A B C D E G H I L M N O P R S U V W

A

addCompartmentReference(CompartmentReference) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Adds a new CompartmentReference to the MultiCompartmentPlugin.listOfCompartmentReferences.

addInSpeciesTypeBond(InSpeciesTypeBond) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Adds a new InSpeciesTypeBond to the SpeciesType.listOfInSpeciesTypeBonds.

addOutwardBindingSite(OutwardBindingSite) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Adds a new OutwardBindingSite to the MultiSpeciesPlugin.listOfOutwardBindingSites.

addPossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Adds a new PossibleSpeciesFeatureValue to the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues.

addSpeciesFeature(SpeciesFeature) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Adds a new SpeciesFeature to the MultiSpeciesPlugin.listOfSpeciesFeatures.

addSpeciesFeatureChange(SpeciesFeatureChange) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Adds a new SpeciesFeatureChange to the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges.

addSpeciesFeatureType(SpeciesFeatureType) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Adds a new SpeciesFeatureType to the SpeciesType.listOfSpeciesFeatureTypes.

addSpeciesFeatureValue(SpeciesFeatureValue) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Adds a new SpeciesFeatureValue to the SpeciesFeature.listOfSpeciesFeatureValues.

addSpeciesType(SpeciesType) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Adds a SpeciesType.

addSpeciesTypeComponentIndex(SpeciesTypeComponentIndex) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Adds a new SpeciesTypeComponentIndex to the SpeciesType.listOfSpeciesTypeComponentIndexes.

addSpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Adds a new SpeciesTypeComponentMapInProduct to the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts.

addSpeciesTypeInstance(SpeciesTypeInstance) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Adds a new SpeciesTypeInstance to the SpeciesType.listOfSpeciesTypeInstances.

B

bindingSite - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

bindingSite1 - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

bindingSite2 - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

bindingSiteReference - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

BindingSiteSpeciesType - Class in org.sbml.jsbml.ext.multi

BindingSiteSpeciesType() - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(int, int) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(BindingSiteSpeciesType) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(String) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingSiteSpeciesType(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

BindingStatus - Enum in org.sbml.jsbml.ext.multi

The BindingStatus enumeration is used in the definition of the OutwardBindingSite class.

bindingStatus - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

bond - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

C

clone() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

clone() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.IntraSpeciesReaction

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

clone() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

clone() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

clone() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

clone() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

clones this class

clone() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

clones this class

compartment - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

CompartmentReference - Class in org.sbml.jsbml.ext.multi

CompartmentReference() - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference

Creates an CompartmentReference instance

CompartmentReference(CompartmentReference) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference

Clone constructor

CompartmentReference(int, int) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference

Creates a CompartmentReference instance with a level and version.

CompartmentReference(String) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference

Creates a CompartmentReference instance with an id.

CompartmentReference(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference

Creates a CompartmentReference instance with an id, level, and version.

CompartmentReference(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.CompartmentReference

Creates a CompartmentReference instance with an id, name, level, and version.

compartmentReference - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

compartmentType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

component - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

connex - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

containedSpeciesType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

createBindingSiteSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Creates a new BindingSiteSpeciesType inside this MultiModelPlugin and returns it.

createBindingSiteSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Creates a new BindingSiteSpeciesType inside this MultiModelPlugin and returns it.

createCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Creates a new CompartmentReference element and adds it to the MultiCompartmentPlugin.listOfCompartmentReferences list.

createCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Creates a new CompartmentReference element and adds it to the MultiCompartmentPlugin.listOfCompartmentReferences list.

createInSpeciesTypeBond() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Creates a new InSpeciesTypeBond element and adds it to the SpeciesType.listOfInSpeciesTypeBonds list.

createInSpeciesTypeBond(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Creates a new InSpeciesTypeBond element and adds it to the SpeciesType.listOfInSpeciesTypeBonds list.

createIntraSpeciesReaction() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Creates a new IntraSpeciesReaction inside this MultiModelPlugin and returns it.

createIntraSpeciesReaction(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Creates a new IntraSpeciesReaction inside this MultiModelPlugin and returns it.

createOutwardBindingSite() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Creates a new OutwardBindingSite element and adds it to the MultiSpeciesPlugin.listOfOutwardBindingSites list.

createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

createPluginFor(ASTNode) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

createPossibleSpeciesFeatureValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Creates a new PossibleSpeciesFeatureValue element and adds it to the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues list.

createPossibleSpeciesFeatureValue(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Creates a new PossibleSpeciesFeatureValue element and adds it to the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues list.

createSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Creates a new SpeciesFeature element and adds it to the MultiSpeciesPlugin.listOfSpeciesFeatures list.

createSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Creates a new SpeciesFeature element and adds it to the MultiSpeciesPlugin.listOfSpeciesFeatures list.

createSpeciesFeatureChange() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Creates a new SpeciesFeatureChange element and adds it to the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges list.

createSpeciesFeatureChange(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Creates a new SpeciesFeatureChange element and adds it to the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges list.

createSpeciesFeatureType() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Creates a new SpeciesFeatureType element and adds it to the SpeciesType.listOfSpeciesFeatureTypes list.

createSpeciesFeatureType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Creates a new SpeciesFeatureType element and adds it to the SpeciesType.listOfSpeciesFeatureTypes list.

createSpeciesFeatureValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Creates a new SpeciesFeatureValue element and adds it to the SpeciesFeature.listOfSpeciesFeatureValues list.

createSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Creates a new SpeciesType inside this MultiModelPlugin and returns it.

createSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Creates a new SpeciesType inside this MultiModelPlugin and returns it.

createSpeciesTypeComponentIndex() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Creates a new SpeciesTypeComponentIndex element and adds it to the SpeciesType.listOfSpeciesTypeComponentIndexes list.

createSpeciesTypeComponentIndex(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Creates a new SpeciesTypeComponentIndex element and adds it to the SpeciesType.listOfSpeciesTypeComponentIndexes list.

createSpeciesTypeComponentMapInProduct() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Creates a new SpeciesTypeComponentMapInProduct element and adds it to the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts list.

createSpeciesTypeInstance() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Creates a new SpeciesTypeInstance element and adds it to the SpeciesType.listOfSpeciesTypeInstances list.

createSpeciesTypeInstance(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Creates a new SpeciesTypeInstance element and adds it to the SpeciesType.listOfSpeciesTypeInstances list.

D

DenotedSpeciesTypeComponentIndex - Class in org.sbml.jsbml.ext.multi

Class removed from the draft specs 1.0 release 0.5 (2015-11-27)

DenotedSpeciesTypeComponentIndex() - Constructor for class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

Creates an DenotedSpeciesTypeComponentIndex instance

DenotedSpeciesTypeComponentIndex(int, int) - Constructor for class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

Creates a DenotedSpeciesTypeComponentIndex instance with a level and version.

DenotedSpeciesTypeComponentIndex(DenotedSpeciesTypeComponentIndex) - Constructor for class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

Clone constructor

denotedSpeciesTypeComponentIndex - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

E

equals(Object) - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

equals(Object) - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

equals(Object) - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

equals(Object) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

G

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

getAllowsChildren() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

getBindingSite1() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Returns the value of InSpeciesTypeBond.bindingSite1.

getBindingSite2() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Returns the value of InSpeciesTypeBond.bindingSite2.

getBindingStatus() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Returns the value of OutwardBindingSite.bindingStatus.

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

getChildAt(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

getChildCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

getCompartment() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

getCompartment() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

getCompartmentInstance() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

getCompartmentInstance() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

getCompartmentReference(int) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Gets an element from the MultiCompartmentPlugin.listOfCompartmentReferences at the given index.

getCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Gets an element from the listOfCompartmentReferences, with the given id.

getCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Returns the value of MultiSimpleSpeciesReferencePlugin.compartmentReference.

getCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Returns the value of SpeciesTypeInstance.compartmentReference.

getCompartmentReferenceCount() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the number of CompartmentReferences in this MultiCompartmentPlugin.

getCompartmentType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the value of MultiCompartmentPlugin.compartmentType.

getComponent() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Returns the value of OutwardBindingSite.component.

getComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the value of SpeciesFeature.component.

getComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Returns the value of SpeciesTypeComponentIndex.component.

getIndentifyingParent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Returns the value of SpeciesTypeComponentIndex.identifyingParent.

getInSpeciesTypeBond(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Gets an element from the SpeciesType.listOfInSpeciesTypeBonds at the given index.

getInSpeciesTypeBond(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Gets an element from the listOfInSpeciesTypeBonds, with the given id.

getInSpeciesTypeBondCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the number of InSpeciesTypeBonds in this SpeciesType.

getIsType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the value of MultiCompartmentPlugin.isType.

getListOfCompartmentReferences() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the MultiCompartmentPlugin.listOfCompartmentReferences.

getListOfInSpeciesTypeBonds() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the SpeciesType.listOfInSpeciesTypeBonds.

getListOfOutwardBindingSites() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the MultiSpeciesPlugin.listOfOutwardBindingSites.

getListOfPossibleSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues.

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getListOfSpeciesFeatureChanges() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges.

getListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the MultiSpeciesPlugin.listOfSpeciesFeatures.

getListOfSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the SpeciesType.listOfSpeciesFeatureTypes.

getListOfSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the SpeciesFeature.listOfSpeciesFeatureValues.

getListOfSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the SpeciesType.listOfSpeciesTypeComponentIndexes.

getListOfSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Returns the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts.

getListOfSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the SpeciesType.listOfSpeciesTypeInstances.

getListOfSpeciesTypes() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Returns the listOfSpeciesTypes.

getModel() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Returns the Model

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.multi.MultiConstants

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getNumCompartmentReferences() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the number of CompartmentReferences in this MultiCompartmentPlugin.

getNumericValue() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Returns the value of PossibleSpeciesFeatureValue.numericValue.

getNumInSpeciesTypeBonds() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the number of InSpeciesTypeBonds in this SpeciesType.

getNumOutwardBindingSites() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of OutwardBindingSites in this MultiSpeciesPlugin.

getNumPossibleSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.

getNumSpeciesFeatureChanges() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the number of SpeciesFeatureChanges in this SpeciesTypeComponentMapInProduct.

getNumSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of SpeciesFeatures in this MultiSpeciesPlugin.

getNumSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the number of SpeciesFeatureTypes in this SpeciesType.

getNumSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the number of SpeciesFeatureValues in this SpeciesFeature.

getNumSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the number of SpeciesTypeComponentIndexs in this SpeciesType.

getNumSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Returns the number of SpeciesTypeComponentMapInProducts in this MultiSpeciesReferencePlugin.

getNumSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the number of SpeciesTypeInstances in this SpeciesType.

getOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the value of SpeciesFeature.occur.

getOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns the value of SpeciesFeatureType.occur.

getOutwardBindingSite(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Gets an element from the MultiSpeciesPlugin.listOfOutwardBindingSites at the given index.

getOutwardBindingSiteCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of OutwardBindingSites in this MultiSpeciesPlugin.

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getPackageName() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getParent() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getParent() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getPossibleSpeciesFeatureValue(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Gets an element from the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues at the given index.

getPossibleSpeciesFeatureValue(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Gets an element from the listOfPossibleSpeciesFeatureValues, with the given id.

getPossibleSpeciesFeatureValueCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getProductComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the value of SpeciesTypeComponentMapInProduct.productComponent.

getProductSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Returns the value of SpeciesFeatureChange.productSpeciesFeature.

getReactant() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the value of SpeciesTypeComponentMapInProduct.reactant.

getReactantComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the value of SpeciesTypeComponentMapInProduct.reactantComponent.

getReactantSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Returns the value of SpeciesFeatureChange.reactantSpeciesFeature.

getRepresentationType() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Returns the value of MultiASTNodePlugin.representationType.

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

getSpeciesFeature(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Gets an element from the MultiSpeciesPlugin.listOfSpeciesFeatures at the given index.

getSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Gets an element from the listOfSpeciesFeatures, with the given id.

getSpeciesFeatureChange(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Gets an element from the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges at the given index.

getSpeciesFeatureChange(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Gets an element from the listOfSpeciesFeatureChanges, with the given id.

getSpeciesFeatureChangeCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns the number of SpeciesFeatureChanges in this SpeciesTypeComponentMapInProduct.

getSpeciesFeatureCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the number of SpeciesFeatures in this MultiSpeciesPlugin.

getSpeciesFeatureType() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the value of SpeciesFeature.speciesFeatureType.

getSpeciesFeatureType(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Gets an element from the SpeciesType.listOfSpeciesFeatureTypes at the given index.

getSpeciesFeatureType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Gets an element from the listOfSpeciesFeatureTypes, with the given id.

getSpeciesFeatureTypeCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the number of SpeciesFeatureTypes in this SpeciesType.

getSpeciesFeatureValue(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Gets an element from the SpeciesFeature.listOfSpeciesFeatureValues at the given index.

getSpeciesFeatureValueCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns the number of SpeciesFeatureValues in this SpeciesFeature.

getSpeciesReference() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Returns the value of MultiASTNodePlugin.speciesReference.

getSpeciesType(int) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Gets the ith SpeciesType.

getSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Gets the SpeciesType that has the given id.

getSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns the value of MultiSpeciesPlugin.speciesType.

getSpeciesType() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Returns the value of SpeciesTypeInstance.speciesType.

getSpeciesTypeComponentIndex() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

Returns the value of DenotedSpeciesTypeComponentIndex.speciesTypeComponentIndex.

getSpeciesTypeComponentIndex(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Gets an element from the SpeciesType.listOfSpeciesTypeComponentIndexes at the given index.

getSpeciesTypeComponentIndex(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Gets an element from the listOfSpeciesTypeComponentIndexes, with the given id.

getSpeciesTypeComponentIndexCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the number of SpeciesTypeComponentIndexs in this SpeciesType.

getSpeciesTypeComponentMapInProduct(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Gets an element from the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts at the given index.

getSpeciesTypeComponentMapInProductCount() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Returns the number of SpeciesTypeComponentMapInProducts in this MultiSpeciesReferencePlugin.

getSpeciesTypeInstance(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Gets an element from the SpeciesType.listOfSpeciesTypeInstances at the given index.

getSpeciesTypeInstance(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Gets an element from the listOfSpeciesTypeInstances, with the given id.

getSpeciesTypeInstanceCount() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns the number of SpeciesTypeInstances in this SpeciesType.

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

getURI() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

getValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Returns the value of SpeciesFeatureValue.value.

H

hashCode() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

hashCode() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

hashCode() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

hashCode() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

hashCode() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

hashCode() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

hashCode() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

hashCode() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

hashCode() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

hashCode() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

hashCode() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

hashCode() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

hashCode() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

hashCode() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

I

identifyingParent - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

initDefaults() - Method in class org.sbml.jsbml.ext.multi.BindingSiteSpeciesType

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.IntraSpeciesReaction

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Initializes the default values.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Initializes the default values using the namespace.

InSpeciesTypeBond - Class in org.sbml.jsbml.ext.multi

InSpeciesTypeBond() - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Creates an InSpeciesTypeBond instance

InSpeciesTypeBond(String) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Creates a InSpeciesTypeBond instance with an id.

InSpeciesTypeBond(int, int) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Creates a InSpeciesTypeBond instance with a level and version.

InSpeciesTypeBond(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Creates a InSpeciesTypeBond instance with an id, level, and version.

InSpeciesTypeBond(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Creates a InSpeciesTypeBond instance with an id, name, level, and version.

InSpeciesTypeBond(InSpeciesTypeBond) - Constructor for class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Clone constructor

IntraSpeciesReaction - Class in org.sbml.jsbml.ext.multi

IntraSpeciesReaction() - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction

Creates an IntraSpeciesReaction instance

IntraSpeciesReaction(String) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction

Creates a IntraSpeciesReaction instance with an id.

IntraSpeciesReaction(int, int) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction

Creates a IntraSpeciesReaction instance with a level and version.

IntraSpeciesReaction(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction

Creates a IntraSpeciesReaction instance with an id, level, and version.

IntraSpeciesReaction(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction

Creates a IntraSpeciesReaction instance with an id, name, level, and version.

IntraSpeciesReaction(IntraSpeciesReaction) - Constructor for class org.sbml.jsbml.ext.multi.IntraSpeciesReaction

Clone constructor

isCompartmentMandatory() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

isCompartmentMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

isIdMandatory() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

isRequired() - Method in class org.sbml.jsbml.xml.parsers.MultiParser

isSetBindingSite1() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Returns whether InSpeciesTypeBond.bindingSite1 is set.

isSetBindingSite2() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Returns whether InSpeciesTypeBond.bindingSite2 is set.

isSetBindingStatus() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Returns whether OutwardBindingSite.bindingStatus is set.

isSetCompartment() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

Returns whether CompartmentReference.compartment is set.

isSetCompartment() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

isSetCompartmentInstance() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

isSetCompartmentInstance() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

isSetCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Returns whether MultiSimpleSpeciesReferencePlugin.compartmentReference is set.

isSetCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Returns whether SpeciesTypeInstance.compartmentReference is set.

isSetCompartmentType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns whether MultiCompartmentPlugin.compartmentType is set.

isSetComponent() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Returns whether OutwardBindingSite.component is set.

isSetComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns whether SpeciesFeature.component is set.

isSetComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Returns whether SpeciesTypeComponentIndex.component is set.

isSetIndentifyingParent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Returns whether SpeciesTypeComponentIndex.identifyingParent is set.

isSetIsType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns whether MultiCompartmentPlugin.isType is set.

isSetListOfCompartmentReferences() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns true if MultiCompartmentPlugin.listOfCompartmentReferences contains at least one element.

isSetListOfInSpeciesTypeBonds() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns true if SpeciesType.listOfInSpeciesTypeBonds contains at least one element.

isSetListOfOutwardBindingSites() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns true if MultiSpeciesPlugin.listOfOutwardBindingSites contains at least one element.

isSetListOfPossibleSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns true if SpeciesFeatureType.listOfPossibleSpeciesFeatureValues contains at least one element.

isSetListOfSpeciesFeatureChanges() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns true if SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges contains at least one element.

isSetListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns true if MultiSpeciesPlugin.listOfSpeciesFeatures contains at least one element.

isSetListOfSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns true if SpeciesType.listOfSpeciesFeatureTypes contains at least one element.

isSetListOfSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns true if SpeciesFeature.listOfSpeciesFeatureValues contains at least one element.

isSetListOfSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns true if SpeciesType.listOfSpeciesTypeComponentIndexes contains at least one element.

isSetListOfSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Returns true if MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts contains at least one element.

isSetListOfSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns true if SpeciesType.listOfSpeciesTypeInstances contains at least one element.

isSetListOfSpeciesTypes() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Returns true if the listOfSpeciesType is set.

isSetNumericValue() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Returns whether PossibleSpeciesFeatureValue.numericValue is set.

isSetOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns whether SpeciesFeature.occur is set.

isSetOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns whether SpeciesFeatureType.occur is set.

isSetProductComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns whether SpeciesTypeComponentMapInProduct.productComponent is set.

isSetProductSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Returns whether SpeciesFeatureChange.productSpeciesFeature is set.

isSetReactant() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns whether SpeciesTypeComponentMapInProduct.reactant is set.

isSetReactantComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns whether SpeciesTypeComponentMapInProduct.reactantComponent is set.

isSetReactantSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Returns whether SpeciesFeatureChange.reactantSpeciesFeature is set.

isSetRepresentationType() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Returns whether MultiASTNodePlugin.representationType is set.

isSetSpeciesFeatureType() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns whether SpeciesFeature.speciesFeatureType is set.

isSetSpeciesReference() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Returns whether MultiASTNodePlugin.speciesReference is set.

isSetSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns whether MultiSpeciesPlugin.speciesType is set.

isSetSpeciesType() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Returns whether SpeciesTypeInstance.speciesType is set.

isSetSpeciesTypeComponentIndex() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

Returns whether DenotedSpeciesTypeComponentIndex.speciesTypeComponentIndex is set.

isSetValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Returns whether SpeciesFeatureValue.value is set.

isType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns the value of MultiCompartmentPlugin.isType, return false if isType is not defined.

isType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

L

listOfBonds - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfCompartmentReferences - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfContainedSpeciesTypes - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfInSpeciesTypeBonds - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfOutwardBindingSites - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfPossibleSpeciesFeatureValues - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfPossibleValues - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSelectors - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesFeatureChanges - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesFeatures - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesFeatureTypes - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesFeatureValues - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesTypeComponentIndexes - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesTypeComponentMapInProducts - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesTypeInstances - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesTypes - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfSpeciesTypeStates - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfStateFeatureInstances - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfStateFeatures - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfStateFeatureValues - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

listOfUnboundBindingSites - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

M

maxOccur - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

minOccur - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

MultiASTNodePlugin - Class in org.sbml.jsbml.ext.multi

MultiASTNodePlugin() - Constructor for class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

MultiASTNodePlugin(MultiASTNodePlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

MultiASTNodePlugin(ASTNode) - Constructor for class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

MultiCompartmentPlugin - Class in org.sbml.jsbml.ext.multi

MultiCompartmentPlugin() - Constructor for class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Creates an MultiCompartmentPlugin instance

MultiCompartmentPlugin(Compartment) - Constructor for class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Creates a MultiCompartmentPlugin instance associated with the given Compartment.

MultiCompartmentPlugin(MultiCompartmentPlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Clone constructor

MultiConstants - Class in org.sbml.jsbml.ext.multi

Contains some constants related to the multi package.

MultiConstants() - Constructor for class org.sbml.jsbml.ext.multi.MultiConstants

MultiModelPlugin - Class in org.sbml.jsbml.ext.multi

In order to encode the structures needed to define and use multistate and multi-component complexes, the element model is extended to be linked to a list of SpeciesTypes.

MultiModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.multi.MultiModelPlugin

MultiModelPlugin(MultiModelPlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiModelPlugin

MultiParser - Class in org.sbml.jsbml.xml.parsers

A MultiParser is used to parse the multi extension package elements and attributes.

MultiParser() - Constructor for class org.sbml.jsbml.xml.parsers.MultiParser

MultiSimpleSpeciesReferencePlugin - Class in org.sbml.jsbml.ext.multi

MultiSimpleSpeciesReferencePlugin() - Constructor for class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Creates an MultiSimpleSpeciesReferencePlugin instance

MultiSimpleSpeciesReferencePlugin(SimpleSpeciesReference) - Constructor for class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Creates a MultiSimpleSpeciesReferencePlugin instance with a SimpleSpeciesReference.

MultiSimpleSpeciesReferencePlugin(MultiSimpleSpeciesReferencePlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Clone constructor

MultiSpeciesPlugin - Class in org.sbml.jsbml.ext.multi

MultiSpeciesPlugin(Species) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

MultiSpeciesPlugin(MultiSpeciesPlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

MultiSpeciesReferencePlugin - Class in org.sbml.jsbml.ext.multi

MultiSpeciesReferencePlugin() - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Creates an MultiSpeciesReferencePlugin instance

MultiSpeciesReferencePlugin(SpeciesReference) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Creates a MultiSpeciesReferencePlugin instance with a SpeciesReference.

MultiSpeciesReferencePlugin(MultiSpeciesReferencePlugin) - Constructor for class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Clone constructor

N

namespaces - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

numericValue - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

O

occur - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

occurrence - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

org.sbml.jsbml.ext.multi - package org.sbml.jsbml.ext.multi

Provides classes for the Multi package.

org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers

outwardBindingSite - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

OutwardBindingSite - Class in org.sbml.jsbml.ext.multi

OutwardBindingSite() - Constructor for class org.sbml.jsbml.ext.multi.OutwardBindingSite

Creates an OutwardBindingSite instance

OutwardBindingSite(int, int) - Constructor for class org.sbml.jsbml.ext.multi.OutwardBindingSite

Creates a OutwardBindingSite instance with a level and version.

OutwardBindingSite(OutwardBindingSite) - Constructor for class org.sbml.jsbml.ext.multi.OutwardBindingSite

Clone constructor

P

packageDisplayName - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

packageName - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

possibleSpeciesFeatureValue - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

PossibleSpeciesFeatureValue - Class in org.sbml.jsbml.ext.multi

Each state feature (SpeciesFeatureType) also requires the definition of all the possible values it can take.

PossibleSpeciesFeatureValue() - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Creates an PossibleSpeciesFeatureValue instance

PossibleSpeciesFeatureValue(String) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Creates a PossibleSpeciesFeatureValue instance with an id.

PossibleSpeciesFeatureValue(int, int) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Creates a PossibleSpeciesFeatureValue instance with a level and version.

PossibleSpeciesFeatureValue(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Creates a PossibleSpeciesFeatureValue instance with an id, level, and version.

PossibleSpeciesFeatureValue(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Creates a PossibleSpeciesFeatureValue instance with an id, name, level, and version.

PossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue) - Constructor for class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Clone constructor

processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

productComponent - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

productSpeciesFeature - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

R

reactant - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

reactantComponent - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

reactantSpeciesFeature - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Relation - Enum in org.sbml.jsbml.ext.multi

The Relation enumeration is used in the definition of the ListOfSpeciesFeatures class.

removeCompartmentReference(CompartmentReference) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Removes an element from the MultiCompartmentPlugin.listOfCompartmentReferences.

removeCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Removes an element from the MultiCompartmentPlugin.listOfCompartmentReferences.

removeCompartmentReference(int) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Removes an element from the MultiCompartmentPlugin.listOfCompartmentReferences at the given index.

removeInSpeciesTypeBond(InSpeciesTypeBond) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfInSpeciesTypeBonds.

removeInSpeciesTypeBond(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfInSpeciesTypeBonds at the given index.

removeInSpeciesTypeBond(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfInSpeciesTypeBonds.

removeOutwardBindingSite(OutwardBindingSite) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Removes an element from the MultiSpeciesPlugin.listOfOutwardBindingSites.

removeOutwardBindingSite(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Removes an element from the MultiSpeciesPlugin.listOfOutwardBindingSites at the given index.

removePossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Removes an element from the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues.

removePossibleSpeciesFeatureValue(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Removes an element from the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues.

removePossibleSpeciesFeatureValue(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Removes an element from the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues at the given index.

removeSpeciesFeature(SpeciesFeature) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Removes an element from the MultiSpeciesPlugin.listOfSpeciesFeatures.

removeSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Removes an element from the MultiSpeciesPlugin.listOfSpeciesFeatures.

removeSpeciesFeature(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Removes an element from the MultiSpeciesPlugin.listOfSpeciesFeatures at the given index.

removeSpeciesFeatureChange(SpeciesFeatureChange) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Removes an element from the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges.

removeSpeciesFeatureChange(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Removes an element from the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges.

removeSpeciesFeatureChange(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Removes an element from the SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges at the given index.

removeSpeciesFeatureType(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesFeatureTypes at the given index.

removeSpeciesFeatureType(SpeciesFeatureType) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesFeatureTypes.

removeSpeciesFeatureType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesFeatureTypes.

removeSpeciesFeatureValue(SpeciesFeatureValue) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Removes an element from the SpeciesFeature.listOfSpeciesFeatureValues.

removeSpeciesFeatureValue(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Removes an element from the SpeciesFeature.listOfSpeciesFeatureValues at the given index.

removeSpeciesTypeComponentIndex(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesTypeComponentIndexes at the given index.

removeSpeciesTypeComponentIndex(SpeciesTypeComponentIndex) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesTypeComponentIndexes.

removeSpeciesTypeComponentIndex(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesTypeComponentIndexes.

removeSpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Removes an element from the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts.

removeSpeciesTypeComponentMapInProduct(int) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Removes an element from the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts at the given index.

removeSpeciesTypeInstance(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesTypeInstances at the given index.

removeSpeciesTypeInstance(SpeciesTypeInstance) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesTypeInstances.

removeSpeciesTypeInstance(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Removes an element from the SpeciesType.listOfSpeciesTypeInstances.

representationType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

RepresentationType - Enum in org.sbml.jsbml.ext.multi

The RepresentationType enumeration is used in the extension of the ci element.

S

saturated - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

selector - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

setBindingSite1(String) - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Sets the value of bindingSite1

setBindingSite2(String) - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Sets the value of bindingSite2

setBindingStatus(BindingStatus) - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Sets the value of bindingStatus

setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

setCompartment(String) - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

setCompartment(Compartment) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

setCompartment(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

setCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Sets the value of compartmentReference

setCompartmentReference(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Sets the value of compartmentReference

setCompartmentType(String) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Sets the value of compartmentType

setComponent(String) - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Sets the value of component

setComponent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Sets the value of component

setComponent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Sets the value of component

setIndentifyingParent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Sets the value of identifyingParent

setIsType(boolean) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Sets the value of isType

setListOfCompartmentReferences(ListOf<CompartmentReference>) - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Sets the given ListOf<CompartmentReference>.

setListOfInSpeciesTypeBonds(ListOf<InSpeciesTypeBond>) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Sets the given ListOf<InSpeciesTypeBond>.

setListOfOutwardBindingSites(ListOf<OutwardBindingSite>) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Sets the given ListOf<OutwardBindingSite>.

setListOfPossibleSpeciesFeatureValues(ListOf<PossibleSpeciesFeatureValue>) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Sets the given ListOf<PossibleSpeciesFeatureValue>.

setListOfSpeciesFeatureChanges(ListOf<SpeciesFeatureChange>) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Sets the given ListOf<SpeciesFeatureChange>.

setListOfSpeciesFeatures(ListOf<SpeciesFeature>) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Sets the given ListOf<SpeciesFeature>.

setListOfSpeciesFeatureTypes(ListOf<SpeciesFeatureType>) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Sets the given ListOf<SpeciesFeatureType>.

setListOfSpeciesFeatureValues(ListOf<SpeciesFeatureValue>) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Sets the given ListOf<SpeciesFeatureValue>.

setListOfSpeciesTypeComponentIndexes(ListOf<SpeciesTypeComponentIndex>) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Sets the given ListOf<SpeciesTypeComponentIndex>.

setListOfSpeciesTypeComponentMapInProducts(ListOf<SpeciesTypeComponentMapInProduct>) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Sets the given ListOf<SpeciesTypeComponentMapInProduct>.

setListOfSpeciesTypeInstances(ListOf<SpeciesTypeInstance>) - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Sets the given ListOf<SpeciesTypeInstance>.

setListOfSpeciesTypes(ListOf<SpeciesType>) - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Sets the listOfSpeciesTypes.

setNumericValue(String) - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Sets the value of numericValue

setOccur(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Sets the value of occur

setOccur(int) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Sets the value of occur

setProductComponent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Sets the value of productComponent

setProductSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Sets the value of productSpeciesFeature

setReactant(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Sets the value of reactant

setReactantComponent(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Sets the value of reactantComponent

setReactantSpeciesFeature(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Sets the value of reactantSpeciesFeature

setRepresentationType(RepresentationType) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Sets the value of representationType

setSpeciesFeatureType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Sets the value of speciesFeatureType

setSpeciesReference(String) - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Sets the value of speciesReference

setSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Sets the value of speciesType

setSpeciesType(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Sets the value of speciesType

setSpeciesTypeComponentIndex(String) - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

Sets the value of speciesTypeComponentIndex

setValue(String) - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Sets the value of value

shortLabel - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

SpeciesFeature - Class in org.sbml.jsbml.ext.multi

SpeciesFeature() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature

Creates an SpeciesFeature instance

SpeciesFeature(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature

Creates a SpeciesFeature instance with an id.

SpeciesFeature(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature

Creates a SpeciesFeature instance with a level and version.

SpeciesFeature(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature

Creates a SpeciesFeature instance with an id, level, and version.

SpeciesFeature(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature

Creates a SpeciesFeature instance with an id, name, level, and version.

SpeciesFeature(SpeciesFeature) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeature

Clone constructor

SpeciesFeatureChange - Class in org.sbml.jsbml.ext.multi

SpeciesFeatureChange() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Creates an SpeciesFeatureChange instance

SpeciesFeatureChange(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Creates a SpeciesFeatureChange instance with an id.

SpeciesFeatureChange(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Creates a SpeciesFeatureChange instance with a level and version.

SpeciesFeatureChange(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Creates a SpeciesFeatureChange instance with an id, level, and version.

SpeciesFeatureChange(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Creates a SpeciesFeatureChange instance with an id, name, level, and version.

SpeciesFeatureChange(SpeciesFeatureChange) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Clone constructor

speciesFeatureType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

SpeciesFeatureType - Class in org.sbml.jsbml.ext.multi

A species type (SpeciesType) can carry any number of features (SpeciesFeatureType), which are characteristic properties specific for this type of species (Species).

SpeciesFeatureType() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Creates an SpeciesFeatureType instance

SpeciesFeatureType(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Creates a SpeciesFeatureType instance with an id.

SpeciesFeatureType(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Creates a SpeciesFeatureType instance with a level and version.

SpeciesFeatureType(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Creates a SpeciesFeatureType instance with an id, level, and version.

SpeciesFeatureType(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Creates a SpeciesFeatureType instance with an id, name, level, and version.

SpeciesFeatureType(SpeciesFeatureType) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Clone constructor

SpeciesFeatureValue - Class in org.sbml.jsbml.ext.multi

SpeciesFeatureValue() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Creates an SpeciesFeatureValue instance

SpeciesFeatureValue(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Creates a SpeciesFeatureValue instance with a level and version.

SpeciesFeatureValue(SpeciesFeatureValue) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Clone constructor

speciesReference - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

speciesType - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

SpeciesType - Class in org.sbml.jsbml.ext.multi

The element SpeciesType, which is part of SBML Level 2 Version 4 specification, is not part of SBML Level 3 Version 1 Core any more.

SpeciesType() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType

Creates an SpeciesType instance

SpeciesType(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType

Creates a SpeciesType instance with a level and version.

SpeciesType(SpeciesType) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType

Clone constructor

SpeciesType(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType

Creates a SpeciesType instance with an id.

SpeciesType(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType

Creates a SpeciesType instance with an id, level, and version.

SpeciesType(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesType

Creates a SpeciesType instance with an id, name, level, and version.

speciesTypeComponentIndex - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

SpeciesTypeComponentIndex - Class in org.sbml.jsbml.ext.multi

SpeciesTypeComponentIndex() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Creates an SpeciesTypeComponentIndex instance

SpeciesTypeComponentIndex(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Creates a SpeciesTypeComponentIndex instance with an id.

SpeciesTypeComponentIndex(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Creates a SpeciesTypeComponentIndex instance with a level and version.

SpeciesTypeComponentIndex(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Creates a SpeciesTypeComponentIndex instance with an id, level, and version.

SpeciesTypeComponentIndex(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Creates a SpeciesTypeComponentIndex instance with an id, name, level, and version.

SpeciesTypeComponentIndex(SpeciesTypeComponentIndex) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Clone constructor

SpeciesTypeComponentMapInProduct - Class in org.sbml.jsbml.ext.multi

SpeciesTypeComponentMapInProduct() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Creates an SpeciesTypeComponentMapInProduct instance

SpeciesTypeComponentMapInProduct(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Creates a SpeciesTypeComponentMapInProduct instance with a level and version.

SpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Clone constructor

SpeciesTypeInstance - Class in org.sbml.jsbml.ext.multi

SpeciesTypeInstance() - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Creates an SpeciesTypeInstance instance

SpeciesTypeInstance(String) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Creates a SpeciesTypeInstance instance with an id.

SpeciesTypeInstance(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Creates a SpeciesTypeInstance instance with a level and version.

SpeciesTypeInstance(String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Creates a SpeciesTypeInstance instance with an id, level, and version.

SpeciesTypeInstance(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Creates a SpeciesTypeInstance instance with an id, name, level, and version.

SpeciesTypeInstance(SpeciesTypeInstance) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Clone constructor

speciesTypeRestriction - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

speciesTypeState - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

stateFeature - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

stateFeatureInstance - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

stateFeatureValue - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

U

unsetBindingSite1() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Unsets the variable bindingSite1.

unsetBindingSite2() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

Unsets the variable bindingSite2.

unsetBindingStatus() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Unsets the variable bindingStatus.

unsetCompartment() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

unsetCompartment() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

unsetCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

Unsets the variable compartmentReference.

unsetCompartmentReference() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Unsets the variable compartmentReference.

unsetCompartmentType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Unsets the variable compartmentType.

unsetComponent() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

Unsets the variable component.

unsetComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Unsets the variable component.

unsetComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Unsets the variable component.

unsetIndentifyingParent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

Unsets the variable identifyingParent.

unsetIsType() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Unsets the variable isType.

unsetListOfCompartmentReferences() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

Returns true if MultiCompartmentPlugin.listOfCompartmentReferences contains at least one element, otherwise false.

unsetListOfInSpeciesTypeBonds() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns true if SpeciesType.listOfInSpeciesTypeBonds contains at least one element, otherwise false.

unsetListOfOutwardBindingSites() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns true if MultiSpeciesPlugin.listOfOutwardBindingSites contains at least one element, otherwise false.

unsetListOfPossibleSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Returns true if SpeciesFeatureType.listOfPossibleSpeciesFeatureValues contains at least one element, otherwise false.

unsetListOfSpeciesFeatureChanges() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Returns true if SpeciesTypeComponentMapInProduct.listOfSpeciesFeatureChanges contains at least one element, otherwise false.

unsetListOfSpeciesFeatures() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Returns true if MultiSpeciesPlugin.listOfSpeciesFeatures contains at least one element, otherwise false.

unsetListOfSpeciesFeatureTypes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns true if SpeciesType.listOfSpeciesFeatureTypes contains at least one element, otherwise false.

unsetListOfSpeciesFeatureValues() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Returns true if SpeciesFeature.listOfSpeciesFeatureValues contains at least one element, otherwise false.

unsetListOfSpeciesTypeComponentIndexes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns true if SpeciesType.listOfSpeciesTypeComponentIndexes contains at least one element, otherwise false.

unsetListOfSpeciesTypeComponentMapInProducts() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesReferencePlugin

Returns true if MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts contains at least one element, otherwise false.

unsetListOfSpeciesTypeInstances() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

Returns true if SpeciesType.listOfSpeciesTypeInstances contains at least one element, otherwise false.

unsetListOfSpeciesTypes() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

Sets the listOfSpeciesTypes to null

unsetNumericValue() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

Unsets the variable numericValue.

unsetOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Unsets the variable occur.

unsetOccur() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Unsets the variable occur.

unsetProductComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Unsets the variable productComponent.

unsetProductSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Unsets the variable productSpeciesFeature.

unsetReactant() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Unsets the variable reactant.

unsetReactantComponent() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

Unsets the variable reactantComponent.

unsetReactantSpeciesFeature() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

Unsets the variable reactantSpeciesFeature.

unsetRepresentationType() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Unsets the variable representationType.

unsetSpeciesFeatureType() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

Unsets the variable speciesFeatureType.

unsetSpeciesReference() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

Unsets the variable speciesReference.

unsetSpeciesType() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

Unsets the variable speciesType.

unsetSpeciesType() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

Unsets the variable speciesType.

unsetSpeciesTypeComponentIndex() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

Unsets the variable speciesTypeComponentIndex.

unsetValue() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

Unsets the variable value.

V

value - Static variable in class org.sbml.jsbml.ext.multi.MultiConstants

valueOf(String) - Static method in enum org.sbml.jsbml.ext.multi.BindingStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.multi.Relation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.sbml.jsbml.ext.multi.RepresentationType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.sbml.jsbml.ext.multi.BindingStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.multi.Relation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.multi.RepresentationType

Returns an array containing the constants of this enum type, in the order they are declared.

W

writeElement(SBMLObjectForXML, Object) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.CompartmentReference

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.DenotedSpeciesTypeComponentIndex

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.InSpeciesTypeBond

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.MultiASTNodePlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.MultiModelPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.MultiSimpleSpeciesReferencePlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.OutwardBindingSite

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeature

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureChange

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureType

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.SpeciesFeatureValue

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.SpeciesType

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentIndex

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeComponentMapInProduct

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.multi.SpeciesTypeInstance

A B C D E G H I L M N O P R S U V W