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

A

AbstractNamedSBaseRef - Class in org.sbml.jsbml.ext.comp

This abstract class is used by Deletion and Port classes.

AbstractNamedSBaseRef() - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

Creates an AbstractNamedSBaseRef.

AbstractNamedSBaseRef(AbstractNamedSBaseRef) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

Creates an AbstractNamedSBaseRef from a given AbstractNamedSBaseRef.

AbstractNamedSBaseRef(int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

Creates an AbstractNamedSBaseRef from a level and version.

AbstractNamedSBaseRef(String) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

Creates an AbstractNamedSBaseRef with the given identifier.

AbstractNamedSBaseRef(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

Creates an AbstractNamedSBaseRef from an id, level and version.

AbstractNamedSBaseRef(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

Creates an AbstractNamedSBaseRef from an id, name, level and version.

accept(SBase) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

addDeletion(Deletion) - Method in class org.sbml.jsbml.ext.comp.Submodel

Adds a new Deletion to the listOfDeletions.

addExternalModelDefinition(ExternalModelDefinition) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Adds a new ExternalModelDefinition to the listOfExternalModelDefinitions.

addModelDefinition(ModelDefinition) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Adds a new ModelDefinition to the listOfModelDefinitions.

addPort(Port) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Adds a new Port to the listOfPorts.

addReplacedElement(ReplacedElement) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Adds a new element to listOfReplacedElements.

addSubmodel(Submodel) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Adds a new Submodel to the listOfSubmodels.

C

clone() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

clone() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

clones this class

clone() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

clone() - Method in class org.sbml.jsbml.ext.comp.Deletion

clone() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

clones this class

clone() - Method in class org.sbml.jsbml.ext.comp.ModelDefinition

clone() - Method in class org.sbml.jsbml.ext.comp.Port

clone() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

clones this class

clone() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

clones this class

clone() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

clone() - Method in class org.sbml.jsbml.ext.comp.Submodel

clones this class

CompConstants - Class in org.sbml.jsbml.ext.comp

Contains some constants related to the comp package.

CompConstants() - Constructor for class org.sbml.jsbml.ext.comp.CompConstants

CompModelPlugin - Class in org.sbml.jsbml.ext.comp

Adds two lists, one for holding Submodels and the other for holding Ports.

CompModelPlugin(CompModelPlugin) - Constructor for class org.sbml.jsbml.ext.comp.CompModelPlugin

Creates a new CompModelPlugin instance that is a copy of the current CompModelPlugin.

CompModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.comp.CompModelPlugin

Creates a new CompModelPlugin instance, associated with the given Model

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

A CompParser is used to parse the comp extension package elements and attributes.

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

CompSBasePlugin - Class in org.sbml.jsbml.ext.comp

Extends the SBase class by adding an optional ListOfReplacedElements child and a single optional ReplacedBy child.

CompSBasePlugin() - Constructor for class org.sbml.jsbml.ext.comp.CompSBasePlugin

Creates an CompSBasePlugin instance

CompSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.comp.CompSBasePlugin

Creates a CompSBasePlugin instance with a level and version.

CompSBasePlugin(CompSBasePlugin) - Constructor for class org.sbml.jsbml.ext.comp.CompSBasePlugin

Clone constructor

CompSBMLDocumentPlugin - Class in org.sbml.jsbml.ext.comp

Allows SBML documents to contain more than one model.

CompSBMLDocumentPlugin(SBMLDocument) - Constructor for class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Creates a new CompSBMLDocumentPlugin instance.

CompSBMLDocumentPlugin(CompSBMLDocumentPlugin) - Constructor for class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Creates a new CompSBMLDocumentPlugin instance.

conversionFactor - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

createDeletion() - Method in class org.sbml.jsbml.ext.comp.Submodel

Creates a new Deletion element and adds it to the ListOfDeletions list

createDeletion(String) - Method in class org.sbml.jsbml.ext.comp.Submodel

Creates a new Deletion element and adds it to the ListOfDeletions list

createExternalModelDefinition() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Creates a new ExternalModelDefinition element and adds it to the ListOfExternalModelDefinitions list

createExternalModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Creates a new ExternalModelDefinition element and adds it to the ListOfExternalModelDefinitions list

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

createModelDefinition() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list

createModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list

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

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

createPort() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Creates a new Port element and adds it to the ListOfPorts list

createPort(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Creates a new Port element and adds it to the ListOfPorts list

createReplacedBy() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Creates a new ReplacedBy element and sets it in this CompSBasePlugin.

createReplacedElement() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Creates a new ReplacedElement element and adds it to the ListOfReplacedElements list.

createSBaseRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Creates a new SBaseRef instance and add it to this SBaseRef

createSubmodel() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Creates a new Submodel element and adds it to the ListOfSubmodels list

createSubmodel(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Creates a new Submodel element and adds it to the ListOfSubmodels list

D

deletion - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

Deletion - Class in org.sbml.jsbml.ext.comp

Defines a deletion operation to be applied when a submodel instantiates a model definition.

Deletion() - Constructor for class org.sbml.jsbml.ext.comp.Deletion

Creates an Deletion instance

Deletion(String) - Constructor for class org.sbml.jsbml.ext.comp.Deletion

Creates a new Deletion instance with an id.

Deletion(int, int) - Constructor for class org.sbml.jsbml.ext.comp.Deletion

Creates a Deletion instance with a level and version.

Deletion(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Deletion

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

Deletion(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Deletion

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

Deletion(Deletion) - Constructor for class org.sbml.jsbml.ext.comp.Deletion

Clone constructor

E

equals(Object) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

equals(Object) - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

equals(Object) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

equals(Object) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

equals(Object) - Method in class org.sbml.jsbml.ext.comp.Submodel

extentConversionFactor - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

ExternalModelDefinition - Class in org.sbml.jsbml.ext.comp

The ExternalModelDefinition objects are model definitions - in and of themselves, they are definitions of the models but not uses of those models.

ExternalModelDefinition() - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Creates an ExternalModelDefinition instance

ExternalModelDefinition(String) - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Creates a ExternalModelDefinition instance with an id.

ExternalModelDefinition(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

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

ExternalModelDefinition(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

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

ExternalModelDefinition(ExternalModelDefinition) - Constructor for class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Clone constructor

F

findPort(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns a Port element that has the given 'id' within this Model or null if no such element can be found.

G

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

getAllowsChildren() - Method in class org.sbml.jsbml.ext.comp.Submodel

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

getChildAt(int) - Method in class org.sbml.jsbml.ext.comp.Submodel

getChildCount() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

getChildCount() - Method in class org.sbml.jsbml.ext.comp.Submodel

getConversionFactor() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns the value of conversionFactor

getDeletion() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns the value of deletion

getDeletionCount() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the number of Deletion objects in this Submodel.

getExtentConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the value of extentConversionFactor

getExternalModelDefinition(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the n-th ExternalModelDefinition object in this CompSBMLDocumentPlugin.

getExternalModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns a ExternalModelDefinition element that has the given 'id' within this CompSBMLDocumentPlugin or null if no such element can be found.

getExternalModelDefinitionCount() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the number of ExternalModelDefinition objects in this CompSBMLDocumentPlugin.

getIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of idRef

getListOfDeletions() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the listOfDeletions.

getListOfExternalModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the listOfExternalModelDefinitions.

getListOfModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the listOfModelDefinitions.

getListOfPorts() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the listOfPorts.

getListOfReplacedElements() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the listOfReplacedElements

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

getListOfSubmodels() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the listOfSubmodels.

getMd5() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns the value of md5 or an empty String if it is not set.

getMetaIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of metaIdRef

getModelDefinition(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the n-th ModelDefinition object in this CompSBMLDocumentPlugin.

getModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns a ModelDefinition element that has the given 'id' within this CompSBMLDocumentPlugin or null if no such element can be found.

getModelDefinitionCount() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the number of ModelDefinition objects in this CompSBMLDocumentPlugin.

getModelRef() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns the value of modelRef or an empty String if it is not set.

getModelRef() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the value of modelRef

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

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

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.comp.CompConstants

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

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

getNumExternalModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the number of ExternalModelDefinition of this CompSBMLDocumentPlugin.

getNumModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns the number of ModelDefinition of this CompSBMLDocumentPlugin.

getNumPorts() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the number of Port of this CompModelPlugin.

getNumReplacedElements() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the number of ReplacedElement of this CompSBasePlugin.

getNumSubmodels() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the number of Submodel of this CompModelPlugin.

getPackageName() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

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

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

getParent() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getPort(int) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the n-th Port object in this CompModelPlugin.

getPort(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns a Port element that has the given 'id' within this CompModelPlugin or null if no such element can be found.

getPortCount() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the number of Port objects in this CompModelPlugin.

getPortRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of portRef

getPrefix() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

getReplacedBy() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the value of replacedBy

getReplacedElement(int) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the n-th ReplacedElement object in this CompSBasePlugin.

getReplacedElement(String) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns a ReplacedElement element that has the given 'id' within this CompSBasePlugin or null if no such element can be found.

getReplacedElementCount() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns the number of ReplacedElement objects in this CompSBasePlugin.

getSBaseRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of sBaseRef

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

getSource() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns the value of source or an empty String if it is not set.

getSubmodel(int) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the n-th Submodel object in this CompModelPlugin.

getSubmodel(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns a Submodel element that has the given 'id' within this CompModelPlugin or null if no such element can be found.

getSubmodelCount() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns the number of Submodel objects in this CompModelPlugin.

getSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

Returns the value of submodelRef

getSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns the value of submodelRef

getTimeConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns the value of timeConversionFactor

getUnitRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns the value of unitRef

getURI() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

H

hashCode() - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

hashCode() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

hashCode() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

hashCode() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

hashCode() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

hashCode() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

hashCode() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

hashCode() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

hashCode() - Method in class org.sbml.jsbml.ext.comp.Submodel

I

idRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

init() - Method in class org.sbml.jsbml.ext.comp.ModelDefinition

initDefaults() - Method in class org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.comp.Deletion

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.comp.Port

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Initializes the default values.

initDefaults() - Method in class org.sbml.jsbml.ext.comp.Submodel

Initializes the default values using the namespace.

isIdMandatory() - Method in class org.sbml.jsbml.ext.comp.Deletion

isIdMandatory() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

isIdMandatory() - Method in class org.sbml.jsbml.ext.comp.Port

isIdMandatory() - Method in class org.sbml.jsbml.ext.comp.Submodel

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

isSetConversionFactor() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns whether conversionFactor is set

isSetDeletion() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns whether deletion is set

isSetExtentConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns whether extentConversionFactor is set

isSetIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns whether idRef is set

isSetListOfDeletions() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns true, if listOfDeletions contains at least one element.

isSetListOfExternalModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns true, if listOfExternalModelDefinitions contains at least one element.

isSetListOfModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns true, if listOfModelDefinitions contains at least one element.

isSetListOfPorts() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns true, if listOfPorts contains at least one element.

isSetListOfReplacedElements() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns true, if listOfReplacedElements contains at least one element, otherwise false

isSetListOfSubmodels() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns true, if listOfSubmodels contains at least one element.

isSetMd5() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns whether md5 is set

isSetMetaIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns whether metaIdRef is set

isSetModelRef() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns whether modelRef is set

isSetModelRef() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns whether modelRef is set

isSetPortRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns whether portRef is set

isSetReplacedBy() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns whether replacedBy is set

isSetSBaseRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns whether sBaseRef is set

isSetSource() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Returns whether source is set

isSetSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

Returns whether submodelRef is set

isSetSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Returns whether submodelRef is set

isSetTimeConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns whether timeConversionFactor is set

isSetUnitRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Returns whether unitRef is set

L

listOfDeletions - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

listOfExternalModelDefinitions - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

listOfModelDefinitions - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

listOfPorts - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

listOfReplacedElements - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

listOfSubmodels - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

M

md5 - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

metaIdRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

ModelDefinition - Class in org.sbml.jsbml.ext.comp

Holder class for model definitions, which are Models.

ModelDefinition() - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition

Creates a new ModelDefinition instance.

ModelDefinition(int, int) - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition

Creates a new ModelDefinition instance.

ModelDefinition(Model) - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition

Creates a new ModelDefinition instance cloned from the given core Model instance.

ModelDefinition(String) - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition

Creates a new ModelDefinition instance.

ModelDefinition(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.ModelDefinition

Creates a new ModelDefinition instance.

modelRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

N

namespaces - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

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

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

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

O

org.sbml.jsbml.ext.comp - package org.sbml.jsbml.ext.comp

Provides classes for the Hierarchical Model Composition package.

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

P

packageName - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

Port - Class in org.sbml.jsbml.ext.comp

The Port allows a modeler to design a Submodel such that other models interact with the Submodel through designated interfaces.

Port() - Constructor for class org.sbml.jsbml.ext.comp.Port

Creates an Port instance

Port(String) - Constructor for class org.sbml.jsbml.ext.comp.Port

Creates a Port instance with an id.

Port(int, int) - Constructor for class org.sbml.jsbml.ext.comp.Port

Creates a Port instance with a level and version.

Port(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Port

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

Port(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Port

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

Port(Port) - Constructor for class org.sbml.jsbml.ext.comp.Port

Clone constructor

portRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

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

R

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.comp.Submodel

register(SBase) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

removeDeletion(Deletion) - Method in class org.sbml.jsbml.ext.comp.Submodel

Removes an element from the listOfDeletions.

removeDeletion(int) - Method in class org.sbml.jsbml.ext.comp.Submodel

Removes an element from the listOfDeletions at the given index.

removeDeletion(String) - Method in class org.sbml.jsbml.ext.comp.Submodel

Removes an element from the listOfDeletions with the given id.

removeExternalModelDefinition(ExternalModelDefinition) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Removes an element from the listOfExternalModelDefinitions.

removeExternalModelDefinition(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Removes an element from the listOfExternalModelDefinitions at the given index.

removeExternalModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Removes an element from the listOfExternalModelDefinitions with the given id.

removeFromParent() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

removeModelDefinition(ModelDefinition) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Removes an element from the listOfModelDefinitions.

removeModelDefinition(int) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Removes an element from the listOfModelDefinitions at the given index.

removeModelDefinition(String) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Removes an element from the listOfModelDefinitions with the given id.

removePort(int) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Removes an element from the listOfPorts at the given index.

removePort(Port) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Removes an element from the listOfPorts.

removeReplacedElement(ReplacedElement) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Removes an element from listOfReplacedElements.

removeReplacedElement(int) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Removes the ith element from the ListOfReplacedElements.

removeSubmodel(int) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Removes an element from the listOfSubmodels at the given index.

removeSubmodel(String) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Removes an element from the listOfSubmodels.

removeSubmodel(Submodel) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Removes an element from the listOfSubmodels.

replacedBy - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

ReplacedBy - Class in org.sbml.jsbml.ext.comp

Indicates when the parent object is to be replaced by another object.

ReplacedBy() - Constructor for class org.sbml.jsbml.ext.comp.ReplacedBy

Creates a ReplacedBy instance

ReplacedBy(int, int) - Constructor for class org.sbml.jsbml.ext.comp.ReplacedBy

Creates a ReplacedBy instance with a level and version.

ReplacedBy(ReplacedBy) - Constructor for class org.sbml.jsbml.ext.comp.ReplacedBy

Clone constructor

replacedElement - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

ReplacedElement - Class in org.sbml.jsbml.ext.comp

Points to a submodel object that should be considered "replaced".

ReplacedElement() - Constructor for class org.sbml.jsbml.ext.comp.ReplacedElement

Creates an ReplacedElement instance

ReplacedElement(int, int) - Constructor for class org.sbml.jsbml.ext.comp.ReplacedElement

Creates a ReplacedElement instance with a level and version.

ReplacedElement(ReplacedElement) - Constructor for class org.sbml.jsbml.ext.comp.ReplacedElement

Clone constructor

S

sBaseRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

SBaseRef - Class in org.sbml.jsbml.ext.comp

Contains the machinery for constructing references to specific components within enclosed models or even within external models located in other files.

SBaseRef() - Constructor for class org.sbml.jsbml.ext.comp.SBaseRef

Creates a SBaseRef instance.

SBaseRef(int, int) - Constructor for class org.sbml.jsbml.ext.comp.SBaseRef

Creates a SBaseRef instance with a level and version.

SBaseRef(SBaseRef) - Constructor for class org.sbml.jsbml.ext.comp.SBaseRef

Clone constructor

setConversionFactor(String) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Sets the value of the optional conversionFactor attribute.

setDeletion(String) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Sets the value of the optional deletion attribute.

setExtentConversionFactor(String) - Method in class org.sbml.jsbml.ext.comp.Submodel

Sets the value of the optional extentConversionFactor

setIdRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Sets the value of the optional idRef attribute.

setListOfDeletions(ListOf<Deletion>) - Method in class org.sbml.jsbml.ext.comp.Submodel

Sets the given ListOf<Deletion>.

setListOfExternalModelDefinitions(ListOf<ExternalModelDefinition>) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

The listOfExternamModelDefinitions is an optional element of CompSBMLDocumentPlugin and defines external SBML document references within the ExternalModelDefinition object.

setListOfModelDefinitions(ListOf<ModelDefinition>) - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

listOfModelDefinitions is an optional list of CompSBMLDocumentPlugin which specifies ModelDefinitions for the SBML document.

setListOfPorts(ListOf<Port>) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Sets the optional ListOf<Port>.

setListOfReplacedElements(ListOf<ReplacedElement>) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Sets the listOfReplacedElements.

setListOfSubmodels(ListOf<Submodel>) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Sets the optional ListOf<Submodel>.

setMd5(String) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Sets the value of the optional md5 attribute.

setMetaIdRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Sets the value of the optional metaIdRef attribute.

setModelRef(String) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Sets the value of the optional modelRef attribute.

setModelRef(String) - Method in class org.sbml.jsbml.ext.comp.Submodel

Sets the value of the required modelRef

setPortRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Sets the value of the optional portRef attribute.

setReplacedBy(ReplacedBy) - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Sets the value of the optional replacedBy element.

setSBaseRef(SBaseRef) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Sets the value of the optional sBaseRef element.

setSource(String) - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Sets the value of the required source attribute.

setSubmodelRef(String) - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

Sets the value of the required submodelRef attribute.

setSubmodelRef(String) - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Sets the value of the required submodelRef attribute.

setTimeConversionFactor(String) - Method in class org.sbml.jsbml.ext.comp.Submodel

Sets the value of the optional timeConversionFactor

setUnitRef(String) - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Sets the value of the optional unitRef attribute

shortLabel - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

source - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

Submodel - Class in org.sbml.jsbml.ext.comp

Submodels are instantiations of models contained within other models.

Submodel() - Constructor for class org.sbml.jsbml.ext.comp.Submodel

Creates an Submodel instance

Submodel(String) - Constructor for class org.sbml.jsbml.ext.comp.Submodel

Creates a Submodel instance with an id.

Submodel(int, int) - Constructor for class org.sbml.jsbml.ext.comp.Submodel

Creates a Submodel instance with a level and version.

Submodel(String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Submodel

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

Submodel(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.comp.Submodel

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

Submodel(Submodel) - Constructor for class org.sbml.jsbml.ext.comp.Submodel

Clone constructor

submodelRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

T

timeConversionFactor - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

U

unitRef - Static variable in class org.sbml.jsbml.ext.comp.CompConstants

unregister(SBase) - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

unsetConversionFactor() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Unsets the variable conversionFactor

unsetDeletion() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Unsets the variable deletion

unsetExtentConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel

Unsets the variable extentConversionFactor

unsetIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Unsets the variable idRef

unsetListOfDeletions() - Method in class org.sbml.jsbml.ext.comp.Submodel

Returns true, if listOfDeletions contain at least one element, otherwise false

unsetListOfExternalModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns true, if listOfExternalModelDefinitions contain at least one element, otherwise false

unsetListOfModelDefinitions() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

Returns true, if listOfModelDefinitions contain at least one element, otherwise false

unsetListOfPorts() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns true, if listOfPorts contain at least one element, otherwise false

unsetListOfReplacedElements() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Returns true, if listOfReplacedElements contained at least one element, otherwise false

unsetListOfSubmodels() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

Returns true, if listOfSubmodels contain at least one element, otherwise false

unsetMd5() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Unsets the variable md5

unsetMetaIdRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Unsets the variable metaIdRef

unsetModelRef() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Unsets the variable modelRef

unsetModelRef() - Method in class org.sbml.jsbml.ext.comp.Submodel

Unsets the variable modelRef

unsetPortRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Unsets the variable portRef

unsetReplacedBy() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

Unsets the variable replacedBy

unsetSBaseRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Unsets the variable sBaseRef

unsetSource() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

Unsets the variable source

unsetSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

Unsets the variable submodelRef

unsetSubmodelRef() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

Unsets the variable submodelRef

unsetTimeConversionFactor() - Method in class org.sbml.jsbml.ext.comp.Submodel

Unsets the variable timeConversionFactor

unsetUnitRef() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

Unsets the variable unitRef

W

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

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.comp.CompModelPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.comp.CompSBasePlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.comp.ExternalModelDefinition

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.comp.ReplacedBy

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.comp.ReplacedElement

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.comp.SBaseRef

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.comp.Submodel

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