public class FluxObjective extends SBase
An integral component in a complete description of a steady-state model is the so-called 'objective function' which generally consists of a linear combination of model variables (fluxes) and a sense (direction). In the FBC package this concept is succinctly captured in the Objective
class.
Constructor and Description |
---|
FluxObjective()
Creates a new
FluxObjective with the given level, version, and package version. |
FluxObjective(FbcPkgNamespaces fbcns)
Creates a new
FluxObjective with the given FbcPkgNamespaces object. |
FluxObjective(FluxObjective source)
Copy constructor.
|
FluxObjective(long level)
Creates a new
FluxObjective with the given level, version, and package version. |
FluxObjective(long level,
long version)
Creates a new
FluxObjective with the given level, version, and package version. |
FluxObjective(long level,
long version,
long pkgVersion)
Creates a new
FluxObjective with the given level, version, and package version. |
Modifier and Type | Method and Description |
---|---|
FluxObjective |
cloneObject()
Creates and returns a deep copy of this
FluxObjective . |
void |
delete()
Explicitly deletes the underlying native object.
|
double |
getCoefficient()
Returns the value of the 'coefficient' attribute of this
FluxObjective . |
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
java.lang.String |
getId()
Returns the value of the 'id' attribute of this
FluxObjective . |
java.lang.String |
getName()
Returns the value of the 'name' attribute of this
FluxObjective . |
java.lang.String |
getReaction()
Returns the string of the 'reaction' attribute of this
FluxObjective . |
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
boolean |
isSetCoefficient()
Predicate returning
true or false depending on whether this
FluxObjective 's 'coefficient' attribute has been set. |
boolean |
isSetId()
Predicate returning
true or false depending on whether this
FluxObjective 'id' attribute has been set. |
boolean |
isSetName()
Predicate returning
true or false depending on whether this
FluxObjective 'name' attribute has been set. |
boolean |
isSetReaction()
Predicate returning
true or false depending on whether this
FluxObjective 's 'reaction' attribute has been set. |
void |
renameSIdRefs(java.lang.String oldid,
java.lang.String newid)
Renames all the
SIdRef attributes on this element, including any
found in MathML content (if such exists). |
int |
setCoefficient(double coefficient)
Sets the value of the 'coefficient' attribute of this
FluxObjective . |
int |
setId(java.lang.String id)
Sets the value of the 'id' attribute of this
FluxObjective . |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
FluxObjective . |
int |
setReaction(java.lang.String reaction)
Sets the SIdRef string of the 'reaction' attribute of this
FluxObjective . |
int |
unsetCoefficient()
Unsets the value of the 'id' attribute of this
FluxObjective . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
FluxObjective . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
FluxObjective . |
int |
unsetReaction()
Unsets the value of the 'id' attribute of this
FluxObjective . |
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 FluxObjective() throws SBMLConstructorException
FluxObjective
with the given level, version, and package version.SBMLConstructorException
public FluxObjective(FbcPkgNamespaces fbcns) throws SBMLConstructorException
FluxObjective
with the given FbcPkgNamespaces
object.SBMLConstructorException
public FluxObjective(FluxObjective source) throws SBMLConstructorException
SBMLConstructorException
public FluxObjective(long level) throws SBMLConstructorException
FluxObjective
with the given level, version, and package version.SBMLConstructorException
public FluxObjective(long level, long version) throws SBMLConstructorException
FluxObjective
with the given level, version, and package version.SBMLConstructorException
public FluxObjective(long level, long version, long pkgVersion) throws SBMLConstructorException
FluxObjective
with the given level, version, and package version.SBMLConstructorException
public FluxObjective cloneObject()
FluxObjective
.
cloneObject
 in class SBase
FluxObjective
.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 FluxObjective.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 FluxObjective.delete()
themselves.
public double getCoefficient()
FluxObjective
.
FluxObjective
.public java.lang.String getElementName()
getElementName
 in class SBase
public java.lang.String getId()
FluxObjective
.
getId
 in class SBase
FluxObjective
.public java.lang.String getName()
FluxObjective
.
getName
 in class SBase
FluxObjective
.public java.lang.String getReaction()
FluxObjective
.
FluxObjective
.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_FBC_FLUXOBJECTIVE
FluxObjective.getElementName()
,
SBase.getPackageName()
public boolean isSetCoefficient()
true
or false
depending on whether this
FluxObjective
's 'coefficient' attribute has been set.
true
if this FluxObjective
's 'coefficient' attribute has been set,
otherwise false
is returned.public boolean isSetId()
true
or false
depending on whether this
FluxObjective
'id' attribute has been set.
isSetId
 in class SBase
true
if this FluxObjective
'id' attribute has been set,
otherwise false
is returned.public boolean isSetName()
true
or false
depending on whether this
FluxObjective
'name' attribute has been set.
isSetName
 in class SBase
true
if this FluxObjective
'id' attribute has been set,
otherwise false
is returned.public boolean isSetReaction()
true
or false
depending on whether this
FluxObjective
's 'reaction' attribute has been set.
true
if this FluxObjective
's 'reaction' attribute has been set,
otherwise false
is returned.public void renameSIdRefs(java.lang.String oldid, java.lang.String newid)
SIdRef
attributes on this element, including any
found in MathML content (if such exists).
This method works by looking at all attributes and (if appropriate)
mathematical formulas, comparing the identifiers to the value of @p
oldid. If any matches are found, the matching identifiers are replaced
with newid
. The method does not descend into child elements.
renameSIdRefs
 in class SBase
oldid
- the old identifiernewid
- the new identifierpublic int setCoefficient(double coefficient)
FluxObjective
.
coefficient
- a double coefficient to be set.
public int setId(java.lang.String id)
FluxObjective
.
public int setName(java.lang.String name)
FluxObjective
.
public int setReaction(java.lang.String reaction)
FluxObjective
.
reaction
- a SIdRef string to be set.
public int unsetCoefficient()
FluxObjective
.
public int unsetId()
FluxObjective
.
public int unsetName()
FluxObjective
.
public int unsetReaction()
FluxObjective
.