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a - Variable in class org.pathvisio.libgpml.model.TestAnnotation
a - Variable in class org.pathvisio.libgpml.model.TestCitation
a - Variable in class org.pathvisio.libgpml.model.TestEvidence
a1 - Variable in class org.pathvisio.libgpml.model.TestAnchor
a1 - Variable in class org.pathvisio.libgpml.model.TestReferenceable
a2 - Variable in class org.pathvisio.libgpml.model.TestAnnotation
a2 - Variable in class org.pathvisio.libgpml.model.TestCitation
a2 - Variable in class org.pathvisio.libgpml.model.TestEvidence
AbstractConnector - Class in org.pathvisio.libgpml.model.connector: Abstract connector shape implementation that deals with cached shapes, segments and waypoints.
AbstractConnector() - Constructor for class org.pathvisio.libgpml.model.connector.AbstractConnector
AbstractPathwayModelFormat - Class in org.pathvisio.libgpml.io: base implementation of PathwayImporter and PathwayExporter warnings mechanism.
AbstractPathwayModelFormat() - Constructor for class org.pathvisio.libgpml.io.AbstractPathwayModelFormat
AbstractShape - Class in org.pathvisio.libgpml.model.shape: Class for shapes.
AbstractShape(Shape, String) - Constructor for class org.pathvisio.libgpml.model.shape.AbstractShape
AbstractShape(Shape, String, boolean, boolean) - Constructor for class org.pathvisio.libgpml.model.shape.AbstractShape: Instantiates.
add(int, E) - Method in class org.pathvisio.libgpml.debug.DebugList
add(E) - Method in class org.pathvisio.libgpml.debug.DebugList
add(E) - Method in class org.pathvisio.libgpml.debug.DebugList.DebugIterator
add(PathwayObject) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds a PathwayObject to this Pathway.
add(LinAlg.Point) - Method in class org.pathvisio.libgpml.util.LinAlg.Point
addAlias(String) - Method in class org.pathvisio.libgpml.model.Group: Creates and returns an Alias data node for this group.
addAll(int, Collection<? extends E>) - Method in class org.pathvisio.libgpml.debug.DebugList
addAll(Collection<? extends E>) - Method in class org.pathvisio.libgpml.debug.DebugList
addAnchor(double, AnchorShapeType) - Method in class org.pathvisio.libgpml.model.LineElement: Adds a new anchor to this line at the given position with anchorShapeType property.
addAnchor(String, double, AnchorShapeType) - Method in class org.pathvisio.libgpml.model.LineElement: Creates and adds a new anchor to this line at the given position with anchorShapeType property.
addAnchor(LineElement.Anchor) - Method in class org.pathvisio.libgpml.model.LineElement: Adds given anchor to anchors list.
addAnnotation(String, String, AnnotationType, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates a annotation with given properties, and adds annotation to pathway model.
addAnnotation(String, String, AnnotationType, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Creates a annotation with given properties, and adds annotation to pathway model.
addAnnotation(String, String, AnnotationType, Xref, String) - Method in interface org.pathvisio.libgpml.model.Referenceable.Annotatable: Creates a annotation with given properties, and adds annotation to pathway model.
addAnnotation(String, AnnotationType, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates a annotation with given properties, and adds annotation to pathway model.
addAnnotation(String, AnnotationType, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Creates a annotation with given properties, and adds annotation to pathway model.
addAnnotation(String, AnnotationType, Xref, String) - Method in interface org.pathvisio.libgpml.model.Referenceable.Annotatable: Creates a annotation with given properties, and adds annotation to pathway model.
addAnnotation(Annotation) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates and adds an annotationRef to annotationRefs list.
addAnnotation(Annotation) - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Creates and adds an annotationRef to annotationRefs list.Sets annotable for the given annotationRef.
addAnnotation(Annotation) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds given annotation to annotations list.
addAnnotation(Annotation) - Method in interface org.pathvisio.libgpml.model.Referenceable.Annotatable: Creates and adds an annotationRef to annotationRefs list.
addAnnotationRef(PathwayElement.AnnotationRef) - Method in class org.pathvisio.libgpml.model.Annotation: Adds the given annotationRef to annotationRefs list of the annotation.
addAuthor(String) - Method in class org.pathvisio.libgpml.model.Pathway: Creates and adds an author to authors list.
addAuthor(Pathway.Author) - Method in class org.pathvisio.libgpml.model.Pathway: Adds the given author to authors list.
addCitation(String, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates a citation with given xref and urlLink, and adds citation to pathway model.
addCitation(String, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Creates a citation with given xref and urlLink, and adds citation to pathway model.
addCitation(String, Xref, String) - Method in interface org.pathvisio.libgpml.model.Referenceable.Citable: Creates a citation with given xref and urlLink, and adds citation to pathway model.
addCitation(Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates a citation with given xref and urlLink, and adds citation to pathway model.
addCitation(Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Creates a citation with given xref and urlLink, and adds citation to pathway model.
addCitation(Xref, String) - Method in interface org.pathvisio.libgpml.model.Referenceable.Citable: Creates a citation with given xref and urlLink, and adds citation to pathway model.
addCitation(Citation) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates and adds an citationRef to citationRefs list.
addCitation(Citation) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Creates and adds an citationRef to citationRefs list.
addCitation(Citation) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds given citation to citations list.
addCitation(Citation) - Method in interface org.pathvisio.libgpml.model.Referenceable.Citable: Creates and adds a citationRefs to citationRefs list.
addCitationRef(PathwayElement.CitationRef) - Method in class org.pathvisio.libgpml.model.Citation: Adds the given citationRef to citationRefs list of this citation.
addComment(String, String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates a comment with given properties and adds to comments list.
addComment(PathwayElement.Comment) - Method in class org.pathvisio.libgpml.model.PathwayElement: Adds given comment to comments list.
addDataNode(DataNode) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds the given dataNode to dataNodes list.
ADDED - Static variable in class org.pathvisio.libgpml.model.PathwayModelEvent
addElementId(String, PathwayObject) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds mapping of elementId key to PathwayObject value in the elementIdToPathwayObject hash map.
addElementRef(GraphLink.LinkableTo, GraphLink.LinkableFrom) - Method in class org.pathvisio.libgpml.model.PathwayModel: Register a link from a elementRef to a linePoint(s).
addEvidence(String, String, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates an evidence with given properties, and adds evidence to pathway model.
addEvidence(String, String, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Creates an evidence with given properties, and adds evidence to pathway model.
addEvidence(String, String, Xref, String) - Method in interface org.pathvisio.libgpml.model.Referenceable.Evidenceable: Creates an evidence with given properties, and adds evidence to pathway model.
addEvidence(String, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates an evidence with given properties, and adds evidence to pathway model.
addEvidence(String, Xref, String) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Creates an evidence with given properties, and adds evidence to pathway model.
addEvidence(String, Xref, String) - Method in interface org.pathvisio.libgpml.model.Referenceable.Evidenceable: Creates an evidence with given properties, and adds evidence to pathway model.
addEvidence(Evidence) - Method in class org.pathvisio.libgpml.model.PathwayElement: Creates and adds an evidenceRef to evidenceRefs list.
addEvidence(Evidence) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Creates and adds an evidenceRef to evidenceRefs list.
addEvidence(Evidence) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds given evidence to evidences.
addEvidence(Evidence) - Method in interface org.pathvisio.libgpml.model.Referenceable.Evidenceable: Creates and adds an evidenceRef to evidenceRefs list.
addEvidenceRef(PathwayElement.EvidenceRef) - Method in class org.pathvisio.libgpml.model.Evidence: Adds the given evidenceRef to evidenceRefs list of this evidence.
addGraphicalLine(GraphicalLine) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds the given graphicalLine to graphicalLines list.
addGroup(Group) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds the given group to groups list.
addInteraction(Interaction) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds the given interaction to interactions list.
addLabel(Label) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds the given label to labels list.
addLinePoints(List<LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.LineElement: Adds all given points to the linePoints list.
addListener(PathwayModelListener) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds listener to this pathway model.
addListener(PathwayObjectListener) - Method in class org.pathvisio.libgpml.model.PathwayObject: Adds pathway object listener.
addPathwayElement(Groupable) - Method in class org.pathvisio.libgpml.model.Group: Adds the given pathway element to pathwayElements list of this group.
addPathwayElements(List<? extends Groupable>) - Method in class org.pathvisio.libgpml.model.Group: Adds the given list of pathway elements to pathwayElements list of this group.
addPathwayObject(PathwayObject) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds the given pathway object to pathway model.
addShape(Shape) - Method in class org.pathvisio.libgpml.model.PathwayModel: Adds the given shape to shapes list.Sets pathwayModel and elementId, and maps to elementIdToPathwayObject.
addState(String, String, StateType, double, double) - Method in class org.pathvisio.libgpml.model.DataNode: Instantiates a state with the given properties including elementId.
addState(String, StateType, double, double) - Method in class org.pathvisio.libgpml.model.DataNode: Instantiates a state with the given properties.
addState(DataNode.State) - Method in class org.pathvisio.libgpml.model.DataNode: Adds given state to states list.
addStatusFlagListener(PathwayModel.StatusFlagListener) - Method in class org.pathvisio.libgpml.model.PathwayModel: Registers a status flag listener
adjustWayPointPreferences(ConnectorShape.WayPoint[]) - Method in class org.pathvisio.libgpml.model.LineElement
affectedData - Variable in class org.pathvisio.libgpml.model.PathwayModelEvent
affectsProperty(String) - Method in class org.pathvisio.libgpml.model.PathwayObjectEvent: Checks if the given dynamic property may have been modified in this event.
affectsProperty(Property) - Method in class org.pathvisio.libgpml.model.PathwayObjectEvent: Check if the given static property may have been modified in this event.
alias - Variable in class org.pathvisio.libgpml.model.TestAlias
ALIAS - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
aliasRef - Variable in class org.pathvisio.libgpml.model.DataNode
ALIASREF - org.pathvisio.libgpml.prop.StaticProperty
ALIASREF - org.pathvisio.libgpml.prop.StaticPropertyType
aliasRefToAliases - Variable in class org.pathvisio.libgpml.model.PathwayModel
almostPerfectAlignment(int) - Method in class org.pathvisio.libgpml.model.LineElement: Check if either the line segment has less than or equal to 10 degree alignment with the side passed
ANALOG - Static variable in class org.pathvisio.libgpml.model.type.GroupType
Anchor(double, AnchorShapeType) - Constructor for class org.pathvisio.libgpml.model.LineElement.Anchor: Instantiates an Anchor pathway element.
ANCHOR - org.pathvisio.libgpml.model.type.ObjectType: An anchor point on a line pathway element.
ANCHOR_CIRCLE_SIZE - Static variable in class org.pathvisio.libgpml.model.shape.AnchorShapeRegistry
ANCHOR_NONE_SIZE - Static variable in class org.pathvisio.libgpml.model.shape.AnchorShapeRegistry: These are all model coordinates:
ANCHOR_SQUARE_SIZE - Static variable in class org.pathvisio.libgpml.model.shape.AnchorShapeRegistry
anchorMap - Static variable in class org.pathvisio.libgpml.model.shape.ShapeRegistry
anchors - Variable in class org.pathvisio.libgpml.model.LineElement
AnchorShape - Class in org.pathvisio.libgpml.model.shape: AnchorShape is responsible for defining the graphic for Anchors, similar to ArrowShape for Arrows.
AnchorShape(Shape) - Constructor for class org.pathvisio.libgpml.model.shape.AnchorShape
AnchorShapeRegistry - Class in org.pathvisio.libgpml.model.shape: Defines and registers all Anchor shapes.
AnchorShapeRegistry() - Constructor for class org.pathvisio.libgpml.model.shape.AnchorShapeRegistry
AnchorShapeType - Class in org.pathvisio.libgpml.model.type: This class contains extensible enum for Anchor type property.
AnchorShapeType(String) - Constructor for class org.pathvisio.libgpml.model.type.AnchorShapeType: Constructor to initialize the state of enum types without disallowLinks.
AnchorShapeType(String, boolean) - Constructor for class org.pathvisio.libgpml.model.type.AnchorShapeType: Constructor to initialize the state of enum types.
ANCHORSHAPETYPE - org.pathvisio.libgpml.prop.StaticProperty
ANCHORSHAPETYPE - org.pathvisio.libgpml.prop.StaticPropertyType
ANCHORSHAPETYPE_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract
angle(LinAlg.Point, LinAlg.Point) - Static method in class org.pathvisio.libgpml.util.LinAlg: Determines angle between two vectors defined by p1 and p2 Both vectors start at 0.0
annotatable - Variable in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef
annotation - Variable in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef
Annotation - Class in org.pathvisio.libgpml.model: This class stores information for an Annotation.
Annotation(String, AnnotationType, Xref, String) - Constructor for class org.pathvisio.libgpml.model.Annotation: Instantiates an Annotation pathway element given all possible parameters: elementId, parent pathway model, value, type, url, and xref.
ANNOTATION - org.pathvisio.libgpml.model.type.ObjectType: A reference with additional information, e.g.
AnnotationRef(Annotation) - Constructor for class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Instantiates an AnnotationRef given source Annotation and initializes citationRefs and evidenceRefs lists.
ANNOTATIONREF - org.pathvisio.libgpml.prop.StaticProperty
ANNOTATIONREF - org.pathvisio.libgpml.prop.StaticPropertyType
annotationRefs - Variable in class org.pathvisio.libgpml.model.Annotation
annotationRefs - Variable in class org.pathvisio.libgpml.model.PathwayElement
annotationRefs - Variable in class org.pathvisio.libgpml.model.PathwayElement.CitationRef
annotations - Variable in class org.pathvisio.libgpml.model.PathwayModel
AnnotationType - Class in org.pathvisio.libgpml.model.type: This class contains extensible enum for Annotation type property.
AnnotationType(String) - Constructor for class org.pathvisio.libgpml.model.type.AnnotationType: The constructor is private.
ANNOTATIONTYPE - org.pathvisio.libgpml.prop.StaticProperty
ANNOTATIONTYPE - org.pathvisio.libgpml.prop.StaticPropertyType
ANNOTATIONTYPE_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract
ar1 - Variable in class org.pathvisio.libgpml.model.TestAnnotation
ar1 - Variable in class org.pathvisio.libgpml.model.TestCitation
ar1 - Variable in class org.pathvisio.libgpml.model.TestEvidence
ar1 - Variable in class org.pathvisio.libgpml.model.TestReferenceable
ar2 - Variable in class org.pathvisio.libgpml.model.TestAnnotation
ar2 - Variable in class org.pathvisio.libgpml.model.TestCitation
ar2 - Variable in class org.pathvisio.libgpml.model.TestEvidence
ar2 - Variable in class org.pathvisio.libgpml.model.TestReferenceable
ARC - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
ARROWHEAD_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract
ArrowHeadType - Class in org.pathvisio.libgpml.model.type: This class contains extensible enum pattern for different arrow head types.
ArrowHeadType(String) - Constructor for class org.pathvisio.libgpml.model.type.ArrowHeadType: Private constructor.
ArrowHeadType(String, boolean) - Constructor for class org.pathvisio.libgpml.model.type.ArrowHeadType: The constructor is private.
ARROWHEADTYPE - org.pathvisio.libgpml.prop.StaticPropertyType
ARROWHEIGHT - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry: These are all model coordinates:
arrowMap - Static variable in class org.pathvisio.libgpml.model.shape.ShapeRegistry
ArrowShape - Class in org.pathvisio.libgpml.model.shape: ArrowShapes determine how the ending of a line can be drawn.
ArrowShape(Shape, ArrowShape.FillType) - Constructor for class org.pathvisio.libgpml.model.shape.ArrowShape: Normally, this constructor is not called directly.
ArrowShape(Shape, ArrowShape.FillType, int) - Constructor for class org.pathvisio.libgpml.model.shape.ArrowShape: Normally, this constructor is not called directly.
ArrowShape.FillType - Enum in org.pathvisio.libgpml.model.shape: Enumerates possible ways to combine the outline and body.
ArrowShapeRegistry - Class in org.pathvisio.libgpml.model.shape: Defines and registers all arrowhead shapes.
ArrowShapeRegistry() - Constructor for class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
ARROWWIDTH - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
asArray() - Method in class org.pathvisio.libgpml.util.LinAlg.Point
asIntArray() - Method in class org.pathvisio.libgpml.util.LinAlg.Point
ATTRIBUTE_INFO - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Attribute info map is initiated with GPML2013aFormatAbstract.initAttributeInfo().
AttributeInfo(String, String, String) - Constructor for class org.pathvisio.libgpml.model.GPML2013aFormatAbstract.AttributeInfo: Creates an object containing the gpml schema definition of a given attribute.
Author(String) - Constructor for class org.pathvisio.libgpml.model.Pathway.Author: Instantiates an author with only required property.
AUTHOR - org.pathvisio.libgpml.prop.StaticProperty
AUTHOR - org.pathvisio.libgpml.prop.StaticPropertyType
authors - Variable in class org.pathvisio.libgpml.model.Citation
authors - Variable in class org.pathvisio.libgpml.model.Pathway
AXIS_X - Static variable in interface org.pathvisio.libgpml.model.connector.ConnectorShape
AXIS_Y - Static variable in interface org.pathvisio.libgpml.model.connector.ConnectorShape

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