Method in class org.sbml.libsbml.QualModelPlugin
Returns the Transition object that belongs to the given index.
getTransition(String) - Method in class org.sbml.libsbml.QualModelPlugin
Returns the qualitativeSpecies object based on its identifier.
getTransitionEffect() - Method in class org.sbml.libsbml.Input
Returns the value of the 'transitionEffect' attribute of this Input.
getTransitionEffect() - Method in class org.sbml.libsbml.Output
Returns the value of the 'transitionEffect' attribute of this Output.
getTrigger() - Method in class org.sbml.libsbml.Event
Get the event trigger portion of this Event.
getType() - Method in class org.sbml.libsbml.Association
Returns the string of the 'type' attribute of this Association object.
getType() - Method in class org.sbml.libsbml.ASTNode
Returns the type of this ASTNode.
getType() - Method in class org.sbml.libsbml.ConversionOption
Returns the type of this option
getType() - Method in class org.sbml.libsbml.Objective
Returns the string of the 'type' attribute of this Objective.
getType() - Method in class org.sbml.libsbml.Rule
Returns a code representing the type of rule this is.
getType(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the type of a given option in this properties object.
getTypeCode() - Method in class org.sbml.libsbml.Association
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.BoundingBox
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.ColorDefinition
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Compartment
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.CompartmentGlyph
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.CompartmentType
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Constraint
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.CubicBezier
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Curve
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.DefaultTerm
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.DefaultValues
Returns the libSBML type code for this DefaultValues object.
getTypeCode() - Method in class org.sbml.libsbml.Delay
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Deletion
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Dimensions
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Ellipse
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Event
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.EventAssignment
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.FbcAnd
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.FbcAssociation
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.FbcOr
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.FluxBound
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.FluxObjective
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.FunctionDefinition
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.FunctionTerm
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.GeneAssociation
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.GeneProduct
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.GeneProductAssociation
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.GeneProductRef
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.GeneralGlyph
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.GlobalRenderInformation
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.GlobalStyle
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.GradientStop
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.GraphicalObject
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Group
Returns the libSBML type code for this Group object.
getTypeCode() - Method in class org.sbml.libsbml.Image
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.InitialAssignment
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Input
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.KineticLaw
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Layout
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.LinearGradient
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.LineEnding
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.LineSegment
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.ListOf
Returns the libSBML type code for this object, namely, SBML_LIST_OF.
getTypeCode() - Method in class org.sbml.libsbml.ListOfFbcAssociations
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfFluxObjectives
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfGeneProducts
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfGlobalStyles
Returns the libSBML type code for the objects contained in this ListOf (i.e., GradientDefinition objects, if the list is non-empty).
getTypeCode() - Method in class org.sbml.libsbml.ListOfGroups
Returns the libSBML type code for this ListOfGroups object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfLocalStyles
Returns the libSBML type code for the objects contained in this ListOf (i.e., GradientDefinition objects, if the list is non-empty).
getTypeCode() - Method in class org.sbml.libsbml.ListOfMembers
Returns the libSBML type code for this ListOfMembers object.
getTypeCode() - Method in class org.sbml.libsbml.ListOfObjectives
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.LocalParameter
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.LocalRenderInformation
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.LocalStyle
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Member
Returns the libSBML type code for this Member object.
getTypeCode() - Method in class org.sbml.libsbml.Model
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ModelDefinition
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Objective
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Output
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Parameter
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Point
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Polygon
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Port
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Priority
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.QualitativeSpecies
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.RadialGradient
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Reaction
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ReactionGlyph
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Rectangle
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.RenderCubicBezier
Returns the libSBML type code for the objects contained in this ListOf (i.e., ColorDefinition objects, if the list is non-empty).
getTypeCode() - Method in class org.sbml.libsbml.RenderCurve
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.RenderGroup
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.RenderPoint
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.ReplacedBy
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.ReplacedElement
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Rule
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.SBase
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.SBaseRef
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.SBMLDocument
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.Species
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.SpeciesGlyph
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.SpeciesReference
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.SpeciesType
Returns the libSBML type code for this SBML object.
getTypeCode() - Method in class org.sbml.libsbml.StoichiometryMath
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Submodel
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Text
Returns the libSBML type code for this object.
getTypeCode() - Method in class org.sbml.libsbml.TextGlyph
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Transition
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Trigger
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.Unit
Returns the libSBML type code of this object instance.
getTypeCode() - Method in class org.sbml.libsbml.UnitDefinition
Returns the libSBML type code for this object instance.
getTypeList() - Method in class org.sbml.libsbml.Style
Returns the type list.
getUnit(long) - Method in class org.sbml.libsbml.UnitDefinition
Returns a specific Unit instance belonging to this UnitDefinition.
getUnitDefinition(long) - Method in class org.sbml.libsbml.Model
Get the nth UnitDefinition object in this Model.
getUnitDefinition(String) - Method in class org.sbml.libsbml.Model
Get a UnitDefinition based on its identifier.
getUnitRef() - Method in class org.sbml.libsbml.SBaseRef
Returns the value of the 'unitRef' attribute of this SBaseRef.
getUnits() - Method in class org.sbml.libsbml.ASTNode
Returns the units of this ASTNode.
getUnits() - Method in class org.sbml.libsbml.Compartment
Get the units of this Compartment object's size.
getUnits() - Method in class org.sbml.libsbml.Parameter
Gets the units defined for this Parameter.
getUnits() - Method in class org.sbml.libsbml.Rule
Returns the units for the mathematical formula of this Rule.
getUnits() - Method in class org.sbml.libsbml.Species
Get the value of the 'units' attribute.
getUpperFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
Returns the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.
getUri() - Method in class org.sbml.libsbml.SBMLUri
Returns the full stored URI, after replacing backslashes with slashes.
getURI() - Method in class org.sbml.libsbml.CompPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.FbcPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.GroupsPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.LayoutPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.QualPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.RenderPkgNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.SBase
Gets the namespace URI to which this element belongs to.
getURI() - Method in class org.sbml.libsbml.SBasePlugin
Returns the XML namespace URI for the package to which this object belongs.
getURI() - Method in class org.sbml.libsbml.SBMLNamespaces
Returns a string representing the SBML XML namespace of this object.
getURI() - Method in class org.sbml.libsbml.XMLNamespaces
Look up the URI of an XML namespace declaration by its prefix.
getURI() - Method in class org.sbml.libsbml.XMLToken
Returns the XML namespace URI of token.
getURI() - Method in class org.sbml.libsbml.XMLTriple
Returns the URI portion of this XMLTriple object.
getURI(int) - Method in class org.sbml.libsbml.XMLAttributes
Returns the XML namespace URI of the nth attribute in this attribute set.
getURI(int) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the URI of an XML namespace declaration by its position.
getURI(long, long, long) - Method in class org.sbml.libsbml.CompExtension
Returns a string representing the SBML XML namespace of this SBML Level 3 package.
getURI(long, long, long) - Method in class org.sbml.libsbml.FbcExtension
Returns a string representing the SBML XML namespace of this SBML Level 3 package.
getURI(long, long, long) - Method in class org.sbml.libsbml.GroupsExtension
Returns a string representing the SBML XML namespace of this SBML Level 3 package.
getURI(long, long, long) - Method in class org.sbml.libsbml.LayoutExtension
Returns a string representing the SBML XML namespace of this SBML Level 3 package.
getURI(long, long, long) - Method in class org.sbml.libsbml.QualExtension
Returns a string representing the SBML XML namespace of this SBML Level 3 package.
getURI(long, long, long) - Method in class org.sbml.libsbml.RenderExtension
Returns the URI (namespace) of the package corresponding to the combination of the given sbml level, sbml version, and package version.
getURI(long, long, long) - Method in class org.sbml.libsbml.SBMLExtension
Returns the XML namespace URI for a given Level and Version.
getURI(String) - Method in class org.sbml.libsbml.XMLNamespaces
Look up the URI of an XML namespace declaration by its prefix.
getUseValuesFromTriggerTime() - Method in class org.sbml.libsbml.Event
Get the value of the 'useValuesFromTriggerTime' attribute of this Event.
getValidityFlag() - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns the flag indicating whether the conversion has been set to 'strict'.
getValue() - Method in class org.sbml.libsbml.ASTNode
Returns the numerical value of this ASTNode.
getValue() - Method in class org.sbml.libsbml.ConversionOption
Returns the value of this option.
getValue() - Method in class org.sbml.libsbml.FluxBound
Returns the value of the 'value' attribute of this FluxBound object.
getValue() - Method in class org.sbml.libsbml.Parameter
Gets the numerical value of this Parameter.
getValue(int) - Method in class org.sbml.libsbml.XMLAttributes
Returns the value of the nth attribute in this list of attributes.
getValue(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns the value of the given option as a string.
getValue(String) - Method in class org.sbml.libsbml.XMLAttributes
Returns a named attribute's value.
getValue(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Returns a named attribute's value.
getValue(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
Return the value of an attribute described by a given XMLTriple object.
getVariable() - Method in class org.sbml.libsbml.EventAssignment
Get the value of this EventAssignment's 'variable' attribute.
getVariable() - Method in class org.sbml.libsbml.Rule
Get the value of the 'variable' attribute of this Rule object.
getVersion() - Method in class org.sbml.libsbml.SBase
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
getVersion() - Method in class org.sbml.libsbml.SBasePlugin
Returns the Version within the SBML Level of the package extension of this plugin object.
getVersion() - Method in class org.sbml.libsbml.SBMLNamespaces
Get the SBML Version of this SBMLNamespaces object.
getVersion() - Method in class org.sbml.libsbml.XMLInputStream
Returns the version of the XML stream.
getVersion(String) - Method in class org.sbml.libsbml.CompExtension
Returns the Version within the SBML Level for the given URI of this package.
getVersion(String) - Method in class org.sbml.libsbml.FbcExtension
Returns the Version within the SBML Level for the given URI of this package.
getVersion(String) - Method in class org.sbml.libsbml.GroupsExtension
Returns the Version within the SBML Level for the given URI of this package.
getVersion(String) - Method in class org.sbml.libsbml.LayoutExtension
Returns the Version within the SBML Level for the given URI of this package.
getVersion(String) - Method in class org.sbml.libsbml.QualExtension
Returns the Version within the SBML Level for the given URI of this package.
getVersion(String) - Method in class org.sbml.libsbml.RenderExtension
Returns the SBML version with the given URI of this package.
getVersion(String) - Method in class org.sbml.libsbml.SBMLExtension
Returns the SBML Version associated with the given XML namespace URI.
getVersionString() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Returns the version as a string.
getVersionString() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Returns the version as a string.
getVolume() - Method in class org.sbml.libsbml.Compartment
Get the volume of this Compartment object.
getVolumeUnits() - Method in class org.sbml.libsbml.Model
Returns the value of the 'volumeUnits' attribute of this Model.
getVTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'vtextAnchor' attribute of this DefaultValues.
getVTextAnchor() - Method in class org.sbml.libsbml.RenderGroup
Returns the vertical text anchor.
getVTextAnchor() - Method in class org.sbml.libsbml.Text
Returns the vertical text anchor.
getVTextAnchorAsString() - Method in class org.sbml.libsbml.DefaultValues
Returns the value of the 'vtextAnchor' attribute of this DefaultValues.
getWidth() - Method in class org.sbml.libsbml.Dimensions
Returns the width.
getWidth() - Method in class org.sbml.libsbml.Image
Returns a reference to the width of the image.
getWidth() - Method in class org.sbml.libsbml.Rectangle
Returns the with of the rectangle
getWriteComment() - Static method in class org.sbml.libsbml.XMLOutputStream
 
getWriteTimestamp() - Static method in class org.sbml.libsbml.XMLOutputStream
 
getX() - Method in class org.sbml.libsbml.Image
Returns a reference to the x coordinate of the image position.
getX() - Method in class org.sbml.libsbml.Rectangle
Returns the x coordinate of the rectangles position
getX() - Method in class org.sbml.libsbml.Text
Returns the x position offset as a reference.
getXmlnsL2() - Static method in class org.sbml.libsbml.LayoutExtension
Returns the XML namespace URI of the SBML Level 2 version of the package implemented by this libSBML Extension.
getXmlnsL2() - Static method in class org.sbml.libsbml.RenderExtension
 
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.CompExtension
Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension.
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.FbcExtension
Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension.
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.GroupsExtension
Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension.
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.LayoutExtension
Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension.
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.QualExtension
Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension.
getXmlnsL3V1V1() - Static method in class org.sbml.libsbml.RenderExtension
Returns URI of supported versions of this package.
getXmlnsL3V1V2() - Static method in class org.sbml.libsbml.FbcExtension
Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension.
getXmlnsXSI() - Static method in class org.sbml.libsbml.LayoutExtension
Returns the XML namespace URI of any additional XML namespaces needed or used by this SBML Level 3 package.
getXOffset() - Method in class org.sbml.libsbml.Point
Returns the x offset.
getXPoint1() - Method in class org.sbml.libsbml.LinearGradient
Returns the x coordinate for the start point as a reference.
getXPoint2() - Method in class org.sbml.libsbml.LinearGradient
Returns the x coordinate for the end point as a reference.
getY() - Method in class org.sbml.libsbml.Image
Returns a reference to the y coordinate of the image position.
getY() - Method in class org.sbml.libsbml.Rectangle
Returns the y coordinate of the rectangles position
getY() - Method in class org.sbml.libsbml.Text
Returns the y position offset as a reference.
getYear() - Method in class org.sbml.libsbml.Date
Returns the year from this Date.
getYOffset() - Method in class org.sbml.libsbml.Point
Returns the y offset.
getYPoint1() - Method in class org.sbml.libsbml.LinearGradient
Returns the y coordinate for the start point as a reference.
getYPoint2() - Method in class org.sbml.libsbml.LinearGradient
Returns the y coordinate for the end point as a reference.
getZ() - Method in class org.sbml.libsbml.Image
Returns a reference to the z coordinate of the image position.
getZ() - Method in class org.sbml.libsbml.Rectangle
Returns the z coordinate of the rectangles position
getZ() - Method in class org.sbml.libsbml.Text
Returns the z position offset as a reference.
getZOffset() - Method in class org.sbml.libsbml.Point
Returns the z offset.
getZOffsetExplicitlySet() - Method in class org.sbml.libsbml.Point
 
getZPoint1() - Method in class org.sbml.libsbml.LinearGradient
Returns the z coordinate for the start point as a reference.
getZPoint2() - Method in class org.sbml.libsbml.LinearGradient
Returns the z coordinate for the end point as a reference.
GlobalRenderInformation - Class in org.sbml.libsbml
GlobalRenderInformation is the render information stored in the ListOfLayouts.
GlobalRenderInformation() - Constructor for class org.sbml.libsbml.GlobalRenderInformation
Creates a new GlobalRenderInformation object with the given SBML level and SBML version.
GlobalRenderInformation(long) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
Creates a new GlobalRenderInformation object with the given SBML level and SBML version.
GlobalRenderInformation(long, long) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
Creates a new GlobalRenderInformation object with the given SBML level and SBML version.
GlobalRenderInformation(long, long, long) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
Creates a new GlobalRenderInformation object with the given SBML level and SBML version.
GlobalRenderInformation(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
Creates a new GlobalRenderInformation object with the given SBMLNamespaces.
GlobalRenderInformation(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GlobalRenderInformation
Constructor which creates a GlobalRenderInformation with the given id and all lists empty.
GlobalStyle - Class in org.sbml.libsbml
implementation of the GlobalStyle concept of the SBML render extension.
GlobalStyle() - Constructor for class org.sbml.libsbml.GlobalStyle
Creates a new GlobalStyle object with the given SBML level and SBML version.
GlobalStyle(long) - Constructor for class org.sbml.libsbml.GlobalStyle
Creates a new GlobalStyle object with the given SBML level and SBML version.
GlobalStyle(long, long) - Constructor for class org.sbml.libsbml.GlobalStyle
Creates a new GlobalStyle object with the given SBML level and SBML version.
GlobalStyle(long, long, long) - Constructor for class org.sbml.libsbml.GlobalStyle
Creates a new GlobalStyle object with the given SBML level and SBML version.
GlobalStyle(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.GlobalStyle
Creates a new GlobalStyle object with the given SBMLNamespaces.
GlobalStyle(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GlobalStyle
Constructor which creates a GlobalStyle with the given id and all lists empty.
GlobalStyle(XMLNode) - Constructor for class org.sbml.libsbml.GlobalStyle
Creates a new GlobalStyle object from the given XMLNode object.
GlobalStyle(XMLNode, long) - Constructor for class org.sbml.libsbml.GlobalStyle
Creates a new GlobalStyle object from the given XMLNode object.
GlobalUnitsNotDeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GradientBase - Class in org.sbml.libsbml
abstract base class for linear and radial gradients
GradientStop - Class in org.sbml.libsbml
LibSBML implementation of the gradient stop concept from the
GradientStop() - Constructor for class org.sbml.libsbml.GradientStop
Creates a new GradientStop object with the given SBML level and SBML version.
GradientStop(long) - Constructor for class org.sbml.libsbml.GradientStop
Creates a new GradientStop object with the given SBML level and SBML version.
GradientStop(long, long) - Constructor for class org.sbml.libsbml.GradientStop
Creates a new GradientStop object with the given SBML level and SBML version.
GradientStop(long, long, long) - Constructor for class org.sbml.libsbml.GradientStop
Creates a new GradientStop object with the given SBML level and SBML version.
GradientStop(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.GradientStop
Creates a new GradientStop object with the given SBMLNamespaces.
GradientStop(XMLNode) - Constructor for class org.sbml.libsbml.GradientStop
Creates a new GradientStop object from the given XMLNode object.
GradientStop(XMLNode, long) - Constructor for class org.sbml.libsbml.GradientStop
Creates a new GradientStop object from the given XMLNode object.
GraphicalObject - Class in org.sbml.libsbml
layout Base class of objects that store layouts.
GraphicalObject() - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject.
GraphicalObject(long) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject.
GraphicalObject(long, long) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject.
GraphicalObject(long, long, long) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject.
GraphicalObject(GraphicalObject) - Constructor for class org.sbml.libsbml.GraphicalObject
Copy constructor.
GraphicalObject(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject with the given LayoutPkgNamespaces
GraphicalObject(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject with the given id.
GraphicalObject(LayoutPkgNamespaces, String, double, double, double, double) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject with the given id and 2D coordinates for the bounding box.
GraphicalObject(LayoutPkgNamespaces, String, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject with the given id and 3D coordinates for the bounding box.
GraphicalObject(LayoutPkgNamespaces, String, BoundingBox) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject with the given id and 3D coordinates for the bounding box.
GraphicalObject(LayoutPkgNamespaces, String, Point, Dimensions) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject with the given id and 3D coordinates for the bounding box.
GraphicalObject(XMLNode) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject from the given XMLNode
GraphicalObject(XMLNode, long) - Constructor for class org.sbml.libsbml.GraphicalObject
Creates a new GraphicalObject from the given XMLNode
GraphicalPrimitive1D - Class in org.sbml.libsbml
base class for all graphical primitives which implements all 1D attributes
GraphicalPrimitive2D - Class in org.sbml.libsbml
base class for all graphical primitives which implements all 2D attributes
Group - Class in org.sbml.libsbml
groups Representation of a group of SBML components.
Group() - Constructor for class org.sbml.libsbml.Group
Creates a new Group using the given SBML Level, Version and “groups” package version.
Group(long) - Constructor for class org.sbml.libsbml.Group
Creates a new Group using the given SBML Level, Version and “groups” package version.
Group(long, long) - Constructor for class org.sbml.libsbml.Group
Creates a new Group using the given SBML Level, Version and “groups” package version.
Group(long, long, long) - Constructor for class org.sbml.libsbml.Group
Creates a new Group using the given SBML Level, Version and “groups” package version.
Group(Group) - Constructor for class org.sbml.libsbml.Group
Copy constructor for Group.
Group(GroupsPkgNamespaces) - Constructor for class org.sbml.libsbml.Group
Creates a new Group using the given GroupsPkgNamespaces object.
GROUP_KIND_CLASSIFICATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GROUP_KIND_COLLECTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GROUP_KIND_PARTONOMY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GROUP_KIND_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupKind_fromString(String) - Static method in class org.sbml.libsbml.libsbml
Returns the enumeration value corresponding to the given string or GROUP_KIND_UNKNOWN if there is no such match.
GroupKind_isValid(int) - Static method in class org.sbml.libsbml.libsbml
Predicate returning 1 (true) or 0 (false) depending on whether the given enumeration value is valid.
GroupKind_isValidString(String) - Static method in class org.sbml.libsbml.libsbml
Predicate returning 1 (true) or 0 (false) depending on whether the given string is a valid enumeration value.
GroupKind_toString(int) - Static method in class org.sbml.libsbml.libsbml
Returns the string version of the provided enumeration value.
GroupsAttributeRequiredMissing - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsAttributeRequiredMustBeBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsAttributeRequiredMustHaveValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsDuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsElementNotInNs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsExtension - Class in org.sbml.libsbml
groups Base extension class for the package.
GroupsExtension() - Constructor for class org.sbml.libsbml.GroupsExtension
Creates a new GroupsExtension instance.
GroupsExtension(GroupsExtension) - Constructor for class org.sbml.libsbml.GroupsExtension
Copy constructor for GroupsExtension.
GroupsGroupAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupEmptyLOElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupKindMustBeGroupKindEnum - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupLOMembersAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupLOMembersAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupLOMembersAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsGroupNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsIdSyntaxRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsLOMembersConsistentReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsLOMembersNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsMemberAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsMemberAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsMemberAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsMemberIdRefMustBeSBase - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsMemberIdRefMustBeSId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsMemberMetaIdRefMustBeID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsMemberMetaIdRefMustBeSBase - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsMemberNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsModelAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsModelEmptyLOElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsModelLOGroupsAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsModelLOGroupsAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsModelPlugin - Class in org.sbml.libsbml
groups Extension of Model.
GroupsModelPlugin(String, String, GroupsPkgNamespaces) - Constructor for class org.sbml.libsbml.GroupsModelPlugin
Creates a new GroupsModelPlugin using the given URI, prefix and package namespace.
GroupsModelPlugin(GroupsModelPlugin) - Constructor for class org.sbml.libsbml.GroupsModelPlugin
Copy constructor for GroupsModelPlugin.
GroupsNotCircularReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsNSUndeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
GroupsPkgNamespaces - Class in org.sbml.libsbml
Set of SBML Level + Version + namespace triples.
GroupsPkgNamespaces() - Constructor for class org.sbml.libsbml.GroupsPkgNamespaces
 
GroupsPkgNamespaces(long) - Constructor for class org.sbml.libsbml.GroupsPkgNamespaces
 
GroupsPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.GroupsPkgNamespaces
 
GroupsPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.GroupsPkgNamespaces
 
GroupsPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.GroupsPkgNamespaces
 
GroupsPkgNamespaces(GroupsPkgNamespaces) - Constructor for class org.sbml.libsbml.GroupsPkgNamespaces
 
GroupsUnknown - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

H

has_key(String) - Method in class org.sbml.libsbml.StringSet
 
hasAttr(int) - Method in class org.sbml.libsbml.XMLToken
Returns true if an attribute with the given index exists.
hasAttr(String) - Method in class org.sbml.libsbml.XMLToken
Returns true if an attribute with a given name and namespace URI exists.
hasAttr(String, String) - Method in class org.sbml.libsbml.XMLToken
Returns true if an attribute with a given name and namespace URI exists.
hasAttr(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Returns true if an attribute defined by a given XMLTriple object exists.
hasAttribute(int) - Method in class org.sbml.libsbml.XMLAttributes
Returns true if an attribute exists at a given index.
hasAttribute(String) - Method in class org.sbml.libsbml.XMLAttributes
Returns true if an attribute with a given name and namespace URI exists.
hasAttribute(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Returns true if an attribute with a given name and namespace URI exists.
hasAttribute(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
Returns true if an attribute with the given properties exists.
hasBzip2() - Static method in class org.sbml.libsbml.SBMLReader
Static method; returns true if this copy of libSBML supports bzip2 format compression.
hasBzip2() - Static method in class org.sbml.libsbml.SBMLWriter
Predicate returning true if this copy of libSBML has been linked with the bzip2 library.
hasChild(String) - Method in class org.sbml.libsbml.XMLNode
Return a boolean indicating whether this XMLNode has a child with the given name.
hasCorrectNumberArguments() - Method in class org.sbml.libsbml.ASTNode
Returns true if this ASTNode has the correct number of children for its type.
hasExpectedXHTMLSyntax(XMLNode) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the given XMLNode object contains valid XHTML content.
hasExpectedXHTMLSyntax(XMLNode, SBMLNamespaces) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the given XMLNode object contains valid XHTML content.
hashCode() - Method in class org.sbml.libsbml.ASTNode
Returns a hashcode for this ASTNode object.
hashCode() - Method in class org.sbml.libsbml.CVTerm
Returns a hashcode for this CVTerm object.
hashCode() - Method in class org.sbml.libsbml.Date
Returns a hashcode for this Date object.
hashCode() - Method in class org.sbml.libsbml.ModelCreator
Returns a hashcode for this ModelCreator object.
hashCode() - Method in class org.sbml.libsbml.ModelHistory
Returns a hashcode for this ModelHistory object.
hashCode() - Method in class org.sbml.libsbml.SBase
Returns a hashcode for this SBase object.
hashCode() - Method in class org.sbml.libsbml.SBMLNamespaces
Returns a hashcode for this SBMLNamespaces object.
hashCode() - Method in class org.sbml.libsbml.SBMLReader
Returns a hashcode for this SBMLReader object.
hashCode() - Method in class org.sbml.libsbml.SBMLWriter
Returns a hashcode for this SBMLWriter object.
hashCode() - Method in class org.sbml.libsbml.XMLAttributes
Returns a hashcode for this XMLAttributes object.
hashCode() - Method in class org.sbml.libsbml.XMLError
Returns a hashcode for this XMLError object.
hashCode() - Method in class org.sbml.libsbml.XMLErrorLog
Returns a hashcode for this XMLErrorLog object.
hashCode() - Method in class org.sbml.libsbml.XMLNamespaces
Returns a hashcode for this XMLNamespaces object.
hashCode() - Method in class org.sbml.libsbml.XMLNode
Returns a hashcode for this XMLNode object.
hashCode() - Method in class org.sbml.libsbml.XMLOutputStream
Returns a hashcode for this XMLOutputStream object.
hashCode() - Method in class org.sbml.libsbml.XMLToken
Returns a hashcode for this XMLToken object.
hashCode() - Method in class org.sbml.libsbml.XMLTriple
Returns a hashcode for this XMLTriple object.
hasNamespaceNS(String, String) - Method in class org.sbml.libsbml.XMLToken
Returns true if this token has an XML namespace with a given prefix and URI combination.
hasNamespacePrefix(String) - Method in class org.sbml.libsbml.XMLToken
Returns true if this token has an XML namespace with a given prefix.
hasNamespaceURI(String) - Method in class org.sbml.libsbml.XMLToken
Returns true if this token has an XML namespace with a given URI.
hasNS(String, String) - Method in class org.sbml.libsbml.XMLNamespaces
Predicate returning true or false depending on whether an XML Namespace with the given URI and prefix pair is contained in this XMLNamespaces list.
HasOnlySubsNoSpatialUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
HasOnlySubstanceUnitsNotinL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
HasOnlySubsUnitsNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
hasOption(String) - Method in class org.sbml.libsbml.ConversionProperties
Returns true if this properties object contains an option with the given key.
hasPrefix(String) - Method in class org.sbml.libsbml.XMLNamespaces
Predicate returning true or false depending on whether an XML Namespace with the given prefix is contained in this XMLNamespaces list.
hasRequiredAttributes() - Method in class org.sbml.libsbml.AlgebraicRule
Predicate returning true if all the required attributes for this AlgebraicRule object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.AssignmentRule
Predicate returning true if all the required attributes for this AssignmentRule object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if all the required attributes for this Compartment object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.CompartmentType
Predicate returning true if all the required attributes for this CompartmentType object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.CVTerm
Predicate returning true if all the required elements for this CVTerm object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.DefaultTerm
Predicate returning true if all the required attributes for this DefaultTerm object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if all the required attributes for this DefaultValues object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Event
Predicate returning true if all the required attributes for this Event object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.EventAssignment
Predicate returning true if all the required attributes for this EventAssignment object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.ExternalModelDefinition
Returns true if the 'modelRef' and 'id' attributes are set, and false if not.
hasRequiredAttributes() - Method in class org.sbml.libsbml.FbcAnd
Predicate returning true if all the required attributes for this FbcAnd object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.FbcAssociation
Predicate returning true if all the required attributes for this FbcAssociation object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.FbcOr
Predicate returning true if all the required attributes for this FbcOr object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.FluxObjective
Predicate returning true if all the required attributes for this FluxObjective object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if all the required attributes for this FunctionDefinition object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.FunctionTerm
Predicate returning true if all the required attributes for this FunctionTerm object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.GeneProduct
Predicate returning true if all the required attributes for this GeneProduct object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.GeneProductAssociation
Predicate returning true if all the required attributes for this GeneProductAssociation object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.GeneProductRef
Predicate returning true if all the required attributes for this GeneProductRef object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Group
Predicate returning true if all the required attributes for this Group object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if all the required attributes for this InitialAssignment object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Input
Predicate returning true if all the required attributes for this Input object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if all the required attributes for this KineticLaw object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.ListOfMembers
Predicate returning true if all the required attributes for this ListOfMembers object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.LocalParameter
Predicate returning true if all the required attributes for this LocalParameter object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Member
Predicate returning true if all the required attributes for this Member object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true if all the required elements for this ModelCreator object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.ModelHistory
Predicate returning true if all the required elements for this ModelHistory object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.ModifierSpeciesReference
Predicate returning true if all the required attributes for this ModifierSpeciesReference object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Objective
Predicate returning true if all the required attributes for this Objective object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Output
Predicate returning true if all the required attributes for this Output object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if all the required attributes for this Parameter object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Port
Returns true if the 'id' attribute is set, and if exactly one of the optional attributes of SBaseRef (portRef, idRef, metaIdRef, and unitRef)are set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.QualitativeSpecies
Predicate returning true if all the required attributes for this QualitativeSpecies object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.RateRule
Predicate returning true if all the required attributes for this RateRule object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if all the required attributes for this Reaction object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Replacing
Returns true if getNumReferents() is exactly 1 and if the submodelRef is set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Rule
Predicate returning true if all the required attributes for this Rule object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.SBaseRef
Returns true if getNumReferents() is exactly 1.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Species
Predicate returning true if all the required attributes for this Species object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.SpeciesReference
Predicate returning true if all the required attributes for this SpeciesReference object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.SpeciesType
Predicate returning true if all the required attributes for this SpeciesType object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Submodel
Returns true if the 'submodel' attribute is set, and if getNumReferents() is exactly 1.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Trigger
Predicate returning true if all the required attributes for this Trigger object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.Unit
Predicate returning true if all the required attributes for this Unit object have been set.
hasRequiredAttributes() - Method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if all the required attributes for this UnitDefinition object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Constraint
Predicate returning true if all the required elements for this Constraint object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Delay
Predicate returning true if all the required elements for this Delay object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Event
Predicate returning true if all the required elements for this Event object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.EventAssignment
Predicate returning true if all the required elements for this EventAssignment object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.FbcAnd
Predicate returning true if all the required elements for this FbcAnd object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.FbcOr
Predicate returning true if all the required elements for this FbcOr object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if all the required elements for this FunctionDefinition object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.FunctionTerm
Predicate returning true if all the required elements for this FunctionTerm object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.GeneProductAssociation
Predicate returning true if all the required elements for this GeneProductAssociation object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if all the required elements for this InitialAssignment object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if all the required elements for this KineticLaw object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Model
Predicate returning true if all the required elements for this Model object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Objective
Predicate returning true if all the required elements for this Objective object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Priority
Predicate returning true if all the required elements for this Priority object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Rule
Predicate returning true if all the required elements for this Rule object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.StoichiometryMath
Predicate returning true if all the required elements for this StoichiometryMath object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Transition
Predicate returning true if all the required attributes for this Transition object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.Trigger
Predicate returning true if all the required elements for this Trigger object have been set.
hasRequiredElements() - Method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if all the required elements for this UnitDefinition object have been set.
hasTargetNamespaces() - Method in class org.sbml.libsbml.ConversionProperties
Returns true if the target SBML namespace has been set.
hasTypeAndNumChildren(int, long) - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is of a certain type with a specific number of children.
hasUnits() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node or any of its children nodes have the attribute sbml:units.
hasURI(String) - Method in class org.sbml.libsbml.XMLNamespaces
Predicate returning true or false depending on whether an XML Namespace with the given URI is contained in this XMLNamespaces list.
hasValidLevelVersionNamespaceCombination() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification.
hasZlib() - Static method in class org.sbml.libsbml.SBMLReader
Static method; returns true if this copy of libSBML supports gzip and zip format compression.
hasZlib() - Static method in class org.sbml.libsbml.SBMLWriter
Predicate returning true if this copy of libSBML has been linked with the zlib library.
height() - Method in class org.sbml.libsbml.BoundingBox
Get the height of the bounding box.
height() - Method in class org.sbml.libsbml.Dimensions
Returns the height.

I

IdCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IdCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IdNameSBaseInL3V2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IdNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Image - Class in org.sbml.libsbml
implementation of the Image concept from the SBML render extension
Image() - Constructor for class org.sbml.libsbml.Image
Creates a new Image object with the given SBML level and SBML version.
Image(long) - Constructor for class org.sbml.libsbml.Image
Creates a new Image object with the given SBML level and SBML version.
Image(long, long) - Constructor for class org.sbml.libsbml.Image
Creates a new Image object with the given SBML level and SBML version.
Image(long, long, long) - Constructor for class org.sbml.libsbml.Image
Creates a new Image object with the given SBML level and SBML version.
Image(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.Image
Creates a new Image object with the given SBMLNamespaces.
Image(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.Image
Instantiates an Image object with the given id.
Image(XMLNode) - Constructor for class org.sbml.libsbml.Image
Creates a new Image object from the given XMLNode object.
Image(XMLNode, long) - Constructor for class org.sbml.libsbml.Image
Creates a new Image object from the given XMLNode object.
InconsistentArgUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentArgUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentExponUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentKineticLawUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InconsistentPowerUnitsWarnings - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectCompartmentSpatialDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
IncorrectOrderInReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INFIX_SYNTAX_CURLY_BRACES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INFIX_SYNTAX_CURLY_BRACES_SEMICOLON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INFIX_SYNTAX_NAMED_SQUARE_BRACKETS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INHERIT - Static variable in class org.sbml.libsbml.GraphicalPrimitive2D
 
InitAssignCompartmenMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignmentAndRuleForSameId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignmentCannotRef0DComp - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitAssignStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
initDefaults() - Method in class org.sbml.libsbml.BoundingBox
Does nothing since there are no defaults for a BoundingBox.
initDefaults() - Method in class org.sbml.libsbml.Compartment
Initializes the fields of this Compartment object to 'typical' default values.
initDefaults() - Method in class org.sbml.libsbml.CompartmentGlyph
Calls initDefaults from GraphicalObject.
initDefaults() - Method in class org.sbml.libsbml.CubicBezier
Calls initDefaults from LineSegment.
initDefaults() - Method in class org.sbml.libsbml.Curve
Does nothing since no defaults are defined for Curve.
initDefaults() - Method in class org.sbml.libsbml.Dimensions
Sets the depth to 0.0.
initDefaults() - Method in class org.sbml.libsbml.Event
Initializes the fields of this Event object to 'typical' default values.
initDefaults() - Method in class org.sbml.libsbml.GeneralGlyph
Calls initDefaults from GraphicalObject.
initDefaults() - Method in class org.sbml.libsbml.GraphicalObject
Does nothing.
initDefaults() - Method in class org.sbml.libsbml.Layout
Does nothing since no defaults are defined for Layout.
initDefaults() - Method in class org.sbml.libsbml.LineSegment
Does nothing since no defaults are defined for LineSegment.
initDefaults() - Method in class org.sbml.libsbml.Parameter
Initializes the fields of this Parameter object to 'typical' defaults values.
initDefaults() - Method in class org.sbml.libsbml.Point
Sets the Z offset to 0.0.
initDefaults() - Method in class org.sbml.libsbml.Reaction
Initializes the fields of this Reaction object to 'typical' default values.
initDefaults() - Method in class org.sbml.libsbml.ReactionGlyph
Calls initDefaults from GraphicalObject.
initDefaults() - Method in class org.sbml.libsbml.ReferenceGlyph
Calls initDefaults on GraphicalObject
initDefaults() - Method in class org.sbml.libsbml.RenderPoint
Sets the Z offset to 0.0.
initDefaults() - Method in class org.sbml.libsbml.Species
Initializes the fields of this Species object to 'typical' defaults values.
initDefaults() - Method in class org.sbml.libsbml.SpeciesGlyph
Calls initDefaults from GraphicalObject.
initDefaults() - Method in class org.sbml.libsbml.SpeciesReference
Initializes the fields of this SpeciesReference object to 'typical' default values.
initDefaults() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Calls initDefaults on GraphicalObject and sets role to SPECIES_ROLE_INVALID.
initDefaults() - Method in class org.sbml.libsbml.TextGlyph
Calls initDefaults from GraphicalObject.
initDefaults() - Method in class org.sbml.libsbml.Unit
Initializes the fields of this Unit object to 'typical' default values.
InitialAssignment - Class in org.sbml.libsbml
An SBML initial assignment, evaluated once only.
InitialAssignment(long, long) - Constructor for class org.sbml.libsbml.InitialAssignment
Creates a new InitialAssignment using the given SBML level and version values.
InitialAssignment(InitialAssignment) - Constructor for class org.sbml.libsbml.InitialAssignment
Copy constructor; creates a copy of this InitialAssignment.
InitialAssignment(SBMLNamespaces) - Constructor for class org.sbml.libsbml.InitialAssignment
Creates a new InitialAssignment using the given SBMLNamespaces object sbmlns.
InitialAssignNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitialValueFalseEventNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InitialValueNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Input - Class in org.sbml.libsbml
qual The input to a QualitativeSpecies.
Input() - Constructor for class org.sbml.libsbml.Input
Creates a new Input with the given level, version, and package version.
Input(long) - Constructor for class org.sbml.libsbml.Input
Creates a new Input with the given level, version, and package version.
Input(long, long) - Constructor for class org.sbml.libsbml.Input
Creates a new Input with the given level, version, and package version.
Input(long, long, long) - Constructor for class org.sbml.libsbml.Input
Creates a new Input with the given level, version, and package version.
Input(Input) - Constructor for class org.sbml.libsbml.Input
Copy constructor for Input.
Input(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.Input
Creates a new Input with the given QualPkgNamespaces object.
INPUT_SIGN_DUAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INPUT_SIGN_NEGATIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INPUT_SIGN_POSITIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INPUT_SIGN_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INPUT_SIGN_VALUE_NOTSET - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INPUT_TRANSITION_EFFECT_CONSUMPTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INPUT_TRANSITION_EFFECT_NONE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
INPUT_TRANSITION_EFFECT_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
insert(int, SBase) - Method in class org.sbml.libsbml.ListOf
Inserts an item at a given position in this ListOf's list of items.
insert(String) - Method in class org.sbml.libsbml.StringSet
 
insertAndOwn(int, SBase) - Method in class org.sbml.libsbml.ListOf
Inserts an item at a given position in this ListOf's list of items.
insertChild(long, ASTNode) - Method in class org.sbml.libsbml.ASTNode
Inserts the given ASTNode node at a given point in the current ASTNode's list of children.
insertChild(long, XMLNode) - Method in class org.sbml.libsbml.XMLNode
Inserts a copy of the given node as the nth child of this XMLNode.
insertDash(long, long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Inserts the dash at the given position.
instantiate() - Method in class org.sbml.libsbml.Submodel
Find and create a local copy of the Model object referenced by this Submodel.
int_array - Class in org.sbml.libsbml
 
int_array(int) - Constructor for class org.sbml.libsbml.int_array
 
IntegerSpatialDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InternalXMLParserError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
intToString(int) - Static method in class org.sbml.libsbml.SBO
Returns the integer as a correctly formatted SBO identifier string.
INVALID - Static variable in class org.sbml.libsbml.GradientBase
 
INVALID - Static variable in class org.sbml.libsbml.GraphicalPrimitive2D
 
Invalid1DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Invalid2DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Invalid3DCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidAfterXMLContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidApplyCiInLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidAreaRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidAssignRuleVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCharInXML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCiInLambda - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCompartmentSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCompartmentTypeRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidCompartmentTypeSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidConstraintContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidConstraintSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidDelaySBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidEventAssignmentSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidEventAssignmentVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidEventSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidFunctionDefReturnType - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidFunctionDefSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidInitAssignSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidInitAssignSymbol - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidKineticLawSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidL1CompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidLengthRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidLocalParameterSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidMathElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidMathMLAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidMetaidSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidModelSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidModifiersList - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidNamespaceOnSBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidNameSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidNoArgsPassedToFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidNotesContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidParameterSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidParameterUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidRateRuleVariable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidReactantsProductsList - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidReactionSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidRuleOrdering - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidRuleSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSBMLElementSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSBMLLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSBOTermSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesCompartmentRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesReference - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesReferenceSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesSusbstanceUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesTypeRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSpeciesTypeSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidSubstanceRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidTargetLevelVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidTimeRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidTriggerSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidUnitDefId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidUnitIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidUnitKind - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidUnitsValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidVolumeRedefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
InvalidXMLConstruct - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
is_open() - Method in class org.sbml.libsbml.OFStream
 
isAlgebraic() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an AlgebraicRule.
isAmpere() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind ampere.
isAssignment() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an AssignmentRule.
isAttributesEmpty() - Method in class org.sbml.libsbml.XMLToken
Returns true if this token has no attributes.
isAvogadro() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents the predefined value for Avogadro's constant.
isAvogadro() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind avogadro.
isBecquerel() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind becquerel
isBoolean() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node has a Boolean type.
isBuiltIn(String, long) - Static method in class org.sbml.libsbml.Unit
Predicate to test whether a given string is the name of a built-in SBML unit, depending on the SBML level, since new predefined units were added between level 2 versions 1 and 2, and then all predefined units were removed again in SBML Level 3.
isCandela() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind candela
isCelsius() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind Celsius
isCompartmentVolume() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an CompartmentVolumeRule or equivalent.
isConservationLaw(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isConstant() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents a MathML constant.
isConstantNumber() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents a MathML constant numeric.
isContinuousFramework(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isCoulomb() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind coulomb
isDimensionless() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind dimensionless.
isDisabledIgnoredPackage(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns true if the given package extension is one of an ignored packages that has been disabled, otherwise returns false.
isDiscreteFramework(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isElement() - Method in class org.sbml.libsbml.XMLToken
Returns true if this token represents an XML element.
isEmpty() - Method in class org.sbml.libsbml.XMLAttributes
Returns true if this list of attributes is empty.
isEmpty() - Method in class org.sbml.libsbml.XMLNamespaces
Predicate returning true or false depending on whether this XMLNamespaces list is empty.
isEmpty() - Method in class org.sbml.libsbml.XMLTriple
Returns true if this XMLTriple object is empty.
isEnabled() - Method in class org.sbml.libsbml.SBMLExtension
Returns true if this package is enabled.
isEnabled(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns true if the given extension is enabled.
isEnabledDefaultNS(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns true if a default namespace is added to each top-level element defined in the given package extension, otherwise returns false.
isEnd() - Method in class org.sbml.libsbml.XMLToken
Returns true if this token represents an XML end element.
isEndFor(XMLToken) - Method in class org.sbml.libsbml.XMLToken
Returns true if this token represents an XML end element for a particular start element.
isEntity(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isEOF() - Method in class org.sbml.libsbml.XMLInputStream
Returns true if end of file (stream) has been reached.
isEOF() - Method in class org.sbml.libsbml.XMLToken
Returns true if this token is an end of file marker.
isError() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error is a significant error.
isError() - Method in class org.sbml.libsbml.XMLInputStream
Returns true if a fatal error occurred while reading from this stream.
isEvent(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isFarad() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind farad
isFatal() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error is a fatal run-time error.
isFbcAnd() - Method in class org.sbml.libsbml.FbcAssociation
Returns true, if this abstract FbcAssociation is of type FbcAnd.
isFbcOr() - Method in class org.sbml.libsbml.FbcAssociation
Returns true, if this abstract FbcAssociation is of type FbcOr.
isFunction() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents a function.
isFunctionalCompartment(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isFunctionalEntity(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isGeneProductRef() - Method in class org.sbml.libsbml.FbcAssociation
Returns true, if this abstract FbcAssociation is of type GeneProductRef.
isGood() - Method in class org.sbml.libsbml.XMLInputStream
Returns true if the stream is in a good state.
isGram() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind gram
isGray() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind gray
isHenry() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind henry
isHertz() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind hertz
isIgnoredPackage(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns true if the given package extension is one of an ignored packages, otherwise returns false.
isIgnoredPkg(String) - Method in class org.sbml.libsbml.SBMLDocument
Deprecated.
Replaced in libSBML 5.2.0 by isIgnoredPackage(String)
isInfinity() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents the special IEEE 754 value for infinity.
isInfo() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error object is for information purposes only.
isInIdList(String) - Method in class org.sbml.libsbml.LocalStyle
Checks whether a given id is in the id list.
isInRoleList(String) - Method in class org.sbml.libsbml.Style
Checks whether a given role is in the role list.
isInteger() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node of type AST_INTEGER.
isInteraction(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isInternal() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error resulted from an internal program error.
isInTypeList(String) - Method in class org.sbml.libsbml.Style
Checks whether a given type string is in the type list.
isInUse(SBMLDocument) - Method in class org.sbml.libsbml.LayoutExtension
Determines whether this extension is being used by the given SBMLDocument
isInUse(SBMLDocument) - Method in class org.sbml.libsbml.RenderExtension
Determines whether this extension is being used by the given SBMLDocument
isInUse(SBMLDocument) - Method in class org.sbml.libsbml.SBMLExtension
Indicates whether this extension is being used by the given SBMLDocument.
isItem() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind item
isJoule() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind joule
isKatal() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind katal
isKelvin() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind kelvin
isKilogram() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind kilogram
isKineticConstant(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isLambda() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is a MathML <lambda>.
isLibSBMLCompiledWith(String) - Static method in class org.sbml.libsbml.libsbml
Returns an indication whether libSBML has been compiled with against a specific library.
isLitre() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind litre
isLog10() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents a log10 function.
isLogical() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is a MathML logical operator.
isLogicalFramework(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isLumen() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind lumen
isLux() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind lux
isMaterialEntity(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isMathematicalExpression(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isMetadataRepresentation(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isMetre() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind metre
isModellingFramework(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isModifier() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Predicate returning true if this is a ModifierSpeciesReference.
isModifier(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isMole() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind mole
isName() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is a user-defined variable name or the symbols for time or Avogadro's constant.
isNamespacesEmpty() - Method in class org.sbml.libsbml.XMLToken
Returns true if there are no namespaces declared on this token.
isNaN() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents the special IEEE 754 value 'not a number' (NaN).
isNegInfinity() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents the special IEEE 754 value 'negative infinity'.
isNewton() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind newton
isNumber() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node contains a number.
isObselete(long) - Static method in class org.sbml.libsbml.SBO
Predicate for checking whether the given term is obsolete.
isOccurringEntityRepresentation(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isOhm() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind ohm
isOperator() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is a mathematical operator.
isPackageEnabled(String) - Method in class org.sbml.libsbml.SBase
Predicate returning true if the given SBML Level 3 package is enabled with this object.
isPackageEnabled(String) - Static method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns true if the named package is enabled.
isPackageURIEnabled(String) - Method in class org.sbml.libsbml.SBase
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.
isParameter() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an ParameterRule or equivalent.
isParticipant(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isParticipantRole(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isPascal() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind pascal
isPhysicalEntityRepresentation(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isPhysicalParticipant(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isPiecewise() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is the MathML <piecewise> construct.
isPkgEnabled(String) - Method in class org.sbml.libsbml.SBase
Deprecated.
Replaced in libSBML 5.2.0 by SBase.isPackageEnabled(String).

isPkgURIEnabled(String) - Method in class org.sbml.libsbml.SBase
Deprecated.
Replaced in libSBML 5.2.0 by SBase.isPackageURIEnabled(String).

isPopulatedAllElementIdList() - Method in class org.sbml.libsbml.Model
Predicate returning true if libSBML has a list of the ids of all components of this model.
isPopulatedAllElementMetaIdList() - Method in class org.sbml.libsbml.Model
Predicate returning true if libSBML has a list of the metaids of all components of this model.
isPopulatedListFormulaUnitsData() - Method in class org.sbml.libsbml.Model
Predicate returning true if libSBML has derived units for the components of this model.
isProduct(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isQualifier() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true if this node is a MathML qualifier.
isQuantitativeParameter(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isQuantitativeSystemsDescriptionParameter(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isRadian() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind radian
isRate() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is a RateRule (SBML Levels 2–3) or has a 'type' attribute value of 'rate' (SBML Level 1).
isRateLaw(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isRational() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents a rational number.
isReactant(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isReal() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node can represent a real number.
isRegistered(String) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Returns true if a package extension is registered for the corresponding package URI.
isRelational() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is a MathML relational operator.
isSBMLNamespace(String) - Static method in class org.sbml.libsbml.SBMLNamespaces
Predicate returning true if the given URL is one of SBML XML namespaces.
isScalar() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is an AssignmentRule (SBML Levels 2–3) or has a 'type' attribute value of 'scalar' (SBML Level 1).
isSecond() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind second
isSemantics() - Method in class org.sbml.libsbml.ASTNode
Predicate returning true if this node is a MathML semantics node.
isSetActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
Predicate returning true if this ListOfObjective's 'activeObjective' attribute is set.
isSetAnnotation() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'annotation' subelement exists and has content.
isSetAreaUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'areaUnits' attribute is set.
isSetAssociatedSpecies() - Method in class org.sbml.libsbml.GeneProduct
Predicate returning true if this GeneProduct's 'associatedSpecies' attribute is set.
isSetAssociation() - Method in class org.sbml.libsbml.GeneAssociation
Predicate returning true if this GeneAssociation's 'association' element is set.
isSetAssociation() - Method in class org.sbml.libsbml.GeneProductAssociation
Predicate returning true if this GeneProductAssociation's 'association' element is set.
isSetBackgroundColor() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'backgroundColor' attribute is set.
isSetBackgroundColor() - Method in class org.sbml.libsbml.RenderInformationBase
Predicate returning true if this RenderInformationBase's 'backgroundColor' attribute is set.
isSetBody() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if the body of this FunctionDefinition has set.
isSetBoundaryCondition() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'boundaryCondition' attribute is set.
isSetCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Predicate returning true or false depending on whether this FbcSpeciesPlugin's 'charge' attribute has been set.
isSetCharge() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'charge' attribute is set.
isSetChemicalFormula() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Predicate returning true or false depending on whether this FbcSpeciesPlugin's 'chemicalFormula' attribute has been set.
isSetClass() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node has a value for the MathML attribute class.
isSetCoefficient() - Method in class org.sbml.libsbml.FluxObjective
Predicate returning true if this FluxObjective's 'coefficient' attribute is set.
isSetCompartment() - Method in class org.sbml.libsbml.QualitativeSpecies
Predicate returning true or false depending on whether this QualitativeSpecies's 'compartment' attribute has been set.
isSetCompartment() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction's 'compartment' attribute is set.
isSetCompartment() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'compartment' attribute is set.
isSetCompartmentId() - Method in class org.sbml.libsbml.CompartmentGlyph
Returns true if the id of the associated compartment is not the empty string.
isSetCompartmentType() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'compartmentType' attribute is set.
isSetConstant() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'constant' attribute is set.
isSetConstant() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if the 'constant' attribute of this Parameter is set.
isSetConstant() - Method in class org.sbml.libsbml.QualitativeSpecies
Predicate returning true or false depending on whether this QualitativeSpecies's 'constant' attribute has been set.
isSetConstant() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'constant' attribute is set.
isSetConstant() - Method in class org.sbml.libsbml.SpeciesReference
Predicate returning true if this SpeciesReference's 'constant' attribute is set
isSetConversionFactor() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'conversionFactor' attribute is set.
isSetConversionFactor() - Method in class org.sbml.libsbml.ReplacedElement
Predicate returning true or false depending on whether this ReplacedElement's 'conversionFactor' attribute has been set.
isSetConversionFactor() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'conversionFactor' attribute is set.
isSetCreatedDate() - Method in class org.sbml.libsbml.ModelHistory
Predicate returning true or false depending on whether this ModelHistory's 'creation date' is set.
isSetCurve() - Method in class org.sbml.libsbml.GeneralGlyph
Returns true if the curve consists of one or more segments.
isSetCurve() - Method in class org.sbml.libsbml.ReactionGlyph
Returns true if the curve consists of one or more segments.
isSetCurve() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns true if the curve consists of one or more segments.
isSetCurve() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns true if the curve consists of one or more segments.
isSetDashArray() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Returns true is the dash array has been set or false otherwise.
isSetDefault_z() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'default_z' attribute is set.
isSetDefaultTerm() - Method in class org.sbml.libsbml.ListOfFunctionTerms
Predicate returning true if the defaultTerm for this ListOfFunctionTerms object has been set.
isSetDefaultTerm() - Method in class org.sbml.libsbml.Transition
Predicate returning true if the defaultTerm for this Transition object has been set.
isSetDefaultValues() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Predicate returning true if this ListOfGlobalRenderInformation's 'defaultValues' element is set.
isSetDefaultValues() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Predicate returning true if this ListOfLocalRenderInformation's 'defaultValues' element is set.
isSetDelay() - Method in class org.sbml.libsbml.Event
Predicate for testing whether the delay for this Event is set.
isSetDeletion() - Method in class org.sbml.libsbml.ReplacedElement
Predicate returning true or false depending on whether this SBaseRef's 'deletion' attribute has been set.
isSetEmail() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'email' part is set.
isSetEnableRotationalMapping() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'enableRotationalMapping' attribute is set.
isSetEndHead() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'endHead' attribute is set.
isSetEndHead() - Method in class org.sbml.libsbml.RenderCurve
Returns true if the end head is set or false otherwise.
isSetEndHead() - Method in class org.sbml.libsbml.RenderGroup
Returns true if the end head is set or false otherwise.
isSetExponent() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'exponent' attribute of this Unit is set.
isSetExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
Predicate returning true or false depending on whether this Submodel's 'extentConversionFactor' attribute has been set.
isSetExtentUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'extentUnits' attribute is set.
isSetFamilyName() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'family name' part is set.
isSetFast() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if the value of the 'fast' attribute on this Reaction is set.
isSetFill() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'fill' attribute is set.
isSetFill() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
Returns true if the fill attribute is set or false otherwise.
isSetFillColor() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
Returns true if the fill attribute is set or false otherwise.
isSetFillRule() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'fillRule' attribute is set.
isSetFillRule() - Method in class org.sbml.libsbml.GraphicalPrimitive2D
Returns true if the fill rule attribute is set or false otherwise.
isSetFontFamily() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'fontFamily' attribute is set.
isSetFontFamily() - Method in class org.sbml.libsbml.RenderGroup
Returns true if the font family has been set or false otherwise.
isSetFontFamily() - Method in class org.sbml.libsbml.Text
Returns true if the font family has been set or false otherwise.
isSetFontSize() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'fontSize' attribute is set.
isSetFontSize() - Method in class org.sbml.libsbml.RenderGroup
Returns true if the font size has been set or false otherwise.
isSetFontSize() - Method in class org.sbml.libsbml.Text
Returns true if the font size has been set or false otherwise.
isSetFontStyle() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'fontStyle' attribute is set.
isSetFontStyle() - Method in class org.sbml.libsbml.RenderGroup
Returns true if the font style has been set or false otherwise.
isSetFontStyle() - Method in class org.sbml.libsbml.Text
Returns true if the font style has been set or false otherwise.
isSetFontWeight() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'fontWeight' attribute is set.
isSetFontWeight() - Method in class org.sbml.libsbml.RenderGroup
Returns true if the font weight has been set or false otherwise.
isSetFontWeight() - Method in class org.sbml.libsbml.Text
Returns true if the font weight has been set or false otherwise.
isSetFormula() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if this KineticLaw's 'formula' attribute is set.
isSetFormula() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule's mathematical expression is set.
isSetGeneProduct() - Method in class org.sbml.libsbml.GeneProductRef
Predicate returning true if this GeneProductRef's 'geneProduct' attribute is set.
isSetGeneProductAssociation() - Method in class org.sbml.libsbml.FbcReactionPlugin
Predicate returning true if this FbcReactionPlugin's 'GeneProductAssociation' element has been set.
isSetGivenName() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'given name' part is set.
isSetGlyphId() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns true if the id of the associated glyph is not the empty string.
isSetGraphicalObjectId() - Method in class org.sbml.libsbml.TextGlyph
Returns true if the id of the associated graphical object is not the empty string.
isSetHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'hasOnlySubstanceUnits' attribute is set.
isSetId() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node has a value for the MathML attribute id.
isSetId() - Method in class org.sbml.libsbml.BoundingBox
Predicate returning true or false depending on whether this BoundingBox's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.ColorDefinition
Predicate returning true or false depending on whether this GraphicalPrimitive's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.CompartmentType
Predicate returning true if this CompartmentType object's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Deletion
Predicate returning true or false depending on whether this object's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Dimensions
Predicate returning true or false depending on whether this Dimensions's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Event
Predicate returning true if this Event's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.ExternalModelDefinition
Predicate returning true or false depending on whether this object's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.FluxBound
Predicate returning true if this FluxBound's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.FluxObjective
Predicate returning true if this FluxObjective's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if this FunctionDefinition's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.GeneAssociation
Predicate returning true if this GeneAssociation's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.GeneProduct
Predicate returning true if this GeneProduct's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.GeneProductAssociation
Predicate returning true if this GeneProductAssociation's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.GeneProductRef
Predicate returning true if this GeneProductRef's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.GradientBase
Predicate returning true if a call to getId() returns a non-empty string.
isSetId() - Method in class org.sbml.libsbml.GraphicalObject
Predicate returning true or false depending on whether this GraphicalObject's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Predicate returning true or false depending on whether this GraphicalPrimitive's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Group
Predicate returning true if this Group's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Image
Predicate returning true or false depending on whether this Image's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Input
Predicate returning true or false depending on whether this Input's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Layout
Predicate returning true or false depending on whether this Layout's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.LineEnding
Predicate returning true or false depending on whether this GraphicalPrimitive's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.ListOfMembers
Predicate returning true if this ListOfMembers's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Member
Predicate returning true if this Member's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Objective
Predicate returning true if this Objective's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Output
Predicate returning true or false depending on whether this Output's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if this Parameter's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Point
Predicate returning true or false depending on whether this Point's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Port
Predicate returning true or false depending on whether this Port's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.QualitativeSpecies
Predicate returning true or false depending on whether this QualitativeSpecies's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.RenderInformationBase
Predicate returning true or false depending on whether this RenderInformationBase's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.SBase
Predicate returning true if a call to getId() returns a non-empty string.
isSetId() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Predicate returning true if this SimpleSpeciesReference's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.SpeciesType
Predicate returning true if this SpeciesType's 'id' attribute is set.
isSetId() - Method in class org.sbml.libsbml.Style
Predicate returning true or false depending on whether this Style's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Submodel
Predicate returning true or false depending on whether this Submodel's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.Transition
Predicate returning true or false depending on whether this Transition's 'id' attribute has been set.
isSetId() - Method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if this UnitDefinition's 'id' attribute is set.
isSetIdAttribute() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'id' attribute is set.
isSetIdRef() - Method in class org.sbml.libsbml.Member
Predicate returning true if this Member's 'idRef' attribute is set.
isSetIdRef() - Method in class org.sbml.libsbml.SBaseRef
Predicate returning true or false depending on whether this SBaseRef's 'idRef' attribute has been set.
isSetImageReference() - Method in class org.sbml.libsbml.Image
Returns true if the image reference has been set.
isSetInitialAmount() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'initialAmount' attribute is set.
isSetInitialConcentration() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'initialConcentration' attribute is set.
isSetInitialLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
Predicate returning true or false depending on whether this QualitativeSpecies's 'initialLevel' attribute has been set.
isSetInitialValue() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Predicate to test whether the 'initialValue' attribute for this trigger is set.
isSetKind() - Method in class org.sbml.libsbml.Group
Predicate returning true if this Group's 'kind' attribute is set.
isSetKind() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'kind' attribute of this Unit is set.
isSetKineticLaw() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction contains a kinetic law object.
isSetLabel() - Method in class org.sbml.libsbml.GeneProduct
Predicate returning true if this GeneProduct's 'label' attribute is set.
isSetLengthUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'lengthUnits' attribute is set.
isSetLinearGradient_x1() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'linearGradient_x1' attribute is set.
isSetLinearGradient_x2() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'linearGradient_x2' attribute is set.
isSetLinearGradient_y1() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'linearGradient_y1' attribute is set.
isSetLinearGradient_y2() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'linearGradient_y2' attribute is set.
isSetLinearGradient_z1() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'linearGradient_z1' attribute is set.
isSetLinearGradient_z2() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'linearGradient_z2' attribute is set.
isSetLowerFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
Predicate returning true if this FbcReactionPlugin's 'lowerFluxBound' attribute is set.
isSetMath() - Method in class org.sbml.libsbml.Constraint
Predicate returning true if a mathematical formula is defined for this Constraint.
isSetMath() - Method in class org.sbml.libsbml.Delay
Predicate to test whether the formula for this delay is set.
isSetMath() - Method in class org.sbml.libsbml.EventAssignment
Predicate for testing whether the 'math' subelement of this EventAssignment is set.
isSetMath() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if this FunctionDefinition's 'math' subelement contains a value.
isSetMath() - Method in class org.sbml.libsbml.FunctionTerm
Predicate returning true or false depending on whether this FunctionTerm's 'math' element has been set.
isSetMath() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if this InitialAssignment's 'math' subelement contains a value.
isSetMath() - Method in class org.sbml.libsbml.KineticLaw
Predicate returning true if this Kinetic's 'math' subelement is set.
isSetMath() - Method in class org.sbml.libsbml.Priority
Predicate to test whether the formula for this delay is set.
isSetMath() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule's mathematical expression is set.
isSetMath() - Method in class org.sbml.libsbml.StoichiometryMath
Predicate to test whether the math for this StoichiometryMath object is set.
isSetMath() - Method in class org.sbml.libsbml.Trigger
Predicate to test whether the math for this trigger is set.
isSetMatrix() - Method in class org.sbml.libsbml.Transformation
Returns true if the matrix has been set or false otherwise.
isSetMaxLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
Predicate returning true or false depending on whether this QualitativeSpecies's 'maxLevel' attribute has been set.
isSetMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
Predicate returning true or false depending on whether this ExternalModelDefinition's 'md5' attribute has been set.
isSetMessage() - Method in class org.sbml.libsbml.Constraint
Predicate returning true if a message is defined for this Constraint.
isSetMetaId() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'metaid' attribute is set.
isSetMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
Predicate returning true or false depending on whether this GraphicalObject's 'metaidRef' attribute has been set.
isSetMetaIdRef() - Method in class org.sbml.libsbml.Member
Predicate returning true if this Member's 'metaIdRef' attribute is set.
isSetMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
Predicate returning true or false depending on whether this SBaseRef's 'metaIdRef' attribute has been set.
isSetModel() - Method in class org.sbml.libsbml.SBMLDocument
Returns true if the Model object has been set, otherwise returns false.
isSetModelHistory() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object has a ModelHistory object attached to it.
isSetModelRef() - Method in class org.sbml.libsbml.ExternalModelDefinition
Predicate returning true or false depending on whether this ExternalModelDefinition's 'modelRef' attribute has been set.
isSetModelRef() - Method in class org.sbml.libsbml.Submodel
Predicate returning true or false depending on whether this Submodel's 'modelRef' attribute has been set.
isSetModifiedDate() - Method in class org.sbml.libsbml.ModelHistory
Predicate returning true or false depending on whether this ModelHistory's 'modified date' is set.
isSetMultiplier() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'multiplier' attribute of this Unit is set.
isSetName() - Method in class org.sbml.libsbml.ColorDefinition
Predicate returning true or false depending on whether this ColorDefinition's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.CompartmentType
Predicate returning true if this CompartmentType object's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Deletion
Predicate returning true or false depending on whether this object's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.Event
Predicate returning true if this Event's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.ExternalModelDefinition
Predicate returning true or false depending on whether this object's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.FluxBound
Predicate returning true if this FluxBound's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.FluxObjective
Predicate returning true if this FluxObjective's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.FunctionDefinition
Predicate returning true if this FunctionDefinition's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.GeneProduct
Predicate returning true if this GeneProduct's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.GeneProductAssociation
Predicate returning true if this GeneProductAssociation's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.GeneProductRef
Predicate returning true if this GeneProductRef's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.GradientBase
Predicate returning true if this object's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Group
Predicate returning true if this Group's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Input
Predicate returning true or false depending on whether this Input's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.Layout
Predicate returning true or false depending on whether this Layout's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.ListOfMembers
Predicate returning true if this ListOfMembers's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Member
Predicate returning true if this Member's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'fn' part is set (when using vCard4).
isSetName() - Method in class org.sbml.libsbml.Objective
Predicate returning true if this Objective's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Output
Predicate returning true or false depending on whether this Output's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if this Parameter's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Port
Predicate returning true or false depending on whether this Port's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.QualitativeSpecies
Predicate returning true or false depending on whether this QualitativeSpecies's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.RenderInformationBase
Predicate returning true or false depending on whether this RenderInformationBase's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Predicate returning true if this SimpleSpeciesReference's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.SpeciesType
Predicate returning true if this SpeciesType's 'name' attribute is set.
isSetName() - Method in class org.sbml.libsbml.Style
Predicate returning true or false depending on whether this Style's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.Submodel
Predicate returning true or false depending on whether this Submodel's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.Transformation
Predicate returning true or false depending on whether this Transformation's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.Transition
Predicate returning true or false depending on whether this Transition's 'name' attribute has been set.
isSetName() - Method in class org.sbml.libsbml.UnitDefinition
Predicate returning true if this UnitDefinition's 'name' attribute is set.
isSetNotes() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'notes' subelement exists and has content.
isSetObjectRole() - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
Returns whether the object role has been set or not.
isSetOffset() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'offset' attribute of this Unit is set.
isSetOperation() - Method in class org.sbml.libsbml.FluxBound
Predicate returning true if this FluxBound's 'operation' attribute is set.
isSetOrder() - Method in class org.sbml.libsbml.CompartmentGlyph
Returns true if the compartment order has been set.
isSetOrganisation() - Method in class org.sbml.libsbml.ModelCreator
(Alternate spelling) Predicate returning true or false depending on whether this ModelCreator's 'organization' part is set.
isSetOrganization() - Method in class org.sbml.libsbml.ModelCreator
Predicate returning true or false depending on whether this ModelCreator's 'organization' part is set.
isSetOriginOfTextId() - Method in class org.sbml.libsbml.TextGlyph
Returns true if the id of the origin of text is not the empty string.
isSetOutputLevel() - Method in class org.sbml.libsbml.Output
Predicate returning true or false depending on whether this Output's 'outputLevel' attribute has been set.
isSetOutside() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'outside' attribute is set.
isSetPackageRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
Returns true if the required attribute of the given package extension is defined, otherwise returns false.
isSetParentSBMLObject() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node has a value for the parent SBML object.
isSetPersistent() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Predicate to test whether the 'persistent' attribute for this trigger is set.
isSetPkgRequired(String) - Method in class org.sbml.libsbml.SBMLDocument
Deprecated.
Replaced in libSBML 5.2.0 by isSetPackageRequired(String)
isSetPortRef() - Method in class org.sbml.libsbml.SBaseRef
Predicate returning true or false depending on whether this SBaseRef's 'portRef' attribute has been set.
isSetPriority() - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Predicate for testing whether the priority for this Event is set.
isSetQualitativeSpecies() - Method in class org.sbml.libsbml.Input
Predicate returning true or false depending on whether this Input's 'qualitativeSpecies' attribute has been set.
isSetQualitativeSpecies() - Method in class org.sbml.libsbml.Output
Predicate returning true or false depending on whether this Output's 'qualitativeSpecies' attribute has been set.
isSetRadialGradient_cx() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'radialGradient_cx' attribute is set.
isSetRadialGradient_cy() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'radialGradient_cy' attribute is set.
isSetRadialGradient_cz() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'radialGradient_cz' attribute is set.
isSetRadialGradient_fx() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'radialGradient_fx' attribute is set.
isSetRadialGradient_fy() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'radialGradient_fy' attribute is set.
isSetRadialGradient_fz() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'radialGradient_fz' attribute is set.
isSetRadialGradient_r() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'radialGradient_r' attribute is set.
isSetRatio() - Method in class org.sbml.libsbml.Ellipse
Predicate returning true if this Ellipse's 'ratio' attribute is set.
isSetRatio() - Method in class org.sbml.libsbml.Rectangle
Predicate returning true if this Rectangle's 'ratio' attribute is set.
isSetReaction() - Method in class org.sbml.libsbml.FluxBound
Predicate returning true if this FluxBound's 'reaction' attribute is set.
isSetReaction() - Method in class org.sbml.libsbml.FluxObjective
Predicate returning true if this FluxObjective's 'reaction' attribute is set.
isSetReaction() - Method in class org.sbml.libsbml.GeneAssociation
Predicate returning true if this GeneAssociation's 'reaction' attribute is set.
isSetReactionId() - Method in class org.sbml.libsbml.ReactionGlyph
Returns true if the id of the associated reaction is not the empty string.
isSetReference() - Method in class org.sbml.libsbml.Association
Predicate returning true if this Association's 'reference' attribute has been set.
isSetReferenceId() - Method in class org.sbml.libsbml.GeneralGlyph
Returns true if the id of the associated element is not the empty string.
isSetReferenceId() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns true if the id of the associated reference is not the empty string.
isSetReferenceRenderInformation() - Method in class org.sbml.libsbml.RenderInformationBase
Predicate returning true if this RenderInformationBase's 'referenceRenderInformation' attribute is set.
isSetReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
Predicate for testing whether the ReplacedBy for this SBase is set.
isSetRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Returns the value of the 'required' attribute.
isSetResultLevel() - Method in class org.sbml.libsbml.DefaultTerm
Predicate returning true or false depending on whether this DefaultTerm's 'resultLevel' attribute has been set.
isSetResultLevel() - Method in class org.sbml.libsbml.FunctionTerm
Predicate returning true or false depending on whether this FunctionTerm's 'resultLevel' attribute has been set.
isSetReversible() - Method in class org.sbml.libsbml.Reaction
Predicate returning true if this Reaction's 'reversible' attribute is set.
isSetRole() - Method in class org.sbml.libsbml.ReferenceGlyph
Returns true of role is different from the empty string.
isSetRole() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns true of role is different from SPECIES_ROLE_INVALID.
isSetSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
Predicate for testing whether the sBaseRef for this SBaseRef is set.
isSetSBOTerm() - Method in class org.sbml.libsbml.SBase
Predicate returning true if this object's 'sboTerm' attribute is set.
isSetScale() - Method in class org.sbml.libsbml.Unit
Predicate to test whether the 'scale' attribute of this Unit is set.
isSetSign() - Method in class org.sbml.libsbml.Input
Predicate returning true or false depending on whether this Input's 'sign' attribute has been set.
isSetSize() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'size' attribute is set.
isSetSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
Predicate returning true or false depending on whether this ExternalModelDefinition's 'source' attribute has been set.
isSetSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'spatialDimensions' attribute is set.
isSetSpatialSizeUnits() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'spatialSizeUnits' attribute is set.
isSetSpecies() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Predicate returning true if this SimpleSpeciesReference's 'species' attribute is set.
isSetSpeciesGlyphId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns true if the id of the associated species glyph is not the empty string.
isSetSpeciesId() - Method in class org.sbml.libsbml.SpeciesGlyph
Returns true if the id of the associated species object is not the empty string.
isSetSpeciesReferenceId() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Returns true if the id of the associated species reference is not the empty string.
isSetSpeciesType() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'speciesType' attribute is set.
isSetSpreadMethod() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'spreadMethod' attribute is set.
isSetStartHead() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'startHead' attribute is set.
isSetStartHead() - Method in class org.sbml.libsbml.RenderCurve
Returns true if the start head is set or false otherwise.
isSetStartHead() - Method in class org.sbml.libsbml.RenderGroup
Returns true if the start head is set or false otherwise.
isSetStoichiometry() - Method in class org.sbml.libsbml.SpeciesReference
Predicate returning true if this SpeciesReference's 'stoichiometry' attribute is set.
isSetStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
Predicate returning true if this SpeciesReference's 'stoichiometryMath' subelement is set
isSetStrict() - Method in class org.sbml.libsbml.FbcModelPlugin
Predicate returning true if this FbcModelPlugin's 'strict' attribute is set.
isSetStroke() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'stroke' attribute is set.
isSetStroke() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Returns true is the stroke has been set or false otherwise.
isSetStrokeWidth() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'strokeWidth' attribute is set.
isSetStrokeWidth() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Returns true is the stroke width has been set or false otherwise.
isSetStyle() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node has a value for the MathML attribute style.
isSetSubmodelRef() - Method in class org.sbml.libsbml.Replacing
Predicate returning true or false depending on whether this SBaseRef's 'submodelRef' attribute has been set.
isSetSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
Returns false, since 'substanceConversionFactor' is not a part of the comp spec.
isSetSubstanceUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's 'substanceUnits' attribute is set.
isSetSubstanceUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'substanceUnits' attribute is set.
isSetSubstanceUnits() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'substanceUnits' attribute is set.
isSetSymbol() - Method in class org.sbml.libsbml.InitialAssignment
Predicate returning true if this InitialAssignment's 'symbol' attribute is set.
isSetText() - Method in class org.sbml.libsbml.Text
Returns true if the text is set to something else than the empty string.
isSetText() - Method in class org.sbml.libsbml.TextGlyph
Returns true if the text is not the empty string.
isSetTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'textAnchor' attribute is set.
isSetTextAnchor() - Method in class org.sbml.libsbml.RenderGroup
Returns true if the horizonal alignment attribute has been set.
isSetTextAnchor() - Method in class org.sbml.libsbml.Text
Returns true if the horizontal alignment attribute has been set.
isSetThresholdLevel() - Method in class org.sbml.libsbml.Input
Predicate returning true or false depending on whether this Input's 'thresholdLevel' attribute has been set.
isSetTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
Predicate returning true or false depending on whether this Submodel's 'timeConversionFactor' attribute has been set.
isSetTimeUnits() - Method in class org.sbml.libsbml.Event
Predicate for testing whether the 'timeUnits' attribute of this Event is set.
isSetTimeUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's 'timeUnits' attribute is set.
isSetTimeUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'timeUnits' attribute is set.
isSetTransformer() - Method in class org.sbml.libsbml.CompModelPlugin
 
isSetTransitionEffect() - Method in class org.sbml.libsbml.Input
Predicate returning true or false depending on whether this Input's 'transitionEffect' attribute has been set.
isSetTransitionEffect() - Method in class org.sbml.libsbml.Output
Predicate returning true or false depending on whether this Output's 'transitionEffect' attribute has been set.
isSetTrigger() - Method in class org.sbml.libsbml.Event
Predicate for testing whether the trigger for this Event is set.
isSetType() - Method in class org.sbml.libsbml.Association
Predicate returning true if this Association's 'type' attribute is set.
isSetType() - Method in class org.sbml.libsbml.Objective
Predicate returning true if this Objective's 'type' attribute is set.
isSetUnitRef() - Method in class org.sbml.libsbml.SBaseRef
Predicate returning true or false depending on whether this SBaseRef's 'unitRef' attribute has been set.
isSetUnits() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node has the attribute sbml:units.
isSetUnits() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'units' attribute is set.
isSetUnits() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if the 'units' attribute of this Parameter is set.
isSetUnits() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule's 'units' attribute is set.
isSetUnits() - Method in class org.sbml.libsbml.Species
Predicate returning true if this Species object's 'units' attribute is set.
isSetUpperFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
Predicate returning true if this FbcReactionPlugin's 'upperFluxBound' attribute is set.
isSetUserData() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node has a user data object.
isSetUserData() - Method in class org.sbml.libsbml.SBase
Predicate returning true or false depending on whether the user data of this element has been set.
isSetUseValuesFromTriggerTime() - Method in class org.sbml.libsbml.Event
Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is set.
isSetValue() - Method in class org.sbml.libsbml.FluxBound
Predicate returning true if this FluxBound's 'value' attribute is set.
isSetValue() - Method in class org.sbml.libsbml.Parameter
Predicate returning true if the 'value' attribute of this Parameter is set.
isSetVariable() - Method in class org.sbml.libsbml.EventAssignment
Predicate for testing whether the attribute 'variable' of this EventAssignment is set.
isSetVariable() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule's 'variable' attribute is set.
isSetVersionMajor() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Predicate returning true if this ListOfGlobalRenderInformation's 'versionMajor' attribute is set.
isSetVersionMajor() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Predicate returning true if this ListOfLocalRenderInformation's 'versionMajor' attribute is set.
isSetVersionMinor() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Predicate returning true if this ListOfGlobalRenderInformation's 'versionMinor' attribute is set.
isSetVersionMinor() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Predicate returning true if this ListOfLocalRenderInformation's 'versionMinor' attribute is set.
isSetVolume() - Method in class org.sbml.libsbml.Compartment
Predicate returning true if this Compartment object's 'volume' attribute is set.
isSetVolumeUnits() - Method in class org.sbml.libsbml.Model
Predicate returning true if this Model's 'volumeUnits' attribute is set.
isSetVTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
Predicate returning true if this DefaultValues's 'vtextAnchor' attribute is set.
isSetVTextAnchor() - Method in class org.sbml.libsbml.RenderGroup
Returns true if the vertical alignment attribute has been set.
isSetVTextAnchor() - Method in class org.sbml.libsbml.Text
Returns true if the vertical alignment attribute has been set.
isSeverityOverridden() - Method in class org.sbml.libsbml.XMLErrorLog
Returns a boolean indicating whether or not the severity has been overridden.
isSiemens() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind siemens
isSievert() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind sievert
isSpeciesConcentration() - Method in class org.sbml.libsbml.Rule
Predicate returning true if this Rule is a SpeciesConcentrationRule or equivalent.
isSqrt() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node represents a square root function.
isStart() - Method in class org.sbml.libsbml.XMLToken
Returns true if this token represents an XML start element.
isSteadyStateExpression(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isSteradian() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind steradian
isStripAllUnrecognizedPackages() - Method in class org.sbml.libsbml.SBMLStripPackageConverter
 
isSupported(String) - Method in class org.sbml.libsbml.SBMLExtension
Returns true if the given XML namespace URI is supported by this package extension.
isSystem() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error was generated by the operating system.
isSystemsDescriptionParameter(long) - Static method in class org.sbml.libsbml.SBO
Returns true if the given term identifier comes from the stated branch of SBO.
isTesla() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind tesla
isText() - Method in class org.sbml.libsbml.XMLToken
Returns true if this token represents an XML text element.
isUMinus() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is a unary minus operator.
isUnitKind(String, long, long) - Static method in class org.sbml.libsbml.Unit
Predicate to test whether a given string is the name of a valid base unit in SBML (such as 'gram' or 'mole').
isUnknown() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node has an unknown type.
isUPlus() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node is a unary plus operator.
isValid() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error resulted from a problem or whether it was logged as an unknown error.
isValidCombination() - Method in class org.sbml.libsbml.SBMLNamespaces
Predicate returning true if the given set of namespaces represent a valid set
isValidSBMLSId(String) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the argument string conforms to the syntax of SBML identifiers.
isValidTypeForList(SBase) - Method in class org.sbml.libsbml.ListOfCurveElements
 
isValidTypeForList(SBase) - Method in class org.sbml.libsbml.ListOfDrawables
 
isValidTypeForList(SBase) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
 
isValidTypeForList(SBase) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
 
isValidTypeForList(SBase) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
 
isValidTypeForList(SBase) - Method in class org.sbml.libsbml.SBasePlugin
 
isValidUnitSId(String) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the argument string conforms to the syntax of SBML unit identifiers.
isValidXMLanyURI(String) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the uri argument string conforms to the XML data type anyURI.
isValidXMLID(String) - Static method in class org.sbml.libsbml.SyntaxChecker
Returns true or false depending on whether the argument string conforms to the XML data type ID.
isVariantOfArea() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'area'.
isVariantOfArea(boolean) - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'area'.
isVariantOfDimensionless() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the unit 'dimensionless'.
isVariantOfDimensionless(boolean) - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the unit 'dimensionless'.
isVariantOfLength() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'length'.
isVariantOfLength(boolean) - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'length'.
isVariantOfMass() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'mass'.
isVariantOfMass(boolean) - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'mass'.
isVariantOfSubstance() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'substance'.
isVariantOfSubstance(boolean) - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'substance'.
isVariantOfSubstancePerTime() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit 'substance' divided by the predefined unit 'time'.
isVariantOfSubstancePerTime(boolean) - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit 'substance' divided by the predefined unit 'time'.
isVariantOfTime() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'time'.
isVariantOfTime(boolean) - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'time'.
isVariantOfVolume() - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'volume'.
isVariantOfVolume(boolean) - Method in class org.sbml.libsbml.UnitDefinition
Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'volume'.
isVolt() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind volt
isWarning() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error object is a warning.
isWatt() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind watt
isWeber() - Method in class org.sbml.libsbml.Unit
Predicate for testing whether this Unit is of the kind weber
isWellFormedASTNode() - Method in class org.sbml.libsbml.ASTNode
Returns true or false depending on whether this ASTNode is well-formed.
isXML() - Method in class org.sbml.libsbml.XMLError
Predicate returning true or false depending on whether this error resulted from a problem in the XML input (e.g., an XML syntax error).

K

KineticLaw - Class in org.sbml.libsbml
The rate expression for an SBML reaction.
KineticLaw(long, long) - Constructor for class org.sbml.libsbml.KineticLaw
Creates a new KineticLaw using the given SBML level and version values.
KineticLaw(KineticLaw) - Constructor for class org.sbml.libsbml.KineticLaw
Copy constructor; creates a copy of this KineticLaw.
KineticLaw(SBMLNamespaces) - Constructor for class org.sbml.libsbml.KineticLaw
Creates a new KineticLaw using the given SBMLNamespaces object sbmlns.
KineticLawNotSubstancePerTime - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
KineticLawParametersAreLocalOnly - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

L

L1V1CompartmentVolumeReqd - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3AreaUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3ConversionFactorOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3ExtentUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3LengthUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3NotSchemaConformant - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3NotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_AVOGADRO_IS_CSYMBOL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_AVOGADRO_IS_NAME - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_COLLAPSE_UNARY_MINUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_COMPARE_BUILTINS_CASE_INSENSITIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_COMPARE_BUILTINS_CASE_SENSITIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_EXPAND_UNARY_MINUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_MODULO_IS_PIECEWISE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_MODULO_IS_REM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_NO_UNITS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_L3V2_FUNCTIONS_AS_GENERIC - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_L3V2_FUNCTIONS_DIRECTLY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_LOG_AS_ERROR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_LOG_AS_LN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_LOG_AS_LOG10 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3P_PARSE_UNITS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3PackageOnLowerSBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3ParserSettings - Class in org.sbml.libsbml
Controls the behavior of the Level 3 formula parser.
L3ParserSettings() - Constructor for class org.sbml.libsbml.L3ParserSettings
Creates a new L3ParserSettings object with default values.
L3ParserSettings(L3ParserSettings) - Constructor for class org.sbml.libsbml.L3ParserSettings
Copy constructor.
L3ParserSettings(Model, int, boolean, boolean, boolean) - Constructor for class org.sbml.libsbml.L3ParserSettings
Creates a new L3ParserSettings object with specific values for all possible settings.
L3ParserSettings(Model, int, boolean, boolean, boolean, boolean) - Constructor for class org.sbml.libsbml.L3ParserSettings
Creates a new L3ParserSettings object with specific values for all possible settings.
L3ParserSettings(Model, int, boolean, boolean, boolean, boolean, SBMLNamespaces) - Constructor for class org.sbml.libsbml.L3ParserSettings
Creates a new L3ParserSettings object with specific values for all possible settings.
L3ParserSettings(Model, int, boolean, boolean, boolean, boolean, SBMLNamespaces, boolean) - Constructor for class org.sbml.libsbml.L3ParserSettings
Creates a new L3ParserSettings object with specific values for all possible settings.
L3ParserSettings(Model, int, boolean, boolean, boolean, boolean, SBMLNamespaces, boolean, boolean) - Constructor for class org.sbml.libsbml.L3ParserSettings
Creates a new L3ParserSettings object with specific values for all possible settings.
L3SpatialDimensionsUnset - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3SubstanceUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3TimeUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3V2FastDeprecated - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3V2SubstanceUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
L3VolumeUnitsOnModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LambdaOnlyAllowedInFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Layout - Class in org.sbml.libsbml
layout The layout of a diagram of an SBML model.
Layout() - Constructor for class org.sbml.libsbml.Layout
Creates a new Layout with the given level, version, and package version.
Layout(long) - Constructor for class org.sbml.libsbml.Layout
Creates a new Layout with the given level, version, and package version.
Layout(long, long) - Constructor for class org.sbml.libsbml.Layout
Creates a new Layout with the given level, version, and package version.
Layout(long, long, long) - Constructor for class org.sbml.libsbml.Layout
Creates a new Layout with the given level, version, and package version.
Layout(Layout) - Constructor for class org.sbml.libsbml.Layout
Copy constructor.
Layout(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Layout
Creates a new Layout with the given LayoutPkgNamespaces object.
Layout(LayoutPkgNamespaces, String, Dimensions) - Constructor for class org.sbml.libsbml.Layout
Creates a new Layout with the given id and dimensions.
Layout(XMLNode) - Constructor for class org.sbml.libsbml.Layout
Creates a new Layout from the given XMLNode (only for SBML Level2)
Layout(XMLNode, long) - Constructor for class org.sbml.libsbml.Layout
Creates a new Layout from the given XMLNode (only for SBML Level2)
LayoutAttributeRequiredMissing - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutAttributeRequiredMustBeBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutBBoxAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutBBoxAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutBBoxAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutBBoxAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutBBoxConsistent3DDefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCBezAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCBezAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCBezAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCBezAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGCompartmentMustRefComp - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGCompartmentSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGMetaIdRefMustBeIDREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGNoDuplicateReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCGOrderMustBeDouble - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCurveAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCurveAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCurveAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutCurveAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutDimsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutDimsAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutDimsAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutDimsAttributesMustBeDouble - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutDuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutElementNotInNs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutExtension - Class in org.sbml.libsbml
layout Base extension class for the package.
LayoutExtension() - Constructor for class org.sbml.libsbml.LayoutExtension
Creates a new LayoutExtension instance.
LayoutExtension(LayoutExtension) - Constructor for class org.sbml.libsbml.LayoutExtension
Copy constructor.
LayoutGGAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGGAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGGAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGGAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGGMetaIdRefMustBeIDREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGGMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGGNoDuplicateReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGGReferenceMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGGReferenceSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGOAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGOAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGOAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGOAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGOMetaIdRefMustBeIDREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGOMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutGOMustContainBoundingBox - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLayoutAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLayoutAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLayoutAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLayoutMustHaveDimensions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLayoutNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOAddGOAllowedAttribut - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOAddGOAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOCompGlyphAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOCompGlyphAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOCurveSegsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOCurveSegsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOCurveSegsNotEmpty - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOLayoutsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOLayoutsAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOLayoutsNotEmpty - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOReferenceGlyphAllowedAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOReferenceGlyphAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLORnGlyphAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLORnGlyphAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOSpeciesGlyphAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOSpeciesGlyphAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOSpeciesRefGlyphAllowedAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOSpeciesRefGlyphAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOSpeciesRefGlyphNotEmpty - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOSubGlyphAllowedAttribs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOSubGlyphAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOTextGlyphAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLOTextGlyphAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLSegAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLSegAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLSegAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutLSegAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutModelPlugin - Class in org.sbml.libsbml
layout Extension of Model.
LayoutModelPlugin(String, String, LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.LayoutModelPlugin
Creates a new LayoutModelPlugin object using the given parameters.
LayoutModelPlugin(LayoutModelPlugin) - Constructor for class org.sbml.libsbml.LayoutModelPlugin
Copy constructor.
LayoutNoEmptyListOfs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutNSUndeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutOnlyOneEachListOf - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutOnlyOneLOLayouts - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutPkgNamespaces - Class in org.sbml.libsbml
Set of SBML Level + Version + namespace triples.
LayoutPkgNamespaces() - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(long) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPkgNamespaces(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.LayoutPkgNamespaces
 
LayoutPointAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutPointAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutPointAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutPointAttributesMustBeDouble - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGGlyphMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGGlyphSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGMetaIdRefMustBeIDREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGNoDuplicateReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGReferenceMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGReferenceSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutREFGRoleSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRequiredFalse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGMetaIdRefMustBeIDREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGNoDuplicateReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGReactionMustRefReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutRGReactionSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGMetaIdRefMustBeIDREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGNoDuplicateReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGSpeciesMustRefSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSGSpeciesSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSIdSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSpeciesReferencePlugin - Class in org.sbml.libsbml
layout Extension of SpeciesReference.
LayoutSpeciesReferencePlugin(String, String, LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.LayoutSpeciesReferencePlugin
Creates a new LayoutSpeciesReferencePlugin object using the given parameters.
LayoutSpeciesReferencePlugin(LayoutSpeciesReferencePlugin) - Constructor for class org.sbml.libsbml.LayoutSpeciesReferencePlugin
Copy constructor.
LayoutSRGAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGMetaIdRefMustBeIDREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGNoDuplicateReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGRoleSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGSpeciesGlyphMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGSpeciesGlyphSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGSpeciesReferenceSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutSRGSpeciesRefMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGAllowedCoreElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGGraphicalObjectMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGGraphicalObjectSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGMetaIdRefMustBeIDREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGMetaIdRefMustReferenceObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGNoDuplicateReferences - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGOriginOfTextMustRefObject - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGOriginOfTextSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutTGTextMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutUnknownError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutXsiTypeAllowedLocations - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LayoutXsiTypeSyntax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LevelPositiveInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
libsbml - Class in org.sbml.libsbml
Wrapper class for global methods and constants defined by libSBML.
LIBSBML_ANNOTATION_NAME_NOT_FOUND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_ANNOTATION_NS_NOT_FOUND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_GENERAL_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_IDENTIFIER_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_INTERNAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_INTERNAL_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_MATHML_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_MODELING_PRACTICE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_OVERDETERMINED_MODEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_COMPATIBILITY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L1_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L2V1_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L2V2_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L2V3_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L2V4_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L3V1_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBML_L3V2_COMPAT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SBO_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_SYSTEM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_UNITS_CONSISTENCY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CAT_XML - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_CONVERSION_NOT_AVAILABLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_INVALID_SRC_DOCUMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_INVALID_TARGET_NAMESPACE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_PKG_CONSIDERED_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_CONV_PKG_CONVERSION_NOT_AVAILABLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_DEPRECATED_ATTRIBUTE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_DOTTED_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_DUPLICATE_ANNOTATION_NS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_DUPLICATE_OBJECT_ID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_INDEX_EXCEEDS_SIZE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_INVALID_ATTRIBUTE_VALUE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_INVALID_OBJECT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_INVALID_XML_OPERATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_LEVEL_MISMATCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_MISSING_METAID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_NAMESPACES_MISMATCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_OPERATION_FAILED - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_OPERATION_SUCCESS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_OVERRIDE_DISABLED - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_OVERRIDE_DONT_LOG - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_OVERRIDE_ERROR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_OVERRIDE_WARNING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_CONFLICT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_CONFLICTED_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_DISABLED - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_UNKNOWN_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_PKG_VERSION_MISMATCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_ERROR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_FATAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_GENERAL_WARNING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_INFO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_NOT_APPLICABLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_SCHEMA_ERROR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_SEV_WARNING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_UNEXPECTED_ATTRIBUTE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_USE_ID_ATTRIBUTE_FUNCTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_VERSION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_VERSION_MISMATCH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LIBSBML_VERSION_STRING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LibSBMLAdditionalCodesLowerBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
libsbmlConstants - Interface in org.sbml.libsbml
 
LinearGradient - Class in org.sbml.libsbml
Representation of a linear gradient object from the SBML render extension.
LinearGradient() - Constructor for class org.sbml.libsbml.LinearGradient
Creates a new LinearGradient object with the given SBML level and SBML version.
LinearGradient(long) - Constructor for class org.sbml.libsbml.LinearGradient
Creates a new LinearGradient object with the given SBML level and SBML version.
LinearGradient(long, long) - Constructor for class org.sbml.libsbml.LinearGradient
Creates a new LinearGradient object with the given SBML level and SBML version.
LinearGradient(long, long, long) - Constructor for class org.sbml.libsbml.LinearGradient
Creates a new LinearGradient object with the given SBML level and SBML version.
LinearGradient(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.LinearGradient
Creates a new LinearGradient object with the given SBMLNamespaces.
LinearGradient(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.LinearGradient
Constructor which creates a LinearGradient with no gradient stops.
LinearGradient(XMLNode) - Constructor for class org.sbml.libsbml.LinearGradient
Creates a new LinearGradient object from the given XMLNode object.
LinearGradient(XMLNode, long) - Constructor for class org.sbml.libsbml.LinearGradient
Creates a new LinearGradient object from the given XMLNode object.
LineEnding - Class in org.sbml.libsbml
a LineEnding is a decoration element for the start and/or end of curves in the SBML render extension, e.g.
LineEnding() - Constructor for class org.sbml.libsbml.LineEnding
Creates a new LineEnding object with the given SBML level and SBML version.
LineEnding(long) - Constructor for class org.sbml.libsbml.LineEnding
Creates a new LineEnding object with the given SBML level and SBML version.
LineEnding(long, long) - Constructor for class org.sbml.libsbml.LineEnding
Creates a new LineEnding object with the given SBML level and SBML version.
LineEnding(long, long, long) - Constructor for class org.sbml.libsbml.LineEnding
Creates a new LineEnding object with the given SBML level and SBML version.
LineEnding(LineEnding) - Constructor for class org.sbml.libsbml.LineEnding
Copy constructor.
LineEnding(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.LineEnding
Creates a new LineEnding object with the given SBMLNamespaces.
LineEnding(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.LineEnding
Constructor which creates a LineEnding with an empty group object, and a viewport with a size of 0.
LineEnding(XMLNode, long) - Constructor for class org.sbml.libsbml.LineEnding
Creates a new LineEnding object from the given XMLNode object.
LineSegment - Class in org.sbml.libsbml
layout Representation of a line.
LineSegment() - Constructor for class org.sbml.libsbml.LineSegment
Creates a line segment with the given SBML level, version, and package version and both points set to (0.0,0.0,0.0)
LineSegment(long) - Constructor for class org.sbml.libsbml.LineSegment
Creates a line segment with the given SBML level, version, and package version and both points set to (0.0,0.0,0.0)
LineSegment(long, long) - Constructor for class org.sbml.libsbml.LineSegment
Creates a line segment with the given SBML level, version, and package version and both points set to (0.0,0.0,0.0)
LineSegment(long, long, long) - Constructor for class org.sbml.libsbml.LineSegment
Creates a line segment with the given SBML level, version, and package version and both points set to (0.0,0.0,0.0)
LineSegment(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.LineSegment
Creates a line segment with the LayoutPkgNamespaces and both points set to (0.0,0.0,0.0)
LineSegment(LayoutPkgNamespaces, double, double, double, double) - Constructor for class org.sbml.libsbml.LineSegment
Creates a new line segment with the given 2D coordinates.
LineSegment(LayoutPkgNamespaces, double, double, double, double, double, double) - Constructor for class org.sbml.libsbml.LineSegment
Creates a new line segment with the given 3D coordinates.
LineSegment(LayoutPkgNamespaces, Point, Point) - Constructor for class org.sbml.libsbml.LineSegment
Creates a new line segment with the two given points.
LineSegment(LineSegment) - Constructor for class org.sbml.libsbml.LineSegment
Copy constructor.
LineSegment(XMLNode) - Constructor for class org.sbml.libsbml.LineSegment
Creates a new LineSegment from the given XMLNode
LineSegment(XMLNode, long) - Constructor for class org.sbml.libsbml.LineSegment
Creates a new LineSegment from the given XMLNode
ListOf - Class in org.sbml.libsbml
Parent class for libSBML's 'ListOfXYZ' classes.
ListOf() - Constructor for class org.sbml.libsbml.ListOf
Creates a new ListOf object.
ListOf(long) - Constructor for class org.sbml.libsbml.ListOf
Creates a new ListOf object.
ListOf(long, long) - Constructor for class org.sbml.libsbml.ListOf
Creates a new ListOf object.
ListOf(ListOf) - Constructor for class org.sbml.libsbml.ListOf
Copy constructor; creates a copy of this ListOf.
ListOf(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOf
Creates a new ListOf with a given SBMLNamespaces object.
ListOfColorDefinitions - Class in org.sbml.libsbml
LibSBML implementation for a container which holds zero or more ColorDefinition objects.
ListOfColorDefinitions() - Constructor for class org.sbml.libsbml.ListOfColorDefinitions
Constructor which instantiates an empty ListOfColorDefinitions object.
ListOfColorDefinitions(long) - Constructor for class org.sbml.libsbml.ListOfColorDefinitions
Constructor which instantiates an empty ListOfColorDefinitions object.
ListOfColorDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfColorDefinitions
Constructor which instantiates an empty ListOfColorDefinitions object.
ListOfColorDefinitions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfColorDefinitions
Constructor which instantiates an empty ListOfColorDefinitions object.
ListOfColorDefinitions(ListOfColorDefinitions) - Constructor for class org.sbml.libsbml.ListOfColorDefinitions
Copy constructor.
ListOfColorDefinitions(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfColorDefinitions
Ctor.
ListOfColorDefinitions(XMLNode) - Constructor for class org.sbml.libsbml.ListOfColorDefinitions
Creates a new ListOfColorDefinitions object from the given XMLNode object.
ListOfCompartmentGlyphs - Class in org.sbml.libsbml
layout A list of CompartmentGlyph objects.
ListOfCompartmentGlyphs() - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
Constructor.
ListOfCompartmentGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
Constructor.
ListOfCompartmentGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
Constructor.
ListOfCompartmentGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
Constructor.
ListOfCompartmentGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfCompartmentGlyphs
Constructor.
ListOfCompartments - Class in org.sbml.libsbml
A list of Compartment objects.
ListOfCompartments(long, long) - Constructor for class org.sbml.libsbml.ListOfCompartments
Creates a new ListOfCompartments object.
ListOfCompartments(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfCompartments
Creates a new ListOfCompartments object.
ListOfCompartmentTypes - Class in org.sbml.libsbml
A list of CompartmentType objects.
ListOfCompartmentTypes(long, long) - Constructor for class org.sbml.libsbml.ListOfCompartmentTypes
Creates a new ListOfCompartmentTypes object.
ListOfCompartmentTypes(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfCompartmentTypes
Creates a new ListOfCompartmentTypes object.
ListOfConstraints - Class in org.sbml.libsbml
A list of Constraint objects.
ListOfConstraints(long, long) - Constructor for class org.sbml.libsbml.ListOfConstraints
Creates a new ListOfConstraints object.
ListOfConstraints(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfConstraints
Creates a new ListOfConstraints object.
ListOfCurveElements - Class in org.sbml.libsbml
A container to store curve elements (RenderPoint and RenderCubicBezier).
ListOfCurveElements() - Constructor for class org.sbml.libsbml.ListOfCurveElements
Constructor which instantiates an empty ListOfCurveElements object.
ListOfCurveElements(long) - Constructor for class org.sbml.libsbml.ListOfCurveElements
Constructor which instantiates an empty ListOfCurveElements object.
ListOfCurveElements(long, long) - Constructor for class org.sbml.libsbml.ListOfCurveElements
Constructor which instantiates an empty ListOfCurveElements object.
ListOfCurveElements(long, long, long) - Constructor for class org.sbml.libsbml.ListOfCurveElements
Constructor which instantiates an empty ListOfCurveElements object.
ListOfCurveElements(ListOfCurveElements) - Constructor for class org.sbml.libsbml.ListOfCurveElements
Copy constructor for ListOfCurveElements objects.
ListOfCurveElements(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfCurveElements
Ctor.
ListOfCurveElements(XMLNode) - Constructor for class org.sbml.libsbml.ListOfCurveElements
Creates a new ListOfCurveElements object from the given XMLNode object.
ListOfCurveElements(XMLNode, long) - Constructor for class org.sbml.libsbml.ListOfCurveElements
Creates a new ListOfCurveElements object from the given XMLNode object.
ListOfDeletions - Class in org.sbml.libsbml
comp A list of Deletion objects.
ListOfDeletions() - Constructor for class org.sbml.libsbml.ListOfDeletions
Creates a new ListOfDeletions with the given level, version, and package version.
ListOfDeletions(long) - Constructor for class org.sbml.libsbml.ListOfDeletions
Creates a new ListOfDeletions with the given level, version, and package version.
ListOfDeletions(long, long) - Constructor for class org.sbml.libsbml.ListOfDeletions
Creates a new ListOfDeletions with the given level, version, and package version.
ListOfDeletions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfDeletions
Creates a new ListOfDeletions with the given level, version, and package version.
ListOfDeletions(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfDeletions
Creates a new ListOfDeletions with the given CompPkgNamespaces object.
ListOfDrawables - Class in org.sbml.libsbml
container class that stores objects derived from Transformation2D.
ListOfDrawables() - Constructor for class org.sbml.libsbml.ListOfDrawables
Constructor which instantiates an empty ListOfDrawables object.
ListOfDrawables(long) - Constructor for class org.sbml.libsbml.ListOfDrawables
Constructor which instantiates an empty ListOfDrawables object.
ListOfDrawables(long, long) - Constructor for class org.sbml.libsbml.ListOfDrawables
Constructor which instantiates an empty ListOfDrawables object.
ListOfDrawables(long, long, long) - Constructor for class org.sbml.libsbml.ListOfDrawables
Constructor which instantiates an empty ListOfDrawables object.
ListOfDrawables(ListOfDrawables) - Constructor for class org.sbml.libsbml.ListOfDrawables
Copy constructor.
ListOfDrawables(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfDrawables
Ctor.
ListOfEventAssignments - Class in org.sbml.libsbml
A list of EventAssignment objects.
ListOfEventAssignments(long, long) - Constructor for class org.sbml.libsbml.ListOfEventAssignments
Creates a new ListOfEventAssignments object.
ListOfEventAssignments(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfEventAssignments
Creates a new ListOfEventAssignments object.
ListOfEvents - Class in org.sbml.libsbml
A list of Event objects.
ListOfEvents(long, long) - Constructor for class org.sbml.libsbml.ListOfEvents
Creates a new ListOfEvents object.
ListOfEvents(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfEvents
Creates a new ListOfEvents object.
ListOfExternalModelDefinitions - Class in org.sbml.libsbml
comp A list of ExternalModelDefinition objects.
ListOfExternalModelDefinitions() - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
Creates a new ListOfExternalModelDefinitions with the given level, version, and package version.
ListOfExternalModelDefinitions(long) - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
Creates a new ListOfExternalModelDefinitions with the given level, version, and package version.
ListOfExternalModelDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
Creates a new ListOfExternalModelDefinitions with the given level, version, and package version.
ListOfExternalModelDefinitions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
Creates a new ListOfExternalModelDefinitions with the given level, version, and package version.
ListOfExternalModelDefinitions(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfExternalModelDefinitions
Creates a new ListOfExternalModelDefinitions with the given CompPkgNamespaces object.
ListOfFbcAssociations - Class in org.sbml.libsbml
fbc A list of FbcAssociation objects.
ListOfFbcAssociations() - Constructor for class org.sbml.libsbml.ListOfFbcAssociations
Creates a new ListOfFbcAssociations with the given SBML Level, Version, and “fbc”package version.
ListOfFbcAssociations(long) - Constructor for class org.sbml.libsbml.ListOfFbcAssociations
Creates a new ListOfFbcAssociations with the given SBML Level, Version, and “fbc”package version.
ListOfFbcAssociations(long, long) - Constructor for class org.sbml.libsbml.ListOfFbcAssociations
Creates a new ListOfFbcAssociations with the given SBML Level, Version, and “fbc”package version.
ListOfFbcAssociations(long, long, long) - Constructor for class org.sbml.libsbml.ListOfFbcAssociations
Creates a new ListOfFbcAssociations with the given SBML Level, Version, and “fbc”package version.
ListOfFbcAssociations(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfFbcAssociations
Creates a new ListOfFbcAssociations with the given FbcPkgNamespaces object.
ListOfFluxBounds - Class in org.sbml.libsbml
fbc A list of FluxBound objects.
ListOfFluxBounds() - Constructor for class org.sbml.libsbml.ListOfFluxBounds
Creates a new ListOfFluxBounds with the given level, version, and package version.
ListOfFluxBounds(long) - Constructor for class org.sbml.libsbml.ListOfFluxBounds
Creates a new ListOfFluxBounds with the given level, version, and package version.
ListOfFluxBounds(long, long) - Constructor for class org.sbml.libsbml.ListOfFluxBounds
Creates a new ListOfFluxBounds with the given level, version, and package version.
ListOfFluxBounds(long, long, long) - Constructor for class org.sbml.libsbml.ListOfFluxBounds
Creates a new ListOfFluxBounds with the given level, version, and package version.
ListOfFluxBounds(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfFluxBounds
Creates a new ListOfFluxBounds with the given FbcPkgNamespaces object.
ListOfFluxObjectives - Class in org.sbml.libsbml
fbc A list of FluxObjective objects.
ListOfFluxObjectives() - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
Creates a new ListOfFluxObjectives with the given level, version, and package version.
ListOfFluxObjectives(long) - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
Creates a new ListOfFluxObjectives with the given level, version, and package version.
ListOfFluxObjectives(long, long) - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
Creates a new ListOfFluxObjectives with the given level, version, and package version.
ListOfFluxObjectives(long, long, long) - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
Creates a new ListOfFluxObjectives with the given level, version, and package version.
ListOfFluxObjectives(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfFluxObjectives
Creates a new ListOfFluxObjectives with the given FbcPkgNamespaces object.
ListOfFunctionDefinitions - Class in org.sbml.libsbml
A list of FunctionDefinition objects.
ListOfFunctionDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfFunctionDefinitions
Creates a new ListOfFunctionDefinitions object.
ListOfFunctionDefinitions(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfFunctionDefinitions
Creates a new ListOfFunctionDefinitions object.
ListOfFunctionTerms - Class in org.sbml.libsbml
qual A list of FunctionTerm objects.
ListOfFunctionTerms() - Constructor for class org.sbml.libsbml.ListOfFunctionTerms
Creates a new ListOfFunctionTerms with the given level, version, and package version.
ListOfFunctionTerms(long) - Constructor for class org.sbml.libsbml.ListOfFunctionTerms
Creates a new ListOfFunctionTerms with the given level, version, and package version.
ListOfFunctionTerms(long, long) - Constructor for class org.sbml.libsbml.ListOfFunctionTerms
Creates a new ListOfFunctionTerms with the given level, version, and package version.
ListOfFunctionTerms(long, long, long) - Constructor for class org.sbml.libsbml.ListOfFunctionTerms
Creates a new ListOfFunctionTerms with the given level, version, and package version.
ListOfFunctionTerms(ListOfFunctionTerms) - Constructor for class org.sbml.libsbml.ListOfFunctionTerms
Creates a new ListOfFunctionTerms from the original.
ListOfFunctionTerms(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfFunctionTerms
Creates a new ListOfFunctionTerms with the given QualPkgNamespaces object.
ListOfGeneAssociations - Class in org.sbml.libsbml
fbc A list of GeneAssociation objects.
ListOfGeneAssociations() - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
Creates a new ListOfGeneAssociations with the given level, version, and package version.
ListOfGeneAssociations(long) - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
Creates a new ListOfGeneAssociations with the given level, version, and package version.
ListOfGeneAssociations(long, long) - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
Creates a new ListOfGeneAssociations with the given level, version, and package version.
ListOfGeneAssociations(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
Creates a new ListOfGeneAssociations with the given level, version, and package version.
ListOfGeneAssociations(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGeneAssociations
Creates a new ListOfGeneAssociations with the given FbcPkgNamespaces object.
ListOfGeneProducts - Class in org.sbml.libsbml
fbc A list of GeneProduct objects.
ListOfGeneProducts() - Constructor for class org.sbml.libsbml.ListOfGeneProducts
Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
ListOfGeneProducts(long) - Constructor for class org.sbml.libsbml.ListOfGeneProducts
Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
ListOfGeneProducts(long, long) - Constructor for class org.sbml.libsbml.ListOfGeneProducts
Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
ListOfGeneProducts(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGeneProducts
Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
ListOfGeneProducts(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGeneProducts
Creates a new ListOfGeneProducts with the given FbcPkgNamespaces object.
ListOfGlobalRenderInformation - Class in org.sbml.libsbml
container class that stores GlobalRenderInformation objects.
ListOfGlobalRenderInformation() - Constructor for class org.sbml.libsbml.ListOfGlobalRenderInformation
Constructor which instantiates an empty ListOfGlobalRenderInformation object.
ListOfGlobalRenderInformation(long) - Constructor for class org.sbml.libsbml.ListOfGlobalRenderInformation
Constructor which instantiates an empty ListOfGlobalRenderInformation object.
ListOfGlobalRenderInformation(long, long) - Constructor for class org.sbml.libsbml.ListOfGlobalRenderInformation
Constructor which instantiates an empty ListOfGlobalRenderInformation object.
ListOfGlobalRenderInformation(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGlobalRenderInformation
Constructor which instantiates an empty ListOfGlobalRenderInformation object.
ListOfGlobalRenderInformation(ListOfGlobalRenderInformation) - Constructor for class org.sbml.libsbml.ListOfGlobalRenderInformation
Copy constructor for ListOfGlobalRenderInformation objects.
ListOfGlobalRenderInformation(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGlobalRenderInformation
Ctor.
ListOfGlobalStyles - Class in org.sbml.libsbml
ListOfGlobalStyles is the container class that stores GlobalStyles in GlobalRenderInformation objects.
ListOfGlobalStyles() - Constructor for class org.sbml.libsbml.ListOfGlobalStyles
Constructor which instantiates an empty ListOfGlobalStyles object.
ListOfGlobalStyles(long) - Constructor for class org.sbml.libsbml.ListOfGlobalStyles
Constructor which instantiates an empty ListOfGlobalStyles object.
ListOfGlobalStyles(long, long) - Constructor for class org.sbml.libsbml.ListOfGlobalStyles
Constructor which instantiates an empty ListOfGlobalStyles object.
ListOfGlobalStyles(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGlobalStyles
Constructor which instantiates an empty ListOfGlobalStyles object.
ListOfGlobalStyles(ListOfGlobalStyles) - Constructor for class org.sbml.libsbml.ListOfGlobalStyles
Copy constructor for ListOfGlobalStyles objects.
ListOfGlobalStyles(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGlobalStyles
Ctor.
ListOfGlobalStyles(XMLNode) - Constructor for class org.sbml.libsbml.ListOfGlobalStyles
Creates a new ListOfGlobalStyles object from the given XMLNode object.
ListOfGradientDefinitions - Class in org.sbml.libsbml
a container class that holds a list of gradient definitions.
ListOfGradientDefinitions() - Constructor for class org.sbml.libsbml.ListOfGradientDefinitions
Constructor which instantiates an empty ListOfGradientDefinitions object.
ListOfGradientDefinitions(long) - Constructor for class org.sbml.libsbml.ListOfGradientDefinitions
Constructor which instantiates an empty ListOfGradientDefinitions object.
ListOfGradientDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfGradientDefinitions
Constructor which instantiates an empty ListOfGradientDefinitions object.
ListOfGradientDefinitions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGradientDefinitions
Constructor which instantiates an empty ListOfGradientDefinitions object.
ListOfGradientDefinitions(ListOfGradientDefinitions) - Constructor for class org.sbml.libsbml.ListOfGradientDefinitions
Copy constructor.
ListOfGradientDefinitions(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGradientDefinitions
Ctor.
ListOfGradientDefinitions(XMLNode) - Constructor for class org.sbml.libsbml.ListOfGradientDefinitions
Creates a new ListOfGradientDefinitions object from the given XMLNode object.
ListOfGradientDefinitions(XMLNode, long) - Constructor for class org.sbml.libsbml.ListOfGradientDefinitions
Creates a new ListOfGradientDefinitions object from the given XMLNode object.
ListOfGradientStops - Class in org.sbml.libsbml
a container that holds zero or more GradientStop objects.
ListOfGradientStops() - Constructor for class org.sbml.libsbml.ListOfGradientStops
Constructor which instantiated an empty ListOfGradientStops object.
ListOfGradientStops(long) - Constructor for class org.sbml.libsbml.ListOfGradientStops
Constructor which instantiated an empty ListOfGradientStops object.
ListOfGradientStops(long, long) - Constructor for class org.sbml.libsbml.ListOfGradientStops
Constructor which instantiated an empty ListOfGradientStops object.
ListOfGradientStops(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGradientStops
Constructor which instantiated an empty ListOfGradientStops object.
ListOfGradientStops(ListOfGradientStops) - Constructor for class org.sbml.libsbml.ListOfGradientStops
Copy constructor; creates a copy of the given ListOfGradientStops object.
ListOfGradientStops(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGradientStops
Ctor.
ListOfGradientStops(XMLNode) - Constructor for class org.sbml.libsbml.ListOfGradientStops
Creates a new ListOfGradientStops object from the given XMLNode object.
ListOfGradientStops(XMLNode, long) - Constructor for class org.sbml.libsbml.ListOfGradientStops
Creates a new ListOfGradientStops object from the given XMLNode object.
ListOfGraphicalObjects - Class in org.sbml.libsbml
layout A list of GraphicalObject objects.
ListOfGraphicalObjects() - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
Constructor.
ListOfGraphicalObjects(long) - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
Constructor.
ListOfGraphicalObjects(long, long) - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
Constructor.
ListOfGraphicalObjects(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
Constructor.
ListOfGraphicalObjects(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGraphicalObjects
Constructor.
ListOfGroups - Class in org.sbml.libsbml
groups A list of Group objects.
ListOfGroups() - Constructor for class org.sbml.libsbml.ListOfGroups
Creates a new ListOfGroups using the given SBML Level, Version and “groups” package version.
ListOfGroups(long) - Constructor for class org.sbml.libsbml.ListOfGroups
Creates a new ListOfGroups using the given SBML Level, Version and “groups” package version.
ListOfGroups(long, long) - Constructor for class org.sbml.libsbml.ListOfGroups
Creates a new ListOfGroups using the given SBML Level, Version and “groups” package version.
ListOfGroups(long, long, long) - Constructor for class org.sbml.libsbml.ListOfGroups
Creates a new ListOfGroups using the given SBML Level, Version and “groups” package version.
ListOfGroups(GroupsPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfGroups
Creates a new ListOfGroups using the given GroupsPkgNamespaces object.
ListOfGroups(ListOfGroups) - Constructor for class org.sbml.libsbml.ListOfGroups
Copy constructor for ListOfGroups.
ListOfInitialAssignments - Class in org.sbml.libsbml
A list of InitialAssignment objects.
ListOfInitialAssignments(long, long) - Constructor for class org.sbml.libsbml.ListOfInitialAssignments
Creates a new ListOfInitialAssignments object.
ListOfInitialAssignments(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfInitialAssignments
Creates a new ListOfInitialAssignments object.
ListOfInputs - Class in org.sbml.libsbml
qual A list of Input objects.
ListOfInputs() - Constructor for class org.sbml.libsbml.ListOfInputs
Creates a new ListOfInputs with the given level, version, and package version.
ListOfInputs(long) - Constructor for class org.sbml.libsbml.ListOfInputs
Creates a new ListOfInputs with the given level, version, and package version.
ListOfInputs(long, long) - Constructor for class org.sbml.libsbml.ListOfInputs
Creates a new ListOfInputs with the given level, version, and package version.
ListOfInputs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfInputs
Creates a new ListOfInputs with the given level, version, and package version.
ListOfInputs(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfInputs
Creates a new ListOfInputs with the given QualPkgNamespaces object.
ListOfLayouts - Class in org.sbml.libsbml
layout A list of Layout objects.
ListOfLayouts() - Constructor for class org.sbml.libsbml.ListOfLayouts
Constructor.
ListOfLayouts(long) - Constructor for class org.sbml.libsbml.ListOfLayouts
Constructor.
ListOfLayouts(long, long) - Constructor for class org.sbml.libsbml.ListOfLayouts
Constructor.
ListOfLayouts(long, long, long) - Constructor for class org.sbml.libsbml.ListOfLayouts
Constructor.
ListOfLayouts(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfLayouts
Constructor.
ListOfLineEndings - Class in org.sbml.libsbml
container class to store LineEnding objects
ListOfLineEndings() - Constructor for class org.sbml.libsbml.ListOfLineEndings
Constructor which instantiates an empty ListOfLineEndings object.
ListOfLineEndings(long) - Constructor for class org.sbml.libsbml.ListOfLineEndings
Constructor which instantiates an empty ListOfLineEndings object.
ListOfLineEndings(long, long) - Constructor for class org.sbml.libsbml.ListOfLineEndings
Constructor which instantiates an empty ListOfLineEndings object.
ListOfLineEndings(long, long, long) - Constructor for class org.sbml.libsbml.ListOfLineEndings
Constructor which instantiates an empty ListOfLineEndings object.
ListOfLineEndings(ListOfLineEndings) - Constructor for class org.sbml.libsbml.ListOfLineEndings
Copy constructor.
ListOfLineEndings(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfLineEndings
Ctor.
ListOfLineEndings(XMLNode) - Constructor for class org.sbml.libsbml.ListOfLineEndings
Creates a new ListOfLineEndings object from the given XMLNode object.
ListOfLineEndings(XMLNode, long) - Constructor for class org.sbml.libsbml.ListOfLineEndings
Creates a new ListOfLineEndings object from the given XMLNode object.
ListOfLineSegments - Class in org.sbml.libsbml
layout A list of LineSegment objects.
ListOfLineSegments() - Constructor for class org.sbml.libsbml.ListOfLineSegments
Constructor.
ListOfLineSegments(long) - Constructor for class org.sbml.libsbml.ListOfLineSegments
Constructor.
ListOfLineSegments(long, long) - Constructor for class org.sbml.libsbml.ListOfLineSegments
Constructor.
ListOfLineSegments(long, long, long) - Constructor for class org.sbml.libsbml.ListOfLineSegments
Constructor.
ListOfLineSegments(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfLineSegments
Constructor.
ListOfLocalParameters - Class in org.sbml.libsbml
A list of LocalParameter objects.
ListOfLocalParameters(long, long) - Constructor for class org.sbml.libsbml.ListOfLocalParameters
Creates a new ListOfLocalParameters object.
ListOfLocalParameters(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfLocalParameters
Creates a new ListOfLocalParameters object.
ListOfLocalRenderInformation - Class in org.sbml.libsbml
container class that stores LocalRenderInformation objects.
ListOfLocalRenderInformation() - Constructor for class org.sbml.libsbml.ListOfLocalRenderInformation
Constructor which instantiates an empty ListOfLocalRenderInformation object.
ListOfLocalRenderInformation(long) - Constructor for class org.sbml.libsbml.ListOfLocalRenderInformation
Constructor which instantiates an empty ListOfLocalRenderInformation object.
ListOfLocalRenderInformation(long, long) - Constructor for class org.sbml.libsbml.ListOfLocalRenderInformation
Constructor which instantiates an empty ListOfLocalRenderInformation object.
ListOfLocalRenderInformation(long, long, long) - Constructor for class org.sbml.libsbml.ListOfLocalRenderInformation
Constructor which instantiates an empty ListOfLocalRenderInformation object.
ListOfLocalRenderInformation(ListOfLocalRenderInformation) - Constructor for class org.sbml.libsbml.ListOfLocalRenderInformation
Copy constructor for ListOfLocalRenderInformation objects.
ListOfLocalRenderInformation(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfLocalRenderInformation
Ctor.
ListOfLocalStyles - Class in org.sbml.libsbml
ListOfLocalStyles is the container class that stores LocalStyles in LocalRenderInformation objects.
ListOfLocalStyles() - Constructor for class org.sbml.libsbml.ListOfLocalStyles
Constructor which instantiates an empty ListOfLocalStyles object.
ListOfLocalStyles(long) - Constructor for class org.sbml.libsbml.ListOfLocalStyles
Constructor which instantiates an empty ListOfLocalStyles object.
ListOfLocalStyles(long, long) - Constructor for class org.sbml.libsbml.ListOfLocalStyles
Constructor which instantiates an empty ListOfLocalStyles object.
ListOfLocalStyles(long, long, long) - Constructor for class org.sbml.libsbml.ListOfLocalStyles
Constructor which instantiates an empty ListOfLocalStyles object.
ListOfLocalStyles(ListOfLocalStyles) - Constructor for class org.sbml.libsbml.ListOfLocalStyles
Copy constructor for ListOfLocalStyles objects.
ListOfLocalStyles(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfLocalStyles
Ctor.
ListOfLocalStyles(XMLNode) - Constructor for class org.sbml.libsbml.ListOfLocalStyles
Creates a new ListOfLocalStyles object from the given XMLNode object.
ListOfMembers - Class in org.sbml.libsbml
groups A list of Member objects.
ListOfMembers() - Constructor for class org.sbml.libsbml.ListOfMembers
Creates a new ListOfMembers using the given SBML Level, Version and “groups” package version.
ListOfMembers(long) - Constructor for class org.sbml.libsbml.ListOfMembers
Creates a new ListOfMembers using the given SBML Level, Version and “groups” package version.
ListOfMembers(long, long) - Constructor for class org.sbml.libsbml.ListOfMembers
Creates a new ListOfMembers using the given SBML Level, Version and “groups” package version.
ListOfMembers(long, long, long) - Constructor for class org.sbml.libsbml.ListOfMembers
Creates a new ListOfMembers using the given SBML Level, Version and “groups” package version.
ListOfMembers(GroupsPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfMembers
Creates a new ListOfMembers using the given GroupsPkgNamespaces object.
ListOfMembers(ListOfMembers) - Constructor for class org.sbml.libsbml.ListOfMembers
Copy constructor for ListOfMembers.
ListOfModelDefinitions - Class in org.sbml.libsbml
comp A list of ModelDefinition objects.
ListOfModelDefinitions() - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
Creates a new ListOfModelDefinitions with the given level, version, and package version.
ListOfModelDefinitions(long) - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
Creates a new ListOfModelDefinitions with the given level, version, and package version.
ListOfModelDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
Creates a new ListOfModelDefinitions with the given level, version, and package version.
ListOfModelDefinitions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
Creates a new ListOfModelDefinitions with the given level, version, and package version.
ListOfModelDefinitions(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfModelDefinitions
Creates a new ListOfModelDefinitions with the given CompPkgNamespaces object.
ListOfObjectives - Class in org.sbml.libsbml
fbc A list of Objective objects.
ListOfObjectives() - Constructor for class org.sbml.libsbml.ListOfObjectives
Creates a new ListOfObjectives with the given SBML Level, Version, and “fbc”package version.
ListOfObjectives(long) - Constructor for class org.sbml.libsbml.ListOfObjectives
Creates a new ListOfObjectives with the given SBML Level, Version, and “fbc”package version.
ListOfObjectives(long, long) - Constructor for class org.sbml.libsbml.ListOfObjectives
Creates a new ListOfObjectives with the given SBML Level, Version, and “fbc”package version.
ListOfObjectives(long, long, long) - Constructor for class org.sbml.libsbml.ListOfObjectives
Creates a new ListOfObjectives with the given SBML Level, Version, and “fbc”package version.
ListOfObjectives(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfObjectives
Creates a new ListOfObjectives with the given FbcPkgNamespaces object.
ListOfObjectives(ListOfObjectives) - Constructor for class org.sbml.libsbml.ListOfObjectives
Copy Constructor.
ListOfOutputs - Class in org.sbml.libsbml
qual A list of Output objects.
ListOfOutputs() - Constructor for class org.sbml.libsbml.ListOfOutputs
Creates a new ListOfOutputs with the given level, version, and package version.
ListOfOutputs(long) - Constructor for class org.sbml.libsbml.ListOfOutputs
Creates a new ListOfOutputs with the given level, version, and package version.
ListOfOutputs(long, long) - Constructor for class org.sbml.libsbml.ListOfOutputs
Creates a new ListOfOutputs with the given level, version, and package version.
ListOfOutputs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfOutputs
Creates a new ListOfOutputs with the given level, version, and package version.
ListOfOutputs(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfOutputs
Creates a new ListOfOutputs with the given QualPkgNamespaces object.
ListOfParameters - Class in org.sbml.libsbml
A list of Parameter objects.
ListOfParameters(long, long) - Constructor for class org.sbml.libsbml.ListOfParameters
Creates a new ListOfParameters object.
ListOfParameters(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfParameters
Creates a new ListOfParameters object.
ListOfPorts - Class in org.sbml.libsbml
comp A list of Port objects.
ListOfPorts() - Constructor for class org.sbml.libsbml.ListOfPorts
Creates a new ListOfPorts with the given level, version, and package version.
ListOfPorts(long) - Constructor for class org.sbml.libsbml.ListOfPorts
Creates a new ListOfPorts with the given level, version, and package version.
ListOfPorts(long, long) - Constructor for class org.sbml.libsbml.ListOfPorts
Creates a new ListOfPorts with the given level, version, and package version.
ListOfPorts(long, long, long) - Constructor for class org.sbml.libsbml.ListOfPorts
Creates a new ListOfPorts with the given level, version, and package version.
ListOfPorts(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfPorts
Creates a new ListOfPorts with the given CompPkgNamespaces object.
ListOfQualitativeSpecies - Class in org.sbml.libsbml
qual A list of QualitativeSpecies objects.
ListOfQualitativeSpecies() - Constructor for class org.sbml.libsbml.ListOfQualitativeSpecies
Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
ListOfQualitativeSpecies(long) - Constructor for class org.sbml.libsbml.ListOfQualitativeSpecies
Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
ListOfQualitativeSpecies(long, long) - Constructor for class org.sbml.libsbml.ListOfQualitativeSpecies
Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
ListOfQualitativeSpecies(long, long, long) - Constructor for class org.sbml.libsbml.ListOfQualitativeSpecies
Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
ListOfQualitativeSpecies(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfQualitativeSpecies
Creates a new ListOfQualitativeSpecies with the given QualPkgNamespaces object.
ListOfReactionGlyphs - Class in org.sbml.libsbml
layout A list of ReactionGlyph objects.
ListOfReactionGlyphs() - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
Constructor.
ListOfReactionGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
Constructor.
ListOfReactionGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
Constructor.
ListOfReactionGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
Constructor.
ListOfReactionGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfReactionGlyphs
Constructor.
ListOfReactions - Class in org.sbml.libsbml
A list of Reaction objects.
ListOfReactions(long, long) - Constructor for class org.sbml.libsbml.ListOfReactions
Creates a new ListOfReactions object.
ListOfReactions(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfReactions
Creates a new ListOfReactions object.
ListOfReferenceGlyphs - Class in org.sbml.libsbml
layout A list of ReferenceGlyph objects.
ListOfReferenceGlyphs() - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
Constructor.
ListOfReferenceGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
Constructor.
ListOfReferenceGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
Constructor.
ListOfReferenceGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
Constructor.
ListOfReferenceGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfReferenceGlyphs
Constructor.
ListOfReplacedElements - Class in org.sbml.libsbml
comp A list of ReplacedElement objects.
ListOfReplacedElements() - Constructor for class org.sbml.libsbml.ListOfReplacedElements
Creates a new ListOfReplacedElements with the given level, version, and package version.
ListOfReplacedElements(long) - Constructor for class org.sbml.libsbml.ListOfReplacedElements
Creates a new ListOfReplacedElements with the given level, version, and package version.
ListOfReplacedElements(long, long) - Constructor for class org.sbml.libsbml.ListOfReplacedElements
Creates a new ListOfReplacedElements with the given level, version, and package version.
ListOfReplacedElements(long, long, long) - Constructor for class org.sbml.libsbml.ListOfReplacedElements
Creates a new ListOfReplacedElements with the given level, version, and package version.
ListOfReplacedElements(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfReplacedElements
Creates a new ListOfReplacedElements with the given CompPkgNamespaces object.
ListOfRules - Class in org.sbml.libsbml
A list of Rule objects.
ListOfRules(long, long) - Constructor for class org.sbml.libsbml.ListOfRules
Creates a new ListOfRules object.
ListOfRules(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfRules
Creates a new ListOfRules object.
ListOfSpecies - Class in org.sbml.libsbml
A list of Species objects.
ListOfSpecies(long, long) - Constructor for class org.sbml.libsbml.ListOfSpecies
Creates a new ListOfSpecies object.
ListOfSpecies(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpecies
Creates a new ListOfSpecies object.
ListOfSpeciesGlyphs - Class in org.sbml.libsbml
layout A list of SpeciesGlyph objects.
ListOfSpeciesGlyphs() - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
Constructor.
ListOfSpeciesGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
Constructor.
ListOfSpeciesGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
Constructor.
ListOfSpeciesGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
Constructor.
ListOfSpeciesGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpeciesGlyphs
Constructor.
ListOfSpeciesReferenceGlyphs - Class in org.sbml.libsbml
layout A list of SpeciesReferenceGlyph objects.
ListOfSpeciesReferenceGlyphs() - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Constructor.
ListOfSpeciesReferenceGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Constructor.
ListOfSpeciesReferenceGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Constructor.
ListOfSpeciesReferenceGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Constructor.
ListOfSpeciesReferenceGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Constructor.
ListOfSpeciesReferences - Class in org.sbml.libsbml
A list of SpeciesReference objects.
ListOfSpeciesReferences(long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferences
Creates a new, empty ListOfSpeciesReferences object.
ListOfSpeciesReferences(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpeciesReferences
Creates a new ListOfSpeciesReferences object.
ListOfSpeciesTypes - Class in org.sbml.libsbml
A list of SpeciesType objects.
ListOfSpeciesTypes(long, long) - Constructor for class org.sbml.libsbml.ListOfSpeciesTypes
Creates a new ListOfSpeciesTypes object.
ListOfSpeciesTypes(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfSpeciesTypes
Creates a new ListOfSpeciesTypes object.
ListOfSubmodels - Class in org.sbml.libsbml
comp A list of Submodel objects.
ListOfSubmodels() - Constructor for class org.sbml.libsbml.ListOfSubmodels
Creates a new ListOfSubmodels with the given level, version, and package version.
ListOfSubmodels(long) - Constructor for class org.sbml.libsbml.ListOfSubmodels
Creates a new ListOfSubmodels with the given level, version, and package version.
ListOfSubmodels(long, long) - Constructor for class org.sbml.libsbml.ListOfSubmodels
Creates a new ListOfSubmodels with the given level, version, and package version.
ListOfSubmodels(long, long, long) - Constructor for class org.sbml.libsbml.ListOfSubmodels
Creates a new ListOfSubmodels with the given level, version, and package version.
ListOfSubmodels(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfSubmodels
Creates a new ListOfSubmodels with the given CompPkgNamespaces object.
ListOfTextGlyphs - Class in org.sbml.libsbml
layout A list of TextGlyph objects.
ListOfTextGlyphs() - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
Constructor.
ListOfTextGlyphs(long) - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
Constructor.
ListOfTextGlyphs(long, long) - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
Constructor.
ListOfTextGlyphs(long, long, long) - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
Constructor.
ListOfTextGlyphs(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfTextGlyphs
Constructor.
ListOfTransitions - Class in org.sbml.libsbml
qual A list of Transition objects.
ListOfTransitions() - Constructor for class org.sbml.libsbml.ListOfTransitions
Creates a new ListOfTransitions with the given level, version, and package version.
ListOfTransitions(long) - Constructor for class org.sbml.libsbml.ListOfTransitions
Creates a new ListOfTransitions with the given level, version, and package version.
ListOfTransitions(long, long) - Constructor for class org.sbml.libsbml.ListOfTransitions
Creates a new ListOfTransitions with the given level, version, and package version.
ListOfTransitions(long, long, long) - Constructor for class org.sbml.libsbml.ListOfTransitions
Creates a new ListOfTransitions with the given level, version, and package version.
ListOfTransitions(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.ListOfTransitions
Creates a new ListOfTransitions with the given QualPkgNamespaces object.
ListOfUnitDefinitions - Class in org.sbml.libsbml
A list of UnitDefinition objects.
ListOfUnitDefinitions(long, long) - Constructor for class org.sbml.libsbml.ListOfUnitDefinitions
Creates a new ListOfUnitDefinitions object.
ListOfUnitDefinitions(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfUnitDefinitions
Creates a new ListOfUnitDefinitions object.
ListOfUnits - Class in org.sbml.libsbml
A list of Unit objects.
ListOfUnits(long, long) - Constructor for class org.sbml.libsbml.ListOfUnits
Creates a new ListOfUnits object.
ListOfUnits(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ListOfUnits
Creates a new ListOfUnits object.
LocalParameter - Class in org.sbml.libsbml
A parameter inside an SBML reaction definition.
LocalParameter(long, long) - Constructor for class org.sbml.libsbml.LocalParameter
Creates a new LocalParameter object with the given SBML level and version values.
LocalParameter(LocalParameter) - Constructor for class org.sbml.libsbml.LocalParameter
Copy constructor; creates a copy of a given LocalParameter object.
LocalParameter(Parameter) - Constructor for class org.sbml.libsbml.LocalParameter
Copy constructor; creates a LocalParameter object by copying the attributes of a given Parameter object.
LocalParameter(SBMLNamespaces) - Constructor for class org.sbml.libsbml.LocalParameter
Creates a new LocalParameter object with the given SBMLNamespaces object sbmlns.
LocalParameterShadowsId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LocalParameterShadowsSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
LocalRenderInformation - Class in org.sbml.libsbml
LocalRenderInformation is the render information stored in Layouts.
LocalRenderInformation() - Constructor for class org.sbml.libsbml.LocalRenderInformation
Creates a new LocalRenderInformation object with the given SBML level and SBML version.
LocalRenderInformation(long) - Constructor for class org.sbml.libsbml.LocalRenderInformation
Creates a new LocalRenderInformation object with the given SBML level and SBML version.
LocalRenderInformation(long, long) - Constructor for class org.sbml.libsbml.LocalRenderInformation
Creates a new LocalRenderInformation object with the given SBML level and SBML version.
LocalRenderInformation(long, long, long) - Constructor for class org.sbml.libsbml.LocalRenderInformation
Creates a new LocalRenderInformation object with the given SBML level and SBML version.
LocalRenderInformation(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.LocalRenderInformation
Creates a new LocalRenderInformation object with the given SBMLNamespaces.
LocalRenderInformation(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.LocalRenderInformation
Constructor which creates a LocalRenderInformation with the given id and all lists empty.
LocalStyle - Class in org.sbml.libsbml
implementation of the LocalStyle concept of the SBML render extension.
LocalStyle() - Constructor for class org.sbml.libsbml.LocalStyle
Creates a new LocalStyle object with the given SBML level and SBML version.
LocalStyle(long) - Constructor for class org.sbml.libsbml.LocalStyle
Creates a new LocalStyle object with the given SBML level and SBML version.
LocalStyle(long, long) - Constructor for class org.sbml.libsbml.LocalStyle
Creates a new LocalStyle object with the given SBML level and SBML version.
LocalStyle(long, long, long) - Constructor for class org.sbml.libsbml.LocalStyle
Creates a new LocalStyle object with the given SBML level and SBML version.
LocalStyle(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.LocalStyle
Creates a new LocalStyle object with the given SBMLNamespaces.
LocalStyle(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.LocalStyle
Constructor which creates a LocalStyle with an empty group and empty id, role and type list.
LocalStyle(XMLNode) - Constructor for class org.sbml.libsbml.LocalStyle
Creates a new LocalStyle object from the given XMLNode object.
LocalStyle(XMLNode, long) - Constructor for class org.sbml.libsbml.LocalStyle
Creates a new LocalStyle object from the given XMLNode object.
logFailure(SBMLError) - Method in class org.sbml.libsbml.SBMLValidator
Adds the given failure to this list of Validators failures.
logInvalidId(String, String) - Method in class org.sbml.libsbml.CompSBasePlugin
Helper to log a common type of error.

M

matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.CobraToFbcConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.CompFlatteningConverter
Returns true if this converter matches the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.FbcToCobraConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.FbcV1ToV2Converter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.FbcV2ToV1Converter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLConverter
Returns true if this converter matches the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLIdConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLInferUnitsConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLInitialAssignmentConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLLevel1Version1Converter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLLevelVersionConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLLocalParameterConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLReactionConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLRuleConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLStripPackageConverter
Returns true if this converter object's properties match the given properties.
matchesProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLUnitsConverter
Returns true if this converter object's properties match the given properties.
matchesRequiredSBMLNamespacesForAddition(SBase) - Method in class org.sbml.libsbml.SBase
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.
matchesSBMLNamespaces(SBase) - Method in class org.sbml.libsbml.SBase
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.
MathCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MathCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MathFilter - Class in org.sbml.libsbml
 
MathML - Class in org.sbml.libsbml
 
MathMLElementNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MathResultMustBeNumeric - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Member - Class in org.sbml.libsbml
groups TODO:Definition of the Member class.
Member() - Constructor for class org.sbml.libsbml.Member
Creates a new Member using the given SBML Level, Version and “groups” package version.
Member(long) - Constructor for class org.sbml.libsbml.Member
Creates a new Member using the given SBML Level, Version and “groups” package version.
Member(long, long) - Constructor for class org.sbml.libsbml.Member
Creates a new Member using the given SBML Level, Version and “groups” package version.
Member(long, long, long) - Constructor for class org.sbml.libsbml.Member
Creates a new Member using the given SBML Level, Version and “groups” package version.
Member(GroupsPkgNamespaces) - Constructor for class org.sbml.libsbml.Member
Creates a new Member using the given GroupsPkgNamespaces object.
Member(Member) - Constructor for class org.sbml.libsbml.Member
Copy constructor for Member.
merge(Unit, Unit) - Static method in class org.sbml.libsbml.Unit
Merges two Unit objects with the same 'kind' attribute value into a single Unit.
MetaIdNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingAnnotationNamespace - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingEventAssignment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingMathElementNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingModel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingOrInconsistentLevel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingOrInconsistentVersion - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingParticipantsNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingSpeciesCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingTriggerElementNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingTriggerInEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLAttributeValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLDecl - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLEncoding - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MissingXMLRequiredAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Model - Class in org.sbml.libsbml
An SBML model.
Model(long, long) - Constructor for class org.sbml.libsbml.Model
Creates a new Model using the given SBML level and version values.
Model(Model) - Constructor for class org.sbml.libsbml.Model
Copy constructor; creates a (deep) copy of the given Model object.
Model(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Model
Creates a new Model using the given SBMLNamespaces object sbmlns.
MODEL_QUALIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModelCreator - Class in org.sbml.libsbml
MIRIAM-compliant data about a model's creator.
ModelCreator() - Constructor for class org.sbml.libsbml.ModelCreator
Creates a new ModelCreator object.
ModelCreator(ModelCreator) - Constructor for class org.sbml.libsbml.ModelCreator
Copy constructor; creates a copy of the ModelCreator.
ModelCreator(XMLNode) - Constructor for class org.sbml.libsbml.ModelCreator
Creates a new ModelCreator from an XMLNode.
ModelCreatorList - Class in org.sbml.libsbml
 
ModelCreatorList() - Constructor for class org.sbml.libsbml.ModelCreatorList
 
ModelDefinition - Class in org.sbml.libsbml
comp A model used in model composition.
ModelDefinition() - Constructor for class org.sbml.libsbml.ModelDefinition
Creates a new ModelDefinition with the given level, version, and package version.
ModelDefinition(long) - Constructor for class org.sbml.libsbml.ModelDefinition
Creates a new ModelDefinition with the given level, version, and package version.
ModelDefinition(long, long) - Constructor for class org.sbml.libsbml.ModelDefinition
Creates a new ModelDefinition with the given level, version, and package version.
ModelDefinition(long, long, long) - Constructor for class org.sbml.libsbml.ModelDefinition
Creates a new ModelDefinition with the given level, version, and package version.
ModelDefinition(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ModelDefinition
Creates a new ModelDefinition with the given CompPkgNamespaces object.
ModelDefinition(Model) - Constructor for class org.sbml.libsbml.ModelDefinition
Copy constructor from base Model object.
ModelHistory - Class in org.sbml.libsbml
MIRIAM-compliant data about a model's history.
ModelHistory() - Constructor for class org.sbml.libsbml.ModelHistory
Creates a new ModelHistory object.
ModelHistory(ModelHistory) - Constructor for class org.sbml.libsbml.ModelHistory
Copy constructor; creates a copy of this ModelHistory object.
ModelQualifierType_fromString(String) - Static method in class org.sbml.libsbml.libsbml
This method takes a string and returns a model qualifier representing the string.
ModelQualifierType_toString(int) - Static method in class org.sbml.libsbml.libsbml
This method takes a model qualifier type code and returns a string representing the code.
ModelSBOBranchChangedBeyondL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModelSBOBranchChangedBeyondL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModelSBOBranchChangedInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModelSBOBranchChangedInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ModifierSpeciesReference - Class in org.sbml.libsbml
A reference to an SBML modifier species.
ModifierSpeciesReference(long, long) - Constructor for class org.sbml.libsbml.ModifierSpeciesReference
Creates a new ModifierSpeciesReference using the given SBML level and version values.
ModifierSpeciesReference(SBMLNamespaces) - Constructor for class org.sbml.libsbml.ModifierSpeciesReference
Creates a new ModifierSpeciesReference using the given SBMLNamespaces object sbmlns.
MultipleAnnotations - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultipleAssignmentOrRateRules - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultipleEventAssignmentsForId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultipleInitAssignments - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultiplierNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
MultSpeciesSameTypeInCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

N

NameNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NeedCompartmentIfHaveSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NestedAnnotationNotAllowed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
next() - Method in class org.sbml.libsbml.XMLInputStream
Returns the next token on this XML input stream.
NoBodyInFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoCompartmentOutsideInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoCompartmentTypeInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoCompartmentTypeInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoCompartmentTypeInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoConcentrationInZeroD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoConstraintsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoConstraintsInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoDelayedEventAssignmentInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoDelayedEventAssignmentInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoDelayedEventAssignmentInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoEventsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoEventTimeUnitsInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoEventTimeUnitsInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoEventTimeUnitsInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoFancyStoichiometryMathInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoFunctionDefinitionsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoIdOnSpeciesReferenceInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoInitialAssignmentsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoInitialAssignmentsInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawSubstanceUnitsInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawSubstanceUnitsInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawSubstanceUnitsInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawSubstanceUnitsInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawTimeUnitsInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawTimeUnitsInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawTimeUnitsInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoKineticLawTimeUnitsInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NonBoundarySpeciesAssignedAndUsed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NonConstantLocalParameter - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NonConstantSpeciesUsed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoNon3DCompartmentsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoNonIntegerStoichiometryInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NonPersistentNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NONZERO - Static variable in class org.sbml.libsbml.GraphicalPrimitive2D
 
NoReactantsOrProducts - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSBOTermsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSBOTermsInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpatialUnitsInZeroD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesSpatialSizeUnitsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesSpatialSizeUnitsInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesSpatialSizeUnitsInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesSpatialSizeUnitsInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesTypeInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesTypeInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoSpeciesTypesInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoStoichiometryMathInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotesContainsDOCTYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotesContainsXMLDecl - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotesNotInXHTMLNamespace - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoTimeSymbolInFunctionDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotSchemaConformant - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NotUTF8 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitMultipliersOrOffsetsInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitOffsetInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitOffsetInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitOffsetInL2v4 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitOffsetInL3v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NoUnitsOnCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
NumericOpsNeedNumericArgs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

O

Objective - Class in org.sbml.libsbml
fbc An objective function.
Objective() - Constructor for class org.sbml.libsbml.Objective
Creates a new Objective with the given SBML Level, Version, and “fbc”package version.
Objective(long) - Constructor for class org.sbml.libsbml.Objective
Creates a new Objective with the given SBML Level, Version, and “fbc”package version.
Objective(long, long) - Constructor for class org.sbml.libsbml.Objective
Creates a new Objective with the given SBML Level, Version, and “fbc”package version.
Objective(long, long, long) - Constructor for class org.sbml.libsbml.Objective
Creates a new Objective with the given SBML Level, Version, and “fbc”package version.
Objective(FbcPkgNamespaces) - Constructor for class org.sbml.libsbml.Objective
Creates a new Objective with the given FbcPkgNamespaces object.
Objective(Objective) - Constructor for class org.sbml.libsbml.Objective
Copy constructor for Objective.
OBJECTIVE_TYPE_MAXIMIZE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OBJECTIVE_TYPE_MINIMIZE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OBJECTIVE_TYPE_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ObseleteSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OffsetNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OffsetNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OFStream - Class in org.sbml.libsbml
 
OFStream(String) - Constructor for class org.sbml.libsbml.OFStream
 
OFStream(String, boolean) - Constructor for class org.sbml.libsbml.OFStream
 
OneDimensionalCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneListOfEventAssignmentsPerEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneListOfPerKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneListOfUnitsPerUnitDef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathElementPerConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathElementPerFunc - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathElementPerInitialAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathElementPerRule - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerDelay - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerEventAssignment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerKineticLaw - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerPriority - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMathPerTrigger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneMessageElementPerConstraint - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneOfEachListOf - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OneSubElementPerReaction - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyCompartmentsInListOfCompartments - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyConstraintsInListOfConstraints - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyEventAssignInListOfEventAssign - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyEventsInListOfEvents - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyFuncDefsInListOfFuncDefs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyInitAssignsInListOfInitAssigns - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyLocalParamsInListOfLocalParams - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyOneDelayPerEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyOneNotesElementAllowed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyOnePriorityPerEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyParametersInListOfParameters - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyReactionsInListOfReactions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyRulesInListOfRules - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlySpeciesInListOfSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyUnitDefsInListOfUnitDefs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OnlyUnitsInListOfUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
open(String) - Method in class org.sbml.libsbml.OFStream
 
open(String, boolean) - Method in class org.sbml.libsbml.OFStream
 
OperationReturnValue_toString(int) - Static method in class org.sbml.libsbml.libsbml
This method takes an SBML operation return value and returns a string representing the code.
OpsNeedCorrectNumberOfArgs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OR_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
org.sbml.libsbml - package org.sbml.libsbml
 
OStream - Class in org.sbml.libsbml
 
OStream() - Constructor for class org.sbml.libsbml.OStream
 
OStream(int) - Constructor for class org.sbml.libsbml.OStream
 
OStringStream - Class in org.sbml.libsbml
 
OStringStream() - Constructor for class org.sbml.libsbml.OStringStream
 
Output - Class in org.sbml.libsbml
qual The output from a QualitativeSpecies.
Output() - Constructor for class org.sbml.libsbml.Output
Creates a new Output with the given level, version, and package version.
Output(long) - Constructor for class org.sbml.libsbml.Output
Creates a new Output with the given level, version, and package version.
Output(long, long) - Constructor for class org.sbml.libsbml.Output
Creates a new Output with the given level, version, and package version.
Output(long, long, long) - Constructor for class org.sbml.libsbml.Output
Creates a new Output with the given level, version, and package version.
Output(Output) - Constructor for class org.sbml.libsbml.Output
Copy constructor for Output.
Output(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.Output
Creates a new Output with the given QualPkgNamespaces object.
OUTPUT_TRANSITION_EFFECT_ASSIGNMENT_LEVEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OUTPUT_TRANSITION_EFFECT_PRODUCTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OUTPUT_TRANSITION_EFFECT_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OverdeterCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OverdeterCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
OverdeterminedSystem - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

P

PackageConversionNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PackageNSMustMatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PackageRequiredShouldBeFalse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PAD - Static variable in class org.sbml.libsbml.GradientBase
 
Parameter - Class in org.sbml.libsbml
An SBML parameter: a named symbol with a value.
Parameter(long, long) - Constructor for class org.sbml.libsbml.Parameter
Creates a new Parameter using the given SBML level and version values.
Parameter(Parameter) - Constructor for class org.sbml.libsbml.Parameter
Copy constructor; creates a copy of a Parameter.
Parameter(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Parameter
Creates a new Parameter using the given SBMLNamespaces object sbmlns.
ParameterShouldHaveUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ParameterShouldHaveValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ParameterUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
parseAnnotation() - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
 
parseCVTerms(SBase) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Takes a list of CVTerm objects and creates a complete SBML annotation around it.
parseFbcInfixAssociation(String, FbcModelPlugin) - Static method in class org.sbml.libsbml.FbcAssociation
Parses a gene association in infix format and returns a corresponding Association object.
parseFbcInfixAssociation(String, FbcModelPlugin, boolean) - Static method in class org.sbml.libsbml.FbcAssociation
Parses a gene association in infix format and returns a corresponding Association object.
parseFbcInfixAssociation(String, FbcModelPlugin, boolean, boolean) - Static method in class org.sbml.libsbml.FbcAssociation
Parses a gene association in infix format and returns a corresponding Association object.
parseFormula(String) - Static method in class org.sbml.libsbml.libsbml
Parses a text string as a mathematical formula and returns an AST representation of it.
parseInfixAssociation(String) - Static method in class org.sbml.libsbml.Association
Parses a gene association in infix format and returns a corresponding Association object.
parseL3Formula(String) - Static method in class org.sbml.libsbml.libsbml
Parses a text string as a mathematical formula and returns an AST representation of it.
parseL3FormulaWithModel(String, Model) - Static method in class org.sbml.libsbml.libsbml
Parses a text string as a mathematical formula using a Model to resolve symbols, and returns an AST representation of the result.
parseL3FormulaWithSettings(String, L3ParserSettings) - Static method in class org.sbml.libsbml.libsbml
Parses a text string as a mathematical formula using specific parser settings and returns an AST representation of the result.
parseLayoutAnnotation(XMLNode, ListOfLayouts) - Static method in class org.sbml.libsbml.libsbml
takes an annotation that has been read into the model identifies the RDF elements and creates a List of Layouts from the annotation
parseLayoutId(SimpleSpeciesReference) - Static method in class org.sbml.libsbml.libsbml
Creates an XMLNode that represents the layoutId annotation of the species reference from the given SpeciesReference object.
parseLayouts(Model) - Static method in class org.sbml.libsbml.libsbml
Creates an XMLNode that represents the layouts of the model from the given Model object.
parseModelHistory(SBase) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Reads the model history and cvTerms stored in obj and creates the XML structure for an SBML annotation representing that metadata if there is a model history stored in obj.
parseOnlyModelHistory(SBase) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Reads the model history stored in obj and creates the XML structure for an SBML annotation representing that history.
parseRDFAnnotation(XMLNode) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Parses an annotation into a ModelHistory class instance.
parseRDFAnnotation(XMLNode, String) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Parses an annotation into a ModelHistory class instance.
parseRDFAnnotation(XMLNode, String, XMLInputStream) - Static method in class org.sbml.libsbml.RDFAnnotationParser
Parses an annotation into a ModelHistory class instance.
parseRDFAnnotation(XMLNode, CVTermList) - Static method in class org.sbml.libsbml.RDFAnnotationParser
 
parseRDFAnnotation(XMLNode, CVTermList, String) - Static method in class org.sbml.libsbml.RDFAnnotationParser
 
parseRDFAnnotation(XMLNode, CVTermList, String, XMLInputStream) - Static method in class org.sbml.libsbml.RDFAnnotationParser
 
parseSpeciesReferenceAnnotation(XMLNode, SimpleSpeciesReference) - Static method in class org.sbml.libsbml.libsbml
takes an annotation that has been read into the species reference identifies the id elements and set the id of the species reference
parseXML(XMLNode) - Method in class org.sbml.libsbml.GlobalRenderInformation
Parses the xml information in the given node and sets the attributes.
parseXML(XMLNode) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Parses the xml information in the given node and sets the attributes.
parseXML(XMLNode) - Method in class org.sbml.libsbml.LocalRenderInformation
Parses the xml information in the given node and sets the attributes.
peek() - Method in class org.sbml.libsbml.XMLInputStream
Returns the next token without consuming it.
performDeletion() - Method in class org.sbml.libsbml.SBaseRef
DEPRECATED FUNCTION: DO NOT USE
performDeletions() - Method in class org.sbml.libsbml.Submodel
Delete elements in the instantiated submodel, based on any Deletions from this Submodel's listOfDeletions.
performReplacement() - Method in class org.sbml.libsbml.Replacing
DEPRECATED FUNCTION: DO NOT USE
PersistentNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PieceNeedsBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PiecewiseNeedsConsistentTypes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Point - Class in org.sbml.libsbml
layout Representation of a point.
Point() - Constructor for class org.sbml.libsbml.Point
Creates a new point with x,y and z set to 0.0.
Point(long) - Constructor for class org.sbml.libsbml.Point
Creates a new point with x,y and z set to 0.0.
Point(long, long) - Constructor for class org.sbml.libsbml.Point
Creates a new point with x,y and z set to 0.0.
Point(long, long, long) - Constructor for class org.sbml.libsbml.Point
Creates a new point with x,y and z set to 0.0.
Point(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.Point
Constructor.
Point(LayoutPkgNamespaces, double, double) - Constructor for class org.sbml.libsbml.Point
Creates a new point with the given coordinates.
Point(LayoutPkgNamespaces, double, double, double) - Constructor for class org.sbml.libsbml.Point
Creates a new point with the given coordinates.
Point(Point) - Constructor for class org.sbml.libsbml.Point
Copy constructor.
Point(XMLNode) - Constructor for class org.sbml.libsbml.Point
Creates a new Point from the given XMLNode
Point(XMLNode, long) - Constructor for class org.sbml.libsbml.Point
Creates a new Point from the given XMLNode
Polygon - Class in org.sbml.libsbml
class representing a polygon from the SBML render extension
Polygon() - Constructor for class org.sbml.libsbml.Polygon
Creates a new Polygon object with the given SBML level and SBML version.
Polygon(long) - Constructor for class org.sbml.libsbml.Polygon
Creates a new Polygon object with the given SBML level and SBML version.
Polygon(long, long) - Constructor for class org.sbml.libsbml.Polygon
Creates a new Polygon object with the given SBML level and SBML version.
Polygon(long, long, long) - Constructor for class org.sbml.libsbml.Polygon
Creates a new Polygon object with the given SBML level and SBML version.
Polygon(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.Polygon
Creates a new Polygon object with the given SBMLNamespaces.
Polygon(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.Polygon
Instanciates a polygon with the given id and no elements.
Polygon(XMLNode) - Constructor for class org.sbml.libsbml.Polygon
Creates a new Polygon object from the given XMLNode object.
Polygon(XMLNode, long) - Constructor for class org.sbml.libsbml.Polygon
Creates a new Polygon object from the given XMLNode object.
populateAllElementIdList() - Method in class org.sbml.libsbml.Model
Populates the internal list of the identifiers of all elements within this Model object.
populateAllElementMetaIdList() - Method in class org.sbml.libsbml.Model
Populates the internal list of the metaids of all elements within this Model object.
populateListFormulaUnitsData() - Method in class org.sbml.libsbml.Model
Populates the internal list of derived units for this Model object.
Port - Class in org.sbml.libsbml
comp An interface to be used in composition.
Port() - Constructor for class org.sbml.libsbml.Port
Creates a new Port with the given level, version, and package version.
Port(long) - Constructor for class org.sbml.libsbml.Port
Creates a new Port with the given level, version, and package version.
Port(long, long) - Constructor for class org.sbml.libsbml.Port
Creates a new Port with the given level, version, and package version.
Port(long, long, long) - Constructor for class org.sbml.libsbml.Port
Creates a new Port with the given level, version, and package version.
Port(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Port
Creates a new Port with the given CompPkgNamespaces object.
Port(Port) - Constructor for class org.sbml.libsbml.Port
Copy constructor.
PracticeCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PracticeCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
prepend(ASTNode) - Method in class org.sbml.libsbml.ASTNodeList
 
prepend(CVTerm) - Method in class org.sbml.libsbml.CVTermList
 
prepend(Date) - Method in class org.sbml.libsbml.DateList
 
prepend(ModelCreator) - Method in class org.sbml.libsbml.ModelCreatorList
 
prepend(SBase) - Method in class org.sbml.libsbml.SBaseList
 
prepend(SBMLNamespaces) - Method in class org.sbml.libsbml.SBMLNamespacesList
 
prependChild(ASTNode) - Method in class org.sbml.libsbml.ASTNode
Adds the given node as a child of this ASTNode.
printErrors() - Method in class org.sbml.libsbml.SBMLDocument
Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document.
printErrors() - Method in class org.sbml.libsbml.XMLErrorLog
Prints all the errors or warnings stored in this error log.
printErrors(OStream) - Method in class org.sbml.libsbml.SBMLDocument
Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document.
printErrors(OStream) - Method in class org.sbml.libsbml.XMLErrorLog
Prints all the errors or warnings stored in this error log.
printErrors(OStream, long) - Method in class org.sbml.libsbml.SBMLDocument
Prints all the errors or warnings with the given severity encountered trying to parse, check, or translate this SBML document.
printErrors(OStream, long) - Method in class org.sbml.libsbml.XMLErrorLog
Prints the errors or warnings with given severity stored in this error log.
printUnits(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Expresses the given definition in a plain-text form.
printUnits(UnitDefinition, boolean) - Static method in class org.sbml.libsbml.UnitDefinition
Expresses the given definition in a plain-text form.
Priority - Class in org.sbml.libsbml
The priority of execution of an SBML event.
Priority(long, long) - Constructor for class org.sbml.libsbml.Priority
Creates a new Priority object using the given SBML level and version values.
Priority(Priority) - Constructor for class org.sbml.libsbml.Priority
Copy constructor; creates a copy of this Priority.
Priority(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Priority
Creates a new Priority object using the given SBMLNamespaces object sbmlns.
PriorityLostFromL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
PriorityUnitsNotDimensionless - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

Q

QualAttributeRequiredMissing - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualAttributeRequiredMustBeBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualCompartmentMustReferExisting - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualConstantMustBeBool - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualConstantQSCannotBeOutput - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualDefaultTermAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualDefaultTermAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualDefaultTermAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualDefaultTermResultMustBeInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualDefaultTermResultMustBeNonNeg - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualDuplicateComponentId - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualElementNotInNs - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualEmptyLONotAllowed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualExtension - Class in org.sbml.libsbml
qual Base extension class for the package.
QualExtension() - Constructor for class org.sbml.libsbml.QualExtension
Creates a new QualExtension instance.
QualExtension(QualExtension) - Constructor for class org.sbml.libsbml.QualExtension
Copy constructor.
QualFuncTermAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualFuncTermAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualFuncTermAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualFuncTermOnlyOneMath - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualFuncTermResultMustBeInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualFuncTermResultMustBeNonNeg - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualFunctionTermBool - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInitalLevelNotNegative - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInitialLevelCannotExceedMax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInitialLevelMustBeInt - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputConstantCannotBeConsumed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputQSMustBeExistingQS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputSignMustBeSignEnum - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputThreshMustBeInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputThreshMustBeNonNegative - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualInputTransEffectMustBeInputEffect - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualitativeSpecies - Class in org.sbml.libsbml
qual Extension of Species.
QualitativeSpecies() - Constructor for class org.sbml.libsbml.QualitativeSpecies
Creates a new QualitativeSpecies with the given level, version, and package version.
QualitativeSpecies(long) - Constructor for class org.sbml.libsbml.QualitativeSpecies
Creates a new QualitativeSpecies with the given level, version, and package version.
QualitativeSpecies(long, long) - Constructor for class org.sbml.libsbml.QualitativeSpecies
Creates a new QualitativeSpecies with the given level, version, and package version.
QualitativeSpecies(long, long, long) - Constructor for class org.sbml.libsbml.QualitativeSpecies
Creates a new QualitativeSpecies with the given level, version, and package version.
QualitativeSpecies(QualitativeSpecies) - Constructor for class org.sbml.libsbml.QualitativeSpecies
Copy constructor for QualitativeSpecies.
QualitativeSpecies(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.QualitativeSpecies
Creates a new QualitativeSpecies with the given QualPkgNamespaces object.
QualLOQualSpeciesAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualLOQualSpeciesAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualLOTransitiondAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualLOTransitionsAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualMathCSymbolDisallowed - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualMaxLevelMustBeInt - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualMaxLevelNotNegative - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualModelPlugin - Class in org.sbml.libsbml
qual Extension of Model.
QualModelPlugin(String, String, QualPkgNamespaces) - Constructor for class org.sbml.libsbml.QualModelPlugin
Creates a new QualModelPlugin object using the given parameters.
QualModelPlugin(QualModelPlugin) - Constructor for class org.sbml.libsbml.QualModelPlugin
Copy constructor.
QualNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualNSUndeclared - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOneListOfTransOrQS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputConstantMustBeFalse - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputLevelMustBeInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputLevelMustBeNonNegative - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputProductionMustHaveLevel - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputQSMustBeExistingQS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualOutputTransEffectMustBeOutput - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualPkgNamespaces - Class in org.sbml.libsbml
Set of SBML Level + Version + namespace triples.
QualPkgNamespaces() - Constructor for class org.sbml.libsbml.QualPkgNamespaces
 
QualPkgNamespaces(long) - Constructor for class org.sbml.libsbml.QualPkgNamespaces
 
QualPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.QualPkgNamespaces
 
QualPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.QualPkgNamespaces
 
QualPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.QualPkgNamespaces
 
QualPkgNamespaces(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.QualPkgNamespaces
 
QualQSAssignedOnlyOnce - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualQualSpeciesAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualQualSpeciesAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualQualSpeciesAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualRequiredTrueIfTransitions - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionAllowedAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionAllowedCoreAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionAllowedElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionEmptyLOElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOFuncTermAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOFuncTermElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOFuncTermExceedMax - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOFuncTermNegative - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOInputAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOInputElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOOutputAttributes - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionLOOutputElements - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualTransitionNameMustBeString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
QualUnknown - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

R

RadialGradient - Class in org.sbml.libsbml
Representation of a radial gradient object from the SBML render extension.
RadialGradient() - Constructor for class org.sbml.libsbml.RadialGradient
Creates a new RadialGradient object with the given SBML level and SBML version.
RadialGradient(long) - Constructor for class org.sbml.libsbml.RadialGradient
Creates a new RadialGradient object with the given SBML level and SBML version.
RadialGradient(long, long) - Constructor for class org.sbml.libsbml.RadialGradient
Creates a new RadialGradient object with the given SBML level and SBML version.
RadialGradient(long, long, long) - Constructor for class org.sbml.libsbml.RadialGradient
Creates a new RadialGradient object with the given SBML level and SBML version.
RadialGradient(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RadialGradient
Creates a new RadialGradient object with the given SBMLNamespaces.
RadialGradient(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.RadialGradient
Constructor which creates a RadialGradient with no gradient stops.
RadialGradient(XMLNode, long) - Constructor for class org.sbml.libsbml.RadialGradient
Creates a new RadialGradient object from the given XMLNode object.
RateOfSpeciesTargetCompartmentNot - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateOfTargetCannotBeAssigned - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateOfTargetMustBeCi - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRule - Class in org.sbml.libsbml
An SBML rate rule representing dx/dt = f(Y).
RateRule(long, long) - Constructor for class org.sbml.libsbml.RateRule
Creates a new RateRule using the given SBML level and version values.
RateRule(SBMLNamespaces) - Constructor for class org.sbml.libsbml.RateRule
Creates a new RateRule using the given SBMLNamespaces object sbmlns.
RateRuleCompartmentMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRuleForConstantEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRuleParameterMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRuleSpeciesMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RateRuleStoichiometryMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFAboutTagNotMetaid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFAnnotationParser - Class in org.sbml.libsbml
MIRIAM-compliant RDF annotation reader/writer.
RDFAnnotationParser() - Constructor for class org.sbml.libsbml.RDFAnnotationParser
 
RDFEmptyAboutTag - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFMissingAboutTag - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFNotCompleteModelHistory - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RDFNotModelHistory - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Reaction - Class in org.sbml.libsbml
An SBML reaction between species in an SBML model.
Reaction(long, long) - Constructor for class org.sbml.libsbml.Reaction
Creates a new Reaction using the given SBML level and version values.
Reaction(Reaction) - Constructor for class org.sbml.libsbml.Reaction
Copy constructor; creates a copy of this Reaction.
Reaction(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Reaction
Creates a new Reaction using the given SBMLNamespaces object sbmlns.
ReactionGlyph - Class in org.sbml.libsbml
layout A glyph for an SBML reaction.
ReactionGlyph() - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a new ReactionGlyph.
ReactionGlyph(long) - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a new ReactionGlyph.
ReactionGlyph(long, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a new ReactionGlyph.
ReactionGlyph(long, long, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a new ReactionGlyph.
ReactionGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a new ReactionGlyph with the given LayoutPkgNamespaces object.
ReactionGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a ResctionGlyph with the given LayoutPkgNamespaces and id.
ReactionGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a ResctionGlyph with the given LayoutPkgNamespaces, id and set the id of the associated reaction to the second argument.
ReactionGlyph(ReactionGlyph) - Constructor for class org.sbml.libsbml.ReactionGlyph
Copy constructor.
ReactionGlyph(XMLNode) - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a new ReactionGlyph from the given XMLNode
ReactionGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.ReactionGlyph
Creates a new ReactionGlyph from the given XMLNode
readMathMLFromString(String) - Static method in class org.sbml.libsbml.libsbml
Reads the MathML from the given XML string, constructs a corresponding abstract syntax tree, and returns a pointer to the root of the tree.
readMathMLFromStringWithNamespaces(String, XMLNamespaces) - Static method in class org.sbml.libsbml.libsbml
Reads the MathML from the given XML string, constructs a corresponding abstract syntax tree, and returns a pointer to the root of the tree.
readSBML(String) - Static method in class org.sbml.libsbml.libsbml
Reads an SBML document from the given file.
readSBML(String) - Method in class org.sbml.libsbml.SBMLReader
Reads an SBML document from the given file.
readSBMLFromFile(String) - Static method in class org.sbml.libsbml.libsbml
Reads an SBML document from the given file.
readSBMLFromFile(String) - Method in class org.sbml.libsbml.SBMLReader
Reads an SBML document from the given file.
readSBMLFromString(String) - Static method in class org.sbml.libsbml.libsbml
Reads an SBML document from a text string.
readSBMLFromString(String) - Method in class org.sbml.libsbml.SBMLReader
Reads an SBML document from a text string.
Rectangle - Class in org.sbml.libsbml
 
Rectangle() - Constructor for class org.sbml.libsbml.Rectangle
Creates a new Rectangle object with the given SBML level and SBML version.
Rectangle(long) - Constructor for class org.sbml.libsbml.Rectangle
Creates a new Rectangle object with the given SBML level and SBML version.
Rectangle(long, long) - Constructor for class org.sbml.libsbml.Rectangle
Creates a new Rectangle object with the given SBML level and SBML version.
Rectangle(long, long, long) - Constructor for class org.sbml.libsbml.Rectangle
Creates a new Rectangle object with the given SBML level and SBML version.
Rectangle(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.Rectangle
Creates a new Rectangle object with the given SBMLNamespaces.
Rectangle(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.Rectangle
Instantiates a new Rectangle object.
Rectangle(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Rectangle
Instantiates a new Rectangle object.
Rectangle(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Rectangle
Instantiates a new Rectangle object.
Rectangle(XMLNode) - Constructor for class org.sbml.libsbml.Rectangle
Creates a new Rectangle object from the given XMLNode object.
Rectangle(XMLNode, long) - Constructor for class org.sbml.libsbml.Rectangle
Creates a new Rectangle object from the given XMLNode object.
RecursiveCompartmentContainment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RecursiveFunctionDefinition - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
reduceToBinary() - Method in class org.sbml.libsbml.ASTNode
Reduces this ASTNode to a binary tree.
ReferenceGlyph - Class in org.sbml.libsbml
layout Connection between an object and a glyph.
ReferenceGlyph() - Constructor for class org.sbml.libsbml.ReferenceGlyph
Creates a new ReferenceGlyph with the given SBML level, version and package version.
ReferenceGlyph(long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
Creates a new ReferenceGlyph with the given SBML level, version and package version.
ReferenceGlyph(long, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
Creates a new ReferenceGlyph with the given SBML level, version and package version.
ReferenceGlyph(long, long, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
Creates a new ReferenceGlyph with the given SBML level, version and package version.
ReferenceGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.ReferenceGlyph
Constructor.
ReferenceGlyph(LayoutPkgNamespaces, String, String, String, String) - Constructor for class org.sbml.libsbml.ReferenceGlyph
Creates a new ReferenceGlyph.
ReferenceGlyph(ReferenceGlyph) - Constructor for class org.sbml.libsbml.ReferenceGlyph
Copy constructor.
ReferenceGlyph(XMLNode) - Constructor for class org.sbml.libsbml.ReferenceGlyph
Creates a new ReferenceGlyph from the given XMLNode
ReferenceGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.ReferenceGlyph
Creates a new ReferenceGlyph from the given XMLNode
REFLECT - Static variable in class org.sbml.libsbml.GradientBase
 
RelAbsVector - Class in org.sbml.libsbml
This class represents a pair of numerical values where one value represents an absolute value and the other value is a relative value in percent.
RelAbsVector() - Constructor for class org.sbml.libsbml.RelAbsVector
Constructor with two values.
RelAbsVector(double) - Constructor for class org.sbml.libsbml.RelAbsVector
Constructor with two values.
RelAbsVector(double, double) - Constructor for class org.sbml.libsbml.RelAbsVector
Constructor with two values.
RelAbsVector(String) - Constructor for class org.sbml.libsbml.RelAbsVector
Constructor with a value string.
relativeTo(String) - Method in class org.sbml.libsbml.SBMLUri
Constructs a new URI relative to this object and the given URI.
remove(int) - Method in class org.sbml.libsbml.XMLAttributes
Removes the nth attribute from this list of attributes.
remove(int) - Method in class org.sbml.libsbml.XMLNamespaces
Removes an XML Namespace stored in the given position of this list.
remove(long) - Method in class org.sbml.libsbml.ASTNodeList
 
remove(long) - Method in class org.sbml.libsbml.CVTermList
 
remove(long) - Method in class org.sbml.libsbml.DateList
 
remove(long) - Method in class org.sbml.libsbml.ListOf
Removes the nth item from this ListOf list of items and returns it.
remove(long) - Method in class org.sbml.libsbml.ListOfColorDefinitions
Removes the nth item from this ListOfColorDefinitions items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Removes the nth item from this ListOfCompartmentGlyphs items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfCompartments
Removes the nth item from this ListOfCompartments items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Removes the nth item from this ListOfCompartmentTypes items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfConstraints
Removes the nth item from this ListOfConstraints items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfCurveElements
Removes the RenderPoint with the given index and returns a pointer to the removed object.
remove(long) - Method in class org.sbml.libsbml.ListOfDeletions
Removes the nth item from this ListOfDeletions items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfDrawables
Removes the nth item from this ListOfDrawables items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfEventAssignments
Removes the nth item from this ListOfEventAssignments items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfEvents
Removes the nth item from this ListOfEvents items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Removes the nth item from this ListOfExternalModelDefinitions items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfFbcAssociations
Removes the nth FbcAssociation
remove(long) - Method in class org.sbml.libsbml.ListOfFluxBounds
Removes the nth item from this ListOfFluxBounds items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfFluxObjectives
Removes the nth FluxObjective from this ListOfFluxObjectives and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Removes the nth item from this ListOfFunctionDefinitions items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfFunctionTerms
Removes the nth FunctionTerm from this ListOfFunctionTerms and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfGeneAssociations
Removes the nth item from this ListOfGeneAssociations items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfGeneProducts
Removes the nth GeneProduct from this ListOfGeneProducts and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Removes the nth item from this ListOfGlobalRenderInformation items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfGlobalStyles
Removes the nth item from this ListOfGlobalStyles items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Removes the nth item from this ListOfGradientDefinitions items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfGradientStops
Removes the nth item from this ListOfGradientStops items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Removes the nth item from this ListOfGraphicalObjects items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfGroups
Removes the nth Group from this ListOfGroups and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfInitialAssignments
Removes the nth item from this ListOfInitialAssignments items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfInputs
Removes the nth Input from this ListOfInputs and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfLayouts
Removes the nth item from this ListOfLayouts items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfLineEndings
Removes the nth item from this ListOfLineEndings items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfLineSegments
Removes the nth item from this ListOfLineSegments items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfLocalParameters
Removes the nth item from this ListOfLocalParameters, and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Removes the nth item from this ListOfLocalRenderInformation items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfLocalStyles
Removes the nth item from this ListOfLocalStyles items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfMembers
Removes the nth Member from this ListOfMembers and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfModelDefinitions
Removes the nth item from this ListOfModelDefinitions items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfObjectives
Removes the nth Objective from this ListOfObjectives and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfOutputs
Removes the nth Output from this ListOfOutputs and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfParameters
Removes the nth item from this ListOfParameters, and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfPorts
Removes the nth item from this ListOfPorts items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
Removes the nth QualitativeSpecies from this ListOfQualitativeSpecies and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Removes the nth item from this ListOfReactionGlyphs items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfReactions
Removes the nth item from this ListOfReactions items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Removes the nth item from this ListOfReferenceGlyphs items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfReplacedElements
Removes the nth item from this ListOfReplacedElements items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfRules
Removes the nth item from this ListOfRules items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfSpecies
Removes the nth item from this ListOfSpeciess items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Removes the nth item from this ListOfSpeciesGlyphs items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Removes the nth item from this ListOfSpeciesReferenceGlyphs items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Removes the nth item from this ListOfSpeciesReferences items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Removes the nth item from this ListOfSpeciesTypes items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfSubmodels
Removes the nth item from this ListOfSubmodels items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfTextGlyphs
Removes the nth item from this ListOfTextGlyphs items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfTransitions
Removes the nth Transition from this ListOfTransitions and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Removes the nth item from this ListOfUnitDefinitions items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ListOfUnits
Removes the nth item from this ListOfUnits items and returns a pointer to it.
remove(long) - Method in class org.sbml.libsbml.ModelCreatorList
 
remove(long) - Method in class org.sbml.libsbml.SBaseList
 
remove(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Removes an error having errorId from the SBMLError list.
remove(long) - Method in class org.sbml.libsbml.SBMLNamespacesList
 
remove(String) - Method in class org.sbml.libsbml.ListOfColorDefinitions
Removes item in this ListOfColorDefinition items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Removes item in this ListOfCompartmentGlyphs items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfCompartments
Removes item in this ListOfCompartments items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfCompartmentTypes
Removes item in this ListOfCompartmentTypes items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfDeletions
Removes an item from this ListOfDeletions items based on its identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfDrawables
Removes item in this ListOfDrawables items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfEventAssignments
Removes item in this ListOfEventAssignments items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfEvents
Removes item in this ListOfEvents items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfExternalModelDefinitions
Removes the item with given sid from this ListOfModelDefinitions items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfFbcAssociations
Removes the FbcAssociation with the given identifier
remove(String) - Method in class org.sbml.libsbml.ListOfFluxBounds
Removes item in this ListOfFluxBounds items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfFluxObjectives
Removes the FluxObjective from this ListOfFluxObjectives with the given identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfFunctionDefinitions
Removes item in this ListOfFunctionDefinitions items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfFunctionTerms
Removes the FunctionTerm from this ListOfFunctionTerms with the given identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfGeneAssociations
Removes item in this ListOfGeneAssociations items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfGeneProducts
Removes the GeneProduct from this ListOfGeneProducts with the given identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Removes item in this ListOfGlobalRenderInformation items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfGlobalStyles
Removes item in this ListOfGlobalStyles items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Removes item in this ListOfGradientDefinitions items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Removes item in this ListOfGraphicalObjects items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfGroups
Removes the Group from this ListOfGroups based on its identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfInitialAssignments
Removes item in this ListOfInitialAssignments items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfInputs
Removes the Input from this ListOfInputs with the given identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfLayouts
Removes item in this ListOfLayouts items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfLineEndings
Removes item in this ListOfLineEndings items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfLocalParameters
Removes the first LocalParameter object in this ListOfLocalParameters matching the given identifier, and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Removes item in this ListOfLocalRenderInformation items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfLocalStyles
Removes item in this ListOfLocalStyles items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfMembers
Removes the Member from this ListOfMembers based on its identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfModelDefinitions
Removes the item with given identifer from this ListOfModelDefinitions items and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfObjectives
Removes the Objective from this ListOfObjectives with the given identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfOutputs
Removes the Output from this ListOfOutputs with the given identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfParameters
Removes the first Parameter object in this ListOfParameters matching the given identifier, and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfPorts
Removes an item from this ListOfPorts items based on the identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfQualitativeSpecies
Removes the QualitativeSpecies from this ListOfQualitativeSpecies with the given identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Removes item in this ListOfReactionGlyphs items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfReactions
Removes item in this ListOfReactions items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Removes item in this ListOfReferenceGlyphs items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfRules
Removes item in this ListOfRules items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfSpecies
Removes item in this ListOfSpeciess items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Removes item in this ListOfSpeciesGlyphs items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Removes item in this ListOfSpeciesReferenceGlyphs items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesReferences
Removes item in this ListOfSpeciesReferences items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfSpeciesTypes
Removes item in this ListOfSpeciesTypes items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfSubmodels
Removes an item from this ListOfSubmodels items based on its identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfTextGlyphs
Removes item in this ListOfTextGlyphs items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.ListOfTransitions
Removes the Transition from this ListOfTransitions with the given identifier and returns a pointer to it.
remove(String) - Method in class org.sbml.libsbml.ListOfUnitDefinitions
Removes item in this ListOfUnitDefinitions items with the given identifier.
remove(String) - Method in class org.sbml.libsbml.XMLAttributes
Removes a named attribute from this list of attributes.
remove(String) - Method in class org.sbml.libsbml.XMLNamespaces
Removes an XML Namespace with the given prefix.
remove(String, String) - Method in class org.sbml.libsbml.XMLAttributes
Removes a named attribute from this list of attributes.
remove(XMLTriple) - Method in class org.sbml.libsbml.XMLAttributes
Removes a specific attribute from this list of attributes.
removeAdditionalGraphicalObject(long) - Method in class org.sbml.libsbml.Layout
Removes the graphical object with the given index from the layout.
removeAdditionalGraphicalObject(String) - Method in class org.sbml.libsbml.Layout
Remove the graphical object with the given id.
removeAll(long) - Method in class org.sbml.libsbml.SBMLErrorLog
Removes all errors having errorId from the SBMLError list.
removeAssociation(int) - Method in class org.sbml.libsbml.Association
Removes the child Associations with the given index from this Association object.
removeAssociation(long) - Method in class org.sbml.libsbml.FbcAnd
Removes the nth FbcAssociation from the ListOfFbcAssociations within this FbcAnd and returns a pointer to it.
removeAssociation(long) - Method in class org.sbml.libsbml.FbcOr
Removes the nth Association from the ListOfFbcAssociations within this FbcOr and returns a pointer to it.
removeAssociation(String) - Method in class org.sbml.libsbml.FbcAnd
Removes the FbcAssociation with the given identifier from the ListOfFbcAssociations within this FbcAnd and returns a pointer to it.
removeAssociation(String) - Method in class org.sbml.libsbml.FbcOr
Removes the Association with the given identifier from the ListOfFbcAssociations within this FbcOr and returns a pointer to it.
removeAttr(int) - Method in class org.sbml.libsbml.XMLToken
Removes the nth attribute from the XML element represented by this token.
removeAttr(String) - Method in class org.sbml.libsbml.XMLToken
Removes an attribute from the XML element represented by this token.
removeAttr(String, String) - Method in class org.sbml.libsbml.XMLToken
Removes an attribute from the XML element represented by this token.
removeAttr(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Removes an attribute from the XML element represented by this token.
removeChild(long) - Method in class org.sbml.libsbml.ASTNode
Removes the nth child of this ASTNode object.
removeChild(long) - Method in class org.sbml.libsbml.XMLNode
Removes the nth child of this XMLNode and returns the removed node.
removeChildren() - Method in class org.sbml.libsbml.XMLNode
Removes all children from this node.
removeColorDefinition(long) - Method in class org.sbml.libsbml.RenderInformationBase
Removes the color definition with the given index from the list of color definitions.
removeCompartment(long) - Method in class org.sbml.libsbml.Model
Removes the nth Compartment object from this Model object and returns a pointer to it.
removeCompartment(String) - Method in class org.sbml.libsbml.Model
Removes the Compartment object with the given identifier from this Model object and returns a pointer to it.
removeCompartmentGlyph(long) - Method in class org.sbml.libsbml.Layout
Removes the compartment glyph with the given index from the layout.
removeCompartmentGlyph(String) - Method in class org.sbml.libsbml.Layout
Remove the compartment glyph with the given id.
removeCompartmentType(long) - Method in class org.sbml.libsbml.Model
Removes the nth CompartmentType object from this Model object and returns a pointer to it.
removeCompartmentType(String) - Method in class org.sbml.libsbml.Model
Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it.
removeConstraint(long) - Method in class org.sbml.libsbml.Model
Removes the nth Constraint object from this Model object and returns a pointer to it.
removeDash(long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Removes the dash at the given index
removeDeletion(long) - Method in class org.sbml.libsbml.Submodel
Removes the deletion with the given index from the Submodel.
removeDeletion(String) - Method in class org.sbml.libsbml.Submodel
Removes the deletion with the given identifier from the Submodel.
removeElement(long) - Method in class org.sbml.libsbml.RenderCurve
Removes the curve segment with the given index.
removeEvent(long) - Method in class org.sbml.libsbml.Model
Removes the nth Event object from this Model object and returns a pointer to it.
removeEvent(String) - Method in class org.sbml.libsbml.Model
Removes the Event object with the given identifier from this Model object and returns a pointer to it.
removeEventAssignment(long) - Method in class org.sbml.libsbml.Event
Removes the nth EventAssignment object from this Event object and returns a pointer to it.
removeEventAssignment(String) - Method in class org.sbml.libsbml.Event
Removes the EventAssignment object with the given 'variable' attribute from this Event object and returns a pointer to it.
removeExternalModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Removes the ExternalModelDefinition with the given index.
removeExternalModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Removes the ExternalModelDefinition with the given id.
removeFluxBound(long) - Method in class org.sbml.libsbml.FbcModelPlugin
Removes the nth FluxBound object from this plugin object and returns a pointer to it.
removeFluxBound(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it.
removeFluxObjective(long) - Method in class org.sbml.libsbml.Objective
Removes the nth FluxObjective from the ListOfFluxObjectives.
removeFluxObjective(String) - Method in class org.sbml.libsbml.Objective
Removes the FluxObjective with the given identifier from the ListOfFluxObjectives.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.Delay
Finds this Delay's Event parent and calls unsetDelay() on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.KineticLaw
Finds this KineticLaw's Reaction parent and calls unsetKineticLaw() on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.ListOf
Removes all items in this ListOf object and deletes its properties too.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.Model
Remove this Model from its parent SBMLDocument object.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.ModelDefinition
Finds this Model's parent ListOfModelDefinitions and removes itself from it and deletes itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.Priority
Finds this Priority's Event parent and calls unsetPriority() on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.ReplacedBy
Finds this ReplacedBy's SBase parent, gets the “comp” plugin from it, and tells that to remove this.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.SBase
Removes this object from its parent.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.SBaseRef
Finds this SBaseRef's parent, which can either be a List or can be another SBaseRef, and tells it to remove this.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.StoichiometryMath
Finds this StoichiometryMath's SpeciesReference parent and calls unsetStoichiometryMath() on it, indirectly deleting itself.
removeFromParentAndDelete() - Method in class org.sbml.libsbml.Trigger
Finds this Trigger's Event parent and calls unsetTrigger() on it, indirectly deleting itself.
removeFunctionDefinition(long) - Method in class org.sbml.libsbml.Model
Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.
removeFunctionDefinition(String) - Method in class org.sbml.libsbml.Model
Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it.
removeFunctionTerm(long) - Method in class org.sbml.libsbml.Transition
Removes the nth FunctionTerm from the ListOfFunctionTerms within this Transition.
removeFunctionTerm(String) - Method in class org.sbml.libsbml.Transition
Removes the FunctionTerm with the given identifier from the ListOfFunctionTerms within this Transition and returns a pointer to it.
removeGeneAssociation(long) - Method in class org.sbml.libsbml.FbcModelPlugin
Removes the nth GeneAssociation annotation object from this plugin object and returns a pointer to it.
removeGeneAssociation(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Removes the GeneAssociation annotation object with the given sid attribute from this plugin object and returns a pointer to it.
removeGeneProduct(long) - Method in class org.sbml.libsbml.FbcModelPlugin
Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin.
removeGeneProduct(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin and returns a pointer to it.
removeGlobalRenderInformation(long) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Removed the render information with the given index from the list.
removeGlobalRenderInformation(String) - Method in class org.sbml.libsbml.RenderListOfLayoutsPlugin
Removed the render information with the given id from the list.
removeGradientDefinition(long) - Method in class org.sbml.libsbml.RenderInformationBase
Removes the gradient definition with the given index.
removeGroup(long) - Method in class org.sbml.libsbml.GroupsModelPlugin
Removes the nth Group from this GroupsModelPlugin and returns a pointer to it.
removeGroup(String) - Method in class org.sbml.libsbml.GroupsModelPlugin
Removes the Group from this GroupsModelPlugin based on its identifier and returns a pointer to it.
removeId(String) - Method in class org.sbml.libsbml.LocalStyle
Removes an id from the set.
removeInitialAssignment(long) - Method in class org.sbml.libsbml.Model
Removes the nth InitialAssignment object from this Model object and returns a pointer to it.
removeInitialAssignment(String) - Method in class org.sbml.libsbml.Model
Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it.
removeInput(long) - Method in class org.sbml.libsbml.Transition
Removes the nth Input from the ListOfInputs within this Transition.
removeInput(String) - Method in class org.sbml.libsbml.Transition
Removes the Input with the given identifier from the ListOfInputs within this Transition and returns a pointer to it.
removeL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.LayoutExtension
Removes the L2 Namespace from a document.
removeL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.RenderExtension
Removes the L2 Namespace from a document.
removeL2Namespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Removes SBML Level 2 namespaces from the namespace list.
removeLayout(long) - Method in class org.sbml.libsbml.LayoutModelPlugin
Removes the nth Layout object from this Model object and returns a pointer to it.
removeLineEnding(long) - Method in class org.sbml.libsbml.RenderInformationBase
Removes the line ending with the given index.
removeLocalParameter(long) - Method in class org.sbml.libsbml.KineticLaw
Removes the nth LocalParameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it.
removeLocalParameter(String) - Method in class org.sbml.libsbml.KineticLaw
Removes a LocalParameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it.
removeLocalRenderInformation(long) - Method in class org.sbml.libsbml.RenderLayoutPlugin
Removed the render information with the given index from the list.
removeLocalRenderInformation(String) - Method in class org.sbml.libsbml.RenderLayoutPlugin
Removed the render information with the given id from the list.
removeMember(long) - Method in class org.sbml.libsbml.Group
Removes the nth Member from this Group and returns a pointer to it.
removeMember(String) - Method in class org.sbml.libsbml.Group
Removes the Member from this Group based on its identifier and returns a pointer to it.
removeModelDefinition(long) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin.
removeModelDefinition(String) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Removes the ModelDefinition with the given id from the CompSBMLDocumentPlugin.
removeModifier(long) - Method in class org.sbml.libsbml.Reaction
Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns a pointer to it.
removeModifier(String) - Method in class org.sbml.libsbml.Reaction
Removes the modifier species (ModifierSpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
removeNamespace(int) - Method in class org.sbml.libsbml.XMLToken
Removes the nth XML namespace declaration.
removeNamespace(String) - Method in class org.sbml.libsbml.SBMLNamespaces
Removes an XML namespace from the set of namespaces within this SBMLNamespaces object.
removeNamespace(String) - Method in class org.sbml.libsbml.XMLToken
Removes an XML namespace declaration having a given prefix.
removeNestedCVTerm(long) - Method in class org.sbml.libsbml.CVTerm
Removes the nth CVTerm in the list of CVTerms of this CVTerm object and returns a pointer to it.
removeObjective(long) - Method in class org.sbml.libsbml.FbcModelPlugin
Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin.
removeObjective(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin and returns a pointer to it.
removeOption(String) - Method in class org.sbml.libsbml.ConversionProperties
Removes the option with the given key from this properties object.
removeOutput(long) - Method in class org.sbml.libsbml.Transition
Removes the nth Output from the ListOfOutputs within this Transition.
removeOutput(String) - Method in class org.sbml.libsbml.Transition
Removes the Output with the given identifier from the ListOfOutputs within this Transition and returns a pointer to it.
removePackageNamespace(long, long, String, long) - Method in class org.sbml.libsbml.SBMLNamespaces
Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object.
removeParameter(long) - Method in class org.sbml.libsbml.KineticLaw
Removes the nth Parameter object in the list of parameters in this KineticLaw instance and returns a pointer to it.
removeParameter(long) - Method in class org.sbml.libsbml.Model
Removes the nth Parameter object from this Model object and returns a pointer to it.
removeParameter(String) - Method in class org.sbml.libsbml.KineticLaw
Removes a Parameter object with the given identifier in the list of parameters in this KineticLaw instance and returns a pointer to it.
removeParameter(String) - Method in class org.sbml.libsbml.Model
Removes the Parameter object with the given identifier from this Model object and returns a pointer to it.
removePort(long) - Method in class org.sbml.libsbml.CompModelPlugin
Removes the port with the given index.
removeProduct(long) - Method in class org.sbml.libsbml.Reaction
Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns a pointer to it.
removeProduct(String) - Method in class org.sbml.libsbml.Reaction
Removes the product species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
removeQualitativeSpecies(long) - Method in class org.sbml.libsbml.QualModelPlugin
Removes the nth QualitativeSpecies object from this plugin object and returns a pointer to it.
removeQualitativeSpecies(String) - Method in class org.sbml.libsbml.QualModelPlugin
Removes the QualitativeSpecies object with the given id attribute from this plugin object and returns a pointer to it.
removeReactant(long) - Method in class org.sbml.libsbml.Reaction
Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns a pointer to it.
removeReactant(String) - Method in class org.sbml.libsbml.Reaction
Removes the reactant species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
removeReaction(long) - Method in class org.sbml.libsbml.Model
Removes the nth Reaction object from this Model object and returns a pointer to it.
removeReaction(String) - Method in class org.sbml.libsbml.Model
Removes the Reaction object with the given identifier from this Model object and returns a pointer to it.
removeReactionGlyph(long) - Method in class org.sbml.libsbml.Layout
Removes the reaction glyph with the given index from the layout.
removeReactionGlyph(String) - Method in class org.sbml.libsbml.Layout
Remove the reaction glyph with the given id.
removeReferenceGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
Remove the reference glyph with the given index.
removeReferenceGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
Remove the reference glyph with the given id.
removeReplacedElement(long) - Method in class org.sbml.libsbml.CompSBasePlugin
Removes the ReplacedElement with the given index.
removeResolver(int) - Method in class org.sbml.libsbml.SBMLResolverRegistry
Removes the resolver with the given index.
removeResource(String) - Method in class org.sbml.libsbml.CVTerm
Removes a resource URI from the set of resources stored in this CVTerm object.
removeRole(String) - Method in class org.sbml.libsbml.Style
Removes the given role from the role list.
removeRule(long) - Method in class org.sbml.libsbml.Model
Removes the nth Rule object from this Model object and returns a pointer to it.
removeRule(String) - Method in class org.sbml.libsbml.Model
Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it.
removeRuleByVariable(String) - Method in class org.sbml.libsbml.Model
Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it.
removeScale(Unit) - Static method in class org.sbml.libsbml.Unit
Manipulates the attributes of the Unit to express the unit with the value of the scale attribute reduced to zero.
removeSpecies(long) - Method in class org.sbml.libsbml.Model
Removes the nth Species object from this Model object and returns a pointer to it.
removeSpecies(String) - Method in class org.sbml.libsbml.Model
Removes the Species object with the given identifier from this Model object and returns a pointer to it.
removeSpeciesGlyph(long) - Method in class org.sbml.libsbml.Layout
Removes the species glyph with the given index from the layout.
removeSpeciesGlyph(String) - Method in class org.sbml.libsbml.Layout
Remove the species glyph with the given id.
removeSpeciesReferenceGlyph(long) - Method in class org.sbml.libsbml.ReactionGlyph
Remove the species reference glyph with the given index.
removeSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.Layout
Remove the species reference glyph with the given id.
removeSpeciesReferenceGlyph(String) - Method in class org.sbml.libsbml.ReactionGlyph
Remove the species reference glyph with the given id.
removeSpeciesType(long) - Method in class org.sbml.libsbml.Model
Removes the nth SpeciesType object from this Model object and returns a pointer to it.
removeSpeciesType(String) - Method in class org.sbml.libsbml.Model
Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it.
removeSubGlyph(long) - Method in class org.sbml.libsbml.GeneralGlyph
Remove the subglyph with the given index.
removeSubGlyph(String) - Method in class org.sbml.libsbml.GeneralGlyph
Remove the subglyph with the given id.
removeSubmodel(long) - Method in class org.sbml.libsbml.CompModelPlugin
Removes the submodel with the given index.
removeTextGlyph(long) - Method in class org.sbml.libsbml.Layout
Removes the text glyph with the given index from the layout.
removeTextGlyph(String) - Method in class org.sbml.libsbml.Layout
Remove the text glyph with the given id.
removeTopLevelAnnotationElement(String) - Method in class org.sbml.libsbml.SBase
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
removeTopLevelAnnotationElement(String, String) - Method in class org.sbml.libsbml.SBase
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
removeTopLevelAnnotationElement(String, String, boolean) - Method in class org.sbml.libsbml.SBase
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
removeTransition(long) - Method in class org.sbml.libsbml.QualModelPlugin
Removes the nth Transition object from this plugin object and returns a pointer to it.
removeTransition(String) - Method in class org.sbml.libsbml.QualModelPlugin
Removes the Transition object with the given id attribute from this plugin object and returns a pointer to it.
removeType(String) - Method in class org.sbml.libsbml.Style
Removes a type string from the type list.
removeUnit(long) - Method in class org.sbml.libsbml.UnitDefinition
Removes the nth Unit object from this UnitDefinition object and returns a pointer to it.
removeUnitDefinition(long) - Method in class org.sbml.libsbml.Model
Removes the nth UnitDefinition object from this Model object and returns a pointer to it.
removeUnitDefinition(String) - Method in class org.sbml.libsbml.Model
Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it.
renameIDs(SBaseList, IdentifierTransformer) - Method in class org.sbml.libsbml.Model
 
renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.GraphicalObject
Renames all the MetaIdRef attributes on this element.
renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.Port
Replaces all uses of a given meta identifier attribute value with another value.
renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
Replaces all uses of a given meta identifier attribute value with another value.
renameMetaIdRefs(String, String) - Method in class org.sbml.libsbml.SBasePlugin
Replaces all uses of a given meta identifier attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.AssignmentRule
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ASTNode
Renames all the SIdRef attributes on this node and its child nodes.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Compartment
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.CompartmentGlyph
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Constraint
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.DefaultValues
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Delay
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.EventAssignment
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.FbcReactionPlugin
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.FluxBound
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.FluxObjective
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.FunctionTerm
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.GeneProduct
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.GeneProductRef
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.GeneralGlyph
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.InitialAssignment
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Input
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.KineticLaw
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ListOfObjectives
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Member
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Model
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Output
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Port
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Priority
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.QualitativeSpecies
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.RateRule
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Reaction
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ReactionGlyph
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ReferenceGlyph
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.RenderCurve
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.ReplacedElement
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Replacing
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Rule
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SBasePlugin
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SBaseRef
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Species
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesGlyph
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.StoichiometryMath
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Submodel
Renames the conversion factor attributes on this element if oldid matches.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.TextGlyph
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(String, String) - Method in class org.sbml.libsbml.Trigger
Replaces all uses of a given SIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.ASTNode
Renames all the UnitSIdRef attributes on this node and its child nodes.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Compartment
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Constraint
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Delay
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.EventAssignment
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.FunctionDefinition
Renames all the UnitSIdRef attributes on this element.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.InitialAssignment
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.KineticLaw
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Model
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Parameter
Renames all the UnitSIdRef attributes on this element.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Port
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Priority
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Rule
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.SBase
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.SBasePlugin
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Species
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.StoichiometryMath
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(String, String) - Method in class org.sbml.libsbml.Trigger
Replaces all uses of a given UnitSIdRef type attribute value with another value.
RenderCubicBezier - Class in org.sbml.libsbml
CubicBezier representation for RenderCurve objects and Polygon objects.
RenderCubicBezier() - Constructor for class org.sbml.libsbml.RenderCubicBezier
Creates a new RenderCubicBezier object with the given SBML level and SBML version.
RenderCubicBezier(long) - Constructor for class org.sbml.libsbml.RenderCubicBezier
Creates a new RenderCubicBezier object with the given SBML level and SBML version.
RenderCubicBezier(long, long) - Constructor for class org.sbml.libsbml.RenderCubicBezier
Creates a new RenderCubicBezier object with the given SBML level and SBML version.
RenderCubicBezier(long, long, long) - Constructor for class org.sbml.libsbml.RenderCubicBezier
Creates a new RenderCubicBezier object with the given SBML level and SBML version.
RenderCubicBezier(RenderCubicBezier) - Constructor for class org.sbml.libsbml.RenderCubicBezier
Copy constructor for RenderCubicBezier objects.
RenderCubicBezier(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderCubicBezier
Creates a new RenderCubicBezier object with the given SBMLNamespaces.
RenderCubicBezier(RenderPkgNamespaces, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.RenderCubicBezier
Creates a CubicBezier with the given points.
RenderCubicBezier(XMLNode) - Constructor for class org.sbml.libsbml.RenderCubicBezier
Creates a new RenderCubicBezier object from the given XMLNode object.
RenderCubicBezier(XMLNode, long) - Constructor for class org.sbml.libsbml.RenderCubicBezier
Creates a new RenderCubicBezier object from the given XMLNode object.
RenderCurve - Class in org.sbml.libsbml
implementation of the Curve concept from the SBML render extension
RenderCurve() - Constructor for class org.sbml.libsbml.RenderCurve
Creates a new RenderCurve object with the given SBML level and SBML version.
RenderCurve(long) - Constructor for class org.sbml.libsbml.RenderCurve
Creates a new RenderCurve object with the given SBML level and SBML version.
RenderCurve(long, long) - Constructor for class org.sbml.libsbml.RenderCurve
Creates a new RenderCurve object with the given SBML level and SBML version.
RenderCurve(long, long, long) - Constructor for class org.sbml.libsbml.RenderCurve
Creates a new RenderCurve object with the given SBML level and SBML version.
RenderCurve(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderCurve
Creates a new RenderCurve object with the given SBMLNamespaces.
RenderCurve(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.RenderCurve
Instantiates an empty curve object with the given id.
RenderCurve(XMLNode) - Constructor for class org.sbml.libsbml.RenderCurve
Creates a new RenderCurve object from the given XMLNode object.
RenderCurve(XMLNode, long) - Constructor for class org.sbml.libsbml.RenderCurve
Creates a new RenderCurve object from the given XMLNode object.
RenderExtension - Class in org.sbml.libsbml
 
RenderExtension() - Constructor for class org.sbml.libsbml.RenderExtension
Constructor
RenderExtension(RenderExtension) - Constructor for class org.sbml.libsbml.RenderExtension
Copy constructor.
RenderGraphicalObjectPlugin - Class in org.sbml.libsbml
 
RenderGraphicalObjectPlugin(String, String, RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderGraphicalObjectPlugin
Constructor
RenderGraphicalObjectPlugin(RenderGraphicalObjectPlugin) - Constructor for class org.sbml.libsbml.RenderGraphicalObjectPlugin
Copy constructor.
RenderGroup - Class in org.sbml.libsbml
The RenderGroup concept from the SBML render extension is used to group graphical primitives together to create composite representations from simple primitives.
RenderGroup() - Constructor for class org.sbml.libsbml.RenderGroup
Creates a new RenderGroup object with the given SBML level and SBML version.
RenderGroup(long) - Constructor for class org.sbml.libsbml.RenderGroup
Creates a new RenderGroup object with the given SBML level and SBML version.
RenderGroup(long, long) - Constructor for class org.sbml.libsbml.RenderGroup
Creates a new RenderGroup object with the given SBML level and SBML version.
RenderGroup(long, long, long) - Constructor for class org.sbml.libsbml.RenderGroup
Creates a new RenderGroup object with the given SBML level and SBML version.
RenderGroup(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderGroup
Creates a new RenderGroup object with the given SBMLNamespaces.
RenderGroup(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.RenderGroup
Instantiates a new RenderGroup object.
RenderGroup(XMLNode) - Constructor for class org.sbml.libsbml.RenderGroup
Creates a new RenderGroup object from the given XMLNode object.
RenderGroup(XMLNode, long) - Constructor for class org.sbml.libsbml.RenderGroup
Creates a new RenderGroup object from the given XMLNode object.
RenderInformationBase - Class in org.sbml.libsbml
abstract base class for local and global render information.
RenderLayoutPlugin - Class in org.sbml.libsbml
 
RenderLayoutPlugin(String, String, RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderLayoutPlugin
Constructor
RenderLayoutPlugin(RenderLayoutPlugin) - Constructor for class org.sbml.libsbml.RenderLayoutPlugin
Copy constructor.
RenderListOfLayoutsPlugin - Class in org.sbml.libsbml
 
RenderListOfLayoutsPlugin(String, String, RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderListOfLayoutsPlugin
Constructor
RenderListOfLayoutsPlugin(RenderListOfLayoutsPlugin) - Constructor for class org.sbml.libsbml.RenderListOfLayoutsPlugin
Copy constructor.
RenderPkgNamespaces - Class in org.sbml.libsbml
Set of SBML Level + Version + namespace triples.
RenderPkgNamespaces() - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
 
RenderPkgNamespaces(long) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
 
RenderPkgNamespaces(long, long) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
 
RenderPkgNamespaces(long, long, long) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
 
RenderPkgNamespaces(long, long, long, String) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
 
RenderPkgNamespaces(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderPkgNamespaces
 
RenderPoint - Class in org.sbml.libsbml
Represents a point where the coordinates can be made up of absolute as well as relative values ( Render objects are often specified relative to the current viewport, i.e.
RenderPoint() - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new RenderPoint object with the given SBML level and SBML version.
RenderPoint(long) - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new RenderPoint object with the given SBML level and SBML version.
RenderPoint(long, long) - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new RenderPoint object with the given SBML level and SBML version.
RenderPoint(long, long, long) - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new RenderPoint object with the given SBML level and SBML version.
RenderPoint(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new RenderPoint object with the given SBMLNamespaces.
RenderPoint(RenderPkgNamespaces, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new point with the given ccordinates.
RenderPoint(RenderPkgNamespaces, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new point with the given ccordinates.
RenderPoint(RenderPoint) - Constructor for class org.sbml.libsbml.RenderPoint
Copy constructor for RenderPoint objects.
RenderPoint(XMLNode) - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new RenderPoint object from the given XMLNode object.
RenderPoint(XMLNode, long) - Constructor for class org.sbml.libsbml.RenderPoint
Creates a new RenderPoint object from the given XMLNode object.
reorder(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Alphabetically orders the Unit objects within the ListOfUnits of a UnitDefinition.
REPEAT - Static variable in class org.sbml.libsbml.GradientBase
 
RepeatedRule10304 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RepeatedRule20611 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
replaceArgument(String, ASTNode) - Method in class org.sbml.libsbml.ASTNode
Replaces occurrences of a given name with a given ASTNode.
replaceChild(long, ASTNode) - Method in class org.sbml.libsbml.ASTNode
Replaces the nth child of this ASTNode with the given ASTNode.
replaceChild(long, ASTNode, boolean) - Method in class org.sbml.libsbml.ASTNode
Replaces the nth child of this ASTNode with the given ASTNode.
ReplacedBy - Class in org.sbml.libsbml
comp Indicates an object replaced by another.
ReplacedBy() - Constructor for class org.sbml.libsbml.ReplacedBy
Creates a new ReplacedBy with the given level, version, and package version.
ReplacedBy(long) - Constructor for class org.sbml.libsbml.ReplacedBy
Creates a new ReplacedBy with the given level, version, and package version.
ReplacedBy(long, long) - Constructor for class org.sbml.libsbml.ReplacedBy
Creates a new ReplacedBy with the given level, version, and package version.
ReplacedBy(long, long, long) - Constructor for class org.sbml.libsbml.ReplacedBy
Creates a new ReplacedBy with the given level, version, and package version.
ReplacedBy(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ReplacedBy
Creates a new ReplacedBy with the given CompPkgNamespaces object.
ReplacedBy(ReplacedBy) - Constructor for class org.sbml.libsbml.ReplacedBy
Copy constructor.
ReplacedElement - Class in org.sbml.libsbml
comp Indicates an object replaces another.
ReplacedElement() - Constructor for class org.sbml.libsbml.ReplacedElement
Creates a new ReplacedElement with the given level, version, and package version.
ReplacedElement(long) - Constructor for class org.sbml.libsbml.ReplacedElement
Creates a new ReplacedElement with the given level, version, and package version.
ReplacedElement(long, long) - Constructor for class org.sbml.libsbml.ReplacedElement
Creates a new ReplacedElement with the given level, version, and package version.
ReplacedElement(long, long, long) - Constructor for class org.sbml.libsbml.ReplacedElement
Creates a new ReplacedElement with the given level, version, and package version.
ReplacedElement(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.ReplacedElement
Creates a new ReplacedElement with the given CompPkgNamespaces object.
ReplacedElement(ReplacedElement) - Constructor for class org.sbml.libsbml.ReplacedElement
Copy constructor.
replaceElement(SBase, SBase) - Method in class org.sbml.libsbml.Submodel
Delete the element in question from the stored instantiated Model, and replace all references to it with references to the replacement object.
replaceTopLevelAnnotationElement(String) - Method in class org.sbml.libsbml.SBase
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
replaceTopLevelAnnotationElement(XMLNode) - Method in class org.sbml.libsbml.SBase
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
Replacing - Class in org.sbml.libsbml
comp Convenience class.
representsValidDate() - Method in class org.sbml.libsbml.Date
Returns true or false depending on whether this date object represents a valid date and time value.
RequiredPackagePresent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
resetElementNamespace(String) - Method in class org.sbml.libsbml.ListOfLayouts
 
resolve(String) - Method in class org.sbml.libsbml.SBMLFileResolver
Resolves the document for the given URI.
resolve(String) - Method in class org.sbml.libsbml.SBMLResolver
Resolves the document for the given URI.
resolve(String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
Resolves the document for the given URI.
resolve(String, String) - Method in class org.sbml.libsbml.SBMLFileResolver
Resolves the document for the given URI.
resolve(String, String) - Method in class org.sbml.libsbml.SBMLResolver
Resolves the document for the given URI.
resolve(String, String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
Resolves the document for the given URI.
resolveUri(String) - Method in class org.sbml.libsbml.SBMLFileResolver
Resolves the full URI for a given URI without actually reading the document.
resolveUri(String) - Method in class org.sbml.libsbml.SBMLResolver
Resolves the full URI for the given URI without actually reading the document.
resolveUri(String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
Resolves the full URI for the given URI without actually reading the document.
resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLFileResolver
Resolves the full URI for a given URI without actually reading the document.
resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLResolver
Resolves the full URI for the given URI without actually reading the document.
resolveUri(String, String) - Method in class org.sbml.libsbml.SBMLResolverRegistry
Resolves the full URI for the given URI without actually reading the document.
returnsBoolean() - Method in class org.sbml.libsbml.ASTNode
Returns true if this node returns a Boolean value.
returnsBoolean(Model) - Method in class org.sbml.libsbml.ASTNode
Returns true if this node returns a Boolean value.
Rule - Class in org.sbml.libsbml
Parent class for SBML rules in libSBML.
Rule(Rule) - Constructor for class org.sbml.libsbml.Rule
Copy constructor; creates a copy of this Rule.
RULE_TYPE_INVALID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RULE_TYPE_RATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RULE_TYPE_SCALAR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
RuleCannotRef0DComp - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

S

saveReferencedElement() - Method in class org.sbml.libsbml.Deletion
Finds and stores the referenced object.
saveReferencedElement() - Method in class org.sbml.libsbml.Port
Finds and stores the referenced object by finding its Model parent, calling 'getReferencedElementFrom()' on that model, and storing the result.
saveReferencedElement() - Method in class org.sbml.libsbml.Replacing
Finds and stores the referenced object.
saveReferencedElement() - Method in class org.sbml.libsbml.SBaseRef
Finds and stores the referenced object by finding the Model it needs to point to, calling 'saveReferencedElement' on its parent (which will also be a SBaseRef or one of its subclasses), and the storing the result.
SBase - Class in org.sbml.libsbml
SBML's SBase class, base class of most SBML objects.
SBaseList - Class in org.sbml.libsbml
 
SBaseList() - Constructor for class org.sbml.libsbml.SBaseList
 
SBasePlugin - Class in org.sbml.libsbml
Base class for extending SBML objects in packages.
SBaseRef - Class in org.sbml.libsbml
comp Base class for references to objects.
SBaseRef() - Constructor for class org.sbml.libsbml.SBaseRef
Creates a new SBaseRef with the given level, version, and package version.
SBaseRef(long) - Constructor for class org.sbml.libsbml.SBaseRef
Creates a new SBaseRef with the given level, version, and package version.
SBaseRef(long, long) - Constructor for class org.sbml.libsbml.SBaseRef
Creates a new SBaseRef with the given level, version, and package version.
SBaseRef(long, long, long) - Constructor for class org.sbml.libsbml.SBaseRef
Creates a new SBaseRef with the given level, version, and package version.
SBaseRef(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.SBaseRef
Creates a new SBaseRef with the given CompPkgNamespaces object.
SBaseRef(SBaseRef) - Constructor for class org.sbml.libsbml.SBaseRef
Copy constructor.
SBML_ALGEBRAIC_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_ASSIGNMENT_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_DELETION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_EXTERNALMODELDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_MODELDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_PORT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_REPLACEDBY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_REPLACEDELEMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_SBASEREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMP_SUBMODEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMPARTMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMPARTMENT_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_COMPARTMENT_VOLUME_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_CONSTRAINT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_DELAY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_DOCUMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_EVENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_EVENT_ASSIGNMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_AND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_FLUXBOUND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_FLUXOBJECTIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_GENEASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_GENEPRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_GENEPRODUCTASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_GENEPRODUCTREF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_OBJECTIVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_OR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FBC_V1ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_FUNCTION_DEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_GENERIC_SBASE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_GROUPS_GROUP - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_GROUPS_MEMBER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_INITIAL_ASSIGNMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_KINETIC_LAW - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_BOUNDINGBOX - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_COMPARTMENTGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_CUBICBEZIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_CURVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_DIMENSIONS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_GENERALGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_GRAPHICALOBJECT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_LAYOUT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_LINESEGMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_POINT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_REACTIONGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_REFERENCEGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_SPECIESGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_SPECIESREFERENCEGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LAYOUT_TEXTGLYPH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LIST_OF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_LOCAL_PARAMETER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_MODEL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_MODIFIER_SPECIES_REFERENCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_PARAMETER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_PARAMETER_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_PRIORITY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_QUAL_DEFAULT_TERM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_QUAL_FUNCTION_TERM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_QUAL_INPUT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_QUAL_OUTPUT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_QUAL_QUALITATIVE_SPECIES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_QUAL_TRANSITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RATE_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_REACTION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_COLORDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_CUBICBEZIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_CURVE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_DEFAULTS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_ELLIPSE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_GLOBALRENDERINFORMATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_GLOBALSTYLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_GRADIENT_STOP - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_GRADIENTDEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_GROUP - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_IMAGE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_LINEARGRADIENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_LINEENDING - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_LINESEGMENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_LISTOFGLOBALSTYLES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_LISTOFLOCALSTYLES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_LOCALRENDERINFORMATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_LOCALSTYLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_POINT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_POLYGON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_RADIALGRADIENT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_RECTANGLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_RELABSVECTOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_TEXT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RENDER_TRANSFORMATION2D - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_SPECIES - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_SPECIES_CONCENTRATION_RULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_SPECIES_REFERENCE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_SPECIES_TYPE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_STOICHIOMETRY_MATH - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_TRIGGER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_UNIT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_UNIT_DEFINITION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBML_UNKNOWN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLCodesUpperBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLConstructorException - Exception in org.sbml.libsbml
Exceptions thrown by some libSBML constructors.
SBMLConstructorException(String) - Constructor for exception org.sbml.libsbml.SBMLConstructorException
Exception thrown by libSBML object constructors if something prevents the object from being properly created.
SBMLConverter - Class in org.sbml.libsbml
Base class for SBML converters.
SBMLConverter() - Constructor for class org.sbml.libsbml.SBMLConverter
Creates a new SBMLConverter object.
SBMLConverter(String) - Constructor for class org.sbml.libsbml.SBMLConverter
Creates a new SBMLConverter object with a given name.
SBMLConverter(SBMLConverter) - Constructor for class org.sbml.libsbml.SBMLConverter
Copy constructor.
SBMLConverterRegistry - Class in org.sbml.libsbml
Registry of all libSBML SBML converters.
SBMLDocument - Class in org.sbml.libsbml
Overall SBML container object.
SBMLDocument() - Constructor for class org.sbml.libsbml.SBMLDocument
Creates a new SBMLDocument, optionally with given values for the SBML Level and Version.
SBMLDocument(long) - Constructor for class org.sbml.libsbml.SBMLDocument
Creates a new SBMLDocument, optionally with given values for the SBML Level and Version.
SBMLDocument(long, long) - Constructor for class org.sbml.libsbml.SBMLDocument
Creates a new SBMLDocument, optionally with given values for the SBML Level and Version.
SBMLDocument(SBMLDocument) - Constructor for class org.sbml.libsbml.SBMLDocument
Copy constructor; creates a copy of this SBMLDocument.
SBMLDocument(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLDocument
Creates a new SBMLDocument using the given SBMLNamespaces object sbmlns.
SBMLDocumentPlugin - Class in org.sbml.libsbml
Base class for extending SBMLDocument in packages.
SBMLDocumentPlugin(String, String, SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLDocumentPlugin
Creates a new SBMLDocumentPlugin object using the given parameters.
SBMLDocumentPlugin(SBMLDocumentPlugin) - Constructor for class org.sbml.libsbml.SBMLDocumentPlugin
Copy constructor.
SBMLError - Class in org.sbml.libsbml
An error, warning or other diagnostic.
SBMLError() - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long, long, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long, long, long, String) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(long, long, long, String, long, long, long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLError
Creates a new SBMLError to report that something occurred during SBML processing.
SBMLError(SBMLError) - Constructor for class org.sbml.libsbml.SBMLError
Copy constructor; creates a copy of this SBMLError.
SBMLErrorLog - Class in org.sbml.libsbml
Log of diagnostics reported during processing.
SBMLExtension - Class in org.sbml.libsbml
Base class for SBML Level 3 package plug-ins.
SBMLExtensionException - Class in org.sbml.libsbml
Exception used by package extensions
SBMLExtensionException(String) - Constructor for class org.sbml.libsbml.SBMLExtensionException
Creates a new SBMLExtensionException object with a given message.
SBMLExtensionRegistry - Class in org.sbml.libsbml
Registry where package extensions are registered.
SBMLFileResolver - Class in org.sbml.libsbml
comp Resolves documents stored on a file system.
SBMLFileResolver() - Constructor for class org.sbml.libsbml.SBMLFileResolver
Creates a new SBMLFileResolver object.
SBMLFileResolver(SBMLFileResolver) - Constructor for class org.sbml.libsbml.SBMLFileResolver
Copy constructor.
SBMLFunctionDefinitionConverter - Class in org.sbml.libsbml
Converter to expand user-defined functions in-line.
SBMLFunctionDefinitionConverter() - Constructor for class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Creates a new SBMLFunctionDefinitionConverter object.
SBMLFunctionDefinitionConverter(SBMLFunctionDefinitionConverter) - Constructor for class org.sbml.libsbml.SBMLFunctionDefinitionConverter
Copy constructor; creates a copy of an SBMLFunctionDefinitionConverter object.
SBMLIdConverter - Class in org.sbml.libsbml
Converter for replacing object identifiers.
SBMLIdConverter() - Constructor for class org.sbml.libsbml.SBMLIdConverter
Creates a new SBMLIdConverter object.
SBMLIdConverter(SBMLIdConverter) - Constructor for class org.sbml.libsbml.SBMLIdConverter
Copy constructor; creates a copy of an SBMLIdConverter object.
SBMLInferUnitsConverter - Class in org.sbml.libsbml
Converter for inferring and setting parameter units.
SBMLInferUnitsConverter() - Constructor for class org.sbml.libsbml.SBMLInferUnitsConverter
Creates a new SBMLInferUnitsConverter object.
SBMLInferUnitsConverter(SBMLInferUnitsConverter) - Constructor for class org.sbml.libsbml.SBMLInferUnitsConverter
Copy constructor; creates a copy of an SBMLInferUnitsConverter object.
SBMLInitialAssignmentConverter - Class in org.sbml.libsbml
Converter that removes SBML initial assignments.
SBMLInitialAssignmentConverter() - Constructor for class org.sbml.libsbml.SBMLInitialAssignmentConverter
Creates a new SBMLInitialAssignmentConverter object.
SBMLInitialAssignmentConverter(SBMLInitialAssignmentConverter) - Constructor for class org.sbml.libsbml.SBMLInitialAssignmentConverter
Copy constructor; creates a copy of an SBMLInitialAssignmentConverter object.
SBMLLevel1Version1Converter - Class in org.sbml.libsbml
Whole-document SBML Level/Version converter.
SBMLLevel1Version1Converter() - Constructor for class org.sbml.libsbml.SBMLLevel1Version1Converter
Creates a new SBMLLevel1Version1Converter object.
SBMLLevel1Version1Converter(SBMLLevel1Version1Converter) - Constructor for class org.sbml.libsbml.SBMLLevel1Version1Converter
Copy constructor; creates a copy of an SBMLLevel1Version1Converter object.
SBMLLevelVersionConverter - Class in org.sbml.libsbml
Whole-document SBML Level/Version converter.
SBMLLevelVersionConverter() - Constructor for class org.sbml.libsbml.SBMLLevelVersionConverter
Creates a new SBMLLevelVersionConverter object.
SBMLLevelVersionConverter(SBMLLevelVersionConverter) - Constructor for class org.sbml.libsbml.SBMLLevelVersionConverter
Copy constructor; creates a copy of an SBMLLevelVersionConverter object.
SBMLLocalParameterConverter - Class in org.sbml.libsbml
Converter to turn local parameters into global ones.
SBMLLocalParameterConverter() - Constructor for class org.sbml.libsbml.SBMLLocalParameterConverter
Creates a new SBMLLocalParameterConverter object.
SBMLLocalParameterConverter(SBMLLocalParameterConverter) - Constructor for class org.sbml.libsbml.SBMLLocalParameterConverter
Copy constructor; creates a copy of an SBMLLocalParameterConverter object.
SBMLNamespaceInAnnotation - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBMLNamespaces - Class in org.sbml.libsbml
Set of SBML Level + Version + namespace triples.
SBMLNamespaces() - Constructor for class org.sbml.libsbml.SBMLNamespaces
Creates a new SBMLNamespaces object corresponding to the given SBML level and version.
SBMLNamespaces(long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
Creates a new SBMLNamespaces object corresponding to the given SBML level and version.
SBMLNamespaces(long, long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
Creates a new SBMLNamespaces object corresponding to the given SBML level and version.
SBMLNamespaces(long, long, String, long) - Constructor for class org.sbml.libsbml.SBMLNamespaces
(For extensions) Creates a new SBMLNamespaces object corresponding to the combination of (1) the given SBML level and version, and (2) the given package with the package version.
SBMLNamespaces(long, long, String, long, String) - Constructor for class org.sbml.libsbml.SBMLNamespaces
(For extensions) Creates a new SBMLNamespaces object corresponding to the combination of (1) the given SBML level and version, and (2) the given package with the package version.
SBMLNamespaces(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SBMLNamespaces
Copy constructor; creates a copy of a SBMLNamespaces.
SBMLNamespacesList - Class in org.sbml.libsbml
 
SBMLNamespacesList() - Constructor for class org.sbml.libsbml.SBMLNamespacesList
 
SBMLReactionConverter - Class in org.sbml.libsbml
Converter to replace reactions with SBML rate rules.
SBMLReactionConverter() - Constructor for class org.sbml.libsbml.SBMLReactionConverter
Creates a new SBMLReactionConverter object.
SBMLReactionConverter(SBMLReactionConverter) - Constructor for class org.sbml.libsbml.SBMLReactionConverter
Copy constructor; creates a copy of an SBMLReactionConverter object.
SBMLReader - Class in org.sbml.libsbml
File and text-string SBML reader.
SBMLReader() - Constructor for class org.sbml.libsbml.SBMLReader
Creates a new SBMLReader object and returns it.
SBMLResolver - Class in org.sbml.libsbml
comp Base class for SBML resolvers.
SBMLResolver() - Constructor for class org.sbml.libsbml.SBMLResolver
Creates a new SBMLResolver object.
SBMLResolver(SBMLResolver) - Constructor for class org.sbml.libsbml.SBMLResolver
Copy constructor.
SBMLResolverRegistry - Class in org.sbml.libsbml
comp Registry of all SBML resolvers.
SBMLRuleConverter - Class in org.sbml.libsbml
Converter that sorts SBML rules and assignments.
SBMLRuleConverter() - Constructor for class org.sbml.libsbml.SBMLRuleConverter
Creates a new SBMLLevelVersionConverter object.
SBMLRuleConverter(SBMLRuleConverter) - Constructor for class org.sbml.libsbml.SBMLRuleConverter
Copy constructor; creates a copy of an SBMLLevelVersionConverter object.
SBMLStripPackageConverter - Class in org.sbml.libsbml
Converter that removes SBML Level 3 packages.
SBMLStripPackageConverter() - Constructor for class org.sbml.libsbml.SBMLStripPackageConverter
Creates a new SBMLStripPackageConverter object.
SBMLStripPackageConverter(SBMLStripPackageConverter) - Constructor for class org.sbml.libsbml.SBMLStripPackageConverter
Copy constructor; creates a copy of an SBMLStripPackageConverter object.
SBMLTypeCode_toString(int, String) - Static method in class org.sbml.libsbml.libsbml
This method takes an SBML type code and returns a string representing the code.
SBMLUnitsConverter - Class in org.sbml.libsbml
Converts a model's existing units to SI units.
SBMLUnitsConverter() - Constructor for class org.sbml.libsbml.SBMLUnitsConverter
Creates a new SBMLUnitsConverter object.
SBMLUnitsConverter(SBMLUnitsConverter) - Constructor for class org.sbml.libsbml.SBMLUnitsConverter
Copy constructor; creates a copy of an SBMLUnitsConverter object.
SBMLUri - Class in org.sbml.libsbml
comp Utility class for handling URIs.
SBMLUri(String) - Constructor for class org.sbml.libsbml.SBMLUri
Creates a new SBMLUri from the given string URI.
SBMLUri(SBMLUri) - Constructor for class org.sbml.libsbml.SBMLUri
Copy constructor.
SBMLValidator - Class in org.sbml.libsbml
Base class for SBML validators.
SBMLValidator() - Constructor for class org.sbml.libsbml.SBMLValidator
Creates a new SBMLValidator.
SBMLValidator(SBMLValidator) - Constructor for class org.sbml.libsbml.SBMLValidator
Copy constructor; creates a copy of an SBMLValidator object.
SBMLWriter - Class in org.sbml.libsbml
File and text-string SBML writer.
SBMLWriter() - Constructor for class org.sbml.libsbml.SBMLWriter
Creates a new SBMLWriter.
SBO - Class in org.sbml.libsbml
Facilities for using the Systems Biology Ontology.
SBO() - Constructor for class org.sbml.libsbml.SBO
 
SBOCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBOCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBOTermNotUniversalInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBOTermNotValidAttributeBeforeL2V2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SBOTermNotValidAttributeBeforeL2V3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
setAbsoluteValue(double) - Method in class org.sbml.libsbml.RelAbsVector
Sets the absolute coordinate value.
setActiveObjective(String) - Method in class org.sbml.libsbml.ListOfObjectives
Sets the value of the 'activeObjective' attribute of this ListOfObjectives.
setActiveObjectiveId(String) - Method in class org.sbml.libsbml.FbcModelPlugin
Sets the id of the active objective.
setAlpha(short) - Method in class org.sbml.libsbml.ColorDefinition
Sets alpha red color component.
setAnnotation(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.
setAnnotation(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'annotation' subelement of this SBML object.
setAnnotation(String) - Method in class org.sbml.libsbml.SpeciesReference
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.
setAnnotation(XMLNode) - Method in class org.sbml.libsbml.Model
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.
setAnnotation(XMLNode) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'annotation' subelement of this SBML object.
setAnnotation(XMLNode) - Method in class org.sbml.libsbml.SpeciesReference
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.
setAreaUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'areaUnits' attribute of this Model.
setAssociatedSpecies(String) - Method in class org.sbml.libsbml.GeneProduct
Sets the value of the 'associatedSpecies' attribute of this GeneProduct.
setAssociation(String) - Method in class org.sbml.libsbml.GeneProductAssociation
Sets the 'association' element of this GeneProductAssociation.
setAssociation(String, boolean) - Method in class org.sbml.libsbml.GeneProductAssociation
Sets the 'association' element of this GeneProductAssociation.
setAssociation(String, boolean, boolean) - Method in class org.sbml.libsbml.GeneProductAssociation
Sets the 'association' element of this GeneProductAssociation.
setAssociation(Association) - Method in class org.sbml.libsbml.GeneAssociation
Sets the Association object of this GeneAssociation.
setAssociation(FbcAssociation) - Method in class org.sbml.libsbml.GeneProductAssociation
Sets the 'association' element of this GeneProductAssociation.
setAttributes(XMLAttributes) - Method in class org.sbml.libsbml.XMLToken
Sets the attributes on the XML element represented by this token.
setAutoIndent(boolean) - Method in class org.sbml.libsbml.XMLOutputStream
Turns automatic indentation on or off for this XMLOutputStream.
setBackgroundColor(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'backgroundColor' attribute of this DefaultValues.
setBackgroundColor(String) - Method in class org.sbml.libsbml.RenderInformationBase
Sets the background color to either the id of a color in the list of color definitions, or a color value.
setBasePoint1(double, double) - Method in class org.sbml.libsbml.CubicBezier
Initializes first base point with the given coordinates.
setBasePoint1(double, double, double) - Method in class org.sbml.libsbml.CubicBezier
Initializes first base point with the given coordinates.
setBasePoint1(Point) - Method in class org.sbml.libsbml.CubicBezier
Initializes first base point with a copy of the given point.
setBasePoint1(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the first basepoint to the given coordinatees.
setBasePoint1(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the first basepoint to the given coordinatees.
setBasePoint1_X(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the x value of the first base point of the curve (the one closer to the starting point).
setBasePoint1_Y(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the y value of the first base point of the curve (the one closer to the starting point).
setBasePoint1_Z(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the z value of the first base point of the curve (the one closer to the starting point).
setBasePoint2(double, double) - Method in class org.sbml.libsbml.CubicBezier
Initializes second base point with the given coordinates.
setBasePoint2(double, double, double) - Method in class org.sbml.libsbml.CubicBezier
Initializes second base point with the given coordinates.
setBasePoint2(Point) - Method in class org.sbml.libsbml.CubicBezier
Initializes second base point with a copy of the given point.
setBasePoint2(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the second basepoint to the given coordinatees.
setBasePoint2(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the second basepoint to the given coordinatees.
setBasePoint2_X(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the x value of the second base point of the curve (the one further from the starting point).
setBasePoint2_Y(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the y value of the second base point of the curve (the one further from the starting point).
setBasePoint2_Z(RelAbsVector) - Method in class org.sbml.libsbml.RenderCubicBezier
Sets the z value of the second base point of the curve (the one further from the starting point).
setBiologicalQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
Sets the biology qualifier type of this CVTerm object.
setBiologicalQualifierType(String) - Method in class org.sbml.libsbml.CVTerm
Sets the biology qualifier type code of this CVTerm object.
setBlue(short) - Method in class org.sbml.libsbml.ColorDefinition
Sets the blue color component.
setBoolValue(boolean) - Method in class org.sbml.libsbml.ConversionOption
Set the value of this option to a given Boolean value.
setBoolValue(String, boolean) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to a Boolean.
setBoundaryCondition(boolean) - Method in class org.sbml.libsbml.Species
Sets the 'boundaryCondition' attribute of this Species object.
setBoundingBox(BoundingBox) - Method in class org.sbml.libsbml.GraphicalObject
Sets the boundingbox for the GraphicalObject.
setBoundingBox(BoundingBox) - Method in class org.sbml.libsbml.LineEnding
Sets the viewport for the LineEnding.
setBounds(double, double) - Method in class org.sbml.libsbml.Dimensions
Sets all sizes of the Dimensions object to the given values.
setBounds(double, double, double) - Method in class org.sbml.libsbml.Dimensions
Sets all sizes of the Dimensions object to the given values.
setCenter(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
Sets the coordinates for the center point.
setCenter(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
Sets the coordinates for the center point.
setCenter2D(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
Sets the 2D coordinates for the center point.
setCenter3D(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
Sets the 3D coordinates for the center point.
setCharacter(char) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given character.
setCharacters(String) - Method in class org.sbml.libsbml.XMLToken
Sets the characters for this XMLToken
setCharge(int) - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Sets the value of the 'charge' attribute of this FbcSpeciesPlugin.
setCharge(int) - Method in class org.sbml.libsbml.Species
Sets the 'charge' attribute of this Species object.
setChemicalFormula(String) - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Sets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.
setClassName(String) - Method in class org.sbml.libsbml.ASTNode
Sets the MathML attribute class of this ASTNode.
setCoefficient(double) - Method in class org.sbml.libsbml.FluxObjective
Sets the value of the 'coefficient' attribute of this FluxObjective.
setColorValue(String) - Method in class org.sbml.libsbml.ColorDefinition
Sets the color value from a given value string.
setColumn(long) - Method in class org.sbml.libsbml.XMLError
Sets the column number where this error occurred.
setComparisonCaseSensitivity(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the parser's behavior with respect to case sensitivity for recognizing predefined symbols.
setCompartment(String) - Method in class org.sbml.libsbml.QualitativeSpecies
Sets the value of the 'compartment' attribute of this QualitativeSpecies.
setCompartment(String) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'compartment' attribute of this Reaction.
setCompartment(String) - Method in class org.sbml.libsbml.Species
Sets the 'compartment' attribute of this Species object.
setCompartmentId(String) - Method in class org.sbml.libsbml.CompartmentGlyph
Sets the id of the associated compartment.
setCompartmentType(String) - Method in class org.sbml.libsbml.Compartment
Sets the 'compartmentType' attribute of this Compartment object.
setConsistencyChecks(int, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Controls the consistency checks that are performed when SBMLDocument.checkConsistency() is called.
setConsistencyChecksForConversion(int, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Controls the consistency checks that are performed when SBMLDocument.setLevelAndVersion(long, long, boolean) is called.
setConstant(boolean) - Method in class org.sbml.libsbml.Compartment
Sets the value of the 'constant' attribute of this Compartment object.
setConstant(boolean) - Method in class org.sbml.libsbml.Parameter
Sets the 'constant' attribute of this Parameter to the given boolean flag.
setConstant(boolean) - Method in class org.sbml.libsbml.QualitativeSpecies
Sets the value of the 'constant' attribute of this QualitativeSpecies.
setConstant(boolean) - Method in class org.sbml.libsbml.Species
Sets the 'constant' attribute of this Species object.
setConstant(boolean) - Method in class org.sbml.libsbml.SpeciesReference
Sets the 'constant' attribute of this SpeciesReference to the given boolean flag.
setConversionFactor(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'conversionFactor' attribute of this Model.
setConversionFactor(String) - Method in class org.sbml.libsbml.ReplacedElement
Sets the value of the 'conversionFactor' attribute of this ReplacedElement.
setConversionFactor(String) - Method in class org.sbml.libsbml.Species
Sets the value of the 'conversionFactor' attribute of this Species object.
setCoordinate(double) - Method in class org.sbml.libsbml.RelAbsVector
Sets the relative and absolute value.
setCoordinate(double, double) - Method in class org.sbml.libsbml.RelAbsVector
Sets the relative and absolute value.
setCoordinate(String) - Method in class org.sbml.libsbml.RelAbsVector
Sets the coordinates from the given string.
setCoordinates(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Image
Sets the position of the image relative to its viewport.
setCoordinates(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
Sets the coordinates of the RenderPoint to the given values.
setCoordinates(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Text
Sets the position of the text within the viewport.
setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Image
Sets the position of the image relative to its viewport.
setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the position of the Rectangle within the viewport.
setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
Sets the coordinates of the RenderPoint to the given values.
setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Text
Sets the position of the text within the viewport.
setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
Sets the 2D coordinates for the start and the end point of the linear gradient vector.
setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
Sets the 2D coordinates for the center and the focal point as well as the radius.
setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
Sets the 3D coordinates for the start and the end point of the linear gradient vector.
setCoordinates(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
Sets the 3D coordinates for the center and the focal point as well as the radius.
setCoordinatesAndSize(RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the position and the size of the Rectangle within the viewport.
setCreatedDate(Date) - Method in class org.sbml.libsbml.ModelHistory
Sets the creation date of this ModelHistory object.
setCurve(Curve) - Method in class org.sbml.libsbml.GeneralGlyph
Sets the curve object for the reaction glyph.
setCurve(Curve) - Method in class org.sbml.libsbml.ReactionGlyph
Sets the curve object for the reaction glyph.
setCurve(Curve) - Method in class org.sbml.libsbml.ReferenceGlyph
Sets the curve object for the reference glyph.
setCurve(Curve) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Sets the curve object for the species reference glyph.
setCX(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
Sets the x coordinates for the center point.
setCY(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
Sets the y coordinates for the center point.
setCZ(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
Sets the z coordinates for the center point.
setDashByIndex(long, long) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Sets the dash at the given position.
setDateAsString(String) - Method in class org.sbml.libsbml.Date
Sets the value of this Date object using a date and time value expressed as a text string.
setDay(long) - Method in class org.sbml.libsbml.Date
Sets the value of the day of this Date object.
setDefault_z(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'default_z' attribute of this DefaultValues.
setDefaultTerm(DefaultTerm) - Method in class org.sbml.libsbml.ListOfFunctionTerms
Sets the given DefaultTerm to this Transition.
setDefaultTerm(DefaultTerm) - Method in class org.sbml.libsbml.Transition
Sets the given DefaultTerm to this Transition.
setDefaultValues(DefaultValues) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Sets the value of the 'defaultValues' element of this ListOfGlobalRenderInformation.
setDefaultValues(DefaultValues) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Sets the value of the 'defaultValues' element of this ListOfLocalRenderInformation.
setDefinitionURL(String) - Method in class org.sbml.libsbml.ASTNode
Sets the MathML attribute definitionURL.
setDefinitionURL(XMLAttributes) - Method in class org.sbml.libsbml.ASTNode
Sets the MathML attribute definitionURL.
setDelay(Delay) - Method in class org.sbml.libsbml.Event
Sets the delay definition of this Event to a copy of the given Delay object instance.
setDeletion(String) - Method in class org.sbml.libsbml.ReplacedElement
Sets the value of the 'deletion' attribute of this ReplacedElement.
setDenominator(int) - Method in class org.sbml.libsbml.SpeciesReference
Set the value of the 'denominator' attribute, for the case of a rational-numbered stoichiometry or a model in SBML Level 1.
setDepth(double) - Method in class org.sbml.libsbml.BoundingBox
Set depth of the bounding box.
setDepth(double) - Method in class org.sbml.libsbml.Dimensions
Sets the depth to the given value.
setDescription(String) - Method in class org.sbml.libsbml.ConversionOption
Sets the description text for this option.
setDimensions(Dimensions) - Method in class org.sbml.libsbml.BoundingBox
Sets the dimensions to a copy of the Dimensions object given.
setDimensions(Dimensions) - Method in class org.sbml.libsbml.Layout
Sets the dimensions of the layout.
setDimensions(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Image
Sets the dimensions of the image.
setDivider(String) - Method in class org.sbml.libsbml.CompModelPlugin
Set the string used as the divider between names when renaming and flattening models.
setDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLConverter
Sets the SBML document to be converted.
setDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLReactionConverter
Sets the current SBML document to the given SBMLDocument object.
setDocument(SBMLDocument) - Method in class org.sbml.libsbml.SBMLValidator
Sets the current SBML document to the given SBMLDocument object.
setDoubleValue(double) - Method in class org.sbml.libsbml.ConversionOption
Set the value of this option to a given double value.
setDoubleValue(String, double) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to a double.
setElementName(String) - Method in class org.sbml.libsbml.Point
Sets the element name to be returned by getElementName().
setElementName(String) - Method in class org.sbml.libsbml.RenderPoint
Sets the element name which is returned by getElementName.
setElementNamespace(String) - Method in class org.sbml.libsbml.SBasePlugin
Sets the XML namespace to which this object belongs.
setEmail(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'email' portion of this ModelCreator object.
setEnabled(boolean) - Method in class org.sbml.libsbml.SBMLExtension
Enable or disable this package.
setEnabled(String, boolean) - Method in class org.sbml.libsbml.SBMLExtensionRegistry
Enables or disable the package with the given URI.
setEnableRotationalMapping(boolean) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'enableRotationalMapping' attribute of this DefaultValues.
setEnableRotationalMapping(boolean) - Method in class org.sbml.libsbml.LineEnding
Sets whether rotational mapping is to be done or not.
setEnd() - Method in class org.sbml.libsbml.XMLToken
Declares that this token represents an XML element end tag.
setEnd(double, double) - Method in class org.sbml.libsbml.LineSegment
Initializes the end point with the given coordinates.
setEnd(double, double, double) - Method in class org.sbml.libsbml.LineSegment
Initializes the end point with the given coordinates.
setEnd(Point) - Method in class org.sbml.libsbml.LineSegment
Initializes the end point with a copy of the given Point object.
setEndHead(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'endHead' attribute of this DefaultValues.
setEndHead(String) - Method in class org.sbml.libsbml.RenderCurve
Sets the id of the end head.
setEndHead(String) - Method in class org.sbml.libsbml.RenderGroup
Sets the id of the end head.
setEOF() - Method in class org.sbml.libsbml.XMLToken
Declares that this token is an end-of-file/input marker.
setErrorLog(XMLErrorLog) - Method in class org.sbml.libsbml.XMLInputStream
Sets the XMLErrorLog this stream will use to log errors.
setExponent(double) - Method in class org.sbml.libsbml.Unit
Sets the 'exponent' attribute value of this Unit.
setExponent(int) - Method in class org.sbml.libsbml.Unit
Sets the 'exponent' attribute value of this Unit.
setExtentConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
Sets the value of the 'extentConversionFactor' attribute of this Submodel.
setExtentUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'extentUnits' attribute of this Model.
setFamilyName(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'family name' portion of this ModelCreator object.
setFast(boolean) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'fast' attribute of this Reaction.
setFill(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fill' attribute of this DefaultValues.
setFillColor(String) - Method in class org.sbml.libsbml.GraphicalPrimitive2D
Set fill color to the id of a color definition, the id of a gradient definition or a color value string.
setFillRule(int) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fillRule' attribute of this DefaultValues.
setFillRule(int) - Method in class org.sbml.libsbml.GraphicalPrimitive2D
Sets the fill rule.
setFillRule(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fillRule' attribute of this DefaultValues.
setFloatValue(float) - Method in class org.sbml.libsbml.ConversionOption
Set the value of this option to a given float value.
setFloatValue(String, float) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to a float.
setFocalPoint(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
Sets the coordinates for the focal point.
setFocalPoint(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
Sets the coordinates for the focal point.
setFontFamily(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fontFamily' attribute of this DefaultValues.
setFontFamily(String) - Method in class org.sbml.libsbml.RenderGroup
Sets the font family.
setFontFamily(String) - Method in class org.sbml.libsbml.Text
Sets the font family.
setFontSize(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fontSize' attribute of this DefaultValues.
setFontSize(RelAbsVector) - Method in class org.sbml.libsbml.RenderGroup
Sets the font size.
setFontSize(RelAbsVector) - Method in class org.sbml.libsbml.Text
Sets the font size.
setFontStyle(int) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fontStyle' attribute of this DefaultValues.
setFontStyle(int) - Method in class org.sbml.libsbml.RenderGroup
Sets the font style.
setFontStyle(int) - Method in class org.sbml.libsbml.Text
Sets the font style.
setFontStyle(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fontStyle' attribute of this DefaultValues.
setFontWeight(int) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fontWeight' attribute of this DefaultValues.
setFontWeight(int) - Method in class org.sbml.libsbml.RenderGroup
Sets the font weight.
setFontWeight(int) - Method in class org.sbml.libsbml.Text
Sets the font weight.
setFontWeight(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'fontWeight' attribute of this DefaultValues.
setFormula(String) - Method in class org.sbml.libsbml.KineticLaw
Sets the mathematical expression of this KineticLaw instance to the given formula.
setFormula(String) - Method in class org.sbml.libsbml.Rule
Sets the 'math' subelement of this Rule to an expression in text-string form.
setGeneProduct(String) - Method in class org.sbml.libsbml.GeneProductRef
Sets the value of the 'geneProduct' attribute of this GeneProductRef.
setGeneProductAssociation(GeneProductAssociation) - Method in class org.sbml.libsbml.FbcReactionPlugin
Sets the GeneProductAssociation element in this FbcReactionPlugin object.
setGivenName(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'given name' portion of this ModelCreator object.
setGlyphId(String) - Method in class org.sbml.libsbml.ReferenceGlyph
Sets the id of the associated glyph.
setGraphicalObjectId(String) - Method in class org.sbml.libsbml.TextGlyph
Sets the id of the associated graphical object.
setGreen(short) - Method in class org.sbml.libsbml.ColorDefinition
Sets the green color component.
setGroup(RenderGroup) - Method in class org.sbml.libsbml.LineEnding
Sets the group of the LineEnding to a copy of the given group.
setGroup(RenderGroup) - Method in class org.sbml.libsbml.Style
Sets the group of the Style.
setHasOnlySubstanceUnits(boolean) - Method in class org.sbml.libsbml.Species
Sets the 'hasOnlySubstanceUnits' attribute of this Species object.
setHeight(double) - Method in class org.sbml.libsbml.BoundingBox
Set height of the bounding box.
setHeight(double) - Method in class org.sbml.libsbml.Dimensions
Sets the height to the given value.
setHeight(RelAbsVector) - Method in class org.sbml.libsbml.Image
Sets the height of the image when rendered.
setHeight(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the height of the Rectangle
setHour(long) - Method in class org.sbml.libsbml.Date
Sets the value of the hour of this Date object.
setHoursOffset(long) - Method in class org.sbml.libsbml.Date
Sets the value of this Date object's time zone hour offset.
setId(String) - Method in class org.sbml.libsbml.ASTNode
Sets the MathML attribute id of this ASTNode.
setId(String) - Method in class org.sbml.libsbml.BoundingBox
Sets the value of the 'id' attribute of this BoundingBox.
setId(String) - Method in class org.sbml.libsbml.ColorDefinition
Sets the value of the 'id' attribute of this GraphicalPrimitive.
setId(String) - Method in class org.sbml.libsbml.Compartment
Sets the value of the 'id' attribute of this Compartment object.
setId(String) - Method in class org.sbml.libsbml.CompartmentType
Sets the value of the 'id' attribute of this CompartmentType.
setId(String) - Method in class org.sbml.libsbml.Deletion
Sets the value of the 'id' attribute of this Deletion.
setId(String) - Method in class org.sbml.libsbml.Dimensions
Sets the value of the 'id' attribute of this Dimensions.
setId(String) - Method in class org.sbml.libsbml.Event
Sets the value of the 'id' attribute of this Event.
setId(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
Sets the value of the 'id' attribute of this ExternalModelDefinition.
setId(String) - Method in class org.sbml.libsbml.FluxBound
Sets the value of the 'id' attribute of this FluxBound.
setId(String) - Method in class org.sbml.libsbml.FluxObjective
Sets the value of the 'id' attribute of this FluxObjective.
setId(String) - Method in class org.sbml.libsbml.FunctionDefinition
Sets the value of the 'id' attribute of this FunctionDefinition.
setId(String) - Method in class org.sbml.libsbml.GeneAssociation
Sets the value of the 'id' attribute of this GeneAssociation.
setId(String) - Method in class org.sbml.libsbml.GeneProduct
Sets the value of the 'id' attribute of this GeneProduct.
setId(String) - Method in class org.sbml.libsbml.GeneProductAssociation
Sets the value of the 'id' attribute of this GeneProductAssociation.
setId(String) - Method in class org.sbml.libsbml.GeneProductRef
Sets the value of the 'id' attribute of this GeneProductRef.
setId(String) - Method in class org.sbml.libsbml.GradientBase
Sets the value of the 'id' attribute of this SBML object.
setId(String) - Method in class org.sbml.libsbml.GraphicalObject
Sets the value of the 'id' attribute of this GraphicalObject.
setId(String) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Sets the value of the 'id' attribute of this GraphicalPrimitive.
setId(String) - Method in class org.sbml.libsbml.Group
Sets the value of the 'id' attribute of this Group.
setId(String) - Method in class org.sbml.libsbml.Image
Sets the value of the 'id' attribute of this Image.
setId(String) - Method in class org.sbml.libsbml.Input
Sets the value of the 'id' attribute of this obInputject.
setId(String) - Method in class org.sbml.libsbml.Layout
Sets the value of the 'id' attribute of this Layout.
setId(String) - Method in class org.sbml.libsbml.LineEnding
Sets the value of the 'id' attribute of this GraphicalPrimitive.
setId(String) - Method in class org.sbml.libsbml.ListOfMembers
Sets the value of the 'id' attribute of this ListOfMembers.
setId(String) - Method in class org.sbml.libsbml.Member
Sets the value of the 'id' attribute of this Member.
setId(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'id' attribute of this Model.
setId(String) - Method in class org.sbml.libsbml.Objective
Sets the value of the 'id' attribute of this Objective.
setId(String) - Method in class org.sbml.libsbml.Output
Sets the value of the 'id' attribute of this Output.
setId(String) - Method in class org.sbml.libsbml.Parameter
Sets the value of the 'id' attribute of this Parameter.
setId(String) - Method in class org.sbml.libsbml.Point
Sets the value of the 'id' attribute of this Point.
setId(String) - Method in class org.sbml.libsbml.Port
Sets the value of the 'id' attribute of this Port.
setId(String) - Method in class org.sbml.libsbml.QualitativeSpecies
Sets the value of the 'id' attribute of this QualitativeSpecies.
setId(String) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'id' attribute of this Reaction.
setId(String) - Method in class org.sbml.libsbml.RenderInformationBase
Sets the value of the 'id' attribute of this RenderInformationBase.
setId(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'id' attribute of this SBML object.
setId(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
Sets the value of the 'id' attribute of this SimpleSpeciesReference.
setId(String) - Method in class org.sbml.libsbml.Species
Sets the value of the 'id' attribute of this Species.
setId(String) - Method in class org.sbml.libsbml.SpeciesType
Sets the value of the 'id' attribute of this SpeciesType.
setId(String) - Method in class org.sbml.libsbml.Style
Sets the value of the 'id' attribute of this Style.
setId(String) - Method in class org.sbml.libsbml.Submodel
Sets the value of the 'id' attribute of this Submodel.
setId(String) - Method in class org.sbml.libsbml.Transition
Sets the value of the 'id' attribute of this Transition.
setId(String) - Method in class org.sbml.libsbml.UnitDefinition
Sets the value of the 'id' attribute of this UnitDefinition.
setIdAttribute(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'id' attribute of this SBML object.
setIdList(StringSet) - Method in class org.sbml.libsbml.LocalStyle
Sets the id list.
setIdRef(String) - Method in class org.sbml.libsbml.Member
Sets the value of the 'idRef' attribute of this Member.
setIdRef(String) - Method in class org.sbml.libsbml.SBaseRef
Sets the value of the 'idRef' attribute of this SBaseRef.
setImageReference(String) - Method in class org.sbml.libsbml.Image
Sets the reference to the image location.
setInitialAmount(double) - Method in class org.sbml.libsbml.Species
Sets the 'initialAmount' attribute of this Species and marks the field as set.
setInitialConcentration(double) - Method in class org.sbml.libsbml.Species
Sets the 'initialConcentration' attribute of this Species and marks the field as set.
setInitialLevel(int) - Method in class org.sbml.libsbml.QualitativeSpecies
Sets the value of the 'initialLevel' attribute of this QualitativeSpecies.
setInitialValue(boolean) - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Sets the 'initialValue' attribute of this Trigger instance.
setIntValue(int) - Method in class org.sbml.libsbml.ConversionOption
Set the value of this option to a given int value.
setIntValue(String, int) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to an integer.
setitem(int, double) - Method in class org.sbml.libsbml.double_array
 
setitem(int, int) - Method in class org.sbml.libsbml.int_array
 
setKey(String) - Method in class org.sbml.libsbml.ConversionOption
Sets the key for this option.
setKind(int) - Method in class org.sbml.libsbml.Group
Sets the value of the 'kind' attribute of this Group.
setKind(int) - Method in class org.sbml.libsbml.Unit
Sets the 'kind' attribute value of this Unit.
setKind(String) - Method in class org.sbml.libsbml.Group
Sets the value of the 'kind' attribute of this Group.
setKineticLaw(KineticLaw) - Method in class org.sbml.libsbml.Reaction
Sets the 'kineticLaw' subelement of this Reaction to a copy of the given KineticLaw object.
setL1TypeCode(int) - Method in class org.sbml.libsbml.Rule
Sets the SBML Level 1 type code for this Rule.
setLabel(String) - Method in class org.sbml.libsbml.GeneProduct
Sets the value of the 'label' attribute of this GeneProduct.
setLengthUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'lengthUnits' attribute of this Model.
setLevelAndVersion(long, long) - Method in class org.sbml.libsbml.SBMLDocument
Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
setLevelAndVersion(long, long, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
setLevelAndVersion(long, long, boolean, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
setLibraryName(String) - Static method in class org.sbml.libsbml.XMLOutputStream
sets the name of the library writing the XML
setLibraryVersion(String) - Static method in class org.sbml.libsbml.XMLOutputStream
sets the name of the library writing the output
setLine(long) - Method in class org.sbml.libsbml.XMLError
Sets the line number where this error occurred.
setLinearGradient_x1(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'linearGradient_x1' attribute of this DefaultValues.
setLinearGradient_x2(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'linearGradient_x2' attribute of this DefaultValues.
setLinearGradient_y1(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'linearGradient_y1' attribute of this DefaultValues.
setLinearGradient_y2(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'linearGradient_y2' attribute of this DefaultValues.
setLinearGradient_z1(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'linearGradient_z1' attribute of this DefaultValues.
setLinearGradient_z2(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'linearGradient_z2' attribute of this DefaultValues.
setLocationURI(String) - Method in class org.sbml.libsbml.SBMLDocument
Sets the location of this SBMLDocument.
setLowerFluxBound(String) - Method in class org.sbml.libsbml.FbcReactionPlugin
Sets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.
setMath(ASTNode) - Method in class org.sbml.libsbml.Constraint
Sets the mathematical expression of this Constraint to a copy of the AST given as math.
setMath(ASTNode) - Method in class org.sbml.libsbml.Delay
Sets the delay expression of this Delay instance to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.EventAssignment
Sets the 'math' subelement of this EventAssignment to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.FunctionDefinition
Sets the 'math' subelement of this FunctionDefinition to the Abstract Syntax Tree given in math.
setMath(ASTNode) - Method in class org.sbml.libsbml.FunctionTerm
Sets the 'math' element of this FunctionTerm.
setMath(ASTNode) - Method in class org.sbml.libsbml.InitialAssignment
Sets the 'math' subelement of this InitialAssignment.
setMath(ASTNode) - Method in class org.sbml.libsbml.KineticLaw
Sets the mathematical expression of this KineticLaw instance to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.Priority
Sets the math expression of this Priority instance to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.Rule
Sets the 'math' subelement of this Rule to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.StoichiometryMath
Sets the 'math' expression of this StoichiometryMath instance to a copy of the given ASTNode.
setMath(ASTNode) - Method in class org.sbml.libsbml.Trigger
Sets the trigger expression of this Trigger instance to a copy of the given ASTNode.
setMatrix(SWIGTYPE_p_double) - Method in class org.sbml.libsbml.Transformation
Sets the matrix to the values given in the array.
setMatrix(SWIGTYPE_p_double) - Method in class org.sbml.libsbml.Transformation2D
Sets the 2D matrix to the values given in the array.
setMatrix2D(SWIGTYPE_p_double) - Method in class org.sbml.libsbml.Transformation2D
Sets the 2D matrix to the values given in the array.
setMaxLevel(int) - Method in class org.sbml.libsbml.QualitativeSpecies
Sets the value of the 'maxLevel' attribute of this QualitativeSpecies.
setMd5(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
Sets the value of the 'md5' attribute of this ExternalModelDefinition.
setMessage(String) - Method in class org.sbml.libsbml.Constraint
Sets the message of this Constraint.
setMessage(String, boolean) - Method in class org.sbml.libsbml.Constraint
Sets the message of this Constraint.
setMessage(XMLNode) - Method in class org.sbml.libsbml.Constraint
Sets the message of this Constraint.
setMetaId(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the meta-identifier attribute of this SBML object.
setMetaIdRef(String) - Method in class org.sbml.libsbml.GraphicalObject
Sets the value of the 'metaidRef' attribute of this GraphicalObject.
setMetaIdRef(String) - Method in class org.sbml.libsbml.Member
Sets the value of the 'metaIdRef' attribute of this Member.
setMetaIdRef(String) - Method in class org.sbml.libsbml.SBaseRef
Sets the value of the 'metaIdRef' attribute of this SBaseRef.
setMinute(long) - Method in class org.sbml.libsbml.Date
Sets the value of the minute of this Date object.
setMinutesOffset(long) - Method in class org.sbml.libsbml.Date
Sets the value of this Date object's time zone minutes offset.
setModel(Model) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the model reference in this L3ParserSettings object.
setModel(Model) - Method in class org.sbml.libsbml.SBMLDocument
Sets the Model for this SBMLDocument to a copy of the given Model.
setModelHistory(ModelHistory) - Method in class org.sbml.libsbml.SBase
Sets the ModelHistory of this object.
setModelQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
Sets the model qualifier type of this CVTerm object.
setModelQualifierType(String) - Method in class org.sbml.libsbml.CVTerm
Sets the model qualifier type value of this CVTerm object.
setModelRef(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
Sets the value of the 'modelRef' attribute of this ExternalModelDefinition.
setModelRef(String) - Method in class org.sbml.libsbml.Submodel
Sets the value of the 'modelRef' attribute of this Submodel.
setModifiedDate(Date) - Method in class org.sbml.libsbml.ModelHistory
Sets the modification date of this ModelHistory object.
setMonth(long) - Method in class org.sbml.libsbml.Date
Sets the value of the month of this Date object.
setMultiplier(double) - Method in class org.sbml.libsbml.Unit
Sets the 'multipler' attribute value of this Unit.
setName(String) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given name.
setName(String) - Method in class org.sbml.libsbml.ColorDefinition
Sets the value of the 'name' attribute of this ColorDefinition.
setName(String) - Method in class org.sbml.libsbml.Compartment
Sets the value of the 'name' attribute of this Compartment object.
setName(String) - Method in class org.sbml.libsbml.CompartmentType
Sets the value of the 'name' attribute of this CompartmentType.
setName(String) - Method in class org.sbml.libsbml.Deletion
Sets the value of the 'name' attribute of this Deletion.
setName(String) - Method in class org.sbml.libsbml.Event
Sets the value of the 'name' attribute of this Event.
setName(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
Sets the value of the 'name' attribute of this ExternalModelDefinition.
setName(String) - Method in class org.sbml.libsbml.FluxBound
Sets the value of the 'name' attribute of this FluxBound.
setName(String) - Method in class org.sbml.libsbml.FluxObjective
Sets the value of the 'name' attribute of this FluxObjective.
setName(String) - Method in class org.sbml.libsbml.FunctionDefinition
Sets the value of the 'name' attribute of this FunctionDefinition.
setName(String) - Method in class org.sbml.libsbml.GeneProduct
Sets the value of the 'name' attribute of this GeneProduct.
setName(String) - Method in class org.sbml.libsbml.GeneProductAssociation
Sets the value of the 'name' attribute of this GeneProductAssociation.
setName(String) - Method in class org.sbml.libsbml.GeneProductRef
Sets the value of the 'name' attribute of this GeneProductRef.
setName(String) - Method in class org.sbml.libsbml.GradientBase
Sets the value of the 'name' attribute of this SBML object.
setName(String) - Method in class org.sbml.libsbml.Group
Sets the value of the 'name' attribute of this Group.
setName(String) - Method in class org.sbml.libsbml.Input
Sets the value of the 'name' attribute of this Input.
setName(String) - Method in class org.sbml.libsbml.Layout
Sets the value of the 'name' attribute of this Layout.
setName(String) - Method in class org.sbml.libsbml.ListOfMembers
Sets the value of the 'name' attribute of this ListOfMembers.
setName(String) - Method in class org.sbml.libsbml.Member
Sets the value of the 'name' attribute of this Member.
setName(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'name' attribute of this Model.
setName(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'fn' portion of this ModelCreator object (when using vCard4).
setName(String) - Method in class org.sbml.libsbml.Objective
Sets the value of the 'name' attribute of this Objective.
setName(String) - Method in class org.sbml.libsbml.Output
Sets the value of the 'name' attribute of this Output.
setName(String) - Method in class org.sbml.libsbml.Parameter
Sets the value of the 'name' attribute of this Parameter.
setName(String) - Method in class org.sbml.libsbml.Port
Sets the value of the 'name' attribute of this Port.
setName(String) - Method in class org.sbml.libsbml.QualitativeSpecies
Sets the value of the 'name' attribute of this QualitativeSpecies.
setName(String) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'name' attribute of this Reaction.
setName(String) - Method in class org.sbml.libsbml.RenderInformationBase
Sets the value of the 'name' attribute of this RenderInformationBase.
setName(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'name' attribute of this SBML object.
setName(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
Sets the value of the 'name' attribute of this SimpleSpeciesReference.
setName(String) - Method in class org.sbml.libsbml.Species
Sets the value of the 'name' attribute of this Species.
setName(String) - Method in class org.sbml.libsbml.SpeciesType
Sets the value of the 'name' attribute of this SpeciesType.
setName(String) - Method in class org.sbml.libsbml.Style
Sets the value of the 'name' attribute of this Style.
setName(String) - Method in class org.sbml.libsbml.Submodel
Sets the value of the 'name' attribute of this Submodel.
setName(String) - Method in class org.sbml.libsbml.Transformation
Sets the value of the 'name' attribute of this Transformation.
setName(String) - Method in class org.sbml.libsbml.Transition
Sets the value of the 'name' attribute of this Transition.
setName(String) - Method in class org.sbml.libsbml.UnitDefinition
Sets the value of the 'name' attribute of this UnitDefinition.
setNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.SBase
Sets the namespaces relevant of this SBML object.
setNamespaces(XMLNamespaces) - Method in class org.sbml.libsbml.XMLToken
Sets the XML namespaces on this XML element.
setNotes(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.
setNotes(String, boolean) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.
setNotes(XMLNode) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'notes' subelement of this SBML object.
setObjectRole(String) - Method in class org.sbml.libsbml.RenderGraphicalObjectPlugin
Sets the object role string for the object.
setOffset(double) - Method in class org.sbml.libsbml.Unit
Sets the 'offset' attribute value of this Unit.
setOffset(double, double) - Method in class org.sbml.libsbml.GradientStop
Sets the offset for the gradient stop.
setOffset(String) - Method in class org.sbml.libsbml.GradientStop
Sets the offset to the value specified by the given string.
setOffset(RelAbsVector) - Method in class org.sbml.libsbml.GradientStop
Sets the offset to the given vector object.
setOffsets(double, double) - Method in class org.sbml.libsbml.Point
Sets the coordinates to the given values.
setOffsets(double, double, double) - Method in class org.sbml.libsbml.Point
Sets the coordinates to the given values.
setOffsets(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
Sets the coordinates of the RenderPoint to the given values.
setOffsets(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
Sets the coordinates of the RenderPoint to the given values.
setOperation(int) - Method in class org.sbml.libsbml.FluxBound
Sets the value of the 'operation' attribute of this FluxBound object.
setOperation(String) - Method in class org.sbml.libsbml.FluxBound
Sets the value of the 'operation' attribute of this FluxBound object.
setOrder(double) - Method in class org.sbml.libsbml.CompartmentGlyph
Sets the compartment order.
setOrganisation(String) - Method in class org.sbml.libsbml.ModelCreator
(Alternate spelling) Sets the 'organization' portion of this ModelCreator object.
setOrganization(String) - Method in class org.sbml.libsbml.ModelCreator
Sets the 'organization' portion of this ModelCreator object.
setOriginOfTextId(String) - Method in class org.sbml.libsbml.TextGlyph
Sets the id of the origin of text.
setOutputLevel(int) - Method in class org.sbml.libsbml.Output
Sets the value of the 'outputLevel' attribute of this Output.
setOutside(String) - Method in class org.sbml.libsbml.Compartment
Sets the 'outside' attribute of this Compartment object.
setPackageRequired(String, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Sets the required attribute value of the given package extension.
setParseAvogadroCsymbol(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the parser's behavior in handling the symbol avogadro in mathematical formulas.
setParseCollapseMinus(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the behavior for handling unary minuses appearing in mathematical formulas.
setParseL3v2Functions(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the behavior for handling functions added in SBML L3v2
setParseLog(int) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the behavior for handling log in mathematical formulas.
setParseModuloL3v2(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the behavior for handling the @% symbol in mathematical formulas.
setParseUnits(boolean) - Method in class org.sbml.libsbml.L3ParserSettings
Sets the parser's behavior in handling units associated with numbers in a mathematical formula.
setPersistent(boolean) - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Sets the 'persistent' attribute of this Trigger instance.
setPkgRequired(String, boolean) - Method in class org.sbml.libsbml.SBMLDocument
Deprecated.
Replaced in libSBML 5.2.0 by setPackageRequired(String, boolean)
setPlugins(SBMLNamespaces) - Method in class org.sbml.libsbml.L3ParserSettings
Set up the plugins for this L3ParserSettings, based on the SBMLNamespaces object.
setPoint1(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
Sets the coordinates for the start point of the linear gradient vector.
setPoint1(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
Sets the coordinates for the start point of the linear gradient vector.
setPoint2(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
Sets the coordinates for the end point of the linear gradient vector.
setPoint2(RelAbsVector, RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.LinearGradient
Sets the coordinates for the end point of the linear gradient vector.
setPortRef(String) - Method in class org.sbml.libsbml.Port
Overrides SBaseRef.setPortRef to always fail, because Port objects themselves cannot refer to model elements by PortSId.
setPortRef(String) - Method in class org.sbml.libsbml.SBaseRef
Sets the value of the 'portRef' attribute of this SBaseRef.
setPosition(Point) - Method in class org.sbml.libsbml.BoundingBox
Sets the position to a copy of the Point object given.
setPriority(Priority) - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Sets the priority definition of this Event to a copy of the given Priority object instance.
setProgramName(String) - Method in class org.sbml.libsbml.RenderInformationBase
Sets the name of the program that created the render information.
setProgramName(String) - Method in class org.sbml.libsbml.SBMLWriter
Sets the name of this program, i.e., the program that is about to write out the SBMLDocument.
setProgramVersion(String) - Method in class org.sbml.libsbml.RenderInformationBase
Sets the version string of the program that created the render information.
setProgramVersion(String) - Method in class org.sbml.libsbml.SBMLWriter
Sets the version of this program, i.e., the program that is about to write out the SBMLDocument.
setProperties(ConversionProperties) - Method in class org.sbml.libsbml.SBMLConverter
Sets the configuration properties to be used by this converter.
setQualifierType(int) - Method in class org.sbml.libsbml.CVTerm
Sets the qualifier code of this CVTerm object.
setQualitativeSpecies(String) - Method in class org.sbml.libsbml.Input
Sets the value of the 'qualitativeSpecies' attribute of this Input.
setQualitativeSpecies(String) - Method in class org.sbml.libsbml.Output
Sets the value of the 'qualitativeSpecies' attribute of this Output.
setRadialGradient_cx(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'radialGradient_cx' attribute of this DefaultValues.
setRadialGradient_cy(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'radialGradient_cy' attribute of this DefaultValues.
setRadialGradient_cz(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'radialGradient_cz' attribute of this DefaultValues.
setRadialGradient_fx(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'radialGradient_fx' attribute of this DefaultValues.
setRadialGradient_fy(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'radialGradient_fy' attribute of this DefaultValues.
setRadialGradient_fz(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'radialGradient_fz' attribute of this DefaultValues.
setRadialGradient_r(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'radialGradient_r' attribute of this DefaultValues.
setRadii(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
Sets the radii of the ellipse
setRadii(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the two corner radii of the rectangle
setRadius(RelAbsVector) - Method in class org.sbml.libsbml.RadialGradient
Sets the radius of the radial gradient.
setRadiusX(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the corner radius along the x axis
setRadiusY(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the corner radius along the y axis
setRatio(double) - Method in class org.sbml.libsbml.Ellipse
Sets the value of the 'ratio' attribute of this Ellipse.
setRatio(double) - Method in class org.sbml.libsbml.Rectangle
Sets the value of the 'ratio' attribute of this Rectangle.
setReaction(String) - Method in class org.sbml.libsbml.FluxBound
Sets the value of the 'reaction' attribute of this FluxBound object.
setReaction(String) - Method in class org.sbml.libsbml.FluxObjective
Sets the value of the 'reaction' attribute of this FluxObjective.
setReaction(String) - Method in class org.sbml.libsbml.GeneAssociation
Sets the SIdRef string of the 'reaction' attribute of this GeneAssociation.
setReactionId(String) - Method in class org.sbml.libsbml.ReactionGlyph
Sets the id of the associated reaction.
setRed(short) - Method in class org.sbml.libsbml.ColorDefinition
Sets the red color component.
setReference(String) - Method in class org.sbml.libsbml.Association
Sets the SIdRef string of the 'reference' attribute of this Association object.
setReferenceId(String) - Method in class org.sbml.libsbml.GeneralGlyph
Sets the id of the associated element.
setReferenceId(String) - Method in class org.sbml.libsbml.ReferenceGlyph
Sets the id of the associated sbml reference.
setReferenceRenderInformationId(String) - Method in class org.sbml.libsbml.RenderInformationBase
Sets the id of the referenced render information object.
setRelativeValue(double) - Method in class org.sbml.libsbml.RelAbsVector
Sets the relative coordinate value.
setReplacedBy(ReplacedBy) - Method in class org.sbml.libsbml.CompSBasePlugin
Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance.
setRequired(boolean) - Method in class org.sbml.libsbml.CompSBMLDocumentPlugin
Sets the boolean value of 'required' attribute of corresponding package in SBMLDocument element.
setRequired(boolean) - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Sets the SBML 'required' attribute value.
setResultLevel(int) - Method in class org.sbml.libsbml.DefaultTerm
Sets the value of the 'resultLevel' attribute of this DefaultTerm.
setResultLevel(int) - Method in class org.sbml.libsbml.FunctionTerm
Sets the value of the 'resultLevel' attribute of this FunctionTerm.
setReversible(boolean) - Method in class org.sbml.libsbml.Reaction
Sets the value of the 'reversible' attribute of this Reaction.
setRGBA(short, short, short) - Method in class org.sbml.libsbml.ColorDefinition
Sets the red green, blue and alpha color component.
setRGBA(short, short, short, short) - Method in class org.sbml.libsbml.ColorDefinition
Sets the red green, blue and alpha color component.
setRole(int) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Sets the role.
setRole(String) - Method in class org.sbml.libsbml.ReferenceGlyph
Sets the role.
setRole(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Sets the role based on a string.
setRoleList(StringSet) - Method in class org.sbml.libsbml.Style
Sets the complete role list to a copy of the given list.
setRX(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
Sets the radius along the x axis
setRY(RelAbsVector) - Method in class org.sbml.libsbml.Ellipse
Sets the radius along the y axis
setSBaseRef(SBaseRef) - Method in class org.sbml.libsbml.SBaseRef
Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance.
setSBMLNamespaces(SBMLNamespaces) - Method in class org.sbml.libsbml.XMLInputStream
Sets the SBML namespaces associated with this XML input stream.
setSBMLNamespaces(SBMLNamespaces) - Method in class org.sbml.libsbml.XMLOutputStream
Sets the SBMLNamespaces object associated with this output stream.
setSBOTerm(int) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'sboTerm' attribute.
setSBOTerm(String) - Method in class org.sbml.libsbml.SBase
Sets the value of the 'sboTerm' attribute by string.
setScale(int) - Method in class org.sbml.libsbml.Unit
Sets the 'scale' attribute value of this Unit.
setSecond(long) - Method in class org.sbml.libsbml.Date
Sets the value of the second of the Date object.
setSeverityOverride(int) - Method in class org.sbml.libsbml.XMLErrorLog
Set the severity override.
setSign(int) - Method in class org.sbml.libsbml.Input
Sets the value of the 'sign' attribute of this Input.
setSignOffset(long) - Method in class org.sbml.libsbml.Date
Sets the value of the sign of the time zone offset of this Date object.
setSize(double) - Method in class org.sbml.libsbml.Compartment
Sets the 'size' attribute (or 'volume' in SBML Level 1) of this Compartment object.
setSize(RelAbsVector, RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the size of the Rectangle
setSource(String) - Method in class org.sbml.libsbml.ExternalModelDefinition
Sets the value of the 'source' attribute of this ExternalModelDefinition.
setSpatialDimensions(double) - Method in class org.sbml.libsbml.Compartment
Sets the 'spatialDimensions' attribute of this Compartment object as a double.
setSpatialDimensions(long) - Method in class org.sbml.libsbml.Compartment
Sets the 'spatialDimensions' attribute of this Compartment object.
setSpatialSizeUnits(String) - Method in class org.sbml.libsbml.Species
(SBML Level 2 Versions 1–2) Sets the 'spatialSizeUnits' attribute of this Species object.
setSpecies(String) - Method in class org.sbml.libsbml.SimpleSpeciesReference
Sets the 'species' attribute of this SimpleSpeciesReference.
setSpeciesGlyphId(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Sets the id of the associated species glyph.
setSpeciesId(String) - Method in class org.sbml.libsbml.SpeciesGlyph
Sets the id of the associated species object.
setSpeciesReferenceId(String) - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Sets the id of the associated species reference.
setSpeciesType(String) - Method in class org.sbml.libsbml.Species
Sets the 'speciesType' attribute of this Species object.
setSpreadMethod(int) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'spreadMethod' attribute of this DefaultValues.
setSpreadMethod(int) - Method in class org.sbml.libsbml.GradientBase
Sets the spread method.
setSpreadMethod(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'spreadMethod' attribute of this DefaultValues.
setStart(double, double) - Method in class org.sbml.libsbml.LineSegment
Initializes the start point with the given coordinates.
setStart(double, double, double) - Method in class org.sbml.libsbml.LineSegment
Initializes the start point with the given coordinates.
setStart(Point) - Method in class org.sbml.libsbml.LineSegment
Initializes the start point with a copy of the given Point object.
setStartHead(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'startHead' attribute of this DefaultValues.
setStartHead(String) - Method in class org.sbml.libsbml.RenderCurve
Sets the id of the start head.
setStartHead(String) - Method in class org.sbml.libsbml.RenderGroup
Sets the id of the start head.
setStoichiometry(double) - Method in class org.sbml.libsbml.SpeciesReference
Sets the value of the 'stoichiometry' attribute of this SpeciesReference.
setStoichiometryMath(StoichiometryMath) - Method in class org.sbml.libsbml.SpeciesReference
Sets the 'stoichiometryMath' subelement of this SpeciesReference.
setStopColor(String) - Method in class org.sbml.libsbml.GradientStop
Sets the stop color id or the stop color value.
setStrict(boolean) - Method in class org.sbml.libsbml.FbcModelPlugin
Sets the value of the 'strict' attribute of this FbcModelPlugin.
setStroke(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'stroke' attribute of this DefaultValues.
setStroke(String) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Sets the stroke color to the given color definition id or color value string.
setStrokeWidth(double) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'strokeWidth' attribute of this DefaultValues.
setStrokeWidth(double) - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Sets the stroke width.
setStyle(String) - Method in class org.sbml.libsbml.ASTNode
Sets the MathML attribute style of this ASTNode.
setSubmodelRef(String) - Method in class org.sbml.libsbml.Replacing
Sets the value of the 'submodelRef' attribute of this SBaseRef.
setSubstanceConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
Automatically fails, since 'substanceConversionFactor' is not a part of the comp spec.
setSubstanceUnits(String) - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Sets the 'substanceUnits' attribute of this KineticLaw object to a copy of the identifier given in sid.
setSubstanceUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'substanceUnits' attribute of this Model.
setSubstanceUnits(String) - Method in class org.sbml.libsbml.Species
Sets the 'substanceUnits' attribute of this Species object.
setSymbol(String) - Method in class org.sbml.libsbml.InitialAssignment
Sets the 'symbol' attribute value of this InitialAssignment.
setTargetNamespaces(SBMLNamespaces) - Method in class org.sbml.libsbml.ConversionProperties
Sets the target namespace.
setText(String) - Method in class org.sbml.libsbml.Text
Sets the text for the text element.
setText(String) - Method in class org.sbml.libsbml.TextGlyph
Sets the text to be displayed by the text glyph.
setTextAnchor(int) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'textAnchor' attribute of this DefaultValues.
setTextAnchor(int) - Method in class org.sbml.libsbml.RenderGroup
Sets the text anchor.
setTextAnchor(int) - Method in class org.sbml.libsbml.Text
Sets the text anchor.
setTextAnchor(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'textAnchor' attribute of this DefaultValues.
setThresholdLevel(int) - Method in class org.sbml.libsbml.Input
Sets the value of the 'thresholdLevel' attribute of this Input.
setTimeConversionFactor(String) - Method in class org.sbml.libsbml.Submodel
Sets the value of the 'timeConversionFactor' attribute of this Submodel.
setTimeUnits(String) - Method in class org.sbml.libsbml.Event
Sets the 'timeUnits' attribute of this Event to a copy of sid.
setTimeUnits(String) - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Sets the 'timeUnits' attribute of this KineticLaw object to a copy of the identifier in sid.
setTimeUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'timeUnits' attribute of this Model.
setTransformer(SWIGTYPE_p_PrefixTransformer) - Method in class org.sbml.libsbml.CompModelPlugin
Sets the custom transformer that is to be used, instead of the standard prefixing with the given divider.
setTransitionEffect(int) - Method in class org.sbml.libsbml.Input
Sets the value of the 'transitionEffect' attribute of this Input.
setTransitionEffect(int) - Method in class org.sbml.libsbml.Output
Sets the value of the 'transitionEffect' attribute of this Output.
setTrigger(Trigger) - Method in class org.sbml.libsbml.Event
Sets the trigger definition of this Event to a copy of the given Trigger object instance.
setTriple(XMLTriple) - Method in class org.sbml.libsbml.XMLToken
Sets the name, namespace prefix and namespace URI of this token.
setType(int) - Method in class org.sbml.libsbml.Association
Sets the SIdRef string of the 'type' attribute of this Association object.
setType(int) - Method in class org.sbml.libsbml.ASTNode
Sets the type of this ASTNode.
setType(int) - Method in class org.sbml.libsbml.ConversionOption
Sets the type of this option.
setType(int) - Method in class org.sbml.libsbml.Objective
Sets the value of the 'type' attribute of this Objective.
setType(String) - Method in class org.sbml.libsbml.Objective
Sets the value of the 'type' attribute of this Objective.
setTypeList(StringSet) - Method in class org.sbml.libsbml.Style
Sets the complete type list to a copy of the given list.
setUnitRef(String) - Method in class org.sbml.libsbml.SBaseRef
Sets the value of the 'unitRef' attribute of this SBaseRef.
setUnits(String) - Method in class org.sbml.libsbml.ASTNode
Sets the units of this ASTNode to units.
setUnits(String) - Method in class org.sbml.libsbml.Compartment
Sets the 'units' attribute of this Compartment object.
setUnits(String) - Method in class org.sbml.libsbml.Parameter
Sets the 'units' attribute of this Parameter to a copy of the given units identifier units.
setUnits(String) - Method in class org.sbml.libsbml.Rule
Sets the units for this Rule.
setUnits(String) - Method in class org.sbml.libsbml.Species
(SBML Level 1 only) Sets the units of this Species object.
setUpperFluxBound(String) - Method in class org.sbml.libsbml.FbcReactionPlugin
Sets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.
setUseValuesFromTriggerTime(boolean) - Method in class org.sbml.libsbml.Event
Sets the 'useValuesFromTriggerTime' attribute of this Event to a value.
setValue(double) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given real (double).
setValue(double) - Method in class org.sbml.libsbml.FluxBound
Sets the value of the 'value' attribute of this FluxBound object.
setValue(double) - Method in class org.sbml.libsbml.Parameter
Sets the 'value' attribute of this Parameter to the given double value and marks the attribute as set.
setValue(double, int) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given real (double)
setValue(int) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given (long) integer
setValue(int, int) - Method in class org.sbml.libsbml.ASTNode
Sets the value of this ASTNode to the given rational.
setValue(String) - Method in class org.sbml.libsbml.ConversionOption
Sets the value for this option.
setValue(String, String) - Method in class org.sbml.libsbml.ConversionProperties
Sets the value of the given option to a string.
setVariable(String) - Method in class org.sbml.libsbml.EventAssignment
Sets the attribute 'variable' of this EventAssignment to a copy of the given identifier string.
setVariable(String) - Method in class org.sbml.libsbml.Rule
Sets the 'variable' attribute value of this Rule object.
setVersion(long, long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Sets the version of the render information list.
setVersion(long, long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Sets the version of the render information list.
setVersionMajor(long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Sets the value of the 'versionMajor' attribute of this ListOfGlobalRenderInformation.
setVersionMajor(long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Sets the value of the 'versionMajor' attribute of this ListOfLocalRenderInformation.
setVersionMinor(long) - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Sets the value of the 'versionMinor' attribute of this ListOfGlobalRenderInformation.
setVersionMinor(long) - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Sets the value of the 'versionMinor' attribute of this ListOfLocalRenderInformation.
setVolume(double) - Method in class org.sbml.libsbml.Compartment
Sets the 'volume' attribute (or 'size' in SBML Level 2) of this Compartment object.
setVolumeUnits(String) - Method in class org.sbml.libsbml.Model
Sets the value of the 'volumeUnits' attribute of this Model.
setVTextAnchor(int) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'vtextAnchor' attribute of this DefaultValues.
setVTextAnchor(int) - Method in class org.sbml.libsbml.RenderGroup
Sets the vertical text anchor.
setVTextAnchor(int) - Method in class org.sbml.libsbml.Text
Sets the vertical text anchor.
setVTextAnchor(String) - Method in class org.sbml.libsbml.DefaultValues
Sets the value of the 'vtextAnchor' attribute of this DefaultValues.
setWidth(double) - Method in class org.sbml.libsbml.BoundingBox
Set width of the bounding box.
setWidth(double) - Method in class org.sbml.libsbml.Dimensions
Sets the width to the given value.
setWidth(RelAbsVector) - Method in class org.sbml.libsbml.Image
Sets the width of the image when rendered.
setWidth(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the siwidth of the Rectangle
setWriteComment(boolean) - Static method in class org.sbml.libsbml.XMLOutputStream
sets a flag, whether the output stream will write an XML comment at the top of the file.
setWriteTimestamp(boolean) - Static method in class org.sbml.libsbml.XMLOutputStream
sets a flag, whether the output stream will write an XML comment with a timestamp at the top of the file.
setX(double) - Method in class org.sbml.libsbml.BoundingBox
Set x offset of the bounding box.
setX(double) - Method in class org.sbml.libsbml.Point
Sets the x offset.
setX(RelAbsVector) - Method in class org.sbml.libsbml.Image
Sets the x coordinate of the image position.
setX(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the x position of the Rectangle within the viewport.
setX(RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
Sets the x ccordiante of the RenderPoint object.
setX(RelAbsVector) - Method in class org.sbml.libsbml.Text
Sets the x position of the text within the viewport.
setXOffset(double) - Method in class org.sbml.libsbml.Point
Sets the x offset.
setY(double) - Method in class org.sbml.libsbml.BoundingBox
Set y offset of the bounding box.
setY(double) - Method in class org.sbml.libsbml.Point
Sets the y offset.
setY(RelAbsVector) - Method in class org.sbml.libsbml.Image
Sets the y coordinate of the image position.
setY(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the y position of the Rectangle within the viewport.
setY(RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
Sets the y ccordiante of the RenderPoint object.
setY(RelAbsVector) - Method in class org.sbml.libsbml.Text
Sets the y position of the text within the viewport.
setYear(long) - Method in class org.sbml.libsbml.Date
Sets the value of the year of this Date object.
setYOffset(double) - Method in class org.sbml.libsbml.Point
Sets the y offset.
setZ(double) - Method in class org.sbml.libsbml.BoundingBox
Set z offset of the bounding box.
setZ(double) - Method in class org.sbml.libsbml.Point
Sets the z offset.
setZ(RelAbsVector) - Method in class org.sbml.libsbml.Image
Sets the z coordinate of the image position.
setZ(RelAbsVector) - Method in class org.sbml.libsbml.Rectangle
Sets the z position of the Rectangle within the viewport.
setZ(RelAbsVector) - Method in class org.sbml.libsbml.RenderPoint
Sets the z ccordiante of the RenderPoint object.
setZ(RelAbsVector) - Method in class org.sbml.libsbml.Text
Sets the z position of the text within the viewport.
setZOffset(double) - Method in class org.sbml.libsbml.Point
Sets the z offset.
SimpleSpeciesReference - Class in org.sbml.libsbml
Abstract class for references to species in reactions.
simplify(UnitDefinition) - Static method in class org.sbml.libsbml.UnitDefinition
Simplifies the UnitDefinition such that any given kind of Unit object occurs only once in the ListOfUnits.
size() - Method in class org.sbml.libsbml.ListOf
Returns number of items in this ListOf list.
size() - Method in class org.sbml.libsbml.StringSet
 
skipPastEnd(XMLToken) - Method in class org.sbml.libsbml.XMLInputStream
Consume zero or more tokens up to and including the corresponding end element or EOF.
skipText() - Method in class org.sbml.libsbml.XMLInputStream
Consume zero or more tokens up to but not including the next XML element or EOF.
SpatialSizeUnitsNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpatialSizeUnitsRemoved - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpatialUnitsInOneD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpatialUnitsInThreeD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpatialUnitsInTwoD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Species - Class in org.sbml.libsbml
An SBML species – a pool of entities.
Species(long, long) - Constructor for class org.sbml.libsbml.Species
Creates a new Species using the given SBML level and version values.
Species(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Species
Creates a new Species using the given SBMLNamespaces object sbmlns.
Species(Species) - Constructor for class org.sbml.libsbml.Species
Copy constructor; creates a copy of this Species object.
SPECIES_ROLE_ACTIVATOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_INHIBITOR - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_INVALID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_MODIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_PRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_SIDEPRODUCT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_SIDESUBSTRATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_SUBSTRATE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SPECIES_ROLE_UNDEFINED - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesCompartmentRequiredInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesGlyph - Class in org.sbml.libsbml
layout A glyph for an SBML species.
SpeciesGlyph() - Constructor for class org.sbml.libsbml.SpeciesGlyph
Creates a new SpeciesGlyph with the given SBML level, version, and package version and the id of the associated species set to the empty string.
SpeciesGlyph(long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Creates a new SpeciesGlyph with the given SBML level, version, and package version and the id of the associated species set to the empty string.
SpeciesGlyph(long, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Creates a new SpeciesGlyph with the given SBML level, version, and package version and the id of the associated species set to the empty string.
SpeciesGlyph(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Creates a new SpeciesGlyph with the given SBML level, version, and package version and the id of the associated species set to the empty string.
SpeciesGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Constructor.
SpeciesGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Creates a new SpeciesGlyph with the given id.
SpeciesGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Creates a new SpeciesGlyph with the given id and the id of the associated species object set to the second argument.
SpeciesGlyph(SpeciesGlyph) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Copy constructor.
SpeciesGlyph(XMLNode) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Creates a new SpeciesGlyph from the given XMLNode
SpeciesGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.SpeciesGlyph
Creates a new SpeciesGlyph from the given XMLNode
SpeciesInvalidExtentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesReference - Class in org.sbml.libsbml
A reference to an SBML species in a reaction.
SpeciesReference(long, long) - Constructor for class org.sbml.libsbml.SpeciesReference
Creates a new SpeciesReference using the given SBML level and version values.
SpeciesReference(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SpeciesReference
Creates a new SpeciesReference using the given SBMLNamespaces object sbmlns.
SpeciesReference(SpeciesReference) - Constructor for class org.sbml.libsbml.SpeciesReference
Copy constructor; creates a copy of this SpeciesReference.
SpeciesReferenceGlyph - Class in org.sbml.libsbml
layout A glyph for an SBML species reference.
SpeciesReferenceGlyph() - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph with the given SBML level, version and package version.
SpeciesReferenceGlyph(long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph with the given SBML level, version and package version.
SpeciesReferenceGlyph(long, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph with the given SBML level, version and package version.
SpeciesReferenceGlyph(long, long, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph with the given SBML level, version and package version.
SpeciesReferenceGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Constructor.
SpeciesReferenceGlyph(LayoutPkgNamespaces, String, String, String, int) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph.
SpeciesReferenceGlyph(SpeciesReferenceGlyph) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Copy constructor.
SpeciesReferenceGlyph(XMLNode) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph from the given XMLNode
SpeciesReferenceGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.SpeciesReferenceGlyph
Creates a new SpeciesReferenceGlyph from the given XMLNode
SpeciesRefIdInMathMLNotSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesShouldHaveValue - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesType - Class in org.sbml.libsbml
A species type in SBML Level 2.
SpeciesType(long, long) - Constructor for class org.sbml.libsbml.SpeciesType
Creates a new SpeciesType using the given SBML level and version values.
SpeciesType(SBMLNamespaces) - Constructor for class org.sbml.libsbml.SpeciesType
Creates a new SpeciesType using the given SBMLNamespaces object sbmlns.
SpeciesType(SpeciesType) - Constructor for class org.sbml.libsbml.SpeciesType
Copy constructor; creates a copy of this SpeciesType.
SpeciesTypeNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpeciesTypeNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SpreadMethod_fromString(String) - Static method in class org.sbml.libsbml.libsbml
 
SpreadMethod_toString(int) - Static method in class org.sbml.libsbml.libsbml
 
startElement(String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given XML start element name to this XMLOutputStream.
startElement(String, String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given XML start element name to this XMLOutputStream.
startElement(XMLTriple) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given XML start element prefix:name on this output stream.
startEndElement(String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given XML start and end element name to this XMLOutputStream.
startEndElement(String, String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given XML start and end element name to this XMLOutputStream.
startEndElement(XMLTriple) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given start element to this output stream.
StoichiometryMath - Class in org.sbml.libsbml
Stochiometry expressions in SBML Level 2 reactions.
StoichiometryMath(long, long) - Constructor for class org.sbml.libsbml.StoichiometryMath
Creates a new StoichiometryMath object using the given SBML level values.
StoichiometryMath(SBMLNamespaces) - Constructor for class org.sbml.libsbml.StoichiometryMath
Creates a new StoichiometryMath object using the given SBMLNamespaces object sbmlns.
StoichiometryMath(StoichiometryMath) - Constructor for class org.sbml.libsbml.StoichiometryMath
Copy constructor; creates a copy of this StoichiometryMath.
StoichiometryMathMissingMath - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StoichiometryMathNotValidComponent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StoichiometryMathNotYetSupported - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
str() - Method in class org.sbml.libsbml.OStringStream
 
str(String) - Method in class org.sbml.libsbml.OStringStream
 
straighten() - Method in class org.sbml.libsbml.CubicBezier
Turns the CubicBezier into a line by setting both 'basepoint1' and 'basepoint2' children to the midpoint between the 'start' and the 'end' points.
StrictSBORequiredInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictSBORequiredInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictUnitsRequiredInL1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictUnitsRequiredInL2v1 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictUnitsRequiredInL2v2 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StrictUnitsRequiredInL2v3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
StringSet - Class in org.sbml.libsbml
 
StringSet() - Constructor for class org.sbml.libsbml.StringSet
 
StringSet(StringSet) - Constructor for class org.sbml.libsbml.StringSet
 
stringToInt(String) - Static method in class org.sbml.libsbml.SBO
Returns the string as a correctly formatted SBO integer portion.
Style - Class in org.sbml.libsbml
abstract base class for local and global styles
STYLE_INVALID - Static variable in class org.sbml.libsbml.Text
 
STYLE_ITALIC - Static variable in class org.sbml.libsbml.Text
 
STYLE_NORMAL - Static variable in class org.sbml.libsbml.Text
 
STYLE_UNSET - Static variable in class org.sbml.libsbml.Text
 
Submodel - Class in org.sbml.libsbml
comp A model instance inside another model.
Submodel() - Constructor for class org.sbml.libsbml.Submodel
Creates a new Submodel with the given level, version, and package version.
Submodel(long) - Constructor for class org.sbml.libsbml.Submodel
Creates a new Submodel with the given level, version, and package version.
Submodel(long, long) - Constructor for class org.sbml.libsbml.Submodel
Creates a new Submodel with the given level, version, and package version.
Submodel(long, long, long) - Constructor for class org.sbml.libsbml.Submodel
Creates a new Submodel with the given level, version, and package version.
Submodel(CompPkgNamespaces) - Constructor for class org.sbml.libsbml.Submodel
Creates a new Submodel with the given CompPkgNamespaces object.
Submodel(Submodel) - Constructor for class org.sbml.libsbml.Submodel
Copy constructor.
SubstanceUnitsOnSpecies - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SubsUnitsAllowedInKL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
SubsUnitsNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
swapChildren(ASTNode) - Method in class org.sbml.libsbml.ASTNode
Swaps the children of this node with the children of another node.
SyntaxChecker - Class in org.sbml.libsbml
Methods for checking the validity of SBML identifiers.
SyntaxChecker() - Constructor for class org.sbml.libsbml.SyntaxChecker
 

T

Text - Class in org.sbml.libsbml
Text element from the SBML render extension.
Text() - Constructor for class org.sbml.libsbml.Text
Creates a new Text object with the given SBML level and SBML version.
Text(long) - Constructor for class org.sbml.libsbml.Text
Creates a new Text object with the given SBML level and SBML version.
Text(long, long) - Constructor for class org.sbml.libsbml.Text
Creates a new Text object with the given SBML level and SBML version.
Text(long, long, long) - Constructor for class org.sbml.libsbml.Text
Creates a new Text object with the given SBML level and SBML version.
Text(RenderPkgNamespaces) - Constructor for class org.sbml.libsbml.Text
Creates a new Text object with the given SBMLNamespaces.
Text(RenderPkgNamespaces, String) - Constructor for class org.sbml.libsbml.Text
Instantiates a new Text object with the given id and position offset.
Text(RenderPkgNamespaces, String, RelAbsVector) - Constructor for class org.sbml.libsbml.Text
Instantiates a new Text object with the given id and position offset.
Text(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Text
Instantiates a new Text object with the given id and position offset.
Text(RenderPkgNamespaces, String, RelAbsVector, RelAbsVector, RelAbsVector) - Constructor for class org.sbml.libsbml.Text
Instantiates a new Text object with the given id and position offset.
Text(XMLNode) - Constructor for class org.sbml.libsbml.Text
Creates a new Text object from the given XMLNode object.
Text(XMLNode, long) - Constructor for class org.sbml.libsbml.Text
Creates a new Text object from the given XMLNode object.
TextAnchor_fromString(String) - Static method in class org.sbml.libsbml.libsbml
 
TextAnchor_toString(int) - Static method in class org.sbml.libsbml.libsbml
 
TextGlyph - Class in org.sbml.libsbml
layout A glyph for a text label.
TextGlyph() - Constructor for class org.sbml.libsbml.TextGlyph
Creates a new TextGlyph with the given SBML level, versin and package version.
TextGlyph(long) - Constructor for class org.sbml.libsbml.TextGlyph
Creates a new TextGlyph with the given SBML level, versin and package version.
TextGlyph(long, long) - Constructor for class org.sbml.libsbml.TextGlyph
Creates a new TextGlyph with the given SBML level, versin and package version.
TextGlyph(long, long, long) - Constructor for class org.sbml.libsbml.TextGlyph
Creates a new TextGlyph with the given SBML level, versin and package version.
TextGlyph(LayoutPkgNamespaces) - Constructor for class org.sbml.libsbml.TextGlyph
Constructor.
TextGlyph(LayoutPkgNamespaces, String) - Constructor for class org.sbml.libsbml.TextGlyph
Creates a new TextGlyph.
TextGlyph(LayoutPkgNamespaces, String, String) - Constructor for class org.sbml.libsbml.TextGlyph
Creates a new TextGlyph.
TextGlyph(TextGlyph) - Constructor for class org.sbml.libsbml.TextGlyph
Copy constructor.
TextGlyph(XMLNode) - Constructor for class org.sbml.libsbml.TextGlyph
Creates a new TextGlyph from the given XMLNode
TextGlyph(XMLNode, long) - Constructor for class org.sbml.libsbml.TextGlyph
Creates a new TextGlyph from the given XMLNode
ThreeDimensionalCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TimeUnitsAllowedInKL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TimeUnitsEvent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TimeUnitsNoLongerValid - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TimeUnitsRemoved - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
toInfix() - Method in class org.sbml.libsbml.Association
Converts this Association object into an infix string representation.
toInfix() - Method in class org.sbml.libsbml.FbcAnd
Converts this FbcAssociation object into an infix string representation.
toInfix() - Method in class org.sbml.libsbml.FbcAssociation
Converts this FbcAssociation object into an infix string representation.
toInfix() - Method in class org.sbml.libsbml.FbcOr
Converts this FbcAssociation object into an infix string representation.
toInfix() - Method in class org.sbml.libsbml.GeneProductRef
Converts this FbcAssociation object into an infix string representation.
toInfix(boolean) - Method in class org.sbml.libsbml.FbcAnd
Converts this FbcAssociation object into an infix string representation.
toInfix(boolean) - Method in class org.sbml.libsbml.FbcAssociation
Converts this FbcAssociation object into an infix string representation.
toInfix(boolean) - Method in class org.sbml.libsbml.FbcOr
Converts this FbcAssociation object into an infix string representation.
toInfix(boolean) - Method in class org.sbml.libsbml.GeneProductRef
Converts this FbcAssociation object into an infix string representation.
toSBML() - Method in class org.sbml.libsbml.SBase
Returns a string consisting of a partial SBML corresponding to just this object.
toString() - Method in class org.sbml.libsbml.RelAbsVector
 
toString() - Method in class org.sbml.libsbml.XMLErrorLog
Writes all errors contained in this log to a string and returns it.
toString() - Method in class org.sbml.libsbml.XMLInputStream
Prints a string representation of the underlying token stream.
toString() - Method in class org.sbml.libsbml.XMLToken
Prints a string representation of the underlying token stream.
toXML() - Method in class org.sbml.libsbml.Association
Creates an XMLNode object from this Association object.
toXML() - Method in class org.sbml.libsbml.BoundingBox
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ColorDefinition
Creates an XMLNode object from this ColorDefinition object.
toXML() - Method in class org.sbml.libsbml.CompartmentGlyph
Creates an XMLNode object from this CompartmentGlyph.
toXML() - Method in class org.sbml.libsbml.CubicBezier
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.Curve
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.Dimensions
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.Ellipse
Creates an XMLNode object from this Ellipse object.
toXML() - Method in class org.sbml.libsbml.GeneAssociation
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.GeneralGlyph
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.GlobalRenderInformation
Creates an XMLNode object from this GlobalRenderInformation object.
toXML() - Method in class org.sbml.libsbml.GradientBase
Creates an Text object from this Group object.
toXML() - Method in class org.sbml.libsbml.GradientStop
Creates an XMLNode object from this GradientStop object.
toXML() - Method in class org.sbml.libsbml.GraphicalObject
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Creates an XMLNode object from this GraphicalPrimitive1D object.
toXML() - Method in class org.sbml.libsbml.Image
Creates an XMLNode object from this Image object.
toXML() - Method in class org.sbml.libsbml.Layout
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.LinearGradient
Creates an XMLNode object from this LinearGradient object.
toXML() - Method in class org.sbml.libsbml.LineEnding
Creates an XMLNode object from this LineEnding object.
toXML() - Method in class org.sbml.libsbml.LineSegment
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfColorDefinitions
Creates an XMLNode object from this ListOfColorDefinitions object.
toXML() - Method in class org.sbml.libsbml.ListOfCompartmentGlyphs
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfCurveElements
Creates an XMLNode object from this ListOfCurveElements object.
toXML() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Creates an XMLNode object from this ListOfGlobalRenderInformation object.
toXML() - Method in class org.sbml.libsbml.ListOfGlobalStyles
Creates an XMLNode object from this ListOfGlobalStyles object.
toXML() - Method in class org.sbml.libsbml.ListOfGradientDefinitions
Creates an XMLNode object from this ListOfGradientDefinitions object.
toXML() - Method in class org.sbml.libsbml.ListOfGradientStops
Creates an XMLNode object from this ListOfGradientStops object.
toXML() - Method in class org.sbml.libsbml.ListOfGraphicalObjects
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfLayouts
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfLineEndings
Creates an XMLNode object from this ListOfLineEndings object.
toXML() - Method in class org.sbml.libsbml.ListOfLineSegments
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Creates an XMLNode object from this ListOfGradientDefinitions object.
toXML() - Method in class org.sbml.libsbml.ListOfLocalStyles
Creates an XMLNode object from this ListOfLocalStyles object.
toXML() - Method in class org.sbml.libsbml.ListOfReactionGlyphs
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfReferenceGlyphs
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfSpeciesGlyphs
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfSpeciesReferenceGlyphs
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.ListOfTextGlyphs
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.LocalRenderInformation
Creates an XMLNode object from this LocalRenderInformation object.
toXML() - Method in class org.sbml.libsbml.LocalStyle
Creates an XMLNode object from this LocalStyle object.
toXML() - Method in class org.sbml.libsbml.Polygon
Creates an XMLNode object from this Polygon object.
toXML() - Method in class org.sbml.libsbml.RadialGradient
Creates an XMLNode object from this RadialGradient object.
toXML() - Method in class org.sbml.libsbml.ReactionGlyph
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.Rectangle
Creates an XMLNode object from this Rectangle object.
toXML() - Method in class org.sbml.libsbml.ReferenceGlyph
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.RenderCurve
Creates an XMLNode object from this RenderCurve object.
toXML() - Method in class org.sbml.libsbml.RenderGroup
Creates an XMLNode object from this RenderGroup object.
toXML() - Method in class org.sbml.libsbml.SpeciesGlyph
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.SpeciesReferenceGlyph
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.Style
Creates an XMLNode object from this Style object.
toXML() - Method in class org.sbml.libsbml.Text
Creates an XMLNode object from this GraphicalPrimitive1D object.
toXML() - Method in class org.sbml.libsbml.TextGlyph
Creates an XMLNode object from this.
toXML() - Method in class org.sbml.libsbml.Transformation2D
Creates an XMLNode object from this Transformation2D object.
toXML(String) - Method in class org.sbml.libsbml.Point
Creates an XMLNode object from this.
toXML(String) - Method in class org.sbml.libsbml.RenderCubicBezier
Creates an XMLNode object from this RenderCubicBezier object.
toXML(String) - Method in class org.sbml.libsbml.RenderPoint
Creates an XMLNode object from this ColorDefinition object.
toXMLNode() - Method in class org.sbml.libsbml.SBase
Returns this element as an XMLNode.
toXMLString() - Method in class org.sbml.libsbml.XMLNode
Returns a string representation of this XMLNode.
Transformation - Class in org.sbml.libsbml
implementation of a 3D transformation matrix.
Transformation2D - Class in org.sbml.libsbml
implementation of a 2D transformation matrix.
Transition - Class in org.sbml.libsbml
qual A transition of a QualitativeSpecies.
Transition() - Constructor for class org.sbml.libsbml.Transition
Creates a new Transition with the given level, version, and package version.
Transition(long) - Constructor for class org.sbml.libsbml.Transition
Creates a new Transition with the given level, version, and package version.
Transition(long, long) - Constructor for class org.sbml.libsbml.Transition
Creates a new Transition with the given level, version, and package version.
Transition(long, long, long) - Constructor for class org.sbml.libsbml.Transition
Creates a new Transition with the given level, version, and package version.
Transition(QualPkgNamespaces) - Constructor for class org.sbml.libsbml.Transition
Creates a new Transition with the given QualPkgNamespaces object.
Transition(Transition) - Constructor for class org.sbml.libsbml.Transition
Copy constructor for Transition.
Trigger - Class in org.sbml.libsbml
The trigger expression for an SBML event.
Trigger(long, long) - Constructor for class org.sbml.libsbml.Trigger
Creates a new Trigger using the given SBML level and version values.
Trigger(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Trigger
Creates a new Trigger using the given SBMLNamespaces object sbmlns.
Trigger(Trigger) - Constructor for class org.sbml.libsbml.Trigger
Copy constructor; creates a copy of this Trigger.
TriggerMathNotBoolean - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
TwoDimensionalCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

U

UnclosedXMLToken - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredExtentUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredObjectUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredSpeciesInStoichMath - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredSpeciesRef - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredTimeUnitsL3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndeclaredUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndefinedOutsideCompartment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UndefinedXMLEntity - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UninterpretableXMLContent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
Unit - Class in org.sbml.libsbml
A single unit referenced in an SBML unit definition.
Unit(long, long) - Constructor for class org.sbml.libsbml.Unit
Creates a new Unit using the given SBML level and version values.
Unit(SBMLNamespaces) - Constructor for class org.sbml.libsbml.Unit
Creates a new Unit using the given SBMLNamespaces object sbmlns.
Unit(Unit) - Constructor for class org.sbml.libsbml.Unit
Copy constructor; creates a copy of this Unit.
UNIT_KIND_AMPERE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_AVOGADRO - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_BECQUEREL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_CANDELA - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_CELSIUS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_COULOMB - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_DIMENSIONLESS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_FARAD - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_GRAM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_GRAY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_HENRY - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_HERTZ - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_INVALID - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_ITEM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_JOULE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_KATAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_KELVIN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_KILOGRAM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_LITER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_LITRE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_LUMEN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_LUX - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_METER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_METRE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_MOLE - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_NEWTON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_OHM - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_PASCAL - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_RADIAN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_SECOND - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_SIEMENS - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_SIEVERT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_STERADIAN - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_TESLA - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_VOLT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_WATT - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNIT_KIND_WEBER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnitDefinition - Class in org.sbml.libsbml
A definition of a unit used in an SBML model.
UnitDefinition(long, long) - Constructor for class org.sbml.libsbml.UnitDefinition
Creates a new UnitDefinition using the given SBML level and version values.
UnitDefinition(SBMLNamespaces) - Constructor for class org.sbml.libsbml.UnitDefinition
Creates a new UnitDefinition using the given SBMLNamespaces object sbmlns.
UnitDefinition(UnitDefinition) - Constructor for class org.sbml.libsbml.UnitDefinition
Copy constructor; creates a copy of this UnitDefinition.
UnitKind_equals(int, int) - Static method in class org.sbml.libsbml.libsbml
Tests for logical equality between two given UNIT_KIND_ code values.
UnitKind_forName(String) - Static method in class org.sbml.libsbml.libsbml
Converts a text string naming a kind of unit to its corresponding libSBML UNIT_KIND_ constant/enumeration value.
UnitKind_isValidUnitKindString(String, long, long) - Static method in class org.sbml.libsbml.libsbml
Predicate for testing whether a given string corresponds to a predefined libSBML unit code.
UnitKind_toString(int) - Static method in class org.sbml.libsbml.libsbml
Converts a unit code to a text string equivalent.
UnitsCheckOFF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnitsCheckON - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnitsNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNKNOWN_ASSOCIATION - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNKNOWN_QUALIFIER - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnknownCoreAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnknownError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnknownPackageAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrecognisedSBOTerm - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrecognizedElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrecognizedXMLElement - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrecognizedXMLParserCode - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UnrequiredPackagePresent - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
UNSET - Static variable in class org.sbml.libsbml.GraphicalPrimitive2D
 
unsetActiveObjective() - Method in class org.sbml.libsbml.ListOfObjectives
Unsets the value of the 'activeObjective' attribute of this ListOfObjectives.
unsetActiveObjectiveId() - Method in class org.sbml.libsbml.FbcModelPlugin
Unsets the 'activeObjective' attribute of the ListOfObjectives.
unsetAnnotation() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'annotation' subelement of this SBML object.
unsetAreaUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'areaUnits' attribute of this Model.
unsetAssociatedSpecies() - Method in class org.sbml.libsbml.GeneProduct
Unsets the value of the 'associatedSpecies' attribute of this GeneProduct.
unsetAssociation() - Method in class org.sbml.libsbml.GeneAssociation
Unsets the Association object of this GeneAssociation.
unsetAssociation() - Method in class org.sbml.libsbml.GeneProductAssociation
Unsets the 'association' element of this GeneProductAssociation.
unsetBackgroundColor() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'backgroundColor' attribute of this DefaultValues.
unsetBackgroundColor() - Method in class org.sbml.libsbml.RenderInformationBase
Unsets the value of the 'backgroundColor' attribute of this RenderInformationBase.
unsetBoundaryCondition() - Method in class org.sbml.libsbml.Species
Unsets the 'boundaryCondition' attribute value of this Species object.
unsetCharge() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Unsets the value of the 'charge' attribute of this FbcSpeciesPlugin.
unsetCharge() - Method in class org.sbml.libsbml.Species
Unsets the 'charge' attribute value of this Species object.
unsetChemicalFormula() - Method in class org.sbml.libsbml.FbcSpeciesPlugin
Unsets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.
unsetClass() - Method in class org.sbml.libsbml.ASTNode
Unsets the MathML class attribute of this ASTNode.
unsetCoefficient() - Method in class org.sbml.libsbml.FluxObjective
Unsets the value of the 'coefficient' attribute of this FluxObjective.
unsetCompartment() - Method in class org.sbml.libsbml.QualitativeSpecies
Unsets the value of the 'compartment' attribute of this QualitativeSpecies.
unsetCompartment() - Method in class org.sbml.libsbml.Reaction
Unsets the value of the 'compartment' attribute of this Reaction.
unsetCompartment() - Method in class org.sbml.libsbml.Species
Unsets the 'compartment' attribute value of this Species object.
unsetCompartmentType() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'compartmentType' attribute of this Compartment object.
unsetConstant() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'constant' attribute of this Compartment object.
unsetConstant() - Method in class org.sbml.libsbml.Parameter
Unsets the value of the 'constant' attribute of this Parameter object.
unsetConstant() - Method in class org.sbml.libsbml.QualitativeSpecies
Unsets the value of the 'constant' attribute of this QualitativeSpecies.
unsetConstant() - Method in class org.sbml.libsbml.Species
Unsets the value of the 'constant' attribute of this Species object.
unsetConstant() - Method in class org.sbml.libsbml.SpeciesReference
Unsets the 'constant' attribute of this SpeciesReference.
unsetConversionFactor() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'conversionFactor' attribute of this Model.
unsetConversionFactor() - Method in class org.sbml.libsbml.ReplacedElement
Unsets the value of the 'conversionFactor' attribute of this ReplacedElement.
unsetConversionFactor() - Method in class org.sbml.libsbml.Species
Unsets the 'conversionFactor' attribute value of this Species object.
unsetCVTerms() - Method in class org.sbml.libsbml.SBase
Clears the list of CVTerm objects attached to this SBML object.
unsetDefault_z() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'default_z' attribute of this DefaultValues.
unsetDefaultValues() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Unsets the value of the 'defaultValues' element of this ListOfGlobalRenderInformation.
unsetDefaultValues() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Unsets the value of the 'defaultValues' element of this ListOfLocalRenderInformation.
unsetDelay() - Method in class org.sbml.libsbml.Event
Unsets the Delay of this Event.
unsetDeletion() - Method in class org.sbml.libsbml.ReplacedElement
Unsets the value of the 'deletion' attribute of this ReplacedElement.
unsetEmail() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'email' portion of this ModelCreator object.
unsetEnableRotationalMapping() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'enableRotationalMapping' attribute of this DefaultValues.
unsetEnd() - Method in class org.sbml.libsbml.XMLToken
Declares that this token no longer represents an XML start/end element.
unsetEndHead() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'endHead' attribute of this DefaultValues.
unsetExponent() - Method in class org.sbml.libsbml.Unit
Unsets the 'exponent' attribute value of this Unit.
unsetExtentConversionFactor() - Method in class org.sbml.libsbml.Submodel
Unsets the value of the 'extentConversionFactor' attribute of this Submodel.
unsetExtentUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'extentUnits' attribute of this Model.
unsetFamilyName() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'family name' portion of this ModelCreator object.
unsetFast() - Method in class org.sbml.libsbml.Reaction
Unsets the value of the 'fast' attribute of this Reaction.
unsetFill() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'fill' attribute of this DefaultValues.
unsetFillRule() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'fillRule' attribute of this DefaultValues.
unsetFontFamily() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'fontFamily' attribute of this DefaultValues.
unsetFontSize() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'fontSize' attribute of this DefaultValues.
unsetFontStyle() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'fontStyle' attribute of this DefaultValues.
unsetFontWeight() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'fontWeight' attribute of this DefaultValues.
unsetGeneProduct() - Method in class org.sbml.libsbml.GeneProductRef
Unsets the value of the 'geneProduct' attribute of this GeneProductRef.
unsetGeneProductAssociation() - Method in class org.sbml.libsbml.FbcReactionPlugin
Unsets the the 'geneProduct' element of this FbcReactionPlugin.
unsetGivenName() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'given name' portion of this ModelCreator object.
unsetHasOnlySubstanceUnits() - Method in class org.sbml.libsbml.Species
Unsets the 'hasOnlySubstanceUnits' attribute value of this Species object.
unsetId() - Method in class org.sbml.libsbml.ASTNode
Unsets the MathML id attribute of this ASTNode.
unsetId() - Method in class org.sbml.libsbml.BoundingBox
Unsets the value of the 'id' attribute of this BoundingBox.
unsetId() - Method in class org.sbml.libsbml.ColorDefinition
Unsets the value of the 'id' attribute of this ColorDefinition.
unsetId() - Method in class org.sbml.libsbml.Deletion
Unsets the value of the 'id' attribute of this Deletion.
unsetId() - Method in class org.sbml.libsbml.Dimensions
Unsets the value of the 'id' attribute of this Dimensions.
unsetId() - Method in class org.sbml.libsbml.Event
Unsets the value of the 'id' attribute of this Event.
unsetId() - Method in class org.sbml.libsbml.ExternalModelDefinition
Unsets the value of the 'id' attribute of this ExternalModelDefinition.
unsetId() - Method in class org.sbml.libsbml.FluxBound
Unsets the value of the 'id' attribute of this FluxBound object.
unsetId() - Method in class org.sbml.libsbml.FluxObjective
Unsets the value of the 'id' attribute of this FluxObjective.
unsetId() - Method in class org.sbml.libsbml.GeneAssociation
Unsets the value of the 'id' attribute of this GeneAssociation.
unsetId() - Method in class org.sbml.libsbml.GeneProduct
Unsets the value of the 'id' attribute of this GeneProduct.
unsetId() - Method in class org.sbml.libsbml.GeneProductAssociation
Unsets the value of the 'id' attribute of this GeneProductAssociation.
unsetId() - Method in class org.sbml.libsbml.GeneProductRef
Unsets the value of the 'id' attribute of this GeneProductRef.
unsetId() - Method in class org.sbml.libsbml.GradientBase
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.GraphicalObject
Unsets the value of the 'id' attribute of this GraphicalObject.
unsetId() - Method in class org.sbml.libsbml.GraphicalPrimitive1D
Unsets the value of the 'id' attribute of this GraphicalPrimitive.
unsetId() - Method in class org.sbml.libsbml.Group
Unsets the value of the 'id' attribute of this Group.
unsetId() - Method in class org.sbml.libsbml.Image
Unsets the value of the 'id' attribute of this Image.
unsetId() - Method in class org.sbml.libsbml.Input
Unsets the value of the 'id' attribute of this Input.
unsetId() - Method in class org.sbml.libsbml.Layout
Unsets the value of the 'id' attribute of this Layout.
unsetId() - Method in class org.sbml.libsbml.LineEnding
Unsets the value of the 'id' attribute of this GraphicalPrimitive.
unsetId() - Method in class org.sbml.libsbml.ListOfMembers
Unsets the value of the 'id' attribute of this ListOfMembers.
unsetId() - Method in class org.sbml.libsbml.Member
Unsets the value of the 'id' attribute of this Member.
unsetId() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'id' attribute of this Model.
unsetId() - Method in class org.sbml.libsbml.Objective
Unsets the value of the 'id' attribute of this Objective.
unsetId() - Method in class org.sbml.libsbml.Output
Unsets the value of the 'id' attribute of this Output.
unsetId() - Method in class org.sbml.libsbml.Point
Unsets the value of the 'id' attribute of this Point.
unsetId() - Method in class org.sbml.libsbml.Port
Unsets the value of the 'id' attribute of this Port.
unsetId() - Method in class org.sbml.libsbml.QualitativeSpecies
Unsets the value of the 'id' attribute of this QualitativeSpecies.
unsetId() - Method in class org.sbml.libsbml.RenderInformationBase
Unsets the value of the 'id' attribute of this RenderInformationBase.
unsetId() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'id' attribute of this SBML object.
unsetId() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Unsets the value of the 'id' attribute of this SimpleSpeciesReference.
unsetId() - Method in class org.sbml.libsbml.Style
Unsets the value of the 'id' attribute of this Style.
unsetId() - Method in class org.sbml.libsbml.Submodel
Unsets the value of the 'id' attribute of this Submodel.
unsetId() - Method in class org.sbml.libsbml.Transition
Unsets the value of the 'id' attribute of this Transition.
unsetIdAttribute() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'id' attribute of this SBML object.
unsetIdRef() - Method in class org.sbml.libsbml.Member
Unsets the value of the 'idRef' attribute of this Member.
unsetIdRef() - Method in class org.sbml.libsbml.SBaseRef
Unsets the value of the 'idRef' attribute of this SBaseRef.
unsetInitialAmount() - Method in class org.sbml.libsbml.Species
Unsets the 'initialAmount' attribute value of this Species object.
unsetInitialConcentration() - Method in class org.sbml.libsbml.Species
Unsets the 'initialConcentration' attribute value of this Species object.
unsetInitialLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
Unsets the value of the 'initialLevel' attribute of this QualitativeSpecies.
unsetInitialValue() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Unsets the 'initialValue' attribute of this Trigger instance.
unsetKind() - Method in class org.sbml.libsbml.Group
Unsets the value of the 'kind' attribute of this Group.
unsetKind() - Method in class org.sbml.libsbml.Unit
Unsets the 'kind' attribute value of this Unit.
unsetKineticLaw() - Method in class org.sbml.libsbml.Reaction
Unsets the 'kineticLaw' subelement of this Reaction.
unsetLabel() - Method in class org.sbml.libsbml.GeneProduct
Unsets the value of the 'label' attribute of this GeneProduct.
unsetLengthUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'lengthUnits' attribute of this Model.
unsetLinearGradient_x1() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'linearGradient_x1' attribute of this DefaultValues.
unsetLinearGradient_x2() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'linearGradient_x2' attribute of this DefaultValues.
unsetLinearGradient_y1() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'linearGradient_y1' attribute of this DefaultValues.
unsetLinearGradient_y2() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'linearGradient_y2' attribute of this DefaultValues.
unsetLinearGradient_z1() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'linearGradient_z1' attribute of this DefaultValues.
unsetLinearGradient_z2() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'linearGradient_z2' attribute of this DefaultValues.
unsetLowerFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
Unsets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.
unsetMath() - Method in class org.sbml.libsbml.FunctionTerm
Unsets the 'math' element of this FunctionTerm.
unsetMaxLevel() - Method in class org.sbml.libsbml.QualitativeSpecies
Unsets the value of the 'maxLevel' attribute of this QualitativeSpecies.
unsetMd5() - Method in class org.sbml.libsbml.ExternalModelDefinition
Unsets the value of the 'md5' attribute of this ExternalModelDefinition.
unsetMessage() - Method in class org.sbml.libsbml.Constraint
Unsets the 'message' subelement of this Constraint.
unsetMetaId() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'metaid' attribute of this SBML object.
unsetMetaIdRef() - Method in class org.sbml.libsbml.GraphicalObject
Unsets the value of the 'metaidRef' attribute of this GraphicalObject.
unsetMetaIdRef() - Method in class org.sbml.libsbml.Member
Unsets the value of the 'metaIdRef' attribute of this Member.
unsetMetaIdRef() - Method in class org.sbml.libsbml.SBaseRef
Unsets the value of the 'metaIdRef' attribute of this SBaseRef.
unsetModel() - Method in class org.sbml.libsbml.L3ParserSettings
Unsets the Model reference in this L3ParserSettings object.
unsetModelHistory() - Method in class org.sbml.libsbml.SBase
Unsets the ModelHistory object attached to this object.
unsetModelRef() - Method in class org.sbml.libsbml.ExternalModelDefinition
Unsets the value of the 'modelRef' attribute of this ExternalModelDefinition.
unsetModelRef() - Method in class org.sbml.libsbml.Submodel
Unsets the value of the 'modelRef' attribute of this Submodel.
unsetMultiplier() - Method in class org.sbml.libsbml.Unit
Unsets the 'multipler' attribute value of this Unit.
unsetName() - Method in class org.sbml.libsbml.ColorDefinition
Unsets the value of the 'name' attribute of this ColorDefinition.
unsetName() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'name' attribute of this Compartment object.
unsetName() - Method in class org.sbml.libsbml.CompartmentType
Unsets the value of the 'name' attribute of this CompartmentType object.
unsetName() - Method in class org.sbml.libsbml.Deletion
Unsets the value of the 'name' attribute of this Deletion.
unsetName() - Method in class org.sbml.libsbml.Event
Unsets the value of the 'name' attribute of this Event.
unsetName() - Method in class org.sbml.libsbml.ExternalModelDefinition
Unsets the value of the 'name' attribute of this ExternalModelDefinition.
unsetName() - Method in class org.sbml.libsbml.FluxBound
Unsets the value of the 'name' attribute of this FluxBound object.
unsetName() - Method in class org.sbml.libsbml.FluxObjective
Unsets the value of the 'name' attribute of this FluxObjective.
unsetName() - Method in class org.sbml.libsbml.FunctionDefinition
Unsets the value of the 'name' attribute of this FunctionDefinition.
unsetName() - Method in class org.sbml.libsbml.GeneProduct
Unsets the value of the 'name' attribute of this GeneProduct.
unsetName() - Method in class org.sbml.libsbml.GeneProductAssociation
Unsets the value of the 'name' attribute of this GeneProductAssociation.
unsetName() - Method in class org.sbml.libsbml.GeneProductRef
Unsets the value of the 'name' attribute of this GeneProductRef.
unsetName() - Method in class org.sbml.libsbml.GradientBase
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.Group
Unsets the value of the 'name' attribute of this Group.
unsetName() - Method in class org.sbml.libsbml.Input
Unsets the value of the 'name' attribute of this Input.
unsetName() - Method in class org.sbml.libsbml.Layout
Unsets the value of the 'name' attribute of this Layout.
unsetName() - Method in class org.sbml.libsbml.ListOfMembers
Unsets the value of the 'name' attribute of this ListOfMembers.
unsetName() - Method in class org.sbml.libsbml.Member
Unsets the value of the 'name' attribute of this Member.
unsetName() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'name' attribute of this Model.
unsetName() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'fn' portion of this ModelCreator object (when using vCard4).
unsetName() - Method in class org.sbml.libsbml.Objective
Unsets the value of the 'name' attribute of this Objective.
unsetName() - Method in class org.sbml.libsbml.Output
Unsets the value of the 'name' attribute of this Output.
unsetName() - Method in class org.sbml.libsbml.Parameter
Unsets the value of the 'name' attribute of this Parameter.
unsetName() - Method in class org.sbml.libsbml.Port
Unsets the value of the 'name' attribute of this Port.
unsetName() - Method in class org.sbml.libsbml.QualitativeSpecies
Unsets the value of the 'name' attribute of this QualitativeSpecies.
unsetName() - Method in class org.sbml.libsbml.Reaction
Unsets the value of the 'name' attribute of this Reaction.
unsetName() - Method in class org.sbml.libsbml.RenderInformationBase
Unsets the value of the 'name' attribute of this RenderInformationBase.
unsetName() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'name' attribute of this SBML object.
unsetName() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Unsets the value of the 'name' attribute of this SimpleSpeciesReference.
unsetName() - Method in class org.sbml.libsbml.Species
Unsets the value of the 'name' attribute of this Species object.
unsetName() - Method in class org.sbml.libsbml.SpeciesType
Unsets the value of the 'name' attribute of this SpeciesType.
unsetName() - Method in class org.sbml.libsbml.Style
Unsets the value of the 'name' attribute of this Style.
unsetName() - Method in class org.sbml.libsbml.Submodel
Unsets the value of the 'name' attribute of this Submodel.
unsetName() - Method in class org.sbml.libsbml.Transformation
Unsets the value of the 'name' attribute of this Transformation.
unsetName() - Method in class org.sbml.libsbml.Transition
Unsets the value of the 'name' attribute of this Transition.
unsetName() - Method in class org.sbml.libsbml.UnitDefinition
Unsets the value of the 'name' attribute of this UnitDefinition.
unsetNotes() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'notes' subelement of this SBML object.
unsetOffset() - Method in class org.sbml.libsbml.Unit
Unsets the 'offset' attribute value of this Unit.
unsetOperation() - Method in class org.sbml.libsbml.FluxBound
Unsets the value of the 'operation' attribute of this FluxBound object.
unsetOrder() - Method in class org.sbml.libsbml.CompartmentGlyph
Unsets the compartment order.
unsetOrganisation() - Method in class org.sbml.libsbml.ModelCreator
(Alternate spelling) Unsets the 'organization' portion of this ModelCreator object.
unsetOrganization() - Method in class org.sbml.libsbml.ModelCreator
Unsets the 'organization' portion of this ModelCreator object.
unsetOutputLevel() - Method in class org.sbml.libsbml.Output
Unsets the value of the 'outputLevel' attribute of this Output.
unsetOutside() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'outside' attribute of this Compartment object.
unsetParentSBMLObject() - Method in class org.sbml.libsbml.ASTNode
Unsets the parent SBML object.
unsetPersistent() - Method in class org.sbml.libsbml.Trigger
(SBML Level 3 only) Unsets the 'persistent' attribute of this Trigger instance.
unsetPortRef() - Method in class org.sbml.libsbml.SBaseRef
Unsets the value of the 'portRef' attribute of this SBaseRef.
unsetPriority() - Method in class org.sbml.libsbml.Event
(SBML Level 3 only) Unsets the Priority of this Event.
unsetQualitativeSpecies() - Method in class org.sbml.libsbml.Input
Unsets the value of the 'qualitativeSpecies' attribute of this Input.
unsetQualitativeSpecies() - Method in class org.sbml.libsbml.Output
Unsets the value of the 'qualitativeSpecies' attribute of this Output.
unsetRadialGradient_cx() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'radialGradient_cx' attribute of this DefaultValues.
unsetRadialGradient_cy() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'radialGradient_cy' attribute of this DefaultValues.
unsetRadialGradient_cz() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'radialGradient_cz' attribute of this DefaultValues.
unsetRadialGradient_fx() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'radialGradient_fx' attribute of this DefaultValues.
unsetRadialGradient_fy() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'radialGradient_fy' attribute of this DefaultValues.
unsetRadialGradient_fz() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'radialGradient_fz' attribute of this DefaultValues.
unsetRadialGradient_r() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'radialGradient_r' attribute of this DefaultValues.
unsetRatio() - Method in class org.sbml.libsbml.Ellipse
Unsets the value of the 'ratio' attribute of this Ellipse.
unsetRatio() - Method in class org.sbml.libsbml.Rectangle
Unsets the value of the 'ratio' attribute of this Rectangle.
unsetReaction() - Method in class org.sbml.libsbml.FluxBound
Unsets the value of the 'reaction' attribute of this FluxBound object.
unsetReaction() - Method in class org.sbml.libsbml.FluxObjective
Unsets the value of the 'reaction' attribute of this FluxObjective.
unsetReaction() - Method in class org.sbml.libsbml.GeneAssociation
Unsets the value of the 'id' attribute of this GeneAssociation.
unsetReference() - Method in class org.sbml.libsbml.Association
Unsets the value of the 'id' attribute of this Association object.
unsetReferenceRenderInformation() - Method in class org.sbml.libsbml.RenderInformationBase
Unsets the value of the 'referenceRenderInformation' attribute of this RenderInformationBase.
unsetReplacedBy() - Method in class org.sbml.libsbml.CompSBasePlugin
Unsets the child ReplacedBy of this SBase.
unsetRequired() - Method in class org.sbml.libsbml.SBMLDocumentPlugin
Unsets the value of the 'required' attribute of this SBMLDocumentPlugin.
unsetResultLevel() - Method in class org.sbml.libsbml.DefaultTerm
Unsets the value of the 'resultLevel' attribute of this DefaultTerm.
unsetResultLevel() - Method in class org.sbml.libsbml.FunctionTerm
Unsets the value of the 'resultLevel' attribute of this FunctionTerm.
unsetReversible() - Method in class org.sbml.libsbml.Reaction
Unsets the value of the 'reversible' attribute of this Reaction.
unsetSBaseRef() - Method in class org.sbml.libsbml.SBaseRef
Unsets the child SBaseRef of this SBaseRef.
unsetSBOTerm() - Method in class org.sbml.libsbml.SBase
Unsets the value of the 'sboTerm' attribute of this SBML object.
unsetScale() - Method in class org.sbml.libsbml.Unit
Unsets the 'scale' attribute value of this Unit.
unsetSeverityOverride() - Method in class org.sbml.libsbml.XMLErrorLog
Usets an existing override.
unsetSign() - Method in class org.sbml.libsbml.Input
Unsets the value of the 'sign' attribute of this Input.
unsetSize() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'size' attribute of this Compartment object.
unsetSource() - Method in class org.sbml.libsbml.ExternalModelDefinition
Unsets the value of the 'source' attribute of this ExternalModelDefinition.
unsetSpatialDimensions() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'spatialDimensions' attribute of this Compartment object.
unsetSpatialSizeUnits() - Method in class org.sbml.libsbml.Species
Unsets the 'spatialSizeUnits' attribute value of this Species object.
unsetSpecies() - Method in class org.sbml.libsbml.SimpleSpeciesReference
Unsets the value of the 'species' attribute of this SimpleSpeciesReference.
unsetSpeciesType() - Method in class org.sbml.libsbml.Species
Unsets the 'speciesType' attribute value of this Species object.
unsetSpreadMethod() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'spreadMethod' attribute of this DefaultValues.
unsetStartHead() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'startHead' attribute of this DefaultValues.
unsetStoichiometry() - Method in class org.sbml.libsbml.SpeciesReference
Unsets the 'stoichiometry' attribute of this SpeciesReference.
unsetStoichiometryMath() - Method in class org.sbml.libsbml.SpeciesReference
Unsets the 'stoichiometryMath' subelement of this SpeciesReference.
unsetStrict() - Method in class org.sbml.libsbml.FbcModelPlugin
Unsets the value of the 'strict' attribute of this FbcModelPlugin.
unsetStroke() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'stroke' attribute of this DefaultValues.
unsetStrokeWidth() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'strokeWidth' attribute of this DefaultValues.
unsetStyle() - Method in class org.sbml.libsbml.ASTNode
Unsets the MathML style attribute of this ASTNode.
unsetSubmodelRef() - Method in class org.sbml.libsbml.Replacing
Unsets the value of the 'SubmodelRef' attribute of this SBaseRef.
unsetSubstanceConversionFactor() - Method in class org.sbml.libsbml.Submodel
Automatically fails, since 'substanceConversionFactor' is not a part of the comp spec.
unsetSubstanceUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Unsets the 'substanceUnits' attribute of this KineticLaw object.
unsetSubstanceUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'substanceUnits' attribute of this Model.
unsetSubstanceUnits() - Method in class org.sbml.libsbml.Species
Unsets the 'substanceUnits' attribute value of this Species object.
unsetSymbol() - Method in class org.sbml.libsbml.InitialAssignment
Unsets the 'symbol' attribute value of this InitialAssignment.
unsetTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'textAnchor' attribute of this DefaultValues.
unsetThresholdLevel() - Method in class org.sbml.libsbml.Input
Unsets the value of the 'thresholdLevel' attribute of this Input.
unsetTimeConversionFactor() - Method in class org.sbml.libsbml.Submodel
Unsets the value of the 'timeConversionFactor' attribute of this Submodel.
unsetTimeUnits() - Method in class org.sbml.libsbml.Event
Unsets the 'timeUnits' attribute of this Event.
unsetTimeUnits() - Method in class org.sbml.libsbml.KineticLaw
(SBML Level 2 Version 1 only) Unsets the 'timeUnits' attribugte of this KineticLaw object.
unsetTimeUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'timeUnits' attribute of this Model.
unsetTransformer() - Method in class org.sbml.libsbml.CompModelPlugin
Unsets any custom prefix transformers.
unsetTransitionEffect() - Method in class org.sbml.libsbml.Input
Unsets the value of the 'transitionEffect' attribute of this Input.
unsetTransitionEffect() - Method in class org.sbml.libsbml.Output
Unsets the value of the 'transitionEffect' attribute of this Output.
unsetTrigger() - Method in class org.sbml.libsbml.Event
Unsets the Trigger of this Event.
unsetType() - Method in class org.sbml.libsbml.Association
Unsets the value of the 'id' attribute of this Association object.
unsetType() - Method in class org.sbml.libsbml.Objective
Unsets the value of the 'type' attribute of this Objective.
unsetUnitRef() - Method in class org.sbml.libsbml.SBaseRef
Unsets the value of the 'unitRef' attribute of this SBaseRef.
unsetUnits() - Method in class org.sbml.libsbml.ASTNode
Unsets the units of this ASTNode.
unsetUnits() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'units' attribute of this Compartment object.
unsetUnits() - Method in class org.sbml.libsbml.Parameter
Unsets the 'units' attribute of this Parameter instance.
unsetUnits() - Method in class org.sbml.libsbml.Rule
Unsets the 'units' for this Rule.
unsetUnits() - Method in class org.sbml.libsbml.Species
Unsets the 'units' attribute value of this Species object.
unsetUpperFluxBound() - Method in class org.sbml.libsbml.FbcReactionPlugin
Unsets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.
unsetUserData() - Method in class org.sbml.libsbml.ASTNode
Unsets the user data of this node.
unsetUserData() - Method in class org.sbml.libsbml.SBase
Unsets the user data of this element.
unsetUseValuesFromTriggerTime() - Method in class org.sbml.libsbml.Event
Unsets the value of the 'useValuesFromTriggerTime' attribute of this Event.
unsetValue() - Method in class org.sbml.libsbml.FluxBound
Unsets the value of the 'value' attribute of this FluxBound object.
unsetValue() - Method in class org.sbml.libsbml.Parameter
Unsets the 'value' attribute of this Parameter instance.
unsetVariable() - Method in class org.sbml.libsbml.EventAssignment
Unsets the attribute 'variable' of this EventAssignment.
unsetVariable() - Method in class org.sbml.libsbml.Rule
Unsets the value of the 'variable' attribute of this Rule object.
unsetVersionMajor() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Unsets the value of the 'versionMajor' attribute of this ListOfGlobalRenderInformation.
unsetVersionMajor() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Unsets the value of the 'versionMajor' attribute of this ListOfLocalRenderInformation.
unsetVersionMinor() - Method in class org.sbml.libsbml.ListOfGlobalRenderInformation
Unsets the value of the 'versionMinor' attribute of this ListOfGlobalRenderInformation.
unsetVersionMinor() - Method in class org.sbml.libsbml.ListOfLocalRenderInformation
Unsets the value of the 'versionMinor' attribute of this ListOfLocalRenderInformation.
unsetVolume() - Method in class org.sbml.libsbml.Compartment
Unsets the value of the 'volume' attribute of this Compartment object.
unsetVolumeUnits() - Method in class org.sbml.libsbml.Model
Unsets the value of the 'volumeUnits' attribute of this Model.
unsetVTextAnchor() - Method in class org.sbml.libsbml.DefaultValues
Unsets the value of the 'vtextAnchor' attribute of this DefaultValues.
upIndent() - Method in class org.sbml.libsbml.XMLOutputStream
Increases the indentation level for this XMLOutputStream.
UpperUnitBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

V

validate() - Method in class org.sbml.libsbml.SBMLValidator
Runs this validator on the current SBML document.
validate(String) - Method in class org.sbml.libsbml.SBMLValidator
Validates the SBML document located at the given filename.
validate(SBMLDocument) - Method in class org.sbml.libsbml.SBMLValidator
Validates the given SBMLDocument object.
validateSBML() - Method in class org.sbml.libsbml.SBMLDocument
Performs consistency checking and validation on this SBML document.
ValuesFromTriggerTimeNeedDelay - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
VariableNotValidAttribute - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
VersionPositiveInteger - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
VolumeLitreDefExponentNotOne - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
VolumeMetreDefExponentNot3 - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

W

WEIGHT_BOLD - Static variable in class org.sbml.libsbml.Text
 
WEIGHT_INVALID - Static variable in class org.sbml.libsbml.Text
 
WEIGHT_NORMAL - Static variable in class org.sbml.libsbml.Text
 
WEIGHT_UNSET - Static variable in class org.sbml.libsbml.Text
 
width() - Method in class org.sbml.libsbml.BoundingBox
Get the width of the bounding box.
width() - Method in class org.sbml.libsbml.Dimensions
Returns the width.
writeAttribute(String, boolean) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given attribute and value to this output stream.
writeAttribute(String, double) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given attribute and value to this output stream.
writeAttribute(String, int) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given attribute and value to this output stream.
writeAttribute(String, String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given attribute and value to this output stream.
writeAttribute(String, String, boolean) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given namespace-prefixed attribute value to this output stream.
writeAttribute(String, String, double) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given namespace-prefixed attribute value to this output stream.
writeAttribute(String, String, int) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given namespace-prefixed attribute value to this output stream.
writeAttribute(String, String, long) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given namespace-prefixed attribute value to this output stream.
writeAttribute(String, String, String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given namespace-prefixed attribute value to this output stream.
writeAttribute(XMLTriple, boolean) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given attribute and value to this output stream.
writeAttribute(XMLTriple, double) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given attribute and value to this output stream.
writeAttribute(XMLTriple, int) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given attribute and value to this output stream.
writeAttribute(XMLTriple, String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes the given attribute and value to this output stream.
writeComment(String, String) - Method in class org.sbml.libsbml.XMLOutputStream
Writes an XML comment with the name and version of this program.
writeComment(String, String, boolean) - Method in class org.sbml.libsbml.XMLOutputStream
Writes an XML comment with the name and version of this program.
writeMathMLToString(ASTNode) - Static method in class org.sbml.libsbml.libsbml
Writes the given AST node (and its children) to a string as MathML, and returns the string.
writeMathMLWithNamespaceToString(ASTNode, SBMLNamespaces) - Static method in class org.sbml.libsbml.libsbml
Writes the given AST node (and its children) to a string as MathML, and returns the string.
writeSBML(SBMLDocument, String) - Static method in class org.sbml.libsbml.libsbml
Writes the given SBML document d to the file named by filename.
writeSBML(SBMLDocument, String) - Method in class org.sbml.libsbml.SBMLWriter
Writes the given SBML document to filename.
writeSBML(SBMLDocument, OStream) - Method in class org.sbml.libsbml.SBMLWriter
Writes the given SBML document to the output stream.
writeSBMLToFile(SBMLDocument, String) - Static method in class org.sbml.libsbml.libsbml
Writes the given SBML document d to the file filename.
writeSBMLToFile(SBMLDocument, String) - Method in class org.sbml.libsbml.SBMLWriter
Writes the given SBML document to filename.
writeSBMLToString(SBMLDocument) - Static method in class org.sbml.libsbml.libsbml
Writes the given SBML document d to an in-memory string and returns a pointer to it.
writeSBMLToString(SBMLDocument) - Method in class org.sbml.libsbml.SBMLWriter
Writes the given SBML document to an in-memory string and returns a pointer to it.
writeXMLDecl() - Method in class org.sbml.libsbml.XMLOutputStream
Writes a standard XML declaration to this output stream.

X

x() - Method in class org.sbml.libsbml.BoundingBox
Get the x offset of the bounding box.
x() - Method in class org.sbml.libsbml.Point
Returns the x offset.
x() - Method in class org.sbml.libsbml.RenderPoint
Returns the x coordinate of the RenderPoint as a reference.
XMLAttributes - Class in org.sbml.libsbml
A list of attributes on an XML element.
XMLAttributes() - Constructor for class org.sbml.libsbml.XMLAttributes
Creates a new, empty XMLAttributes object.
XMLAttributes(XMLAttributes) - Constructor for class org.sbml.libsbml.XMLAttributes
Copy constructor; creates a copy of this XMLAttributes object.
XMLAttributeTypeMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLBadColon - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLBadNumber - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLBadUTF8Content - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLConstructorException - Exception in org.sbml.libsbml
Exceptions thrown by some libSBML constructors.
XMLConstructorException(String) - Constructor for exception org.sbml.libsbml.XMLConstructorException
 
XMLContentEmpty - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLEmptyValueNotPermitted - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
xmlEquals(XMLNode) - Method in class org.sbml.libsbml.XMLNode
Compare this XMLNode against another XMLNode returning true if both nodes represent the same XML tree, or false otherwise.
xmlEquals(XMLNode, boolean) - Method in class org.sbml.libsbml.XMLNode
Compare this XMLNode against another XMLNode returning true if both nodes represent the same XML tree, or false otherwise.
xmlEquals(XMLNode, boolean, boolean) - Method in class org.sbml.libsbml.XMLNode
Compare this XMLNode against another XMLNode returning true if both nodes represent the same XML tree, or false otherwise.
XMLError - Class in org.sbml.libsbml
XML-level errors, warnings and other diagnostics.
XMLError() - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String, long) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String, long, long) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String, long, long, long) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(int, String, long, long, long, long) - Constructor for class org.sbml.libsbml.XMLError
Creates a new XMLError to report that something occurred during XML processing.
XMLError(XMLError) - Constructor for class org.sbml.libsbml.XMLError
Copy constructor; creates a copy of this XMLError.
XMLErrorCodesUpperBound - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLErrorLog - Class in org.sbml.libsbml
Log of diagnostics reported during XML processing.
XMLExpectedQuotedString - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLFileOperationError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLFileUnreadable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLFileUnwritable - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLInputStream - Class in org.sbml.libsbml
An interface to an XML input stream.
XMLInputStream(String) - Constructor for class org.sbml.libsbml.XMLInputStream
Creates a new XMLInputStream.
XMLInputStream(String, boolean) - Constructor for class org.sbml.libsbml.XMLInputStream
Creates a new XMLInputStream.
XMLInputStream(String, boolean, String) - Constructor for class org.sbml.libsbml.XMLInputStream
Creates a new XMLInputStream.
XMLInputStream(String, boolean, String, XMLErrorLog) - Constructor for class org.sbml.libsbml.XMLInputStream
Creates a new XMLInputStream.
XMLNamespaces - Class in org.sbml.libsbml
An XML Namespace.
XMLNamespaces() - Constructor for class org.sbml.libsbml.XMLNamespaces
Creates a new empty list of XML namespace declarations.
XMLNamespaces(XMLNamespaces) - Constructor for class org.sbml.libsbml.XMLNamespaces
Copy constructor; creates a copy of this XMLNamespaces list.
XMLNetworkAccessError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLNode - Class in org.sbml.libsbml
A node in libSBML's XML document tree.
XMLNode() - Constructor for class org.sbml.libsbml.XMLNode
Creates a new empty XMLNode with no children.
XMLNode(String) - Constructor for class org.sbml.libsbml.XMLNode
Creates a text XMLNode.
XMLNode(String, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a text XMLNode.
XMLNode(String, long, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a text XMLNode.
XMLNode(XMLNode) - Constructor for class org.sbml.libsbml.XMLNode
Copy constructor; creates a copy of this XMLNode.
XMLNode(XMLToken) - Constructor for class org.sbml.libsbml.XMLNode
Creates a new XMLNode by copying an XMLToken object.
XMLNode(XMLTriple) - Constructor for class org.sbml.libsbml.XMLNode
Creates an end element XMLNode.
XMLNode(XMLTriple, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates an end element XMLNode.
XMLNode(XMLTriple, long, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates an end element XMLNode.
XMLNode(XMLTriple, XMLAttributes) - Constructor for class org.sbml.libsbml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, XMLAttributes, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, XMLAttributes, long, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a start element XMLNode with the given set of attributes.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces) - Constructor for class org.sbml.libsbml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLNode(XMLTriple, XMLAttributes, XMLNamespaces, long, long) - Constructor for class org.sbml.libsbml.XMLNode
Creates a new start element XMLNode with the given set of attributes and namespace declarations.
XMLOutOfMemory - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLOutputStream - Class in org.sbml.libsbml
Interface to an XML output stream.
XMLOutputStream(OStream) - Constructor for class org.sbml.libsbml.XMLOutputStream
Creates a new XMLOutputStream that wraps the given stream.
XMLOutputStream(OStream, String) - Constructor for class org.sbml.libsbml.XMLOutputStream
Creates a new XMLOutputStream that wraps the given stream.
XMLOutputStream(OStream, String, boolean) - Constructor for class org.sbml.libsbml.XMLOutputStream
Creates a new XMLOutputStream that wraps the given stream.
XMLOutputStream(OStream, String, boolean, String) - Constructor for class org.sbml.libsbml.XMLOutputStream
Creates a new XMLOutputStream that wraps the given stream.
XMLOutputStream(OStream, String, boolean, String, String) - Constructor for class org.sbml.libsbml.XMLOutputStream
Creates a new XMLOutputStream that wraps the given stream.
XMLOwningOutputFileStream - Class in org.sbml.libsbml
 
XMLOwningOutputStringStream - Class in org.sbml.libsbml
 
XMLTagMismatch - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLToken - Class in org.sbml.libsbml
A token in an XML stream.
XMLToken() - Constructor for class org.sbml.libsbml.XMLToken
Creates a new empty XMLToken object.
XMLToken(String) - Constructor for class org.sbml.libsbml.XMLToken
Creates a text object.
XMLToken(String, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates a text object.
XMLToken(String, long, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates a text object.
XMLToken(XMLToken) - Constructor for class org.sbml.libsbml.XMLToken
Copy constructor; creates a copy of this XMLToken object.
XMLToken(XMLTriple) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML end element.
XMLToken(XMLTriple, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML end element.
XMLToken(XMLTriple, long, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML end element.
XMLToken(XMLTriple, XMLAttributes) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML start element with attributes.
XMLToken(XMLTriple, XMLAttributes, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML start element with attributes.
XMLToken(XMLTriple, XMLAttributes, long, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML start element with attributes.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML start element with attributes and namespace declarations.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML start element with attributes and namespace declarations.
XMLToken(XMLTriple, XMLAttributes, XMLNamespaces, long, long) - Constructor for class org.sbml.libsbml.XMLToken
Creates an XML start element with attributes and namespace declarations.
XMLTranscoderError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLTriple - Class in org.sbml.libsbml
A qualified XML name.
XMLTriple() - Constructor for class org.sbml.libsbml.XMLTriple
Creates a new, empty XMLTriple object.
XMLTriple(String) - Constructor for class org.sbml.libsbml.XMLTriple
Creates an XMLTriple object by splitting a given string at a given separator character.
XMLTriple(String, char) - Constructor for class org.sbml.libsbml.XMLTriple
Creates an XMLTriple object by splitting a given string at a given separator character.
XMLTriple(String, String, String) - Constructor for class org.sbml.libsbml.XMLTriple
Creates a new XMLTriple object with a given name, uri and and prefix.
XMLTriple(XMLTriple) - Constructor for class org.sbml.libsbml.XMLTriple
Copy constructor; creates a copy of this XMLTriple object.
XMLUnexpectedEOF - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
XMLUnknownError - Static variable in interface org.sbml.libsbml.libsbmlConstants
 

Y

y() - Method in class org.sbml.libsbml.BoundingBox
Get the y offset of the bounding box.
y() - Method in class org.sbml.libsbml.Point
Returns the y offset.
y() - Method in class org.sbml.libsbml.RenderPoint
Returns the y coordinate of the RenderPoint as a reference.

Z

z() - Method in class org.sbml.libsbml.BoundingBox
Get the z offset of the bounding box.
z() - Method in class org.sbml.libsbml.Point
Returns the z offset.
z() - Method in class org.sbml.libsbml.RenderPoint
Returns the z coordinate of the RenderPoint as a reference.
ZeroDCompartmentContainment - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ZeroDimensionalCompartmentConst - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ZeroDimensionalCompartmentSize - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
ZeroDimensionalCompartmentUnits - Static variable in interface org.sbml.libsbml.libsbmlConstants
 
A B C D E F G H I K L M N O P Q R S T U V W X Y Z 
Skip navigation links
libSBML
5.16.0


LibSBML %%version%%, an application programming interface (API) library for SBML.