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.

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints

addErrorCodesForAttribute(Set<Integer>, int, int, String, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints

addErrorCodesForCheck(Set<Integer>, int, int, SBMLValidator.CHECK_CATEGORY, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints

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

Adds a new InSpeciesTypeBond to the MultiSpeciesType.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.

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

Adds a new SpeciesFeatureType to the MultiSpeciesType.listOfSpeciesFeatureTypes.

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

Adds a new SpeciesFeatureValue to the SpeciesFeature.listOfSpeciesFeatureValues.

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

Adds a MultiSpeciesType.

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

Adds a new SpeciesTypeComponentIndex to the MultiSpeciesType.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.MultiSpeciesType

Adds a new SpeciesTypeInstance to the MultiSpeciesType.listOfSpeciesTypeInstances.

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

Adds a new SubListOfSpeciesFeature to the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures.

and - org.sbml.jsbml.ext.multi.Relation

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

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

A BindingSiteSpeciesType object is a binding site, and therefore its instance can further define the bindingStatus attribute and can participate a binding internally and explicitly in an InSpeciesTypeBond object, or externally and implicitly defined by an OutwardBindingSite object.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance.

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

Creates a new BindingSiteSpeciesType instance, cloned from the given object.

BindingSiteSpeciesTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

BindingSiteSpeciesTypeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints

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

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

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

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

bound - org.sbml.jsbml.ext.multi.BindingStatus

C

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

Creates a new BindingSiteSpeciesType instance, cloned from itself.

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

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.MultiSpeciesType

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.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.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

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

clones this class

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

compartmentReference - 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 a new CompartmentReference instance.

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

Creates a new CompartmentReference instance, cloned from the given object.

CompartmentReferenceConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

CompartmentReferenceConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints

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.MultiSpeciesType

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

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

Creates a new InSpeciesTypeBond element and adds it to the MultiSpeciesType.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.

createListOfChild(ListOf<?>, String) - Method in class org.sbml.jsbml.xml.parsers.MultiParser

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

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

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

createPluginFor(SBase) - 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.

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

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

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

Creates a new SpeciesFeatureType element and adds it to the MultiSpeciesType.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 MultiSpeciesType inside this MultiModelPlugin and returns it.

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

Creates a new MultiSpeciesType inside this MultiModelPlugin and returns it.

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

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

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

Creates a new SpeciesTypeComponentIndex element and adds it to the MultiSpeciesType.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.MultiSpeciesType

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

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

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

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

Creates a new SubListOfSpeciesFeature element and adds it to the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures list.

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

Creates a new SubListOfSpeciesFeature element and adds it to the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures list.

D

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

E

either - org.sbml.jsbml.ext.multi.BindingStatus

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

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.MultiCompartmentPlugin

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

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

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

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

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.SpeciesFeatureType

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

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

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

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

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

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

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.MultiSpeciesType

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

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

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.MultiSpeciesType

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

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

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

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

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

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

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.

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.

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.

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

Returns the value of SubListOfSpeciesFeature.component.

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

getElementName() - Method in class org.sbml.jsbml.ext.multi.MultiSpeciesType

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.MultiSpeciesType

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

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

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

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

Returns the number of InSpeciesTypeBonds in this MultiSpeciesType.

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.MultiSpeciesType

Returns the MultiSpeciesType.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

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

Returns the MultiSpeciesPlugin.listOfSpeciesFeatures.

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

Returns the MultiSpeciesType.listOfSpeciesFeatureTypes.

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

Returns the SpeciesFeature.listOfSpeciesFeatureValues.

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

Returns the MultiSpeciesType.listOfSpeciesTypeComponentIndexes.

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

Returns the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts.

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

Returns the MultiSpeciesType.listOfSpeciesTypeInstances.

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

Returns the listOfSpeciesTypes.

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

Returns the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures.

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

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

Returns a namespace corresponding to the given SBML level and version or null.

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.MultiSpeciesType

Returns the number of InSpeciesTypeBonds in this MultiSpeciesType.

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.

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.MultiSpeciesType

Returns the number of SpeciesFeatureTypes in this MultiSpeciesType.

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.MultiSpeciesType

Returns the number of SpeciesTypeComponentIndexs in this MultiSpeciesType.

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.MultiSpeciesType

Returns the number of SpeciesTypeInstances in this MultiSpeciesType.

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

Returns the number of SubListOfSpeciesFeatures in this MultiSpeciesPlugin.

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.

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.

getRelation() - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature

Returns the value of SubListOfSpeciesFeature.relation.

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.

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.MultiSpeciesType

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

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

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

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

Returns the number of SpeciesFeatureTypes in this MultiSpeciesType.

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() - 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.

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

Gets the ith MultiSpeciesType.

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

Gets the MultiSpeciesType that has the given id.

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

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

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

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

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

Returns the number of SpeciesTypeComponentIndexs in this MultiSpeciesType.

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.MultiSpeciesType

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

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

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

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

Returns the number of SpeciesTypeInstances in this MultiSpeciesType.

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

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

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

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

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

Returns the number of SubListOfSpeciesFeatures in this MultiSpeciesPlugin.

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

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.BindingSiteSpeciesTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.CompartmentReferenceConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints

getValidationFunction(int, ValidationContext) - Method in class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints

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.CompartmentReference

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.MultiCompartmentPlugin

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

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

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

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

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.SpeciesFeatureType

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

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

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

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

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

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.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.MultiSpeciesType

Initializes the default values.

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.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.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.

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

Initializes the default values using the namespace.

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

Defines a bond existing within a MultiSpeciesType.

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

Creates an InSpeciesTypeBond instance

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

Creates a InSpeciesTypeBond instance with a level and version.

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

Creates a InSpeciesTypeBond instance with an id.

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

InSpeciesTypeBondConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

InSpeciesTypeBondConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.InSpeciesTypeBondConstraints

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

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

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

Creates an IntraSpeciesReaction instance

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

Creates a IntraSpeciesReaction instance with a level and version.

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

Creates a IntraSpeciesReaction instance with an id.

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.MultiSpeciesType

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.MultiSpeciesType

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.SpeciesFeatureType

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.MultiSpeciesType

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

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

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.

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

Returns whether SubListOfSpeciesFeature.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.MultiSpeciesType

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

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

Returns true if MultiSpeciesPlugin.listOfOutwardBindingSites is not null.

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

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

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

Returns true if MultiSpeciesPlugin.listOfSpeciesFeatures is not null.

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

Returns true if MultiSpeciesType.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.MultiSpeciesType

Returns true if MultiSpeciesType.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.MultiSpeciesType

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

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

Returns true if the listOfSpeciesType is set.

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

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

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.

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.

isSetRelation() - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature

Returns whether SubListOfSpeciesFeature.relation 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.

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

Returns whether SpeciesFeatureValue.value is set.

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

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

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

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

ListOfSpeciesFeatureContent - Interface in org.sbml.jsbml.ext.multi.util

Represents elements that can go into the combined ListOfSpeciesFeatures, meaning SpeciesFeature and SubListOfSpeciesFeature.

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

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

MultiASTNodePlugin(MultiASTNodePlugin) - 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.

MultiCompartmentPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

MultiCompartmentPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.MultiCompartmentPluginConstraints

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 MultiSpeciesTypes.

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

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

MultiModelPluginConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

MultiModelPluginConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.MultiModelPluginConstraints

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

Clone constructor

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

Creates a MultiSimpleSpeciesReferencePlugin instance with a SimpleSpeciesReference.

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

A species in the Multi package is extended from a pool to a template or pattern which multiple pools may map to.

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

Creates a new MultiSpeciesPlugin instance copied from the given MultiSpeciesPlugin.

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

Creates a new MultiSpeciesPlugin instance, connected to the given 'core' Species.

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

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

Creates an MultiSpeciesReferencePlugin instance

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

Clone constructor

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

Creates a MultiSpeciesReferencePlugin instance with a SpeciesReference.

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

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

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

Creates an MultiSpeciesType instance

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

Creates a MultiSpeciesType instance with a level and version.

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

Creates a MultiSpeciesType instance with an id.

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

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

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

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

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

Creates a new MultiSpeciesType instance cloned from the given MultiSpeciesType.

MultiSpeciesTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

MultiSpeciesTypeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.MultiSpeciesTypeConstraints

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.

not - org.sbml.jsbml.ext.multi.Relation

numericValue - org.sbml.jsbml.ext.multi.RepresentationType

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

or - org.sbml.jsbml.ext.multi.Relation

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

Provides classes for the Multi package.

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

org.sbml.jsbml.validator.offline.constraints - package org.sbml.jsbml.validator.offline.constraints

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

A binding site not involved in any InSpeciesTypeBond object in the MultiSpeciesType referenced by a Species is an outwardBindingSite.

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

Creates a PossibleSpeciesFeatureValue instance with a level and version.

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

Creates a PossibleSpeciesFeatureValue instance with an id.

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

PossibleSpeciesFeatureValueConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

PossibleSpeciesFeatureValueConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.PossibleSpeciesFeatureValueConstraints

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.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.MultiSpeciesType

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.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.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

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

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

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

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

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

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

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

Removes an element from the MultiCompartmentPlugin.listOfCompartmentReferences.

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

Removes an element from the MultiCompartmentPlugin.listOfCompartmentReferences.

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

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

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

Removes an element from the MultiSpeciesType.listOfInSpeciesTypeBonds.

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

Removes an element from the MultiSpeciesType.listOfInSpeciesTypeBonds.

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

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

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

Removes an element from the MultiSpeciesPlugin.listOfOutwardBindingSites.

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

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

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

Removes an element from the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues.

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

Removes an element from the SpeciesFeatureType.listOfPossibleSpeciesFeatureValues.

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

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

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

Removes an element from the MultiSpeciesPlugin.listOfSpeciesFeatures.

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

Removes an element from the MultiSpeciesPlugin.listOfSpeciesFeatures.

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

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

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

Removes an element from the MultiSpeciesType.listOfSpeciesFeatureTypes.

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

Removes an element from the MultiSpeciesType.listOfSpeciesFeatureTypes.

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

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

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

Removes an element from the SpeciesFeature.listOfSpeciesFeatureValues.

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

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

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

Removes an element from the MultiSpeciesType.listOfSpeciesTypeComponentIndexes.

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

Removes an element from the MultiSpeciesType.listOfSpeciesTypeComponentIndexes.

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

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

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

Removes an element from the MultiSpeciesReferencePlugin.listOfSpeciesTypeComponentMapInProducts.

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

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

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

Removes an element from the MultiSpeciesType.listOfSpeciesTypeInstances.

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

Removes an element from the MultiSpeciesType.listOfSpeciesTypeInstances.

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

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

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

Removes an element from the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures.

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

Removes an element from the MultiSpeciesPlugin.listOfSubListOfSpeciesFeatures.

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

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

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

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

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

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

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.MultiSpeciesType

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>.

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.MultiSpeciesType

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.MultiSpeciesType

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.MultiSpeciesType

Sets the given ListOf<SpeciesTypeInstance>.

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

Sets the listOfSpeciesTypes.

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

Sets the given ListOf<SubListOfSpeciesFeature>.

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

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

setRelation(Relation) - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature

Sets the value of relation

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

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

Defines the state of a component in a species by selecting values from the listOfPossibleSpeciesFeatureValues of the referenced SpeciesFeatureType.

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

Creates an SpeciesFeature instance

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

Creates a SpeciesFeature instance with a level and version.

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

Creates a SpeciesFeature instance with an id.

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

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

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

A species type (MultiSpeciesType) 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(int, int) - Constructor for class org.sbml.jsbml.ext.multi.SpeciesFeatureType

Creates a SpeciesFeatureType instance with a level and version.

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

Creates a SpeciesFeatureType instance with an id.

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

SpeciesFeatureTypeConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

SpeciesFeatureTypeConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesFeatureTypeConstraints

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

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

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

Provides a way to identify or index a component within a MultiSpeciesType.

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

Creates an SpeciesTypeComponentIndex instance

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

Creates a SpeciesTypeComponentIndex instance with a level and version.

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

Creates a SpeciesTypeComponentIndex instance with an id.

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

SpeciesTypeComponentIndexConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

SpeciesTypeComponentIndexConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeComponentIndexConstraints

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

A speciesTypeComponentMapInProduct defines the mapping between a component in a reactant and a component in a product.

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

Provides a way to construct MultiSpeciesTypes and Species with multiple components.

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

Creates an SpeciesTypeInstance instance

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

Creates a SpeciesTypeInstance instance with a level and version.

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

Creates a SpeciesTypeInstance instance with an id.

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

SpeciesTypeInstanceConstraints - Class in org.sbml.jsbml.validator.offline.constraints

Constraints declaration for the MultiCompartmentPlugin class.

SpeciesTypeInstanceConstraints() - Constructor for class org.sbml.jsbml.validator.offline.constraints.SpeciesTypeInstanceConstraints

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

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

Allows to regroup a set of SpeciesFeature that have a specific Relation between them.

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

Creates an SubListOfSpeciesFeature instance

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

Creates a SubListOfSpeciesFeature instance with a level and version.

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

Creates a SubListOfSpeciesFeature instance with an id.

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

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

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

Clone constructor

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

sum - org.sbml.jsbml.ext.multi.RepresentationType

U

unbound - org.sbml.jsbml.ext.multi.BindingStatus

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.MultiSpeciesType

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.

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

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.MultiSpeciesType

Returns true if MultiSpeciesType.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.

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.MultiSpeciesType

Returns true if MultiSpeciesType.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.MultiSpeciesType

Returns true if MultiSpeciesType.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.MultiSpeciesType

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

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

Sets the listOfSpeciesTypes to null

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

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

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.

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.

unsetRelation() - Method in class org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature

Unsets the variable relation.

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.

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.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.MultiSpeciesType

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.SpeciesFeatureType

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

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

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

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