Uses of Class
org.pathvisio.libgpml.model.Group

Packages that use Group

Package	Description
org.pathvisio.libgpml.model	Classes representing the pathway "model".

Uses of Group in org.pathvisio.libgpml.model

Fields in org.pathvisio.libgpml.model declared as Group

Modifier and Type	Field	Description
private Group	DataNode.aliasRef
private Group	TestAlias.g
(package private) Group	TestGroup.g1
(package private) Group	TestGroupNested.g1
(package private) Group	TestGroup.g2
(package private) Group	TestGroupNested.g2
private Group	LineElement.groupRef
private Group	ShapedElement.groupRef

Fields in org.pathvisio.libgpml.model with type parameters of type Group

Modifier and Type	Field	Description
private java.util.Map<Group,java.util.Set<DataNode>>	PathwayModel.aliasRefToAliases
private java.util.List<Group>	PathwayModel.groups

Methods in org.pathvisio.libgpml.model that return Group

Modifier and Type	Method	Description
Group	DataNode.getAliasRef()	Returns the pathway element to which the data node refers to as an alias.
Group	DataNode.State.getGroupRef()	Returns the parent group of the dataNode of this state.
Group	Groupable.getGroupRef()	Returns the parent group of this pathway element.
Group	LineElement.getGroupRef()	Returns the parent group of this pathway element.
Group	ShapedElement.getGroupRef()	Returns the parent group of this pathway element.

Methods in org.pathvisio.libgpml.model that return types with arguments of type Group

Modifier and Type	Method	Description
java.util.Set<Group>	PathwayModel.getAliasRefs()	Returns the set of Group aliasRef keys for this pathway model.
java.util.List<Group>	PathwayModel.getGroups()	Returns the list of group pathway elements.

Methods in org.pathvisio.libgpml.model with parameters of type Group

Modifier and Type	Method	Description
void	PathwayModel.addGroup(Group group)	Adds the given group to groups list.
void	Group.copyValuesFrom(Group src)	Copies values from the given source pathway element.
java.util.Set<DataNode>	PathwayModel.getLinkedAliases(Group aliasRef)	Returns the set of DataNode aliases for a Group aliasRef.
boolean	PathwayModel.hasAliasRef(Group aliasRef)	Returns true if pathway model has Group aliasRef.
protected boolean	PathwayModel.hasLinkedAlias(Group aliasRef, DataNode alias)	Returns true if pathway model has DataNode alias and Group aliasRef.
protected void	PathwayModel.linkAlias(Group aliasRef, DataNode alias)	Adds mapping of aliasRef to data node alias in the aliasRefToAliases hash map.
protected void	PathwayModel.removeAliasRef(Group aliasRef)	Removes the mapping of given elementRef key from the elementRefToDataNode hash map.
void	PathwayModel.removeGroup(Group group)	Removes the given group from groups list and elementIdToPathwayObject map.
void	DataNode.setAliasRef(Group v)	Sets the group aliasRef to which this data node refers to as an alias.
protected void	GPML2013aReader.setGroupGraphicsProperty(Group group, GroupType type)	Reads and sets graphics properties for Group.
private void	LineElement.setGroupRef(Group v)	Sets the parent group for this pathway element.
private void	ShapedElement.setGroupRef(Group v)	Sets the parent group for this pathway element.
void	DataNode.State.setGroupRefTo(Group v)	Do not allow groupRef to be set for this state.
void	Groupable.setGroupRefTo(Group groupRef)	Verifies if given parent group is new and valid.
void	LineElement.setGroupRefTo(Group v)	Verifies if given parent group is new and valid.
void	ShapedElement.setGroupRefTo(Group v)	Verifies if given parent group is new and valid.
protected void	PathwayModel.unlinkAlias(Group aliasRef, DataNode alias)	Removes the link between given aliasRef and alias, and removes mapping from aliasRefToAliases of this pathway model.
protected void	GPML2021Writer.writeAliasRef(Group aliasRef, org.jdom2.Element e)	Writes aliasRef property information for a data node.
protected void	GPML2013aWriter.writeGroupRef(Group groupRef, org.jdom2.Element e)	Writes groupRef property information.
protected void	GPML2021Writer.writeGroupRef(Group groupRef, org.jdom2.Element e)	Writes groupRef property information.

Method parameters in org.pathvisio.libgpml.model with type arguments of type Group

Modifier and Type	Method	Description
protected void	GPML2013aReader.readGroupGroupRef(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads groupRef property ShapedElement.setGroupRef(org.pathvisio.libgpml.model.Group) information of group pathway element.
protected void	GPML2013aReader.readGroupRef(ShapedElement shapedElement, org.jdom2.Element se, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads and sets groupRef for given (shaped) pathway element and jdom Element.
protected void	GPML2013aReader.readPointElementRefs(PathwayModel pathwayModel, java.util.Map<java.lang.String,Group> graphIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads LineElement.LinePoint elementRefs.
protected void	GPML2013aWriter.writeGroups(java.util.List<Group> groups, org.jdom2.Element root)	Writes group Group information.
protected void	GPML2021Writer.writeGroups(java.util.List<Group> groups, org.jdom2.Element root)	Writes group Group information.

Constructors in org.pathvisio.libgpml.model with parameters of type Group

Constructor	Description
DataNode(java.lang.String textLabel, DataNodeType type, org.bridgedb.Xref xref, Group aliasRef)	Instantiates a DataNode given all possible parameters.