Index (jsbml-groups 1.1 API)

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: 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.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() - 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

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.
getId() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
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
getName() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
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.
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
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.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.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.ListOfMemberConstraint: Deprecated.
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
isSetId() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
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
isSetName() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.

L

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.
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: 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
setId(String) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
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(ListOf<Member>) - 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
setName(String) - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
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: Deprecated.

Unsets the variable distinctAttribute
unsetId() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.
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
unsetName() - Method in class org.sbml.jsbml.ext.groups.ListOfMemberConstraint: Deprecated.

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.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 T U V W