public class ModifierSpeciesReference extends SimpleSpeciesReference
Sometimes a species appears in the kinetic rate formula of a reaction
but is itself neither created nor destroyed in that reaction (for
example, because it acts as a catalyst or inhibitor). In SBML, all such
species are simply called modifiers without regard to the detailed
role of those species in the model. The Reaction
structure provides a
way to express which species act as modifiers in a given reaction. This
is the purpose of the list of modifiers available in Reaction
. The list
contains instances of ModifierSpeciesReference
structures.
The ModifierSpeciesReference
structure inherits the mandatory attribute
'species' and optional attributes 'id' and 'name' from the parent class
SimpleSpeciesReference
. See the description of SimpleSpeciesReference
for more information about these.
The value of the 'species' attribute must be the identifier of a species
defined in the enclosing Model
this species is designated as a modifier
for the current reaction. A reaction may have any number of modifiers.
It is permissible for a modifier species to appear simultaneously in the
list of reactants and products of the same reaction where it is
designated as a modifier, as well as to appear in the list of reactants,
products and modifiers of other reactions in the model.
Constructor and Description |
---|
ModifierSpeciesReference(long level,
long version)
|
ModifierSpeciesReference(SBMLNamespaces sbmlns)
|
Modifier and Type | Method and Description |
---|---|
SBase |
cloneObject()
Creates and returns a deep copy of this
ModifierSpeciesReference
instance. |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getElementName()
Returns the XML element name of this object, which for
Species , is
always 'modifierSpeciesReference'. |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if
all the required attributes for this ModifierSpeciesReference object
have been set. |
getId, getName, getSpecies, isModifier, isSetId, isSetName, isSetSpecies, renameSIdRefs, setId, setName, setSpecies, unsetId, unsetName
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm
public ModifierSpeciesReference(long level, long version) throws SBMLConstructorException
level
- a long integer, the SBML Level to assign to this
ModifierSpeciesReference
version
- a long integer, the SBML Version to assign to this
ModifierSpeciesReference
SBMLConstructorException
ModifierSpeciesReference
object to an
SBMLDocument
(e.g., using Reaction.addModifier(ModifierSpeciesReference msr)
), the
SBML Level, SBML Version and XML namespace of the document
override the values used when creating the ModifierSpeciesReference
object via this constructor. This is necessary to ensure that an SBML
document is a consistent structure. Nevertheless, the ability to
supply the values at the time of creation of a
ModifierSpeciesReference
is an important aid to producing valid SBML.
Knowledge of the intented SBML Level and Version determine whether it
is valid to assign a particular value to an attribute, or whether it
is valid to add an object to an existing SBMLDocument
.public ModifierSpeciesReference(SBMLNamespaces sbmlns) throws SBMLConstructorException
sbmlns
- an SBMLNamespaces
object.
SBMLConstructorException
ModifierSpeciesReference
object to an
SBMLDocument
(e.g., using Reaction.addModifier(ModifierSpeciesReference msr)
), the
SBML Level, SBML Version and XML namespace of the document
override the values used when creating the ModifierSpeciesReference
object via this constructor. This is necessary to ensure that an SBML
document is a consistent structure. Nevertheless, the ability to
supply the values at the time of creation of a
ModifierSpeciesReference
is an important aid to producing valid SBML.
Knowledge of the intented SBML Level and Version determine whether it
is valid to assign a particular value to an attribute, or whether it
is valid to add an object to an existing SBMLDocument
.public SBase cloneObject()
ModifierSpeciesReference
instance.
cloneObject
 in class SBase
ModifierSpeciesReference
.public void delete()
In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize()
methods for the objects. The finalize()
methods in turn call the ModifierSpeciesReference.delete()
method on the libSBML object.
This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke ModifierSpeciesReference.delete()
themselves.
delete
 in class SimpleSpeciesReference
public java.lang.String getElementName()
Species
, is
always 'modifierSpeciesReference'.
getElementName
 in class SBase
'modifierSpeciesReference'.
public int getTypeCode()
LibSBML attaches an identifying code to every kind of SBML object. These
are integer constants known as SBML type codes. The names of all
the codes begin with the characters &ldquoSBML_
&rdquo.
In the Java language interface for libSBML, the
type codes are defined as static integer constants in the interface class
libsbmlConstants
. Note that different Level 3
package plug-ins may use overlapping type codes to identify the package
to which a given object belongs, call the getPackageName()
method on the object.
getTypeCode
 in class SBase
SBML_MODIFIER_SPECIES_REFERENCE
(default).
ModifierSpeciesReference.getElementName()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if
all the required attributes for this ModifierSpeciesReference
object
have been set.
hasRequiredAttributes
 in class SBase
ModifierSpeciesReference
object are:
species