All Classes

Class	Description
AbstractConnector	Abstract connector shape implementation that deals with cached shapes, segments and waypoints.
AbstractPathwayModelFormat	base implementation of PathwayImporter and PathwayExporter warnings mechanism.
AbstractShape	Class for shapes.
AnchorShape	AnchorShape is responsible for defining the graphic for Anchors, similar to ArrowShape for Arrows.
AnchorShapeRegistry	Defines and registers all Anchor shapes.
AnchorShapeType	This class contains extensible enum for Anchor type property.
Annotation	This class stores information for an Annotation.
AnnotationType	This class contains extensible enum for Annotation type property.
ArrowHeadType	This class contains extensible enum pattern for different arrow head types.
ArrowShape	ArrowShapes determine how the ending of a line can be drawn.
ArrowShape.FillType	Enumerates possible ways to combine the outline and body.
ArrowShapeRegistry	Defines and registers all arrowhead shapes.
Citation	This class stores information for a Citation.
ColorUtils	This utils class contains methods for converting `Color` to hexBinary or color name `String`, and vice versa.
ConnectorRestrictions	Methods to provide restrictions for the connector path
ConnectorShape	Implement this to provide a line shape for connectors.
ConnectorShape.Segment	A single segment of the connector path.
ConnectorShape.WayPoint	The class for a waypoint, a point through which the connector passes.
ConnectorShapeFactory	Constructs connector shapes.
ConnectorType	This class contains extensible enum for different connectorType property.
ConverterException	Exception that occurs during import, export, save or load of a pathway model.
CopyElement	This class stores information for copied `PathwayElement`.
CurvedConnectorShape	Implements a curved connector that draws curved lines between the segments.
DataNode	This class stores information for a DataNode pathway element.
DataNodeType	This class contains extensible enum for DataNode type property.
DebugList<E>	This is a List that helps in the search for ConcurrentModification problems.
DebugList.DebugIterator<E>	An iterator to go with the DebugList.
Drawable	Interface for classes which can be drawn a pathway model canvas.
ElbowConnectorShape	ConnectorShape implementation for the elbow connector.
EventDispatchThreadOnly	Indicates that this class or method should only be accessed by the Event Dispatch Thread
Evidence	This class stores information for an Evidence.
FileUtils	Collection of static utility methods dealing with files.
FreeConnectorShape	Implements a connector that draws straight lines between multiple waypoints.
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.
GPMLFormatReader	Interface for GPML reading.
GPMLFormatVersion	Interface for GPML format versions.
GPMLFormatWriter	Interface for GPML writing.
GraphicalLine	This class stores information for GraphicalLine pathway element.
GraphLink	This class only contains static methods and should not be instantiated.
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.
Group	This class stores all information relevant to a Group pathway element.
Groupable	Interface for classes which can belong in a `Group`.
GroupType	This class contains extensible enum for Group type property.
HAlignType	This enum class contains possible values for horizontal text alignment property.
Interaction	This class stores information for an Interaction pathway element.
IShape	Interface for shapes.
Label	This class stores all information relevant to a Label pathway element.
LinAlg	Helper class for rotation calculations.
LinAlg.Point	Point, pair of doubles.
LineElement	This abstract class stores information for a Line pathway element, e.g.
LineStyleType	This class contains extensible enum for lineStyle or borderStyle property.
Logger	Logs output to a stream, with the option to filter for types of messages
ObjectType	Possible values for PathwayElement.getObjectType(), such as "DataNode" or "Shape"
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
PathwayModel.StatusFlagListener	Implement this interface if you want to be notified when the "changed" status changes.
PathwayModelEvent	Used to notify listeners of changes to the model, i.e a Pathway or PathwayElement.
PathwayModelExporter	Interface for an exporter that writes a pathway to a file.
PathwayModelImporter	Implemented by classes that can import a pathway from various different types.
PathwayModelIO	Common methods for `PathwayModelImporter`s and `PathwayModelExporter`s
PathwayModelListener	Implement this if you want to be notified of changes to a PathwayModel.
PathwayObject	Abstract class of pathway elements which are part of a pathway and have an elementId.
PathwayObjectEvent	This event is used to notify `PathwayObjectListener`s of changes to properties of a PathwayElement.
PathwayObjectListener	Implement this if you want to be notified of changes to properties of a PathwayElement.
Property	This interface defines a typed property.
PropertyManager	This PropertyManager handles the registration/lookups of everything related to TypedProperties.
PropertyType	This interface represents a type (the Type in Property).
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`.
RootElementFinder	This is similar to com.sun.xml.internal.ws.message.RootElementSniffer, perhaps can be re-used.
RootElementFinder.RootElementHandler	Root element handler class.
SegmentedConnector	Base class for segmented connectors.
Shape	This class stores all information relevant to a Shape pathway element.
ShapeCatalog	This class defines some shapes.
ShapeCatalog.Internal	these constants are internal, only for the switch statement below.
ShapedElement	This class stores information for shaped pathway element `DataNode`, `DataNode.State`, `Label`, `Shape`, and `Group`.
ShapeRegistry	The Shape registry stores all arrow heads and shapes at this moment the shape registry initializes itself, by calling registerShape() on BasicShapes, GenMAPPShapes and MIMShapes.
ShapeType	This enum class contains extensible enum for Shape type property.
StateType	This class contains extensible enum for state types.
StaticProperty	Static properties for ObjectTypes, linked in `PathwayObject`.
StaticPropertyType	The properties in `StaticProperty` define properties of different types, all the possible types are defined here.
StopWatch	A simple helper class for speed optimizations.
StraightConnectorShape	Implements a straight connector Shape, i.e.
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
TestColorUtils	Tests for ColorUtils class.
TestCopy	Test for Clone methods.
TestDataNodeType	Test for extensible enum class.
TestDebug	Tests for debug.
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).
TestGroupRectPropertyUtils	Tests for GroupRectPropertyUtils class, the utility class for finding group bounds.
TestLinePoint	Test for `LineElement.LinePoint`.
TestReferenceable	Tests for `Referenceable`:
TestSegmentedConnector	Test for segmented connector.
TestState	Test for `DataNode.State`.
TestTemporary	Test for random things.
TestXrefUtils	Tests for XrefUtils class.
ThreadSafe	Use this annotation to indicate that this method is Thread-safe, i.e.
Utils	Various utility functions.
VAlignType	This enum class contains possible values for vertical text alignment property.
WorkerThreadOnly	Indicates that this class or method should only be accessed by threads other than the Event Dispatch Thread
Xrefable	Interface for classes which can have an `Xref`.
XrefUtils	This utils class contains methods for checking DataSource and creating Xref.