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

A

addGroup(Group) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

addMember(Member) - Method in class org.sbml.jsbml.ext.groups.Group

addMemberConstraint(MemberConstraint) - Method in class org.sbml.jsbml.ext.groups.Group

Adds a new MemberConstraint to the listOfMemberConstraints.

C

clone() - Method in class org.sbml.jsbml.ext.groups.Group

clone() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

clone() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

clone() - Method in class org.sbml.jsbml.ext.groups.Member

clone() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

createGroup() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Creates a new instance of Group and add it to this GroupsModelPlugin.

createGroup(String) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Creates a new instance of Group and add it to this GroupsModelPlugin.

createGroup(String, String...) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Creates a new instance of Group and add it to this GroupsModelPlugin.

createMember(String) - Method in class org.sbml.jsbml.ext.groups.Group

Creates a new instance of Member and add it to this Group.

createMemberConstraint() - Method in class org.sbml.jsbml.ext.groups.Group

Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list

createMemberConstraint(String) - Method in class org.sbml.jsbml.ext.groups.Group

Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list

createMemberWithIdRef(String) - Method in class org.sbml.jsbml.ext.groups.Group

Creates a new instance of Member and add it to this Group.

createMemberWithIdRef(String, String) - Method in class org.sbml.jsbml.ext.groups.Group

Creates a new instance of Member and add it to this Group.

createMemberWithMetaIdRef(String) - Method in class org.sbml.jsbml.ext.groups.Group

Creates a new instance of Member and add it to this Group.

createMemberWithMetaIdRef(String, String) - Method in class org.sbml.jsbml.ext.groups.Group

Creates a new instance of Member and add it to this Group.

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

D

distinctAttribute - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

E

equals(Object) - Method in class org.sbml.jsbml.ext.groups.Group

equals(Object) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

equals(Object) - Method in class org.sbml.jsbml.ext.groups.Member

equals(Object) - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

G

getAllowsChildren() - Method in class org.sbml.jsbml.ext.groups.Group

getAllowsChildren() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.groups.Group

getChildAt(int) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.groups.Group

getChildCount() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getDistinctAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Returns the value of distinctAttribute

getElementNamespace() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getGroup(int) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getGroup(String) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Gets the Group that has the given id.

getGroupCount() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Returns the number of Groups of this GroupsModelPlugin.

getId() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

getIdenticalAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Returns the value of identicalAttribute

getIdRef() - Method in class org.sbml.jsbml.ext.groups.Member

Returns the value of idRef

getKind() - Method in class org.sbml.jsbml.ext.groups.Group

getListOfGroups() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getListOfMemberConstraints() - Method in class org.sbml.jsbml.ext.groups.Group

Returns the listOfMemberConstraints.

getListOfMembers() - Method in class org.sbml.jsbml.ext.groups.Group

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

getMember(int) - Method in class org.sbml.jsbml.ext.groups.Group

getMemberConstraintCount() - Method in class org.sbml.jsbml.ext.groups.Group

Returns the number of MemberConstraints of this Group.

getMemberCount() - Method in class org.sbml.jsbml.ext.groups.Group

Returns the number of Members of this Group.

getMembersShareType() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

Returns the value of membersShareType

getMetaIdRef() - Method in class org.sbml.jsbml.ext.groups.Member

Returns the value of metaIdRef

getName() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

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

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

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.groups.GroupsConstants

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

getNumGroups() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Returns the number of Groups of this GroupsModelPlugin.

getNumMemberConstraints() - Method in class org.sbml.jsbml.ext.groups.Group

Returns the number of MemberConstraints of this Group.

getNumMembers() - Method in class org.sbml.jsbml.ext.groups.Group

Returns the number of Members of this Group.

getPackageName() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

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

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

getParent() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getPrefix() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

getSBaseInstance() - Method in class org.sbml.jsbml.ext.groups.Member

Gets the actual SBase instance referred by the idRef or metaIdRef, returns null if nothing is found.

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

getURI() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Group - Class in org.sbml.jsbml.ext.groups

Group() - Constructor for class org.sbml.jsbml.ext.groups.Group

Group(Group) - Constructor for class org.sbml.jsbml.ext.groups.Group

Group(int, int) - Constructor for class org.sbml.jsbml.ext.groups.Group

GroupKind - Enum in org.sbml.jsbml.ext.groups

This is a collection of possible values for the kind attribute within a Group.

GroupsConstants - Class in org.sbml.jsbml.ext.groups

Contains some constants related to the groups package.

GroupsConstants() - Constructor for class org.sbml.jsbml.ext.groups.GroupsConstants

GroupsModelPlugin - Class in org.sbml.jsbml.ext.groups

GroupsModelPlugin(Model) - Constructor for class org.sbml.jsbml.ext.groups.GroupsModelPlugin

GroupsModelPlugin(GroupsModelPlugin) - Constructor for class org.sbml.jsbml.ext.groups.GroupsModelPlugin

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

This class is used to parse the groups extension package elements and attributes.

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

H

hashCode() - Method in class org.sbml.jsbml.ext.groups.Group

hashCode() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

hashCode() - Method in class org.sbml.jsbml.ext.groups.Member

hashCode() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

I

identicalAttribute - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

idRef - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

initDefaults() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Initializes the default values using the namespace.

isIdMandatory() - Method in class org.sbml.jsbml.ext.groups.Group

isIdMandatory() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

isIdMandatory() - Method in class org.sbml.jsbml.ext.groups.Member

isIdMandatory() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

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

isSetDistinctAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Returns whether distinctAttribute is set

isSetId() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

isSetIdenticalAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Returns whether identicalAttribute is set

isSetIdRef() - Method in class org.sbml.jsbml.ext.groups.Member

Returns whether idRef is set

isSetKind() - Method in class org.sbml.jsbml.ext.groups.Group

isSetListOfGroups() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

isSetListOfMemberConstraints() - Method in class org.sbml.jsbml.ext.groups.Group

Returns true, if listOfMemberConstraints contains at least one element.

isSetListOfMembers() - Method in class org.sbml.jsbml.ext.groups.Group

isSetMembersShareType() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

Returns whether membersShareType is set

isSetMetaIdRef() - Method in class org.sbml.jsbml.ext.groups.Member

Returns whether metaIdRef is set

isSetName() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

L

listOfGroups - Variable in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

ListOfMemberConstraint - Class in org.sbml.jsbml.ext.groups

ListOfMemberConstraint() - Constructor for class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

ListOfMemberConstraint(int, int) - Constructor for class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

ListOfMemberConstraint(ListOfMemberConstraint) - Constructor for class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

listOfMembers - Variable in class org.sbml.jsbml.ext.groups.Group

M

Member - Class in org.sbml.jsbml.ext.groups

Member() - Constructor for class org.sbml.jsbml.ext.groups.Member

Member(int, int) - Constructor for class org.sbml.jsbml.ext.groups.Member

Member(Member) - Constructor for class org.sbml.jsbml.ext.groups.Member

memberConstraint - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

MemberConstraint - Class in org.sbml.jsbml.ext.groups

MemberConstraint() - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

Creates an MemberConstraint instance

MemberConstraint(String) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

Creates a MemberConstraint instance with an id.

MemberConstraint(int, int) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

Creates a MemberConstraint instance with a level and version.

MemberConstraint(String, int, int) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

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

MemberConstraint(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

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

MemberConstraint(MemberConstraint) - Constructor for class org.sbml.jsbml.ext.groups.MemberConstraint

Clone constructor

membersShareType - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

metaIdRef - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

N

namespaces - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

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

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

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

O

org.sbml.jsbml.ext.groups - package org.sbml.jsbml.ext.groups

Provides classes for the Groups package.

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

P

packageName - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

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

R

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.groups.Group

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.groups.Member

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

removeMemberConstraint(MemberConstraint) - Method in class org.sbml.jsbml.ext.groups.Group

Removes an element from the listOfMemberConstraints.

removeMemberConstraint(int) - Method in class org.sbml.jsbml.ext.groups.Group

Removes an element from the listOfMemberConstraints at the given index.

removeMemberConstraint(String) - Method in class org.sbml.jsbml.ext.groups.Group

S

setDistinctAttribute(String) - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Sets the value of distinctAttribute

setId(String) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

setIdenticalAttribute(String) - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Sets the value of identicalAttribute

setIdRef(String) - Method in class org.sbml.jsbml.ext.groups.Member

Sets the value of idRef

setIdRef(NamedSBase) - Method in class org.sbml.jsbml.ext.groups.Member

Sets the value of idRef, using the id defined in the given NamedSBase

setKind(GroupKind) - Method in class org.sbml.jsbml.ext.groups.Group

setListOfGroups(ListOf<Group>) - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

setListOfMemberConstraints(ListOfMemberConstraint) - Method in class org.sbml.jsbml.ext.groups.Group

Sets the given ListOf<MemberConstraint>.

setMembersShareType(boolean) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

Sets the value of membersShareType

setMetaIdRef(String) - Method in class org.sbml.jsbml.ext.groups.Member

Sets the value of metaIdRef

setMetaIdRef(SBase) - Method in class org.sbml.jsbml.ext.groups.Member

Sets the value of metaIdRef, using the metaid defined in the given SBase

setName(String) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

shortLabel - Static variable in class org.sbml.jsbml.ext.groups.GroupsConstants

T

toString() - Method in class org.sbml.jsbml.ext.groups.Group

toString() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

toString() - Method in class org.sbml.jsbml.ext.groups.Member

U

unsetDistinctAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Unsets the variable distinctAttribute

unsetId() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

unsetIdenticalAttribute() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

Unsets the variable identicalAttribute

unsetIdRef() - Method in class org.sbml.jsbml.ext.groups.Member

Unsets the variable idRef

unsetListOfGroups() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

Removes the GroupsModelPlugin.listOfGroups from this Model and notifies all registered instances of TreeNodeChangeListener.

unsetListOfMemberConstraints() - Method in class org.sbml.jsbml.ext.groups.Group

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

unsetListOfMembers() - Method in class org.sbml.jsbml.ext.groups.Group

Removes the Group.listOfMembers from this Model and notifies all registered instances of TreeNodeChangeListener.

unsetMembersShareType() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

Unsets the variable membersShareType

unsetMetaIdRef() - Method in class org.sbml.jsbml.ext.groups.Member

Unsets the variable metaIdRef

unsetName() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

V

valueOf(String) - Static method in enum org.sbml.jsbml.ext.groups.GroupKind

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

values() - Static method in enum org.sbml.jsbml.ext.groups.GroupKind

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

W

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.groups.Group

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.groups.GroupsModelPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.groups.Member

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.groups.MemberConstraint

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