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

A

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

Adds a new element to the listOfGroups.

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

Adds a new Member to the Group.listOfMembers.

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

Deprecated.

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

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

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

Deprecated.

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, SBase) - Method in class org.sbml.jsbml.ext.groups.Group

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

Creates a new Member element and adds it to the Group.listOfMembers list.

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

Creates a new Member element and adds it to the Group.listOfMembers 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

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

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

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

Deprecated.

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

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

Deprecated.

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

Deprecated.

Returns the value of distinctAttribute

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

Returns the n-th Group object in this 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.

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

Deprecated.

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

Returns the listOfGroups.

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

Returns the Group.listOfMembers.

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

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

Gets an element from the Group.listOfMembers at the given index.

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

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

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

Deprecated.

Returns the value of membersShareType

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

Returns the value of metaIdRef

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

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

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.

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

Creates a new Group instance.

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

Creates a new Group instance from the given Group.

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

Creates a new Group instance.

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

Creates a new GroupsModelPlugin instance cloned from the given parameter.

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

Creates a new GroupsModelPlugin instance

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

Deprecated.

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

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

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

Deprecated.

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.ListOfMemberConstraint

Deprecated.

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

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

Deprecated.

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.Member

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

Deprecated.

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

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

Deprecated.

Returns whether distinctAttribute is set

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

Deprecated.

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

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

Returns true if Group.listOfMembers is not null.

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

Deprecated.

Returns whether membersShareType is set

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

Returns whether metaIdRef is set

L

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

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

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

Deprecated.

This class was removed from the specifications as of version 0.7 (2015-11-24) as no software wanted to implement support for it. It might be added back in a future version of the specifications if somebody want to implement it.

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

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

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

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

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

Creates a new instance of ListOfMembers.

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

Creates a new instance of ListOfMembers.

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

Creates a new instance of ListOfMembers, cloned from the given listOf.

M

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

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

Creates a new Member instance.

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

Creates a new Member instance.

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

Creates a new Member instance.

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

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

Deprecated.

This class was removed from the specifications as of version 0.7 (2015-11-24) as no software wanted to implement support for it. It might be added back in a future version of the specifications if somebody want to implement it.

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

Deprecated.

Creates an MemberConstraint instance

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

Deprecated.

Creates a MemberConstraint instance with an id.

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

Deprecated.

Creates a MemberConstraint instance with a level and version.

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

Deprecated.

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

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

Deprecated.

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

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

Removes an element from the Group.listOfMembers.

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

Removes an element from the Group.listOfMembers.

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

Removes an element from the Group.listOfMembers at the given index.

S

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

Deprecated.

Sets the value of distinctAttribute

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

Deprecated.

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

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

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

Sets the given ListOf<Member>.

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

Deprecated.

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

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

U

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

Deprecated.

Unsets the variable distinctAttribute

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

Deprecated.

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.

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

Returns true if Group.listOfMembers contains at least one element, otherwise false.

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

Deprecated.

Unsets the variable membersShareType

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

Unsets the variable metaIdRef

V

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

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

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

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

Deprecated.

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

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

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

Deprecated.

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