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

The extended Model class 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

The CompSBasePlugin class 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

The top level of an SBMLDocument is a container whose structure is defined by the object class SBML in the SBML Level 3 Version 1 Core specification.

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

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

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

The Deletion object class is used to define 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 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

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 using the namespace.

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

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

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

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

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

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

A ReplacedBy object 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

A ReplacedElement object is essentially a pointer 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

The optional extentConversionFactor attribute is provided to allow references and assumptions about the scale of a model's reaction extent to be converted to the scale of the containing model.

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

This list specifies objects to be removed from the submodel when composing the overall model.

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

The whole purpose of a Submodel object is to instantiate a model definition, which is to say, either a Model object defined in the same enclosing SBML document, or a model defined in an external SBML document.

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

The required attribute submodelRef takes a value which must be the identifier of a Submodel object in the containing model.

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

The optional timeConversionFactor attribute is provided to allow references and assumptions about the scale of time in the Submodel to be converted to the scale of time in the containing model.

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

Sets the value of the optional unitRef attribute This attribute is used to refer to the identifier of a UnitDefinition object.

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