Package org.pathvisio.libgpml.model

Classes representing the pathway "model". Also includes classes for reading and writing.

Interface Summary

Interface	Description
Drawable	Interface for classes which can be drawn a pathway model canvas.
GPMLFormatReader	Interface for GPML reading.
GPMLFormatVersion	Interface for GPML format versions.
GPMLFormatWriter	Interface for GPML writing.
GraphLink.LinkableFrom	Classes which want to refer *to* a GraphLink.LinkableTo PathwayElement must implement this interface.
GraphLink.LinkableTo	PathwayElements which can be referred to must implement this interface.
Groupable	Interface for classes which can belong in a Group.
PathwayModel.StatusFlagListener	Implement this interface if you want to be notified when the "changed" status changes.
PathwayModelListener	Implement this if you want to be notified of changes to a PathwayModel.
PathwayObjectListener	Implement this if you want to be notified of changes to properties of a PathwayElement.
Referenceable	Interface for Referenceable.Annotatable, Referenceable.Citable, and Referenceable.Evidenceable.
Referenceable.Annotatable	Interface for classes which can hold a List of PathwayElement.AnnotationRef.
Referenceable.Citable	Interface for classes which can hold a List of PathwayElement.CitationRef.
Referenceable.Evidenceable	Interface for classes which can hold a List of PathwayElement.EvidenceRef.
Xrefable	Interface for classes which can have an Xref.

Class Summary

Class	Description
Annotation	This class stores information for an Annotation.
Citation	This class stores information for a Citation.
CopyElement	This class stores information for copied PathwayElement.
DataNode	This class stores information for a DataNode pathway element.
Evidence	This class stores information for an Evidence.
GPML2013aFormatAbstract	Abstract class for GPML2013a format.
GPML2013aFormatAbstract.AttributeInfo	Name of resource containing the gpml schema definition.
GPML2013aReader	This class reads a PathwayModel from an input source (GPML 2013a).
GPML2013aWriter	This class writes a PathwayModel to an output (GPML 2013a).
GPML2021FormatAbstract	Read / write GPML files.
GPML2021Reader	This class reads a PathwayModel from an input source (GPML 2021).
GPML2021Writer	This class writes a PathwayModel to an output (GPML 2021).
GPMLFormat	Class responsible for interaction with Gpml format.
GPMLFormatAbstract	Abstract class for GPML format.
GraphicalLine	This class stores information for GraphicalLine pathway element.
GraphLink	This class only contains static methods and should not be instantiated.
Group	This class stores all information relevant to a Group pathway element.
Interaction	This class stores information for an Interaction pathway element.
Label	This class stores all information relevant to a Label pathway element.
LineElement	This abstract class stores information for a Line pathway element, e.g.
Pathway	The Pathway class stores information or metadata for a Pathway Model.
PathwayElement	Abstract class of pathway elements which are part of a pathway, have an elementId, have Comment, Children: DataNode, State, Interaction, GraphicalLine, Label, Shape, Group.
PathwayModel	This class stores information for a Pathway model.
PathwayModel.StatusFlagEvent	Event for a change in the "changed" status of this Pathway
PathwayModelEvent	Used to notify listeners of changes to the model, i.e a Pathway or PathwayElement.
PathwayObject	Abstract class of pathway elements which are part of a pathway and have an elementId.
PathwayObjectEvent	This event is used to notify PathwayObjectListeners of changes to properties of a PathwayElement.
Shape	This class stores all information relevant to a Shape pathway element.
ShapedElement	This class stores information for shaped pathway element DataNode, DataNode.State, Label, Shape, and Group.
Test	Tests for libgpml model classes.
TestAlias	Tests for aliasRef of DataNode.
TestAnchor	Test for LineElement.Anchor.
TestAnnotation	Tests for Annotation class.
TestCitation	For testing Citation methods
TestCopy	Test for Clone methods.
TestElementId	Tests for elementId.
TestEvidence	For testing Evidence methods
TestGraph	Test graph properties of a pathway model.
TestGraphLink	For testing methods for elementRef:
TestGroup	Test for Group.
TestGroupNested	Tests for nested Group(s).
TestLinePoint	Test for LineElement.LinePoint.
TestReferenceable	Tests for Referenceable:
TestState	Test for DataNode.State.
TestTemporary	Test for random things.