-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmember-search-index.js
1 lines (1 loc) · 216 KB
/
member-search-index.js
1
memberSearchIndex = [{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"a"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"a"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"a"},{"p":"org.pathvisio.libgpml.model","c":"TestAnchor","l":"a1"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"a1"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"a2"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"a2"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"a2"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"AbstractConnector()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.io","c":"AbstractPathwayModelFormat","l":"AbstractPathwayModelFormat()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"AbstractShape(Shape, String)","u":"%3Cinit%3E(java.awt.Shape,java.lang.String)"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"AbstractShape(Shape, String, boolean, boolean)","u":"%3Cinit%3E(java.awt.Shape,java.lang.String,boolean,boolean)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"add(E)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"add(E)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"add(int, E)","u":"add(int,E)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"add(LinAlg.Point)","u":"add(org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"add(PathwayObject)","u":"add(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"addAlias(String)","u":"addAlias(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"addAll(Collection<? extends E>)","u":"addAll(java.util.Collection)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"addAll(int, Collection<? extends E>)","u":"addAll(int,java.util.Collection)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"addAnchor(double, AnchorShapeType)","u":"addAnchor(double,org.pathvisio.libgpml.model.type.AnchorShapeType)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"addAnchor(LineElement.Anchor)","u":"addAnchor(org.pathvisio.libgpml.model.LineElement.Anchor)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"addAnchor(String, double, AnchorShapeType)","u":"addAnchor(java.lang.String,double,org.pathvisio.libgpml.model.type.AnchorShapeType)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addAnnotation(Annotation)","u":"addAnnotation(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"addAnnotation(Annotation)","u":"addAnnotation(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addAnnotation(Annotation)","u":"addAnnotation(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Annotatable","l":"addAnnotation(Annotation)","u":"addAnnotation(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addAnnotation(String, AnnotationType, Xref, String)","u":"addAnnotation(java.lang.String,org.pathvisio.libgpml.model.type.AnnotationType,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"addAnnotation(String, AnnotationType, Xref, String)","u":"addAnnotation(java.lang.String,org.pathvisio.libgpml.model.type.AnnotationType,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Annotatable","l":"addAnnotation(String, AnnotationType, Xref, String)","u":"addAnnotation(java.lang.String,org.pathvisio.libgpml.model.type.AnnotationType,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addAnnotation(String, String, AnnotationType, Xref, String)","u":"addAnnotation(java.lang.String,java.lang.String,org.pathvisio.libgpml.model.type.AnnotationType,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"addAnnotation(String, String, AnnotationType, Xref, String)","u":"addAnnotation(java.lang.String,java.lang.String,org.pathvisio.libgpml.model.type.AnnotationType,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Annotatable","l":"addAnnotation(String, String, AnnotationType, Xref, String)","u":"addAnnotation(java.lang.String,java.lang.String,org.pathvisio.libgpml.model.type.AnnotationType,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"addAnnotationRef(PathwayElement.AnnotationRef)","u":"addAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"addAuthor(Pathway.Author)","u":"addAuthor(org.pathvisio.libgpml.model.Pathway.Author)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"addAuthor(String)","u":"addAuthor(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addCitation(Citation)","u":"addCitation(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"addCitation(Citation)","u":"addCitation(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addCitation(Citation)","u":"addCitation(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Citable","l":"addCitation(Citation)","u":"addCitation(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addCitation(String, Xref, String)","u":"addCitation(java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"addCitation(String, Xref, String)","u":"addCitation(java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Citable","l":"addCitation(String, Xref, String)","u":"addCitation(java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addCitation(Xref, String)","u":"addCitation(org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"addCitation(Xref, String)","u":"addCitation(org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Citable","l":"addCitation(Xref, String)","u":"addCitation(org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"addCitationRef(PathwayElement.CitationRef)","u":"addCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addComment(PathwayElement.Comment)","u":"addComment(org.pathvisio.libgpml.model.PathwayElement.Comment)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addComment(String, String)","u":"addComment(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addDataNode(DataNode)","u":"addDataNode(org.pathvisio.libgpml.model.DataNode)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelEvent","l":"ADDED"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addElementId(String, PathwayObject)","u":"addElementId(java.lang.String,org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addElementRef(GraphLink.LinkableTo, GraphLink.LinkableFrom)","u":"addElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo,org.pathvisio.libgpml.model.GraphLink.LinkableFrom)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addEvidence(Evidence)","u":"addEvidence(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"addEvidence(Evidence)","u":"addEvidence(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addEvidence(Evidence)","u":"addEvidence(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Evidenceable","l":"addEvidence(Evidence)","u":"addEvidence(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addEvidence(String, String, Xref, String)","u":"addEvidence(java.lang.String,java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"addEvidence(String, String, Xref, String)","u":"addEvidence(java.lang.String,java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Evidenceable","l":"addEvidence(String, String, Xref, String)","u":"addEvidence(java.lang.String,java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"addEvidence(String, Xref, String)","u":"addEvidence(java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"addEvidence(String, Xref, String)","u":"addEvidence(java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Evidenceable","l":"addEvidence(String, Xref, String)","u":"addEvidence(java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"addEvidenceRef(PathwayElement.EvidenceRef)","u":"addEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addGraphicalLine(GraphicalLine)","u":"addGraphicalLine(org.pathvisio.libgpml.model.GraphicalLine)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addGroup(Group)","u":"addGroup(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addInteraction(Interaction)","u":"addInteraction(org.pathvisio.libgpml.model.Interaction)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addLabel(Label)","u":"addLabel(org.pathvisio.libgpml.model.Label)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"addLinePoints(List<LineElement.LinePoint>)","u":"addLinePoints(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addListener(PathwayModelListener)","u":"addListener(org.pathvisio.libgpml.model.PathwayModelListener)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"addListener(PathwayObjectListener)","u":"addListener(org.pathvisio.libgpml.model.PathwayObjectListener)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"addPathwayElement(Groupable)","u":"addPathwayElement(org.pathvisio.libgpml.model.Groupable)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"addPathwayElements(List<? extends Groupable>)","u":"addPathwayElements(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addPathwayObject(PathwayObject)","u":"addPathwayObject(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addShape(Shape)","u":"addShape(org.pathvisio.libgpml.model.Shape)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"addState(DataNode.State)","u":"addState(org.pathvisio.libgpml.model.DataNode.State)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"addState(String, StateType, double, double)","u":"addState(java.lang.String,org.pathvisio.libgpml.model.type.StateType,double,double)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"addState(String, String, StateType, double, double)","u":"addState(java.lang.String,java.lang.String,org.pathvisio.libgpml.model.type.StateType,double,double)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"addStatusFlagListener(PathwayModel.StatusFlagListener)","u":"addStatusFlagListener(org.pathvisio.libgpml.model.PathwayModel.StatusFlagListener)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"adjustWayPointPreferences(ConnectorShape.WayPoint[])","u":"adjustWayPointPreferences(org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint[])"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelEvent","l":"affectedData"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"affectsProperty(Property)","u":"affectsProperty(org.pathvisio.libgpml.prop.Property)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"affectsProperty(String)","u":"affectsProperty(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"alias"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"ALIAS"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"aliasRef"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ALIASREF"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"ALIASREF"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"aliasRefToAliases"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"almostPerfectAlignment(int)"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"ANALOG"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"ANCHOR"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShapeRegistry","l":"ANCHOR_CIRCLE_SIZE"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShapeRegistry","l":"ANCHOR_NONE_SIZE"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShapeRegistry","l":"ANCHOR_SQUARE_SIZE"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"Anchor(double, AnchorShapeType)","u":"%3Cinit%3E(double,org.pathvisio.libgpml.model.type.AnchorShapeType)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"anchorMap"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"anchors"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShape","l":"AnchorShape(Shape)","u":"%3Cinit%3E(java.awt.Shape)"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShapeRegistry","l":"AnchorShapeRegistry()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ANCHORSHAPETYPE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"ANCHORSHAPETYPE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"ANCHORSHAPETYPE_DEFAULT"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"AnchorShapeType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"AnchorShapeType(String, boolean)","u":"%3Cinit%3E(java.lang.String,boolean)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"angle(LinAlg.Point, LinAlg.Point)","u":"angle(org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"annotatable"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"annotation"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"ANNOTATION"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"Annotation(String, AnnotationType, Xref, String)","u":"%3Cinit%3E(java.lang.String,org.pathvisio.libgpml.model.type.AnnotationType,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ANNOTATIONREF"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"ANNOTATIONREF"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"AnnotationRef(Annotation)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"annotationRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"annotationRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"annotationRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"annotations"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ANNOTATIONTYPE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"ANNOTATIONTYPE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"ANNOTATIONTYPE_DEFAULT"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"AnnotationType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"ar1"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"ar1"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"ar1"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"ar1"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"ar2"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"ar2"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"ar2"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"ar2"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"ARC"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"ARROWHEAD_DEFAULT"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"ARROWHEADTYPE"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"ArrowHeadType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"ArrowHeadType(String, boolean)","u":"%3Cinit%3E(java.lang.String,boolean)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"ARROWHEIGHT"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"arrowMap"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape","l":"ArrowShape(Shape, ArrowShape.FillType)","u":"%3Cinit%3E(java.awt.Shape,org.pathvisio.libgpml.model.shape.ArrowShape.FillType)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape","l":"ArrowShape(Shape, ArrowShape.FillType, int)","u":"%3Cinit%3E(java.awt.Shape,org.pathvisio.libgpml.model.shape.ArrowShape.FillType,int)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"ArrowShapeRegistry()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"ARROWWIDTH"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"asArray()"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"asIntArray()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"ATTRIBUTE_INFO"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract.AttributeInfo","l":"AttributeInfo(String, String, String)","u":"%3Cinit%3E(java.lang.String,java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"AUTHOR"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"AUTHOR"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"Author(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"authors"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"authors"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"AXIS_X"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"AXIS_Y"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"backgroundColor"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"BACKGROUNDCOLOR"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"BACKGROUNDCOLOR_DEFAULT"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"bezier(double, double, double, double, double)","u":"bezier(double,double,double,double,double)"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"BINDING"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"BINDING_LIST"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"BIOPAX_NAMESPACE"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"BIOPAX_NAMESPACE"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"boardHeight"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"BOARDHEIGHT"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"boardWidth"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"BOARDWIDTH"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"BOOLEAN"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"borderColor"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"BORDERCOLOR"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"BORDERCOLOR_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"borderStyle"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"BORDERSTYLE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"BORDERSTYLE_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"borderWidth"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"BORDERWIDTH"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"BORDERWIDTH_DEFAULT"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"BOTTOM"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"BRACE"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"BRACE"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"c"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"c1"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape.CurvedSegment","l":"c1"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape.CurvedSegment","l":"c2"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"calculateAdjustedShape(double, double)","u":"calculateAdjustedShape(double,double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"calculateAdjustedShape(double, double)","u":"calculateAdjustedShape(double,double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"calculateCurve(int)"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"calculateCurvedSegments(ConnectorShape.Segment[])","u":"calculateCurvedSegments(org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"calculateNewEndPoint(double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"calculateNewStartPoint(double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"calculateSegments(ConnectorRestrictions, ConnectorShape.WayPoint[])","u":"calculateSegments(org.pathvisio.libgpml.model.connector.ConnectorRestrictions,org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"calculateSegments(ConnectorRestrictions, ConnectorShape.WayPoint[])","u":"calculateSegments(org.pathvisio.libgpml.model.connector.ConnectorRestrictions,org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"FreeConnectorShape","l":"calculateSegments(ConnectorRestrictions, ConnectorShape.WayPoint[])","u":"calculateSegments(org.pathvisio.libgpml.model.connector.ConnectorRestrictions,org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"calculateShape()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"calculateShape()"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"calculateShape(ConnectorShape.Segment[])","u":"calculateShape(org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"calculateShape(ConnectorShape.Segment[])","u":"calculateShape(org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"SegmentedConnector","l":"calculateShape(ConnectorShape.Segment[])","u":"calculateShape(org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"StraightConnectorShape","l":"calculateShape(ConnectorShape.Segment[])","u":"calculateShape(org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"calculateWayPoint(Point2D, Point2D, int, int)","u":"calculateWayPoint(java.awt.geom.Point2D,java.awt.geom.Point2D,int,int)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"calculateWayPoints(ConnectorRestrictions)","u":"calculateWayPoints(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"CATALYSIS"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"CATALYSIS_DIAM"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"CATALYSIS_GAP"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"CATALYSIS_GAP_HEIGHT"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"CATALYSIS_LIST"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"cause"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"CELL"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"CELL_CMPNT_KEY"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"CELL_CMPNT_MAP"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"CELL_ICON"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"CELL_ICON"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"CELL_NODE"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"CENTER"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"centerX"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"CENTERX"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"centerY"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"CENTERY"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"changed"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"checkMBoardSize(PathwayObject)","u":"checkMBoardSize(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"childModified(PathwayObjectEvent)","u":"childModified(org.pathvisio.libgpml.model.PathwayObjectEvent)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"CIRCLE"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"citable"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"citation"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"CITATION"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"Citation(Xref, String)","u":"%3Cinit%3E(org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"CITATIONREF"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"CITATIONREF"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"CitationRef(Citation)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"citationRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"citationRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"citationRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"citations"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"clear()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"clearChangedFlag()"},{"p":"org.pathvisio.libgpml.io","c":"AbstractPathwayModelFormat","l":"clearWarnings()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"clone()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"clone()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"clone()"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"clone()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape.FillType","l":"CLOSED"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"collection2String(Collection<?>, String, String)","u":"collection2String(java.util.Collection,java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"COLOR"},{"p":"org.pathvisio.libgpml.util","c":"ColorUtils","l":"colorMap"},{"p":"org.pathvisio.libgpml.util","c":"ColorUtils","l":"colorToHex(Color, boolean)","u":"colorToHex(java.awt.Color,boolean)"},{"p":"org.pathvisio.libgpml.util","c":"ColorUtils","l":"ColorUtils()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"COMMENT"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"COMMENT"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"Comment(String, String)","u":"%3Cinit%3E(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"comments"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"commentText"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"compareTo(AnchorShapeType)","u":"compareTo(org.pathvisio.libgpml.model.type.AnchorShapeType)"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"compareTo(ConnectorType)","u":"compareTo(org.pathvisio.libgpml.model.type.ConnectorType)"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"compareTo(GroupType)","u":"compareTo(org.pathvisio.libgpml.model.type.GroupType)"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"COMPLEX"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"COMPLEX"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"COMPLEX_M_MARGIN"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShapeFactory","l":"ConnectorShapeFactory()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"connectorType"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"CONNECTORTYPE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"CONNECTORTYPE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"CONNECTORTYPE_DEFAULT"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"ConnectorType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"contains(Object)","u":"contains(java.lang.Object)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"containsAll(Collection<?>)","u":"containsAll(java.util.Collection)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"containsCaseInsensitive(String, List<String>)","u":"containsCaseInsensitive(java.lang.String,java.util.List)"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"CONVERSION"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"CONVERSION_LIST"},{"p":"org.pathvisio.libgpml.io","c":"ConverterException","l":"ConverterException(Exception)","u":"%3Cinit%3E(java.lang.Exception)"},{"p":"org.pathvisio.libgpml.io","c":"ConverterException","l":"ConverterException(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"convertStateCommentToRefs(DataNode.State, Set<String>)","u":"convertStateCommentToRefs(org.pathvisio.libgpml.model.DataNode.State,java.util.Set)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"convertStateRefToComments(DataNode.State, Element)","u":"convertStateRefToComments(org.pathvisio.libgpml.model.DataNode.State,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"coordinateChange"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"coordinatesChanged()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"GraphicalLine","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"copy()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"copyAnnotationRefs(List<PathwayElement.AnnotationRef>)","u":"copyAnnotationRefs(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"copyCitationRefs(List<PathwayElement.CitationRef>)","u":"copyCitationRefs(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"CopyElement","l":"CopyElement(PathwayElement, PathwayElement)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.PathwayElement,org.pathvisio.libgpml.model.PathwayElement)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"copyEvidenceRefs(List<PathwayElement.EvidenceRef>)","u":"copyEvidenceRefs(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"copyRef()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"copyRef()"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"copyRef()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"copyReferencesFrom(PathwayElement)","u":"copyReferencesFrom(org.pathvisio.libgpml.model.PathwayElement)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"copyReferencesFrom(PathwayElement)","u":"copyReferencesFrom(org.pathvisio.libgpml.model.PathwayElement)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"copyValuesFrom(Annotation)","u":"copyValuesFrom(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"copyValuesFrom(Citation)","u":"copyValuesFrom(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"copyValuesFrom(DataNode)","u":"copyValuesFrom(org.pathvisio.libgpml.model.DataNode)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"copyValuesFrom(DataNode.State)","u":"copyValuesFrom(org.pathvisio.libgpml.model.DataNode.State)"},{"p":"org.pathvisio.libgpml.model","c":"GraphicalLine","l":"copyValuesFrom(DataNode.State)","u":"copyValuesFrom(org.pathvisio.libgpml.model.DataNode.State)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"copyValuesFrom(Evidence)","u":"copyValuesFrom(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"copyValuesFrom(Group)","u":"copyValuesFrom(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"copyValuesFrom(Interaction)","u":"copyValuesFrom(org.pathvisio.libgpml.model.Interaction)"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"copyValuesFrom(Label)","u":"copyValuesFrom(org.pathvisio.libgpml.model.Label)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"copyValuesFrom(LineElement)","u":"copyValuesFrom(org.pathvisio.libgpml.model.LineElement)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"copyValuesFrom(Pathway)","u":"copyValuesFrom(org.pathvisio.libgpml.model.Pathway)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"copyValuesFrom(PathwayElement)","u":"copyValuesFrom(org.pathvisio.libgpml.model.PathwayElement)"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"copyValuesFrom(Shape)","u":"copyValuesFrom(org.pathvisio.libgpml.model.Shape)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"copyValuesFrom(ShapedElement)","u":"copyValuesFrom(org.pathvisio.libgpml.model.ShapedElement)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"CORONAVIRUS_ICON"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"CORONAVIRUS_ICON"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"cr"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"cr1"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"cr2"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"createAllPropertiesEvent(PathwayObject)","u":"createAllPropertiesEvent(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShapeFactory","l":"createConnectorShape(String)","u":"createConnectorShape(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"createCoordinatePropertyEvent(PathwayObject)","u":"createCoordinatePropertyEvent(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"createJdom(PathwayModel)","u":"createJdom(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"createJdom(PathwayModel)","u":"createJdom(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"createJdom(PathwayModel)","u":"createJdom(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatWriter","l":"createJdom(PathwayModel)","u":"createJdom(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"createSinglePropertyEvent(PathwayObject, Object)","u":"createSinglePropertyEvent(org.pathvisio.libgpml.model.PathwayObject,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"createStraightSegment(Point2D, Point2D, int)","u":"createStraightSegment(java.awt.geom.Point2D,java.awt.geom.Point2D,int)"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"createXref(String, DataSource)","u":"createXref(java.lang.String,org.bridgedb.DataSource)"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"createXref(String, String)","u":"createXref(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"CURVED"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"CurvedConnectorShape()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape.CurvedSegment","l":"CurvedSegment(Point2D, Point2D, Point2D, Point2D)","u":"%3Cinit%3E(java.awt.geom.Point2D,java.awt.geom.Point2D,java.awt.geom.Point2D,java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"curvedSegments"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"curveHigh"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"curveLow"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"d"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"d1"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"d1"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"d1"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"d1"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"d1"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"d1"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"d1"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"d2"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"d2"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"d3"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"d3"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"DASHED"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"data"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"DATANODE"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"DataNode(String, DataNodeType)","u":"%3Cinit%3E(java.lang.String,org.pathvisio.libgpml.model.type.DataNodeType)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"DataNode(String, DataNodeType, Xref, Group)","u":"%3Cinit%3E(java.lang.String,org.pathvisio.libgpml.model.type.DataNodeType,org.bridgedb.Xref,org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"dataNodes"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"DATANODETYPE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"DATANODETYPE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"DATANODETYPE_DEFAULT"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"DataNodeType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"DATASOURCE"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"debug(String)","u":"debug(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"debugEnabled"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"DebugIterator(DebugList<E>)","u":"%3Cinit%3E(org.pathvisio.libgpml.debug.DebugList)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"DebugIterator(DebugList<E>, int)","u":"%3Cinit%3E(org.pathvisio.libgpml.debug.DebugList,int)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"DebugList()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract.AttributeInfo","l":"def"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"DEFAULT_M_MARGIN"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"DEFAULT_SHAPE"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"defaultAnchor"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"defaultArrow"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"defaultShape"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"DEGRADATION"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"DEGRADATION"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"delegate"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"delegate"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelEvent","l":"DELETED"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"DEPRECATED_MAP"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"description"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"DESCRIPTION"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"DESCRIPTION"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"DIRECTED"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"DIRECTED_LIST"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"DIRECTION"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"direction(LinAlg.Point, LinAlg.Point)","u":"direction(org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"disallowLinks"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"DISEASE"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"distance(LinAlg.Point, LinAlg.Point)","u":"distance(org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"DNA"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"DNA_ICON"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"DNA_ICON"},{"p":"org.pathvisio.libgpml.io","c":"PathwayModelExporter","l":"doExport(File, PathwayModel)","u":"doExport(java.io.File,org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"doExport(File, PathwayModel)","u":"doExport(java.io.File,org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.io","c":"PathwayModelExporter","l":"doExport(File, PathwayModel, int)","u":"doExport(java.io.File,org.pathvisio.libgpml.model.PathwayModel,int)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"doExport(File, PathwayModel, int)","u":"doExport(java.io.File,org.pathvisio.libgpml.model.PathwayModel,int)"},{"p":"org.pathvisio.libgpml.io","c":"PathwayModelImporter","l":"doImport(File)","u":"doImport(java.io.File)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"doImport(File)","u":"doImport(java.io.File)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"dontFireEvents(int)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"dot(LinAlg.Point, LinAlg.Point)","u":"dot(org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"DOUBLE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"DOUBLE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"DOUBLE_LINE_KEY"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"downloadFile(URL, File)","u":"downloadFile(java.net.URL,java.io.File)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"dynamicProperties"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"e1"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"EDGE"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"ELBOW"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"ElbowConnectorShape()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"elbowSegments"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader.PublicationXref","l":"element"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader.PublicationXref","l":"elementId"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"elementId"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ELEMENTID"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"elementIdToPathwayObject"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"elementRef"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"elementRefToLinePoints"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"ellipse"},{"p":"org.pathvisio.libgpml.io","c":"AbstractPathwayModelFormat","l":"emitWarning(String)","u":"emitWarning(java.lang.String)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"encodeFont(Font)","u":"encodeFont(java.awt.Font)"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"end"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"end"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"endArrowHeadType"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ENDARROWHEADTYPE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ENDELEMENTREF"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"ENDOPLASMIC_RETICULUM"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"ENDOPLASMIC_RETICULUM"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ENDX"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ENDY"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"EPIGENETIC_MODIFICATION"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"equalsAnnotation(Annotation)","u":"equalsAnnotation(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"equalsCitation(Citation)","u":"equalsCitation(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"equalsEvidence(Evidence)","u":"equalsEvidence(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"equivalentXrefs(Xref, Xref)","u":"equivalentXrefs(org.bridgedb.Xref,org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"er1"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"er2"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"error(String)","u":"error(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"error(String, Throwable)","u":"error(java.lang.String,java.lang.Throwable)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"errorEnabled"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"EVENT"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"evidence"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"EVIDENCE"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"Evidence(String, Xref, String)","u":"%3Cinit%3E(java.lang.String,org.bridgedb.Xref,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"evidenceable"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"EVIDENCEREF"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"EVIDENCEREF"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"EvidenceRef(Evidence)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"evidenceRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"evidenceRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"evidenceRefs"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"evidences"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"expectedModCount"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"EXTRACELLULAR_REGION"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"fatal(String)","u":"fatal(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"fatalEnabled"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"FileUtils()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"fillColor"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"FILLCOLOR"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"FILLCOLOR_DEFAULT"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape","l":"fillType"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape.FillType","l":"FillType()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"findAnchorSegment(LineElement, double)","u":"findAnchorSegment(org.pathvisio.libgpml.model.LineElement,double)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"findComment(String)","u":"findComment(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"fireObjectModifiedEvent(PathwayModelEvent)","u":"fireObjectModifiedEvent(org.pathvisio.libgpml.model.PathwayModelEvent)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"fireObjectModifiedEvent(PathwayObjectEvent)","u":"fireObjectModifiedEvent(org.pathvisio.libgpml.model.PathwayObjectEvent)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"fireStatusFlagEvent(PathwayModel.StatusFlagEvent)","u":"fireStatusFlagEvent(org.pathvisio.libgpml.model.PathwayModel.StatusFlagEvent)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"fontDecoration"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"FONTDECORATION"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"FONTDECORATION_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"fontName"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"FONTNAME"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"FONTNAME"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"FONTNAME_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"fontSize"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"FONTSIZE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"FONTSIZE_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"fontStrikethru"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"FONTSTRIKETHRU"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"FONTSTRIKETHRU_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"fontStyle"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"FONTSTYLE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"FONTSTYLE_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"fontWeight"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"FONTWEIGHT"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"FONTWEIGHT_DEFAULT"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"FORMAT_STRING"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"formatExceptionMsg(String)","u":"formatExceptionMsg(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.connector","c":"FreeConnectorShape","l":"FreeConnectorShape()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"fromCamelCase(String)","u":"fromCamelCase(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"fromLineCoordinate(double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"fromLineCoordinate(double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"SegmentedConnector","l":"fromLineCoordinate(double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"StraightConnectorShape","l":"fromLineCoordinate(double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"SegmentedConnector","l":"fromLineCoordinate(double, ConnectorShape.Segment[])","u":"fromLineCoordinate(double,org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"fromName(String)","u":"fromName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"g"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"g1"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"g1"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"g2"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"g2"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape","l":"gap"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"GENEPRODUCT"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.GenericPoint","l":"GenericPoint()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"GENETIC_VARIANT"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"get(int)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"getAbsolute()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelEvent","l":"getAffectedData()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"getAliasRef()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getAliasRefs()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"getAnchor(String)","u":"getAnchor(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShapeRegistry","l":"getAnchorCircle()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShapeRegistry","l":"getAnchorNone()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getAnchors()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShapeRegistry","l":"getAnchorSquare()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"getAnnotatable()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"getAnnotation()"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"getAnnotationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getAnnotationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"getAnnotationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Annotatable","l":"getAnnotationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getAnnotations()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"getArrow(String)","u":"getArrow(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getArrowHead()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"getArrowHeadTypeStr(ArrowHeadType)","u":"getArrowHeadTypeStr(org.pathvisio.libgpml.model.type.ArrowHeadType)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getAttachedLineDirection(LineElement.Anchor)","u":"getAttachedLineDirection(org.pathvisio.libgpml.model.LineElement.Anchor)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"getAttr(String, String, Element)","u":"getAttr(java.lang.String,java.lang.String,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"getAttributeInfo()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"getAuthors()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getAuthors()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getBackgroundColor()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getBinding()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getBoardHeight()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getBoardWidth()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getBorderColor()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getBorderStyle()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getBorderWidth()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getBounds()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getBounds()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getBounds()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getBounds()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"getByTag(String)","u":"getByTag(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape.CurvedSegment","l":"getC1()"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape.CurvedSegment","l":"getC2()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getCatalysis()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getCenterX()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getCenterX()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getCenterX()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getCenterY()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getCenterY()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getCenterY()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"getCitable()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"getCitation()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"getCitationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getCitationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"getCitationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Citable","l":"getCitationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getCitations()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getClockwisePerpendicularSide(int)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getComments()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"getCommentText()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getConnectorShape()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getConnectorType()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getDataNode()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getDataNodes()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getDataNodeXrefs()"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"getDataSource(Xref)","u":"getDataSource(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getDescription()"},{"p":"org.pathvisio.libgpml.prop","c":"Property","l":"getDescription()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"getDescription()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getDirectionX()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"getDirectionX(Point2D, Point2D)","u":"getDirectionX(java.awt.geom.Point2D,java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"getDirectionX(Point2D, Point2D)","u":"getDirectionX(java.awt.geom.Point2D,java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getDirectionY()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"getDirectionY(Point2D, Point2D)","u":"getDirectionY(java.awt.geom.Point2D,java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"getDirectionY(Point2D, Point2D)","u":"getDirectionY(java.awt.geom.Point2D,java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getDynamicProperties()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getDynamicProperty(String)","u":"getDynamicProperty(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getDynamicPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader.PublicationXref","l":"getElement()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader.PublicationXref","l":"getElementId()"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableTo","l":"getElementId()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"getElementId()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getElementIds()"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableFrom","l":"getElementRef()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"getElementRef()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getEndArrowHeadType()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getEndElementRef()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getEndLinePoint()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getEndLinePointX()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getEndLinePointY()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getEndPoint2D()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"getEndPoint2D()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getEndSide()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"getEndSide()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"getEvidence()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"getEvidenceable()"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"getEvidenceRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getEvidenceRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"getEvidenceRefs()"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Evidenceable","l":"getEvidenceRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getEvidences()"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"getExtension(String)","u":"getExtension(java.lang.String)"},{"p":"org.pathvisio.libgpml.io","c":"PathwayModelIO","l":"getExtensions()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"getExtensions()"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"getFiles(File, boolean)","u":"getFiles(java.io.File,boolean)"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"getFiles(File, String, boolean)","u":"getFiles(java.io.File,java.lang.String,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getFillColor()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape","l":"getFillType()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getFontDecoration()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getFontName()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getFontSize()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getFontStrikethru()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getFontStyle()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getFontWeight()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape","l":"getGap()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"getGpmlNamespace()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatVersion","l":"getGpmlNamespace()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getGraphicalLines()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getGroups()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getGroupXrefs()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getHAlign()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader.PublicationXref","l":"getHasRef()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getHeight()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getHeight()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getHeight()"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"getHref()"},{"p":"org.pathvisio.libgpml.prop","c":"Property","l":"getId()"},{"p":"org.pathvisio.libgpml.prop","c":"PropertyType","l":"getId()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"getId()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"getId()"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"getIdentifier(Xref)","u":"getIdentifier(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShapeFactory","l":"getImplementingClass(String)","u":"getImplementingClass(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"getInteractionPanelType(String)","u":"getInteractionPanelType(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getInteractions()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getInteractionXrefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getLabels()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getLeft()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getLeft()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getLeft()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getLicense()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getLigand()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getLineColor()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.GenericPoint","l":"getLineElement()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getLineElements()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getLinePoints()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getLineStyle()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getLineWidth()"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableTo","l":"getLinkableFroms()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"getLinkableFroms()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getLinkableFroms()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getLinkedAliases(Group)","u":"getLinkedAliases(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"getListeners()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getLRound()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getMargin()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"getMCenter()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"getMEnd()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getMinBounds(boolean)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"getMLength()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"getModifiedPathwayObject()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"getMStart()"},{"p":"org.pathvisio.libgpml.io","c":"PathwayModelIO","l":"getName()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"getName()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"getName()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"getName()"},{"p":"org.pathvisio.libgpml.model.shape","c":"IShape","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"getName()"},{"p":"org.pathvisio.libgpml.prop","c":"Property","l":"getName()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"getName()"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"getNames()"},{"p":"org.pathvisio.libgpml.model","c":"CopyElement","l":"getNewElement()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel.StatusFlagEvent","l":"getNewStatus()"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"getNrLines(String)","u":"getNrLines(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"getNrSegments(ConnectorRestrictions)","u":"getNrSegments(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.connector","c":"FreeConnectorShape","l":"getNrSegments(ConnectorRestrictions)","u":"getNrSegments(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"getNrWaypoints(int, int, int)","u":"getNrWaypoints(int,int,int)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"Drawable","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableTo","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"GraphicalLine","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"getObjectType()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"getOppositeAxis(int)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getOppositeSide(int)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"getOrder()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"getOrder()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getOrganism()"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"getOS()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getPathway()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getPathwayElements()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getPathwayElements()"},{"p":"org.pathvisio.libgpml.model","c":"Drawable","l":"getPathwayModel()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"getPathwayModel()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getPathwayObject(String)","u":"getPathwayObject(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getPathwayObjects()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog","l":"getPluggableShape(ShapeCatalog.Internal)","u":"getPluggableShape(org.pathvisio.libgpml.model.shape.ShapeCatalog.Internal)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getPoints2D()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"getPosition()"},{"p":"org.pathvisio.libgpml.prop","c":"PropertyManager","l":"getProperty(String)","u":"getProperty(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getPropertyEx(Object)","u":"getPropertyEx(java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"getPropertyEx(Object)","u":"getPropertyEx(java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"getPropertyKeys()"},{"p":"org.pathvisio.libgpml.prop","c":"PropertyManager","l":"getPropertyType(String)","u":"getPropertyType(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"getReaderForNamespace(Namespace)","u":"getReaderForNamespace(org.jdom2.Namespace)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getReceptor()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getReceptorSquare()"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink","l":"getReferences(GraphLink.LinkableTo, PathwayModel)","u":"getReferences(org.pathvisio.libgpml.model.GraphLink.LinkableTo,org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getReferringLinkableFroms(GraphLink.LinkableTo)","u":"getReferringLinkableFroms(org.pathvisio.libgpml.model.GraphLink.LinkableTo)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog","l":"getRegularPolygon(int, double, double)","u":"getRegularPolygon(int,double,double)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getRelX()"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableFrom","l":"getRelX()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"getRelX()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getRelY()"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableFrom","l":"getRelY()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"getRelY()"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder.RootElementHandler","l":"getRootQName()"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder.RootElementHandler","l":"getRootUri()"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder","l":"getRootUri(File)","u":"getRootUri(java.io.File)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getRotatedBounds()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getRotatedBounds()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getRotatedBounds()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getRotatedBounds()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getRotation()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getRRound()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"getSchemaFile()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatVersion","l":"getSchemaFile()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"getSegmentAxis(int)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"getSegmentDirection(int)"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"getSegments()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"getSegments()"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"getShape()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"getShape()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShape","l":"getShape()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape","l":"getShape()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"getShape(double, double)","u":"getShape(double,double)"},{"p":"org.pathvisio.libgpml.model.shape","c":"IShape","l":"getShape(double, double)","u":"getShape(double,double)"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"getShape(double, double)","u":"getShape(double,double)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getShapedElements()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getShapedElementsExclStates()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getShapes()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"getShapeType()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getShapeType()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getSide(double, double)","u":"getSide(double,double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getSide(double, double, double, double)","u":"getSide(double,double,double,double)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"getSource()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getSource()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"getSource()"},{"p":"org.pathvisio.libgpml.model","c":"CopyElement","l":"getSourceElement()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getSourceFile()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStartArrowHeadType()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStartElementRef()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStartLinePoint()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStartLinePointX()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStartLinePointY()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStartPoint2D()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"getStartPoint2D()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStartSide()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"getStartSide()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"getStates()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getStateXrefs()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getStaticProperty(StaticProperty)","u":"getStaticProperty(org.pathvisio.libgpml.prop.StaticProperty)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getStaticPropertyKeys()"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"getStream()"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"getTag()"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"getTagMapping(String)","u":"getTagMapping(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getTBar()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getTextColor()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"getTextLabel()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getTextLabel()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getTextLabel()"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"getTextLabel()"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"getTextLabel()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getTextLabel()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"getTitle()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getTitle()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getTop()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getTop()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getTop()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.InfoRef","l":"getTopPathwayElement()"},{"p":"org.pathvisio.libgpml.model.connector","c":"SegmentedConnector","l":"getTotalLength(ConnectorShape.Segment[])","u":"getTotalLength(org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"getTranscriptionTranslation()"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"getType()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"getType()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getType()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getType()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelEvent","l":"getType()"},{"p":"org.pathvisio.libgpml.prop","c":"Property","l":"getType()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"getType()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getUniqueElementId()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"getUniqueId(Set<String>)","u":"getUniqueId(java.util.Set)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"getUrlLink()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"getUrlLink()"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"getUrlLink()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"getUsername()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getVAlign()"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"getValue()"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"getValue()"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"getValues()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getVersion()"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"getVisibleNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"getVisibleNames()"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"getVisibleValues()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"getVisibleValues()"},{"p":"org.pathvisio.libgpml.io","c":"AbstractPathwayModelFormat","l":"getWarnings()"},{"p":"org.pathvisio.libgpml.io","c":"PathwayModelIO","l":"getWarnings()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getWayPointPreferences()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"getWayPointPreferences()"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"getWayPoints()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"getWayPoints()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"getWidth()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getWidth()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getWidth()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"getX()"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"getXref()"},{"p":"org.pathvisio.libgpml.model","c":"Xrefable","l":"getXref()"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"getXrefDataSource(String)","u":"getXrefDataSource(java.lang.String)"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"getXrefDataSourceStr(DataSource)","u":"getXrefDataSourceStr(org.bridgedb.DataSource)"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"getXrefDataSourceStrGPML2013a(DataSource)","u":"getXrefDataSourceStrGPML2013a(org.bridgedb.DataSource)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"getY()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"getYear()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"getZOrder()"},{"p":"org.pathvisio.libgpml.model","c":"Drawable","l":"getZOrder()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"getZOrder()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"getZOrder()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"getZOrder()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"getZOrder()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"gmmlObjectModified(PathwayModelEvent)","u":"gmmlObjectModified(org.pathvisio.libgpml.model.PathwayModelEvent)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectListener","l":"gmmlObjectModified(PathwayObjectEvent)","u":"gmmlObjectModified(org.pathvisio.libgpml.model.PathwayObjectEvent)"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"gmmlObjectModified(PathwayObjectEvent)","u":"gmmlObjectModified(org.pathvisio.libgpml.model.PathwayObjectEvent)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"GOLGI_APPARATUS"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"GOLGI_APPARATUS"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"GPML2013a"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"GPML2013A_KEY_SET"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"GPML2013aFormatAbstract(String, Namespace)","u":"%3Cinit%3E(java.lang.String,org.jdom2.Namespace)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"GPML2013aREADER"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"GPML2013aReader(String, Namespace)","u":"%3Cinit%3E(java.lang.String,org.jdom2.Namespace)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"GPML2013aWRITER"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"GPML2013aWriter(String, Namespace)","u":"%3Cinit%3E(java.lang.String,org.jdom2.Namespace)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"GPML2021"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"GPML2021FormatAbstract(String, Namespace)","u":"%3Cinit%3E(java.lang.String,org.jdom2.Namespace)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"GPML2021READER"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"GPML2021Reader(String, Namespace)","u":"%3Cinit%3E(java.lang.String,org.jdom2.Namespace)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"GPML2021WRITER"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"GPML2021Writer(String, Namespace)","u":"%3Cinit%3E(java.lang.String,org.jdom2.Namespace)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"GPMLFormat(GPMLFormatWriter)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.GPMLFormatWriter)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"GPMLFormatAbstract(String, Namespace)","u":"%3Cinit%3E(java.lang.String,org.jdom2.Namespace)"},{"p":"org.pathvisio.libgpml.model","c":"GraphicalLine","l":"GraphicalLine()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"graphicalLines"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"GRAPHLINE"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink","l":"GraphLink()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"GROUP"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"GROUP"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"Group(GroupType)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.type.GroupType)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"Group(GroupType, Xref)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.type.GroupType,org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"groupRef"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"groupRef"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"GROUPREF"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"groups"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"GROUPTYPE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"GROUPTYPE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"GROUPTYPE_DEFAULT"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"GroupType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"hAlign"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"HALIGN"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"HALIGN_DEFAULT"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"HALIGNTYPE"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"HAlignType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"hasAliasRef(Group)","u":"hasAliasRef(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"hasAnchor(LineElement.Anchor)","u":"hasAnchor(org.pathvisio.libgpml.model.LineElement.Anchor)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"hasAnnotatable()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"hasAnnotation()"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"hasAnnotationRef(PathwayElement.AnnotationRef)","u":"hasAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"hasAnnotationRef(PathwayElement.AnnotationRef)","u":"hasAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"hasAnnotationRef(PathwayElement.AnnotationRef)","u":"hasAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Annotatable","l":"hasAnnotationRef(PathwayElement.AnnotationRef)","u":"hasAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"hasChanged()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"hasCitable()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"hasCitation()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"hasCitationRef(PathwayElement.CitationRef)","u":"hasCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"hasCitationRef(PathwayElement.CitationRef)","u":"hasCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"hasCitationRef(PathwayElement.CitationRef)","u":"hasCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Citable","l":"hasCitationRef(PathwayElement.CitationRef)","u":"hasCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"hasEqualAnnotation(Annotation)","u":"hasEqualAnnotation(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"hasEqualCitation(Citation)","u":"hasEqualCitation(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"hasEqualEvidence(Evidence)","u":"hasEqualEvidence(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"hasEvidence()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"hasEvidenceable()"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"hasEvidenceRef(PathwayElement.EvidenceRef)","u":"hasEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"hasEvidenceRef(PathwayElement.EvidenceRef)","u":"hasEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"hasEvidenceRef(PathwayElement.EvidenceRef)","u":"hasEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Evidenceable","l":"hasEvidenceRef(PathwayElement.EvidenceRef)","u":"hasEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"hasGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"hasGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"hasGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"hasLinkedAlias(Group, DataNode)","u":"hasLinkedAlias(org.pathvisio.libgpml.model.Group,org.pathvisio.libgpml.model.DataNode)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"hasNext()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"hasPathwayElement(Groupable)","u":"hasPathwayElement(org.pathvisio.libgpml.model.Groupable)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"hasPathwayModel()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"hasPathwayObject(PathwayObject)","u":"hasPathwayObject(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"hasPrevious()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader.PublicationXref","l":"hasRef"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"hasState(DataNode.State)","u":"hasState(org.pathvisio.libgpml.model.DataNode.State)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"hasValidWaypoints(ConnectorRestrictions)","u":"hasValidWaypoints(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"hasValidWaypoints(ConnectorRestrictions)","u":"hasValidWaypoints(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.connector","c":"FreeConnectorShape","l":"hasValidWaypoints(ConnectorRestrictions)","u":"hasValidWaypoints(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.connector","c":"StraightConnectorShape","l":"hasValidWaypoints(ConnectorRestrictions)","u":"hasValidWaypoints(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"height"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"HEIGHT"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"helper()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"HEXAGON"},{"p":"org.pathvisio.libgpml.util","c":"ColorUtils","l":"hexToColor(String)","u":"hexToColor(java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"hidden"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"href"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"HREF"},{"p":"org.pathvisio.libgpml.model","c":"TestGraphLink","l":"i"},{"p":"org.pathvisio.libgpml.model","c":"TestAnchor","l":"i1"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"i1"},{"p":"org.pathvisio.libgpml.model","c":"TestLinePoint","l":"i1"},{"p":"org.pathvisio.libgpml.model","c":"TestGraphLink","l":"i2"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"IA_PANEL_MAP"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"id"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"indexOf(Object)","u":"indexOf(java.lang.Object)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"info(String)","u":"info(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"INFOBOX_CENTER_X"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"INFOBOX_CENTER_Y"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"infoEnabled"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.InfoRef","l":"InfoRef()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"INHIBITION"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"INHIBITION_LIST"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"initAttributeInfo()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"initTagMapping()"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder","l":"inputStreamToReader(InputStream)","u":"inputStreamToReader(java.io.InputStream)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"INTEGER"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"INTERACTION"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"Interaction()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"Interaction(Xref)","u":"%3Cinit%3E(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"interactions"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"Internal()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"isAdvanced"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"isAdvanced()"},{"p":"org.pathvisio.libgpml.prop","c":"Property","l":"isCollection()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"isCollection()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"isCoordinate"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"isCoordinateChange()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"isCoordinateChange()"},{"p":"org.pathvisio.libgpml.io","c":"AbstractPathwayModelFormat","l":"isCorrectType(File)","u":"isCorrectType(java.io.File)"},{"p":"org.pathvisio.libgpml.io","c":"PathwayModelImporter","l":"isCorrectType(File)","u":"isCorrectType(java.io.File)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"isCorrectType(File)","u":"isCorrectType(java.io.File)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"isDisallowLinks()"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"isEmpty()"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"isEmpty(String)","u":"isEmpty(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"isEqualsColor(String, String)","u":"isEqualsColor(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"isEqualsNumber(String, String)","u":"isEqualsNumber(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"isEqualsString(String, String)","u":"isEqualsString(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"isHidden()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"isPointOnSegment(Double, Double, Double)","u":"isPointOnSegment(java.lang.Double,java.lang.Double,java.lang.Double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"isRelative()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"isResizeable"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"isResizeable"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"isResizeable()"},{"p":"org.pathvisio.libgpml.model.shape","c":"IShape","l":"isResizeable()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"isResizeable()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"isRotatable"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"isRotatable"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"isRotatable()"},{"p":"org.pathvisio.libgpml.model.shape","c":"IShape","l":"isRotatable()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"isRotatable()"},{"p":"org.pathvisio.libgpml.util","c":"ColorUtils","l":"isTransparent(Color)","u":"isTransparent(java.awt.Color)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"iterator()"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"join(String, Collection<?>)","u":"join(java.lang.String,java.util.Collection)"},{"p":"org.pathvisio.libgpml.debug","c":"TestDebug","l":"l"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"l"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"l"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"LABEL"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"Label(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"labels"},{"p":"org.pathvisio.libgpml.debug","c":"StopWatch","l":"last"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"lastIndexOf(Object)","u":"lastIndexOf(java.lang.Object)"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"LEFT"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"LEGEND_CENTER_X"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"LEGEND_CENTER_Y"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"len()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"license"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"LICENSE"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"LIGANDHEIGHT"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"LIGANDWIDTH"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"LinAlg()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"lineColor"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"LINECOLOR"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"LINECOLOR_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"LineElement()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"LINEPOINT"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"LinePoint(double, double)","u":"%3Cinit%3E(double,double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"linePoints"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"lineStyle"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"LINESTYLE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"LINESTYLE_DEFAULT"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"LINESTYLETYPE"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"LineStyleType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"lineWidth"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"LINEWIDTH"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"LINEWIDTH_DEFAULT"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"LINKABLETO"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"linkAlias(Group, DataNode)","u":"linkAlias(org.pathvisio.libgpml.model.Group,org.pathvisio.libgpml.model.DataNode)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"linkTo(GraphLink.LinkableTo)","u":"linkTo(org.pathvisio.libgpml.model.GraphLink.LinkableTo)"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableFrom","l":"linkTo(GraphLink.LinkableTo, double, double)","u":"linkTo(org.pathvisio.libgpml.model.GraphLink.LinkableTo,double,double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"linkTo(GraphLink.LinkableTo, double, double)","u":"linkTo(org.pathvisio.libgpml.model.GraphLink.LinkableTo,double,double)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"listeners"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"listeners"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"listIterator()"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"listIterator(int)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"log"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"Logger()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"logTimer"},{"p":"org.pathvisio.libgpml.debug","c":"StopWatch","l":"look()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"LRDIAM"},{"p":"org.pathvisio.libgpml.util","c":"ColorUtils","l":"makeTransparent(Color, int)","u":"makeTransparent(java.awt.Color,int)"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"mapFileTree(File, File, File)","u":"mapFileTree(java.io.File,java.io.File,java.io.File)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"markChanged()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"mayCross(Point2D)","u":"mayCross(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"mayCross(Point2D)","u":"mayCross(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"MEMBRANE_ICON"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"MEMBRANE_ICON"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"METABOLITE"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"MIDDLE"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"MITOCHONDRIA"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"MITOCHONDRIA"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"modCount"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"moveBy(double, double)","u":"moveBy(double,double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"moveTo(double, double)","u":"moveTo(double,double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"moveTo(LineElement.LinePoint)","u":"moveTo(org.pathvisio.libgpml.model.LineElement.LinePoint)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"multimapPut(Map<U, Set<V>>, U, V)","u":"multimapPut(java.util.Map,U,V)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"multimapValues(Map<U, Set<V>>)","u":"multimapValues(java.util.Map)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"multiply(double)"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"n1"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"n2"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"name"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"name"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"name"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"nameToAnchorShapeType"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"nameToAnnotationType"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"nameToArrowHeadType"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"nameToConnectorType"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"nameToDataNodeType"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"nameToGroupType"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"nameToHAlignType"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"nameToLineStyleType"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"nameToStateType"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"nameToVAlignType"},{"p":"org.pathvisio.libgpml.model","c":"CopyElement","l":"newElement"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel.StatusFlagEvent","l":"newStatus"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"next()"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"nextIndex()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"noFire"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"NONE"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"NONE"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"norm()"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"NRSTEP_HIGH"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"NRSTEP_LOW"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"nsGPML"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"NUCLEUS"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"o"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"o1"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"ObjectType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"OCTAGON"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"OCTAGON"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"OCV_ONTOLOGY_MAP"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"oneOf(Set<T>)","u":"oneOf(java.util.Set)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"ONTOLOGY"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape.FillType","l":"OPEN"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"order"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"order"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"ORGAN"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"ORGANELLE"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"organism"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ORGANISM"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"ORGANISM"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"OS_LINUX"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"OS_MAC"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"OS_UNSUPPORTED"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"OS_WINDOWS"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"OVAL"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"OWL_NAMESPACE"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"OWL_NAMESPACE"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestAnchor","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestGraphLink","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestLinePoint","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"p"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"p"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"PARALOG"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"parent"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PARENT"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PARENTID"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PARENTID_DB"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PARENTSYMBOL"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PARENTSYMBOL_DB"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder","l":"parse(File)","u":"parse(java.io.File)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"pathway"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"PATHWAY"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"PATHWAY"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"PATHWAY"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PATHWAY_AUTHOR"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PATHWAY_EMAIL"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PATHWAY_LASTMODIFIED"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PATHWAY_MAINTAINER"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"Pathway()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"PathwayElement()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"pathwayElements"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"pathwayModel"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"PathwayModel()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelEvent","l":"PathwayModelEvent(PathwayObject, int)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.PathwayObject,int)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelListener","l":"pathwayModified(PathwayModelEvent)","u":"pathwayModified(org.pathvisio.libgpml.model.PathwayModelEvent)"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"pathwayModified(PathwayModelEvent)","u":"pathwayModified(org.pathvisio.libgpml.model.PathwayModelEvent)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"PathwayObject()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"PathwayObjectEvent(PathwayObject, Object, boolean)","u":"%3Cinit%3E(org.pathvisio.libgpml.model.PathwayObject,java.lang.Object,boolean)"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"PENTAGON"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"PHENOTYPE"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"Point(double, double)","u":"%3Cinit%3E(double,double)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"Point(Point2D)","u":"%3Cinit%3E(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"position"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"POSITION"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"pow(double, double)","u":"pow(double,double)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"previous()"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"previousIndex()"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"printx(PrintStream, String, Object)","u":"printx(java.io.PrintStream,java.lang.String,java.lang.Object)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"project(LinAlg.Point, LinAlg.Point)","u":"project(org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"project(LinAlg.Point, LinAlg.Point, LinAlg.Point)","u":"project(org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.prop","c":"PropertyManager","l":"PROPERTIES"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"property"},{"p":"org.pathvisio.libgpml.prop","c":"PropertyManager","l":"PROPERTY_TYPES"},{"p":"org.pathvisio.libgpml.prop","c":"PropertyManager","l":"PropertyManager()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"PROTEIN"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"PROTEIN_MODIFICATION"},{"p":"org.pathvisio.libgpml.model","c":"TestLinePoint","l":"pt3"},{"p":"org.pathvisio.libgpml.model","c":"TestLinePoint","l":"pt4"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"PTM"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader.PublicationXref","l":"PublicationXref(Element, String)","u":"%3Cinit%3E(org.jdom2.Element,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObjectEvent","l":"pwElement"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"RDF_NAMESPACE"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"RDF_NAMESPACE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"RDF_STRING"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"RDF_STRING"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"RDFS_NAMESPACE"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"RDFS_NAMESPACE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readAllElementIds(Element, Set<String>)","u":"readAllElementIds(org.jdom2.Element,java.util.Set)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readAnchors(LineElement, Element)","u":"readAnchors(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readAnchors(LineElement, Element, Set<String>)","u":"readAnchors(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element,java.util.Set)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readAnnotationRefs(PathwayModel, Referenceable.Annotatable, Element, Map<String, Element>)","u":"readAnnotationRefs(org.pathvisio.libgpml.model.PathwayModel,org.pathvisio.libgpml.model.Referenceable.Annotatable,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readArrowHeadType(Element, String)","u":"readArrowHeadType(org.jdom2.Element,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readAuthors(Pathway, Element)","u":"readAuthors(org.pathvisio.libgpml.model.Pathway,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readCitationRefs(PathwayModel, Referenceable.Citable, Element, Map<String, Element>)","u":"readCitationRefs(org.pathvisio.libgpml.model.PathwayModel,org.pathvisio.libgpml.model.Referenceable.Citable,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readCommentGroup(PathwayElement, Element, Map<String, GPML2013aReader.PublicationXref>)","u":"readCommentGroup(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readCommentGroup(PathwayModel, PathwayElement, Element, Map<String, Element>)","u":"readCommentGroup(org.pathvisio.libgpml.model.PathwayModel,org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readComments(PathwayElement, Element)","u":"readComments(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readComments(PathwayElement, Element)","u":"readComments(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readDataNodes(PathwayModel, Element, Map<String, Element>)","u":"readDataNodes(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readDataNodes(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>)","u":"readDataNodes(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Set,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readDynamicProperties(PathwayElement, Element)","u":"readDynamicProperties(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readDynamicProperties(PathwayElement, Element)","u":"readDynamicProperties(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readElementId(String, Element, Set<String>)","u":"readElementId(java.lang.String,org.jdom2.Element,java.util.Set)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readEvidenceRefs(PathwayModel, Referenceable.Evidenceable, Element, Map<String, Element>)","u":"readEvidenceRefs(org.pathvisio.libgpml.model.PathwayModel,org.pathvisio.libgpml.model.Referenceable.Evidenceable,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readFontProperty(ShapedElement, Element)","u":"readFontProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readFontProperty(ShapedElement, Element)","u":"readFontProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readFromRoot(PathwayModel, Element)","u":"readFromRoot(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readFromRoot(PathwayModel, Element)","u":"readFromRoot(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatReader","l":"readFromRoot(PathwayModel, Element)","u":"readFromRoot(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"readFromXml(File, boolean)","u":"readFromXml(java.io.File,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"readFromXml(InputStream, boolean)","u":"readFromXml(java.io.InputStream,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"readFromXml(PathwayModel, File, boolean)","u":"readFromXml(org.pathvisio.libgpml.model.PathwayModel,java.io.File,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"readFromXml(PathwayModel, InputStream, boolean)","u":"readFromXml(org.pathvisio.libgpml.model.PathwayModel,java.io.InputStream,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"readFromXml(PathwayModel, Reader, boolean)","u":"readFromXml(org.pathvisio.libgpml.model.PathwayModel,java.io.Reader,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"readFromXml(Reader, boolean)","u":"readFromXml(java.io.Reader,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"readFromXmlImpl(PathwayModel, InputSource, boolean)","u":"readFromXmlImpl(org.pathvisio.libgpml.model.PathwayModel,org.xml.sax.InputSource,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readGraphicalLines(PathwayModel, Element, Map<String, Element>, Map<Element, LineElement.LinePoint>)","u":"readGraphicalLines(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readGraphicalLines(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>, Map<Element, LineElement.LinePoint>)","u":"readGraphicalLines(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Set,java.util.Map,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readGroupGroupRef(PathwayModel, Element, Map<String, Group>)","u":"readGroupGroupRef(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readGroupRef(PathwayModel, ShapedElement, Element)","u":"readGroupRef(org.pathvisio.libgpml.model.PathwayModel,org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readGroupRef(ShapedElement, Element, Map<String, Group>)","u":"readGroupRef(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readGroups(PathwayModel, Element, Map<String, Element>)","u":"readGroups(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readGroups(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>, Map<String, Group>)","u":"readGroups(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Set,java.util.Map,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readInfoBox(Pathway, Element)","u":"readInfoBox(org.pathvisio.libgpml.model.Pathway,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readInfoMap(Element, Map<String, Element>)","u":"readInfoMap(org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readInteractions(PathwayModel, Element, Map<String, Element>, Map<Element, LineElement.LinePoint>)","u":"readInteractions(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readInteractions(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>, Map<Element, LineElement.LinePoint>)","u":"readInteractions(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Set,java.util.Map,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readLabels(PathwayModel, Element, Map<String, Element>)","u":"readLabels(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readLabels(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>)","u":"readLabels(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Set,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readLegend(Pathway, Element)","u":"readLegend(org.pathvisio.libgpml.model.Pathway,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readLineElement(LineElement, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>)","u":"readLineElement(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element,java.util.Set,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readLineElement(PathwayModel, LineElement, Element, Map<String, Element>, Map<Element, LineElement.LinePoint>)","u":"readLineElement(org.pathvisio.libgpml.model.PathwayModel,org.pathvisio.libgpml.model.LineElement,org.jdom2.Element,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readLineStyleProperty(LineElement, Element)","u":"readLineStyleProperty(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readLineStyleProperty(LineElement, Element)","u":"readLineStyleProperty(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readOpenControlledVocabulary(PathwayModel, Element, Set<String>)","u":"readOpenControlledVocabulary(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Set)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readPathway(Pathway, Element)","u":"readPathway(org.pathvisio.libgpml.model.Pathway,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readPathway(Pathway, Element)","u":"readPathway(org.pathvisio.libgpml.model.Pathway,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readPointElementRefs(PathwayModel, Map<Element, LineElement.LinePoint>)","u":"readPointElementRefs(org.pathvisio.libgpml.model.PathwayModel,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readPointElementRefs(PathwayModel, Map<String, Group>, Map<Element, LineElement.LinePoint>)","u":"readPointElementRefs(org.pathvisio.libgpml.model.PathwayModel,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readPoints(LineElement, Element, Map<Element, LineElement.LinePoint>)","u":"readPoints(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readPoints(LineElement, Element, Set<String>, Map<Element, LineElement.LinePoint>)","u":"readPoints(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element,java.util.Set,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readPublicationXrefInfo(List<Element>)","u":"readPublicationXrefInfo(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readPublicationXrefMap(Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>)","u":"readPublicationXrefMap(org.jdom2.Element,java.util.Set,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readPublicationXrefs(PathwayElement, Element, Map<String, GPML2013aReader.PublicationXref>)","u":"readPublicationXrefs(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readRectProperty(ShapedElement, Element)","u":"readRectProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readRectProperty(ShapedElement, Element)","u":"readRectProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readShapedElement(PathwayModel, ShapedElement, Element, Map<String, Element>)","u":"readShapedElement(org.pathvisio.libgpml.model.PathwayModel,org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readShapedElement(ShapedElement, Element, Map<String, GPML2013aReader.PublicationXref>)","u":"readShapedElement(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readShapes(PathwayModel, Element, Map<String, Element>)","u":"readShapes(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readShapes(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>)","u":"readShapes(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Set,java.util.Map,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readShapeStyleProperty(ShapedElement, Element)","u":"readShapeStyleProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readShapeStyleProperty(ShapedElement, Element)","u":"readShapeStyleProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readStates(PathwayModel, DataNode, Element, Map<String, Element>)","u":"readStates(org.pathvisio.libgpml.model.PathwayModel,org.pathvisio.libgpml.model.DataNode,org.jdom2.Element,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readStates(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>)","u":"readStates(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element,java.util.Set,java.util.Map)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readUrl(Element)","u":"readUrl(org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"readXref(Element)","u":"readXref(org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Reader","l":"readXref(Element)","u":"readXref(org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"recalculateShape(ConnectorRestrictions)","u":"recalculateShape(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"recalculateShape(ConnectorRestrictions)","u":"recalculateShape(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.connector","c":"FreeConnectorShape","l":"recalculateShape(ConnectorRestrictions)","u":"recalculateShape(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model.connector","c":"StraightConnectorShape","l":"recalculateShape(ConnectorRestrictions)","u":"recalculateShape(org.pathvisio.libgpml.model.connector.ConnectorRestrictions)"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"received"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"receivedElementEvents"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"RECEPHEIGHT"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"RECEPWIDTH"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"rectangle"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"RECTANGLE"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableFrom","l":"refeeChanged()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"refeeChanged()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"refreshLineElements(PathwayModel)","u":"refreshLineElements(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"register(String)","u":"register(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"register(String)","u":"register(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"register(String)","u":"register(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"register(String)","u":"register(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"register(String)","u":"register(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"register(String)","u":"register(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"register(String)","u":"register(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"register(String)","u":"register(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"register(String, Shape)","u":"register(java.lang.String,java.awt.Shape)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"registerAnchor(String, Shape)","u":"registerAnchor(java.lang.String,java.awt.Shape)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"registerArrow(String, Shape, ArrowShape.FillType)","u":"registerArrow(java.lang.String,java.awt.Shape,org.pathvisio.libgpml.model.shape.ArrowShape.FillType)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"registerArrow(String, Shape, ArrowShape.FillType, int)","u":"registerArrow(java.lang.String,java.awt.Shape,org.pathvisio.libgpml.model.shape.ArrowShape.FillType,int)"},{"p":"org.pathvisio.libgpml.prop","c":"PropertyManager","l":"registerProperty(Property)","u":"registerProperty(org.pathvisio.libgpml.prop.Property)"},{"p":"org.pathvisio.libgpml.prop","c":"PropertyManager","l":"registerPropertyType(PropertyType)","u":"registerPropertyType(org.pathvisio.libgpml.prop.PropertyType)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"registerShape(IShape)","u":"registerShape(org.pathvisio.libgpml.model.shape.IShape)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShapeFactory","l":"registerShape(String, Class<? extends ConnectorShape>)","u":"registerShape(java.lang.String,java.lang.Class)"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShapeRegistry","l":"registerShapes()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"registerShapes()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog","l":"registerShapes()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"relX"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"relX"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"RELX"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"relY"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"relY"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"RELY"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"remove()"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"remove(int)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"remove(Object)","u":"remove(java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"remove(PathwayObject)","u":"remove(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeAliasRef(Group)","u":"removeAliasRef(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"removeAll(Collection<?>)","u":"removeAll(java.util.Collection)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"removeAnchor(LineElement.Anchor)","u":"removeAnchor(org.pathvisio.libgpml.model.LineElement.Anchor)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"removeAnchors()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeAnnotation(Annotation)","u":"removeAnnotation(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"removeAnnotationRef(PathwayElement.AnnotationRef)","u":"removeAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"removeAnnotationRef(PathwayElement.AnnotationRef)","u":"removeAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"removeAnnotationRef(PathwayElement.AnnotationRef)","u":"removeAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Annotatable","l":"removeAnnotationRef(PathwayElement.AnnotationRef)","u":"removeAnnotationRef(org.pathvisio.libgpml.model.PathwayElement.AnnotationRef)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"removeAnnotationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"removeAnnotationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"removeAnnotationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Annotatable","l":"removeAnnotationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"removeAuthor(Pathway.Author)","u":"removeAuthor(org.pathvisio.libgpml.model.Pathway.Author)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeCitation(Citation)","u":"removeCitation(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"removeCitationRef(PathwayElement.CitationRef)","u":"removeCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"removeCitationRef(PathwayElement.CitationRef)","u":"removeCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"removeCitationRef(PathwayElement.CitationRef)","u":"removeCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Citable","l":"removeCitationRef(PathwayElement.CitationRef)","u":"removeCitationRef(org.pathvisio.libgpml.model.PathwayElement.CitationRef)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"removeCitationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"removeCitationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"removeCitationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Citable","l":"removeCitationRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"removeComment(PathwayElement.Comment)","u":"removeComment(org.pathvisio.libgpml.model.PathwayElement.Comment)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeDataNode(DataNode)","u":"removeDataNode(org.pathvisio.libgpml.model.DataNode)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeElementId(String)","u":"removeElementId(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeElementRef(GraphLink.LinkableTo, GraphLink.LinkableFrom)","u":"removeElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo,org.pathvisio.libgpml.model.GraphLink.LinkableFrom)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeEvidence(Evidence)","u":"removeEvidence(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"removeEvidenceRef(PathwayElement.EvidenceRef)","u":"removeEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"removeEvidenceRef(PathwayElement.EvidenceRef)","u":"removeEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"removeEvidenceRef(PathwayElement.EvidenceRef)","u":"removeEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Evidenceable","l":"removeEvidenceRef(PathwayElement.EvidenceRef)","u":"removeEvidenceRef(org.pathvisio.libgpml.model.PathwayElement.EvidenceRef)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"removeEvidenceRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"removeEvidenceRefs()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"removeEvidenceRefs()"},{"p":"org.pathvisio.libgpml.model","c":"Referenceable.Evidenceable","l":"removeEvidenceRefs()"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"removeExtension(String)","u":"removeExtension(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeGraphicalLine(GraphicalLine)","u":"removeGraphicalLine(org.pathvisio.libgpml.model.GraphicalLine)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeGroup(Group)","u":"removeGroup(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeInteraction(Interaction)","u":"removeInteraction(org.pathvisio.libgpml.model.Interaction)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeLabel(Label)","u":"removeLabel(org.pathvisio.libgpml.model.Label)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"removeLinePoints(List<LineElement.LinePoint>)","u":"removeLinePoints(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeListener(PathwayModelListener)","u":"removeListener(org.pathvisio.libgpml.model.PathwayModelListener)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"removeListener(PathwayObjectListener)","u":"removeListener(org.pathvisio.libgpml.model.PathwayObjectListener)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeOldPathway(Pathway)","u":"removeOldPathway(org.pathvisio.libgpml.model.Pathway)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"removePathwayElement(Groupable)","u":"removePathwayElement(org.pathvisio.libgpml.model.Groupable)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"removePathwayElements()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removePathwayObject(PathwayObject)","u":"removePathwayObject(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeShape(Shape)","u":"removeShape(org.pathvisio.libgpml.model.Shape)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"removeState(DataNode.State)","u":"removeState(org.pathvisio.libgpml.model.DataNode.State)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"removeStates()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"removeStatusFlagListener(PathwayModel.StatusFlagListener)","u":"removeStatusFlagListener(org.pathvisio.libgpml.model.PathwayModel.StatusFlagListener)"},{"p":"org.pathvisio.libgpml.util","c":"FileUtils","l":"replaceExtension(File, String)","u":"replaceExtension(java.io.File,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"replacePathway(Pathway)","u":"replacePathway(org.pathvisio.libgpml.model.Pathway)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"resetWayPointPreferences()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelEvent","l":"RESIZED"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"retainAll(Collection<?>)","u":"retainAll(java.util.Collection)"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"RIGHT"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"RNA"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"RNA_ICON"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"RNA_ICON"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder","l":"RootElementFinder()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder.RootElementHandler","l":"RootElementHandler()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder.RootElementHandler","l":"rootQName"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder.RootElementHandler","l":"rootUri"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"rotate(LinAlg.Point, double)","u":"rotate(org.pathvisio.libgpml.util.LinAlg.Point,double)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"rotation"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ROTATION"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"ROTATION"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"ROUNDED_RECTANGLE"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"RRDIAM"},{"p":"org.pathvisio.libgpml.debug","c":"StopWatch","l":"running"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"s"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"s1"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"SARCOPLASMIC_RETICULUM"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"SARCOPLASMIC_RETICULUM"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract.AttributeInfo","l":"schemaType"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"SEGMENT_OFFSET"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"Segment(Point2D, Point2D)","u":"%3Cinit%3E(java.awt.geom.Point2D,java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"SEGMENTED"},{"p":"org.pathvisio.libgpml.model.connector","c":"SegmentedConnector","l":"SegmentedConnector()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"segments"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList.DebugIterator","l":"set(E)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"set(int, E)","u":"set(int,E)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"setAliasRef(Group)","u":"setAliasRef(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"setAnnotatable(Referenceable.Annotatable)","u":"setAnnotatable(org.pathvisio.libgpml.model.Referenceable.Annotatable)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"setAnnotatableTo(Referenceable.Annotatable)","u":"setAnnotatableTo(org.pathvisio.libgpml.model.Referenceable.Annotatable)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"setAnnotation(Annotation)","u":"setAnnotation(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"setAnnotationTo(Annotation)","u":"setAnnotationTo(org.pathvisio.libgpml.model.Annotation)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"setAttr(String, String, Element, String)","u":"setAttr(java.lang.String,java.lang.String,org.jdom2.Element,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"setAuthors(List<String>)","u":"setAuthors(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setBackgroundColor(Color)","u":"setBackgroundColor(java.awt.Color)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setBoardHeight(double)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setBoardWidth(double)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setBorderColor(Color)","u":"setBorderColor(java.awt.Color)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setBorderStyle(LineStyleType)","u":"setBorderStyle(org.pathvisio.libgpml.model.type.LineStyleType)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setBorderWidth(double)"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"setCenterX(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setCenterX(double)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setCenterX(double)"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"setCenterY(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setCenterY(double)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setCenterY(double)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"setCitable(Referenceable.Citable)","u":"setCitable(org.pathvisio.libgpml.model.Referenceable.Citable)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"setCitableTo(Referenceable.Citable)","u":"setCitableTo(org.pathvisio.libgpml.model.Referenceable.Citable)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"setCitation(Citation)","u":"setCitation(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"setCitationTo(Citation)","u":"setCitationTo(org.pathvisio.libgpml.model.Citation)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"setComments(List<PathwayElement.Comment>)","u":"setComments(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"setCommentText(String)","u":"setCommentText(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setConnectorType(ConnectorType)","u":"setConnectorType(org.pathvisio.libgpml.model.type.ConnectorType)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setDescription(String)","u":"setDescription(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"setDest(String)","u":"setDest(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"setDynamicProperty(String, String)","u":"setDynamicProperty(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"setElementId(String)","u":"setElementId(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"setElementRef(GraphLink.LinkableTo)","u":"setElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setEndArrowHeadType(ArrowHeadType)","u":"setEndArrowHeadType(org.pathvisio.libgpml.model.type.ArrowHeadType)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setEndElementRef(GraphLink.LinkableTo)","u":"setEndElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setEndLinePoint(LineElement.LinePoint)","u":"setEndLinePoint(org.pathvisio.libgpml.model.LineElement.LinePoint)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setEndLinePointX(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setEndLinePointY(double)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"setEvidence(Evidence)","u":"setEvidence(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"setEvidenceable(Referenceable.Evidenceable)","u":"setEvidenceable(org.pathvisio.libgpml.model.Referenceable.Evidenceable)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"setEvidenceableTo(Referenceable.Evidenceable)","u":"setEvidenceableTo(org.pathvisio.libgpml.model.Referenceable.Evidenceable)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"setEvidenceTo(Evidence)","u":"setEvidenceTo(org.pathvisio.libgpml.model.Evidence)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setFillColor(Color)","u":"setFillColor(java.awt.Color)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setFontDecoration(boolean)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setFontName(String)","u":"setFontName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setFontSize(double)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setFontStrikethru(boolean)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setFontStyle(boolean)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setFontWeight(boolean)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"setGeneratedElementId()"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader","l":"setGroupGraphicsProperty(Group, GroupType)","u":"setGroupGraphicsProperty(org.pathvisio.libgpml.model.Group,org.pathvisio.libgpml.model.type.GroupType)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setGroupRef(Group)","u":"setGroupRef(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setGroupRef(Group)","u":"setGroupRef(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setGroupRefTo(Group)","u":"setGroupRefTo(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"setGroupRefTo(Group)","u":"setGroupRefTo(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setGroupRefTo(Group)","u":"setGroupRefTo(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setGroupRefTo(Group)","u":"setGroupRefTo(org.pathvisio.libgpml.model.Group)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setHAlign(HAlignType)","u":"setHAlign(org.pathvisio.libgpml.model.type.HAlignType)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aReader.PublicationXref","l":"setHasRef(boolean)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setHeight(double)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"setHidden(boolean)"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"setHref(String)","u":"setHref(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"setLeft(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setLeft(double)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setLeft(double)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setLicense(String)","u":"setLicense(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setLineColor(Color)","u":"setLineColor(java.awt.Color)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setLinePoints(List<LineElement.LinePoint>)","u":"setLinePoints(java.util.List)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setLineStyle(LineStyleType)","u":"setLineStyle(org.pathvisio.libgpml.model.type.LineStyleType)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setLineWidth(double)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"setLogLevel(boolean, boolean, boolean, boolean, boolean, boolean)","u":"setLogLevel(boolean,boolean,boolean,boolean,boolean,boolean)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"setMEnd(Point2D)","u":"setMEnd(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"setMStart(Point2D)","u":"setMStart(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"setName(String)","u":"setName(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"CopyElement","l":"setNewElement(PathwayElement)","u":"setNewElement(org.pathvisio.libgpml.model.PathwayElement)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"setNewPathway(Pathway)","u":"setNewPathway(org.pathvisio.libgpml.model.Pathway)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"setOf(T)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"setOrder(int)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setOrganism(String)","u":"setOrganism(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"setPathwayModel(PathwayModel)","u":"setPathwayModel(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"setPathwayModelTo(PathwayModel)","u":"setPathwayModelTo(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setPathwayModelTo(PathwayModel)","u":"setPathwayModelTo(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setPathwayModelTo(PathwayModel)","u":"setPathwayModelTo(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.GenericPoint","l":"setPathwayModelTo(PathwayModel)","u":"setPathwayModelTo(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"setPathwayModelTo(PathwayModel)","u":"setPathwayModelTo(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"setPosition(double)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"setPropertyEx(Object, Object)","u":"setPropertyEx(java.lang.Object,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"setPropertyEx(Object, Object)","u":"setPropertyEx(java.lang.Object,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"setRelativePosition(double, double)","u":"setRelativePosition(double,double)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setRelX(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"setRelX(double)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setRelY(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"setRelY(double)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"setRotation(Double)","u":"setRotation(java.lang.Double)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setRotation(Double)","u":"setRotation(java.lang.Double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"setSegments(ConnectorShape.Segment[])","u":"setSegments(org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"setShape(Shape)","u":"setShape(java.awt.Shape)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"setShapeType(AnchorShapeType)","u":"setShapeType(org.pathvisio.libgpml.model.type.AnchorShapeType)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setShapeType(IShape)","u":"setShapeType(org.pathvisio.libgpml.model.shape.IShape)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"setSource(String)","u":"setSource(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setSource(String)","u":"setSource(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"setSource(String)","u":"setSource(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"CopyElement","l":"setSourceElement(PathwayElement)","u":"setSourceElement(org.pathvisio.libgpml.model.PathwayElement)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"setSourceFile(File)","u":"setSourceFile(java.io.File)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setStartArrowHeadType(ArrowHeadType)","u":"setStartArrowHeadType(org.pathvisio.libgpml.model.type.ArrowHeadType)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setStartElementRef(GraphLink.LinkableTo)","u":"setStartElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setStartLinePoint(LineElement.LinePoint)","u":"setStartLinePoint(org.pathvisio.libgpml.model.LineElement.LinePoint)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setStartLinePointX(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setStartLinePointY(double)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setStaticProperty(StaticProperty, Object)","u":"setStaticProperty(org.pathvisio.libgpml.prop.StaticProperty,java.lang.Object)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"setStream(PrintStream)","u":"setStream(java.io.PrintStream)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setTextColor(Color)","u":"setTextColor(java.awt.Color)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"setTextLabel(String)","u":"setTextLabel(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setTextLabel(String)","u":"setTextLabel(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"setTextLabel(String)","u":"setTextLabel(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"setTextLabel(String)","u":"setTextLabel(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"setTextLabel(String)","u":"setTextLabel(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setTextLabel(String)","u":"setTextLabel(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"setTitle(String)","u":"setTitle(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setTitle(String)","u":"setTitle(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"setTop(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setTop(double)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setTop(double)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"setType(AnnotationType)","u":"setType(org.pathvisio.libgpml.model.type.AnnotationType)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"setType(DataNodeType)","u":"setType(org.pathvisio.libgpml.model.type.DataNodeType)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"setType(GroupType)","u":"setType(org.pathvisio.libgpml.model.type.GroupType)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setType(StateType)","u":"setType(org.pathvisio.libgpml.model.type.StateType)"},{"p":"org.pathvisio.libgpml.debug","c":"TestDebug","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestAnchor","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestGraphLink","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestLinePoint","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"setUp()"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"setUrlLink(String)","u":"setUrlLink(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"setUrlLink(String)","u":"setUrlLink(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"setUrlLink(String)","u":"setUrlLink(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"setUsername(String)","u":"setUsername(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setVAlign(VAlignType)","u":"setVAlign(org.pathvisio.libgpml.model.type.VAlignType)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"setValue(String)","u":"setValue(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"setValue(String)","u":"setValue(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setVersion(String)","u":"setVersion(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"setWayPoints(ConnectorShape.WayPoint[])","u":"setWayPoints(org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint[])"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setWidth(double)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"setX(double)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"Xrefable","l":"setXref(Xref)","u":"setXref(org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"setY(double)"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"setYear(String)","u":"setYear(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"setZOrder(int)"},{"p":"org.pathvisio.libgpml.model","c":"Drawable","l":"setZOrder(int)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"setZOrder(int)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"setZOrder(int)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"setZOrder(int)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"setZOrder(int)"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"sh"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"shape"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"shape"},{"p":"org.pathvisio.libgpml.model.shape","c":"AnchorShape","l":"shape"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape","l":"shape"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"shape"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"SHAPE"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"Shape()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog","l":"ShapeCatalog()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"ShapedElement()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"shapeMap"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeRegistry","l":"ShapeRegistry()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"shapes"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShapeFactory","l":"shapes"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"shapeType"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"shapeType"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"SHAPETYPE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"SHAPETYPE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"SHAPETYPE_DEFAULT"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"SHAPETYPE_MAP"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"SHAPETYPE_TO_CAMELCASE"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"ShapeType(String, Shape)","u":"%3Cinit%3E(java.lang.String,java.awt.Shape)"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"ShapeType(String, Shape, boolean, boolean)","u":"%3Cinit%3E(java.lang.String,java.awt.Shape,boolean,boolean)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"SIDE_EAST"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"SIDE_NORTH"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"SIDE_SOUTH"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorRestrictions","l":"SIDE_WEST"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"SITE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"SITEGRPID"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"SITEGRPID_DB"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"size()"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"SOLID"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"source"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"source"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"source"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"SOURCE"},{"p":"org.pathvisio.libgpml.model","c":"CopyElement","l":"sourceElement"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"sourceFile"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"SQUARE"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"st1"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"st2"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"st3"},{"p":"org.pathvisio.libgpml.debug","c":"StopWatch","l":"start"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"start"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"start"},{"p":"org.pathvisio.libgpml.debug","c":"StopWatch","l":"start()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"startArrowHeadType"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"STARTARROWHEADTYPE"},{"p":"org.pathvisio.libgpml.util","c":"RootElementFinder.RootElementHandler","l":"startElement(String, String, String, Attributes)","u":"startElement(java.lang.String,java.lang.String,java.lang.String,org.xml.sax.Attributes)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"STARTELEMENTREF"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"STARTX"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"STARTY"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"STATE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"STATE_DIRECTION_MAP"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"STATE_PTM_MAP"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"STATE_REF_LIST"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"STATE_ROTATION"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"State(String, StateType, double, double)","u":"%3Cinit%3E(java.lang.String,org.pathvisio.libgpml.model.type.StateType,double,double)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"State(String, StateType, double, double, Xref)","u":"%3Cinit%3E(java.lang.String,org.pathvisio.libgpml.model.type.StateType,double,double,org.bridgedb.Xref)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"states"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"STATETYPE"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"STATETYPE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"STATETYPE_DEFAULT"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"StateType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"StaticProperty(String, String, StaticPropertyType, int)","u":"%3Cinit%3E(java.lang.String,java.lang.String,org.pathvisio.libgpml.prop.StaticPropertyType,int)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"StaticProperty(String, String, StaticPropertyType, int, boolean, boolean, boolean)","u":"%3Cinit%3E(java.lang.String,java.lang.String,org.pathvisio.libgpml.prop.StaticPropertyType,int,boolean,boolean,boolean)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"StaticPropertyType()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel.StatusFlagListener","l":"statusFlagChanged(PathwayModel.StatusFlagEvent)","u":"statusFlagChanged(org.pathvisio.libgpml.model.PathwayModel.StatusFlagEvent)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel.StatusFlagEvent","l":"StatusFlagEvent(boolean)","u":"%3Cinit%3E(boolean)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"statusFlagListeners"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"STIMULATION"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"STIMULATION_LIST"},{"p":"org.pathvisio.libgpml.debug","c":"StopWatch","l":"stop()"},{"p":"org.pathvisio.libgpml.debug","c":"StopWatch","l":"stopToLog(String)","u":"stopToLog(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"StopWatch","l":"StopWatch()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"STRAIGHT"},{"p":"org.pathvisio.libgpml.model.connector","c":"StraightConnectorShape","l":"StraightConnectorShape()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"STRING"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"stringEquals(String, String)","u":"stringEquals(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"stringNullEqualsEmpty(String, String)","u":"stringNullEqualsEmpty(java.lang.String,java.lang.String)"},{"p":"org.pathvisio.libgpml.util","c":"ColorUtils","l":"stringToColor(String)","u":"stringToColor(java.lang.String)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"stringToInputStream(String)","u":"stringToInputStream(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"subList(int, int)","u":"subList(int,int)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"subtract(LinAlg.Point)","u":"subtract(org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"summary()"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"summary(PathwayObject)","u":"summary(org.pathvisio.libgpml.model.PathwayObject)"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"summaryHelper(PathwayObject, StringBuilder, StaticProperty, String)","u":"summaryHelper(org.pathvisio.libgpml.model.PathwayObject,java.lang.StringBuilder,org.pathvisio.libgpml.prop.StaticProperty,java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"tag"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"tag"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"TAG_MAP"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"tag()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"tagMapping"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"TAIL"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"TAXONOMY"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"TBAR_GAP"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"TBARHEIGHT"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShapeRegistry","l":"TBARWIDTH"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"terminate()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"Test()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.debug","c":"TestDebug","l":"test1()"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"TestAlias()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestAnchor","l":"TestAnchor()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"TestAnnotation()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.util","c":"TestXrefUtils","l":"testBridgeDb()"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"testCheckSetUp()"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"TestCitation()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"testClonePathway()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"testColor()"},{"p":"org.pathvisio.libgpml.util","c":"TestColorUtils","l":"TestColorUtils()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"TestCopy()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"testCopyDataNode()"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"testCopyGraphicalLine()"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"testCopyInteraction()"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"testCopyLabel()"},{"p":"org.pathvisio.libgpml.model","c":"TestCopy","l":"testCopyShape()"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"testDataNode()"},{"p":"org.pathvisio.libgpml.model.type","c":"TestDataNodeType","l":"testDataNodeType()"},{"p":"org.pathvisio.libgpml.model.type","c":"TestDataNodeType","l":"TestDataNodeType()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.debug","c":"TestDebug","l":"TestDebug()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"testDuplicateAnnotation()"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"testDuplicateCitation()"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"testDuplicateEvidence()"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"TestElementId()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.util","c":"TestXrefUtils","l":"testEquivalentXrefs()"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"TestEvidence()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"testFields()"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"TestGraph()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"testGraphicalLine()"},{"p":"org.pathvisio.libgpml.model","c":"TestGraphLink","l":"TestGraphLink()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"testGroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"TestGroup()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"TestGroupNested()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.util","c":"TestGroupRectPropertyUtils","l":"testGroupRectPropertyCalculation()"},{"p":"org.pathvisio.libgpml.util","c":"TestGroupRectPropertyUtils","l":"TestGroupRectPropertyUtils()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model.type","c":"TestDataNodeType","l":"testGroupType()"},{"p":"org.pathvisio.libgpml.util","c":"TestColorUtils","l":"testHexToColorToHex()"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"testInteraction()"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"testLabel()"},{"p":"org.pathvisio.libgpml.model.connector","c":"TestSegmentedConnector","l":"testLineCoordinates()"},{"p":"org.pathvisio.libgpml.model","c":"TestLinePoint","l":"TestLinePoint()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestGraphLink","l":"testLinkToAnchor()"},{"p":"org.pathvisio.libgpml.model","c":"TestGraphLink","l":"testLinkToShapedElement()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"testMappInfo()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"testParent()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"testRef()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"testRef2()"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"TestReferenceable()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"testRelative()"},{"p":"org.pathvisio.libgpml.model","c":"TestGraph","l":"testRemove()"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"testRemoveAlias()"},{"p":"org.pathvisio.libgpml.model","c":"TestAnchor","l":"testRemoveAnchor()"},{"p":"org.pathvisio.libgpml.model","c":"TestAnnotation","l":"testRemoveAnnotation()"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"testRemoveAnnotation()"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"testRemoveAnnotationRef()"},{"p":"org.pathvisio.libgpml.model","c":"TestCitation","l":"testRemoveCitation()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"testRemoveDataNode()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"testRemoveDataNode()"},{"p":"org.pathvisio.libgpml.model","c":"TestReferenceable","l":"testRemoveDataNode()"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"testRemoveDataNode()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"testRemoveDataNode2()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"testRemoveDataNodeFromGroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"testRemoveDataNodeFromGroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestEvidence","l":"testRemoveEvidence()"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"testRemoveGroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"testRemoveGroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"testRemoveGroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestAnchor","l":"testRemoveLine()"},{"p":"org.pathvisio.libgpml.model","c":"TestLinePoint","l":"testRemoveLine()"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"testRemoveState()"},{"p":"org.pathvisio.libgpml.model.connector","c":"TestSegmentedConnector","l":"TestSegmentedConnector()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestLinePoint","l":"testSetLinePoints()"},{"p":"org.pathvisio.libgpml.model","c":"TestElementId","l":"testShape()"},{"p":"org.pathvisio.libgpml.model","c":"TestState","l":"TestState()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.util","c":"TestColorUtils","l":"testStringToColor()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"testSwitchGroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"testSwitchGroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestTemporary","l":"TestTemporary()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"TestTemporary","l":"testThis()"},{"p":"org.pathvisio.libgpml.util","c":"TestColorUtils","l":"testTransparency()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroup","l":"testUngroup()"},{"p":"org.pathvisio.libgpml.model","c":"TestAlias","l":"testWriteGPML2021()"},{"p":"org.pathvisio.libgpml.model","c":"TestGroupNested","l":"testWriteGPML2021()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"testWrongFormat()"},{"p":"org.pathvisio.libgpml.model","c":"Test","l":"testXRefEquals()"},{"p":"org.pathvisio.libgpml.util","c":"TestXrefUtils","l":"TestXrefUtils()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"textColor"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"TEXTCOLOR"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"TEXTCOLOR_DEFAULT"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"textLabel"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"textLabel"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"textLabel"},{"p":"org.pathvisio.libgpml.model","c":"Label","l":"textLabel"},{"p":"org.pathvisio.libgpml.model","c":"Shape","l":"textLabel"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"TEXTLABEL"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"title"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"title"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"TITLE"},{"p":"org.pathvisio.libgpml.model","c":"Drawable","l":"toAbsoluteCoordinate(Point2D)","u":"toAbsoluteCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableTo","l":"toAbsoluteCoordinate(Point2D)","u":"toAbsoluteCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"toAbsoluteCoordinate(Point2D)","u":"toAbsoluteCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"toAbsoluteCoordinate(Point2D)","u":"toAbsoluteCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"toAbsoluteCoordinate(Point2D)","u":"toAbsoluteCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"toAbsoluteCoordinate(Point2D)","u":"toAbsoluteCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"toAbsoluteCoordinate(Point2D)","u":"toAbsoluteCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"toArray()"},{"p":"org.pathvisio.libgpml.debug","c":"DebugList","l":"toArray(T[])"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"toCamelCase(String)","u":"toCamelCase(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape","l":"toLineCoordinate(Point2D)","u":"toLineCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model.connector","c":"SegmentedConnector","l":"toLineCoordinate(Point2D)","u":"toLineCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model.connector","c":"StraightConnectorShape","l":"toLineCoordinate(Point2D)","u":"toLineCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg","l":"toLineCoordinates(LinAlg.Point, LinAlg.Point, LinAlg.Point)","u":"toLineCoordinates(org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point,org.pathvisio.libgpml.util.LinAlg.Point)"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"TOP"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"toPoint2D()"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"toPoint2D()"},{"p":"org.pathvisio.libgpml.model","c":"Drawable","l":"toRelativeCoordinate(Point2D)","u":"toRelativeCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableTo","l":"toRelativeCoordinate(Point2D)","u":"toRelativeCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"toRelativeCoordinate(Point2D)","u":"toRelativeCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"toRelativeCoordinate(Point2D)","u":"toRelativeCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"toRelativeCoordinate(Point2D)","u":"toRelativeCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"toRelativeCoordinate(Point2D)","u":"toRelativeCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"toRelativeCoordinate(Point2D)","u":"toRelativeCoordinate(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"toString()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"toString()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"toString()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"toString()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.Comment","l":"toString()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"toString()"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.Segment","l":"toString()"},{"p":"org.pathvisio.libgpml.model.shape","c":"AbstractShape","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"AnchorShapeType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"ConnectorType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"LineStyleType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"toString()"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"toString()"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"toString()"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"trace(String)","u":"trace(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"traceEnabled"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"TRANSCRIPTION_TRANSLATION"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"TRANSCRIPTION_TRANSLATION_LIST"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"transferStatusFlagListeners(PathwayModel)","u":"transferStatusFlagListeners(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"TRANSLOCATION"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"TRANSLOCATION_LIST"},{"p":"org.pathvisio.libgpml.model.type","c":"GroupType","l":"TRANSPARENT"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"TRIANGLE"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"type"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"type"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"type"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"type"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModelEvent","l":"type"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"type"},{"p":"org.pathvisio.libgpml.model.type","c":"AnnotationType","l":"UNDEFINED"},{"p":"org.pathvisio.libgpml.model.type","c":"DataNodeType","l":"UNDEFINED"},{"p":"org.pathvisio.libgpml.model.type","c":"StateType","l":"UNDEFINED"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"UNDIRECTED"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"UNDIRECTED_LIST"},{"p":"org.pathvisio.libgpml.model","c":"GraphLink.LinkableFrom","l":"unlink()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"unlink()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"unlinkAlias(Group, DataNode)","u":"unlinkAlias(org.pathvisio.libgpml.model.Group,org.pathvisio.libgpml.model.DataNode)"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"unsetAliasRef()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.Anchor","l":"unsetAllLinkableFroms()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"unsetAllLinkableFroms()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"unsetAnnotatable()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.AnnotationRef","l":"unsetAnnotation()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"unsetCitable()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.CitationRef","l":"unsetCitation()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"unsetEvidence()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayElement.EvidenceRef","l":"unsetEvidenceable()"},{"p":"org.pathvisio.libgpml.model","c":"Groupable","l":"unsetGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"unsetGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"unsetGroupRef()"},{"p":"org.pathvisio.libgpml.model","c":"PathwayObject","l":"unsetPathwayModel()"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"updateCoordinates()"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"updateDimensions()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"updateGroups(PathwayModel)","u":"updateGroups(org.pathvisio.libgpml.model.PathwayModel)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"urlLink"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"urlLink"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"urlLink"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract.AttributeInfo","l":"use"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"username"},{"p":"org.pathvisio.libgpml.util","c":"Utils","l":"Utils()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"validateDocument(Document)","u":"validateDocument(org.jdom2.Document)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatVersion","l":"validateDocument(Document)","u":"validateDocument(org.jdom2.Document)"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"vAlign"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"VALIGN"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021FormatAbstract","l":"VALIGN_DEFAULT"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"VALIGNTYPE"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"VAlignType(String)","u":"%3Cinit%3E(java.lang.String)"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"value"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"value"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape.FillType","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"values"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape.FillType","l":"values()"},{"p":"org.pathvisio.libgpml.model.shape","c":"ShapeCatalog.Internal","l":"values()"},{"p":"org.pathvisio.libgpml.model.type","c":"HAlignType","l":"values()"},{"p":"org.pathvisio.libgpml.model.type","c":"ObjectType","l":"values()"},{"p":"org.pathvisio.libgpml.model.type","c":"VAlignType","l":"values()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"values()"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"values()"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"version"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"VERSION"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"VESICLE"},{"p":"org.pathvisio.libgpml.model.type","c":"ArrowHeadType","l":"visible"},{"p":"org.pathvisio.libgpml.model.type","c":"ShapeType","l":"VISIBLE_VALUES"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"warn(String)","u":"warn(java.lang.String)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"warn(String, Throwable)","u":"warn(java.lang.String,java.lang.Throwable)"},{"p":"org.pathvisio.libgpml.debug","c":"Logger","l":"warnEnabled"},{"p":"org.pathvisio.libgpml.io","c":"AbstractPathwayModelFormat","l":"warnings"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.WayPoint","l":"WayPoint(double, double)","u":"%3Cinit%3E(double,double)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ConnectorShape.WayPoint","l":"WayPoint(Point2D)","u":"%3Cinit%3E(java.awt.geom.Point2D)"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"waypointNumbers"},{"p":"org.pathvisio.libgpml.model.connector","c":"AbstractConnector","l":"waypoints"},{"p":"org.pathvisio.libgpml.model.connector","c":"CurvedConnectorShape","l":"wayPointsToCenter(ConnectorShape.WayPoint[], ConnectorShape.Segment[])","u":"wayPointsToCenter(org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint[],org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model.connector","c":"ElbowConnectorShape","l":"wayPointsToCenter(ConnectorShape.WayPoint[], ConnectorShape.Segment[])","u":"wayPointsToCenter(org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint[],org.pathvisio.libgpml.model.connector.ConnectorShape.Segment[])"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"width"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"WIDTH"},{"p":"org.pathvisio.libgpml.model.shape","c":"ArrowShape.FillType","l":"WIRE"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aFormatAbstract","l":"WP_DESCRIPTION"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeAliasRef(Group, Element)","u":"writeAliasRef(org.pathvisio.libgpml.model.Group,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeAnchors(List<LineElement.Anchor>, Element)","u":"writeAnchors(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeAnchors(List<LineElement.Anchor>, Element)","u":"writeAnchors(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeAnnotationRefs(List<PathwayElement.AnnotationRef>, Element)","u":"writeAnnotationRefs(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeAnnotations(List<Annotation>, Element)","u":"writeAnnotations(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeArrowHeadType(ArrowHeadType, String, Element)","u":"writeArrowHeadType(org.pathvisio.libgpml.model.type.ArrowHeadType,java.lang.String,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeAuthors(List<Pathway.Author>, Element)","u":"writeAuthors(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeBiopax(PathwayModel, Element)","u":"writeBiopax(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeBiopaxRefs(List<PathwayElement.CitationRef>, Element)","u":"writeBiopaxRefs(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeCitationRefs(List<PathwayElement.CitationRef>, Element)","u":"writeCitationRefs(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeCitations(List<Citation>, Element)","u":"writeCitations(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeColor(ShapedElement, Element)","u":"writeColor(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeComments(List<PathwayElement.Comment>, Element)","u":"writeComments(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeComments(List<PathwayElement.Comment>, Element)","u":"writeComments(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeDataNodes(List<DataNode>, Element)","u":"writeDataNodes(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeDataNodes(List<DataNode>, Element)","u":"writeDataNodes(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeDynamicProperties(Map<String, String>, Element)","u":"writeDynamicProperties(java.util.Map,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeElementId(String, Element)","u":"writeElementId(java.lang.String,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeElementId(String, Element)","u":"writeElementId(java.lang.String,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeElementInfo(PathwayElement, Element)","u":"writeElementInfo(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeElementInfo(PathwayElement, Element)","u":"writeElementInfo(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeElementRef(GraphLink.LinkableTo, Element)","u":"writeElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeEvidenceRefs(List<PathwayElement.EvidenceRef>, Element)","u":"writeEvidenceRefs(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeEvidences(List<Evidence>, Element)","u":"writeEvidences(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeFontProperty(ShapedElement, Element)","u":"writeFontProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeFontProperty(ShapedElement, Element)","u":"writeFontProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeGraphicalLines(List<GraphicalLine>, Element)","u":"writeGraphicalLines(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeGraphicalLines(List<GraphicalLine>, Element)","u":"writeGraphicalLines(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeGroupRef(Group, Element)","u":"writeGroupRef(org.pathvisio.libgpml.model.Group,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeGroupRef(Group, Element)","u":"writeGroupRef(org.pathvisio.libgpml.model.Group,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeGroups(List<Group>, Element)","u":"writeGroups(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeGroups(List<Group>, Element)","u":"writeGroups(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeInfoBox(Pathway, Element)","u":"writeInfoBox(org.pathvisio.libgpml.model.Pathway,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeInteractions(List<Interaction>, Element)","u":"writeInteractions(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeInteractions(List<Interaction>, Element)","u":"writeInteractions(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeLabels(List<Label>, Element)","u":"writeLabels(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeLabels(List<Label>, Element)","u":"writeLabels(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeLegend(Pathway, Element)","u":"writeLegend(org.pathvisio.libgpml.model.Pathway,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeLineDynamicProperties(Map<String, String>, LineElement, Element)","u":"writeLineDynamicProperties(java.util.Map,org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeLineElement(LineElement, Element)","u":"writeLineElement(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeLineElement(LineElement, Element)","u":"writeLineElement(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeLineStyleProperty(LineElement, Element)","u":"writeLineStyleProperty(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeLineStyleProperty(LineElement, Element)","u":"writeLineStyleProperty(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeOpenControlledVocabulary(PathwayModel, Element)","u":"writeOpenControlledVocabulary(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writePathwayDynamicProperties(Pathway, Element)","u":"writePathwayDynamicProperties(org.pathvisio.libgpml.model.Pathway,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writePathwayInfo(PathwayModel, Element)","u":"writePathwayInfo(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writePathwayInfo(PathwayModel, Element)","u":"writePathwayInfo(org.pathvisio.libgpml.model.PathwayModel,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writePointElementRef(GraphLink.LinkableTo, Element)","u":"writePointElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writePoints(LineElement, Element)","u":"writePoints(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writePoints(LineElement, Element)","u":"writePoints(org.pathvisio.libgpml.model.LineElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writePublicationXref(List<Citation>, Element)","u":"writePublicationXref(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writePublicationXrefInfo(String, String, Element)","u":"writePublicationXrefInfo(java.lang.String,java.lang.String,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"writer"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeRectProperty(ShapedElement, Element)","u":"writeRectProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeRectProperty(ShapedElement, Element)","u":"writeRectProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeShapedElement(ShapedElement, Element)","u":"writeShapedElement(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeShapedElement(ShapedElement, Element)","u":"writeShapedElement(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeShapedOrStateDynamicProperties(Map<String, String>, ShapedElement, Element)","u":"writeShapedOrStateDynamicProperties(java.util.Map,org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeShapes(List<Shape>, Element)","u":"writeShapes(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeShapes(List<Shape>, Element)","u":"writeShapes(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeShapeStyleProperty(ShapedElement, Element)","u":"writeShapeStyleProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeShapeStyleProperty(ShapedElement, Element)","u":"writeShapeStyleProperty(org.pathvisio.libgpml.model.ShapedElement,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeStates(List<DataNode.State>, Element)","u":"writeStates(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeStates(List<DataNode>, Element)","u":"writeStates(java.util.List,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"PathwayModel","l":"writeToXml(File, boolean)","u":"writeToXml(java.io.File,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeToXml(PathwayModel, File, boolean)","u":"writeToXml(org.pathvisio.libgpml.model.PathwayModel,java.io.File,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeToXml(PathwayModel, File, boolean)","u":"writeToXml(org.pathvisio.libgpml.model.PathwayModel,java.io.File,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"writeToXml(PathwayModel, File, boolean)","u":"writeToXml(org.pathvisio.libgpml.model.PathwayModel,java.io.File,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatWriter","l":"writeToXml(PathwayModel, File, boolean)","u":"writeToXml(org.pathvisio.libgpml.model.PathwayModel,java.io.File,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeToXml(PathwayModel, OutputStream, boolean)","u":"writeToXml(org.pathvisio.libgpml.model.PathwayModel,java.io.OutputStream,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeToXml(PathwayModel, OutputStream, boolean)","u":"writeToXml(org.pathvisio.libgpml.model.PathwayModel,java.io.OutputStream,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormat","l":"writeToXml(PathwayModel, OutputStream, boolean)","u":"writeToXml(org.pathvisio.libgpml.model.PathwayModel,java.io.OutputStream,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatWriter","l":"writeToXml(PathwayModel, OutputStream, boolean)","u":"writeToXml(org.pathvisio.libgpml.model.PathwayModel,java.io.OutputStream,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeUrl(String, Element)","u":"writeUrl(java.lang.String,org.jdom2.Element)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2013aWriter","l":"writeXref(Xref, Element, boolean)","u":"writeXref(org.bridgedb.Xref,org.jdom2.Element,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"GPML2021Writer","l":"writeXref(Xref, Element, boolean)","u":"writeXref(org.bridgedb.Xref,org.jdom2.Element,boolean)"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"x"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"x"},{"p":"org.pathvisio.libgpml.model","c":"Annotation","l":"xref"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"xref"},{"p":"org.pathvisio.libgpml.model","c":"DataNode","l":"xref"},{"p":"org.pathvisio.libgpml.model","c":"DataNode.State","l":"xref"},{"p":"org.pathvisio.libgpml.model","c":"Evidence","l":"xref"},{"p":"org.pathvisio.libgpml.model","c":"Group","l":"xref"},{"p":"org.pathvisio.libgpml.model","c":"Interaction","l":"xref"},{"p":"org.pathvisio.libgpml.model","c":"Pathway","l":"xref"},{"p":"org.pathvisio.libgpml.model","c":"Pathway.Author","l":"xref"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"XREF"},{"p":"org.pathvisio.libgpml.prop","c":"StaticPropertyType","l":"XREF"},{"p":"org.pathvisio.libgpml.util","c":"XrefUtils","l":"XrefUtils()","u":"%3Cinit%3E()"},{"p":"org.pathvisio.libgpml.model","c":"GPMLFormatAbstract","l":"xsdFile"},{"p":"org.pathvisio.libgpml.model","c":"LineElement.LinePoint","l":"y"},{"p":"org.pathvisio.libgpml.util","c":"LinAlg.Point","l":"y"},{"p":"org.pathvisio.libgpml.model","c":"Citation","l":"year"},{"p":"org.pathvisio.libgpml.model","c":"LineElement","l":"zOrder"},{"p":"org.pathvisio.libgpml.model","c":"ShapedElement","l":"zOrder"},{"p":"org.pathvisio.libgpml.prop","c":"StaticProperty","l":"ZORDER"}];updateSearchResults();