G-Index

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G

g - Variable in class org.pathvisio.libgpml.model.TestAlias
g1 - Variable in class org.pathvisio.libgpml.model.TestGroup
g1 - Variable in class org.pathvisio.libgpml.model.TestGroupNested
g2 - Variable in class org.pathvisio.libgpml.model.TestGroup
g2 - Variable in class org.pathvisio.libgpml.model.TestGroupNested
gap - Variable in class org.pathvisio.libgpml.model.shape.ArrowShape
GENEPRODUCT - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
GenericPoint() - Constructor for class org.pathvisio.libgpml.model.LineElement.GenericPoint: Constructor for a generic point.
GENETIC_VARIANT - Static variable in class org.pathvisio.libgpml.model.type.StateType
get(int) - Method in class org.pathvisio.libgpml.debug.DebugList
getAbsolute() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns absolute coordinates based on elementRef.
getAffectedData() - Method in class org.pathvisio.libgpml.model.PathwayModelEvent: Returns the affected data.
getAliasRef() - Method in class org.pathvisio.libgpml.model.DataNode: Returns the pathway element to which the data node refers to as an alias.
getAliasRefs() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the set of Group aliasRef keys for this pathway model.
getAnchor(String) - Static method in class org.pathvisio.libgpml.model.shape.ShapeRegistry: Returns an anchor shape
getAnchorCircle() - Static method in class org.pathvisio.libgpml.model.shape.AnchorShapeRegistry: Returns circle anchor shape.
getAnchorNone() - Static method in class org.pathvisio.libgpml.model.shape.AnchorShapeRegistry: Returns anchor shape none, which appears invisible.
getAnchors() - Method in class org.pathvisio.libgpml.model.LineElement: Get the anchors for this line.
getAnchorSquare() - Static method in class org.pathvisio.libgpml.model.shape.AnchorShapeRegistry: Returns default square anchor shape.
getAnnotatable() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Returns the target pathway, pathway element, or citationRef Referenceable.Annotatable for this annotationRef.
getAnnotation() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Returns the annotation referenced.
getAnnotationRefs() - Method in class org.pathvisio.libgpml.model.Annotation: Returns the list of annotationRefs which reference the annotation.
getAnnotationRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Returns the list of annotation references.
getAnnotationRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns the list of annotation references.
getAnnotationRefs() - Method in interface org.pathvisio.libgpml.model.Referenceable.Annotatable: Returns the list of annotation references.
getAnnotations() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of annotations.
getArrow(String) - Static method in class org.pathvisio.libgpml.model.shape.ShapeRegistry: Returns a named arrow head.
getArrowHead() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry: Returns standard arrowhead shape.
getArrowHeadTypeStr(ArrowHeadType) - Method in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Returns the prioritized GPML2013a arrowHead type string for given GPML2021 Interaction Panel arrow head type.
getAttachedLineDirection(LineElement.Anchor) - Method in class org.pathvisio.libgpml.model.LineElement
getAttr(String, String, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Gets a certain attribute value, and replaces it with a suitable default under certain conditions.
getAttributeInfo() - Method in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Returns Map ATTRIBUTE_INFO collection that contains String as key and GPML2013aFormatAbstract.AttributeInfo as value.
getAuthors() - Method in class org.pathvisio.libgpml.model.Citation: Returns list of authors for this citation (for GPML2013a Biopax).
getAuthors() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the list of authors for this pathway model.
getBackgroundColor() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the background color of this pathway.
getBinding() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry: Returns binding arrowhead shape.
getBoardHeight() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the board height.
getBoardWidth() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the board width.
getBorderColor() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the border color of this shaped pathway element.
getBorderStyle() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the visual appearance of a border, e.g.
getBorderWidth() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the pixel value for the border of this shaped pathway element.
getBounds() - Method in class org.pathvisio.libgpml.model.Group: Iterates over all group elements to find the TOTAL rectangular bounds.
getBounds() - Method in interface org.pathvisio.libgpml.model.Groupable: Get the rectangular bounds of the object without rotation taken into account.
getBounds() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the rectangular bounds for this line pathway element.
getBounds() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the rectangular bounds of this shaped pathway element without rotation taken into account.
getByTag(String) - Static method in enum org.pathvisio.libgpml.prop.StaticProperty
getC1() - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape.CurvedSegment: Returns the c1 bezier control point.
getC2() - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape.CurvedSegment: Returns the c2 bezier control point.
getCatalysis() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry: Returns catalysis arrowhead shape.
getCenterX() - Method in interface org.pathvisio.libgpml.model.Groupable: Returns the center x coordinate of the bounding box around (start, end) this pathway element.
getCenterX() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the center x coordinate of the bounding box around (start, end) this line pathway element.
getCenterX() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the center x coordinate for this shaped pathway element.
getCenterY() - Method in interface org.pathvisio.libgpml.model.Groupable: Returns the center y coordinate of the bounding box around (start, end) this pathway element.
getCenterY() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the center y coordinate of the bounding box around (start, end) this line pathway element.
getCenterY() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the center y coordinate for this shaped pathway element.
getCitable() - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Returns the target pathway, pathway element, or annotationRef Referenceable.Citable for this citationRef.
getCitation() - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Returns the citation referenced.
getCitationRefs() - Method in class org.pathvisio.libgpml.model.Citation: Returns the list of citationRefs which reference this citation.
getCitationRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Returns the list of citation references.
getCitationRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns the list of citation references.
getCitationRefs() - Method in interface org.pathvisio.libgpml.model.Referenceable.Citable: Returns the list of citation references.
getCitations() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of citations.
getClockwisePerpendicularSide(int) - Method in class org.pathvisio.libgpml.model.LineElement: Returns the Perpendicular for a SIDE_* constant (e.g.
getComments() - Method in class org.pathvisio.libgpml.model.PathwayElement
getCommentText() - Method in class org.pathvisio.libgpml.model.PathwayElement.Comment: Returns the text of this Comment.
getConnectorShape() - Method in class org.pathvisio.libgpml.model.LineElement: The Connector Shape for this line - the connector shape can calculate a Shape based on the connector type (straight, elbow or curved) and possibly way points
getConnectorType() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the value of the connectorType property.
getDataNode() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the parent data node, outer class, to which the state belongs.
getDataNodes() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of data node pathway elements.
getDataNodeXrefs() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the Xref of all DataNodes in this pathway as a List.
getDataSource(Xref) - Static method in class org.pathvisio.libgpml.util.XrefUtils: Returns the identifier for given Xref if valid, otherwise returns null.
getDescription() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the description of this pathway.
getDescription() - Method in interface org.pathvisio.libgpml.prop.Property: Description of property, used e.g.
getDescription() - Method in enum org.pathvisio.libgpml.prop.StaticProperty: inheritDoc Used to be desc()
getDirectionX() - Method in class org.pathvisio.libgpml.model.LineElement: returns the sign of end.x - start.x
getDirectionX(Point2D, Point2D) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape: Get the direction of the line on the x axis
getDirectionX(Point2D, Point2D) - Static method in class org.pathvisio.libgpml.util.Utils: Get the direction of the line on the x axis
getDirectionY() - Method in class org.pathvisio.libgpml.model.LineElement: returns the sign of end.y - start.y
getDirectionY(Point2D, Point2D) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape: Get the direction of the line on the y axis
getDirectionY(Point2D, Point2D) - Static method in class org.pathvisio.libgpml.util.Utils: Get the direction of the line on the y axis
getDynamicProperties() - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns the map of dynamic properties.
getDynamicProperty(String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns a dynamic property string value.
getDynamicPropertyKeys() - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns a set of all dynamic property keys.
getElement() - Method in class org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref: Returns the jdom gpml:Biopax:PublicationXref element.
getElementId() - Method in class org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref: Returns the assigned unique elementId for this PublicationXref.
getElementId() - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableTo: Returns the elementId for this pathway element.
getElementId() - Method in class org.pathvisio.libgpml.model.PathwayObject: Returns the elementId of the pathway element.
getElementIds() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns a set view of String elementId keys from the elementIdToPathwayObject hash map.
getElementRef() - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableFrom: Returns the GraphLink.LinkableTo pathway element this GraphLink.LinkableFrom elementRef refers to.
getElementRef() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns the pathway element to which this point refers to.
getEndArrowHeadType() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the arrowHead property of the end point.
getEndElementRef() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the elementRef of the end point.
getEndLinePoint() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the end (last) point of points list.
getEndLinePointX() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the x coordinate of the end point.
getEndLinePointY() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the y coordinate of the end point.
getEndPoint2D() - Method in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: Returns the end point to which the connector must connect
getEndPoint2D() - Method in class org.pathvisio.libgpml.model.LineElement: converts end point from MPoint to Point2D
getEndSide() - Method in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: Returns the side of the object to which the end of the connector connects
getEndSide() - Method in class org.pathvisio.libgpml.model.LineElement: Calculate on which side of a PathwayElement (SIDE_NORTH, SIDE_EAST, SIDE_SOUTH or SIDE_WEST) the end of this line is connected to.
getEvidence() - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef: Returns the evidence referenced.
getEvidenceable() - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef: Returns the target pathway, pathway element, or evidenceRef Referenceable.Evidenceable for this evidenceRef.
getEvidenceRefs() - Method in class org.pathvisio.libgpml.model.Evidence: Returns the list of evidenceRefs which reference this evidence.
getEvidenceRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Returns the list of evidence references.
getEvidenceRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns the list of evidence references.
getEvidenceRefs() - Method in interface org.pathvisio.libgpml.model.Referenceable.Evidenceable: Returns the list of evidence references.
getEvidences() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of evidences.
getExtension(String) - Static method in class org.pathvisio.libgpml.util.FileUtils: Returns file name extension.
getExtensions() - Method in interface org.pathvisio.libgpml.io.PathwayModelIO: Get the possible extensions this importer/exporter can read (e.g.
getExtensions() - Method in class org.pathvisio.libgpml.model.GPMLFormat
getFiles(File, boolean) - Static method in class org.pathvisio.libgpml.util.FileUtils: Returns all files in a directory
getFiles(File, String, boolean) - Static method in class org.pathvisio.libgpml.util.FileUtils: Returns all files in a directory
getFillColor() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the color used to paint the area of this shaped pathway element., not including its border.
getFillType() - Method in class org.pathvisio.libgpml.model.shape.ArrowShape
getFontDecoration() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the typographic style for underline or normal.
getFontName() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the name of the set of printable text characters to be used for visualization, e.g., Arial.
getFontSize() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the point value for the size of the font.
getFontStrikethru() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the typographic style for strikethru or normal.
getFontStyle() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the typographic style applied to displayed text, e.g.
getFontWeight() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the thickness of the font used, a bold font would have more weight.
getGap() - Method in class org.pathvisio.libgpml.model.shape.ArrowShape
getGpmlNamespace() - Method in class org.pathvisio.libgpml.model.GPMLFormatAbstract: Returns the GPML namespace.
getGpmlNamespace() - Method in interface org.pathvisio.libgpml.model.GPMLFormatVersion: Returns the GPML namespace.
getGraphicalLines() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of graphical line pathway elements.
getGroupRef() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the parent group of the dataNode of this state.
getGroupRef() - Method in interface org.pathvisio.libgpml.model.Groupable: Returns the parent group of this pathway element.
getGroupRef() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the parent group of this pathway element.
getGroupRef() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the parent group of this pathway element.
getGroups() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of group pathway elements.
getGroupXrefs() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the Xref of all Groups in this pathway as a List.
getHAlign() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the horizontal alignment of displayed text, e.g., Left, Center, Right.
getHasRef() - Method in class org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref: Returns true if there is at least one gpml:CommentGroup:BiopaxRef which refers to this gpml:Biopax:PublicationXref, false otherwise.
getHeight() - Method in interface org.pathvisio.libgpml.model.Groupable: Calculates and returns the height of the bounding box around (start, end) this pathway element.
getHeight() - Method in class org.pathvisio.libgpml.model.LineElement: Calculates and returns the height of the bounding box around (start, end) this line pathway element.
getHeight() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the height of this shaped pathway element.
getHref() - Method in class org.pathvisio.libgpml.model.Label: Returns the hyperlink for this label.
getId() - Method in interface org.pathvisio.libgpml.prop.Property: Returns the Id for this property.
getId() - Method in interface org.pathvisio.libgpml.prop.PropertyType: The id for this type.
getId() - Method in enum org.pathvisio.libgpml.prop.StaticProperty
getId() - Method in enum org.pathvisio.libgpml.prop.StaticPropertyType
getIdentifier(Xref) - Static method in class org.pathvisio.libgpml.util.XrefUtils: Returns the identifier for given Xref if valid, otherwise returns empty String.
getImplementingClass(String) - Static method in class org.pathvisio.libgpml.model.connector.ConnectorShapeFactory: Returns the class that implements ConnectorShape identified by the given name
getInteractionPanelType(String) - Method in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Returns the GPML2021 Interaction Panel arrow head type for given GPML2013a arrowHead type string.
getInteractions() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of interaction pathway elements.
getInteractionXrefs() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the Xref of all Interactions in this pathway as a List.
getLabels() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of label pathway elements.
getLeft() - Method in interface org.pathvisio.libgpml.model.Groupable: Returns the left x coordinate of the bounding box around (start, end) this pathway element.
getLeft() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the left x coordinate of the bounding box around (start, end) this line pathway element.
getLeft() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the left x coordinate of the bounding box around (start, end) this shaped pathway element.
getLicense() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the license of this pathway.
getLigand() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
getLineColor() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the color of a line.
getLineElement() - Method in class org.pathvisio.libgpml.model.LineElement.GenericPoint: Returns the parent interaction or graphicalLine for this point.
getLineElements() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns all line pathway elements for the pathway model (interactions and graphicalLines).
getLinePoints() - Method in class org.pathvisio.libgpml.model.LineElement: Get the points for this line.
getLineStyle() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the visual appearance of a line, e.g.
getLineWidth() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the pixel value for the width of a line.
getLinkableFroms() - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableTo: Returns GraphLink.LinkableFroms LineElement.LinePoint for this pathway element.
getLinkableFroms() - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Returns GraphLink.LinkableFrom pathway elements, at this time that only goes for LineElement.LinePoint, for this GraphLink.LinkableTo pathway element.
getLinkableFroms() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns GraphLink.LinkableFrom pathway elements, at this time that only goes for LineElement.LinePoint, for this GraphLink.LinkableTo pathway element.
getLinkedAliases(Group) - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the set of DataNode aliases for a Group aliasRef.
getListeners() - Method in class org.pathvisio.libgpml.model.PathwayObject: Returns the listeners for this pathway object.
getLRound() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
getMargin() - Method in class org.pathvisio.libgpml.model.Group: Returns margin for group bounding-box around contained elements depending on group type, as specified in GPML2013a.
getMCenter() - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment: the center of the bounding box around start, end
getMEnd() - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment
getMinBounds(boolean) - Method in class org.pathvisio.libgpml.model.Group: Iterates over all group elements to find the MINIMAL total rectangular bounds.
getMLength() - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment
getModifiedPathwayObject() - Method in class org.pathvisio.libgpml.model.PathwayObjectEvent: Gets the PathwayElement whose properties have been modified.
getMStart() - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment
getName() - Method in interface org.pathvisio.libgpml.io.PathwayModelIO
getName() - Method in class org.pathvisio.libgpml.model.GPMLFormat
getName() - Method in class org.pathvisio.libgpml.model.Pathway.Author: Returns the name of this author.
getName() - Method in class org.pathvisio.libgpml.model.shape.AbstractShape: Returns String name of this shape.
getName() - Method in interface org.pathvisio.libgpml.model.shape.IShape
getName() - Method in class org.pathvisio.libgpml.model.type.AnchorShapeType: Returns the name key for this AnchorType.
getName() - Method in class org.pathvisio.libgpml.model.type.AnnotationType: Returns the name key for this AnnotationType.
getName() - Method in class org.pathvisio.libgpml.model.type.ArrowHeadType: Returns the name key for this ArrowHeadType.
getName() - Method in class org.pathvisio.libgpml.model.type.ConnectorType: Returns the name key for this ConnectorType.
getName() - Method in class org.pathvisio.libgpml.model.type.DataNodeType: Returns the name key for this DataNodeType.
getName() - Method in class org.pathvisio.libgpml.model.type.GroupType: Returns the name key for this GroupType.
getName() - Method in enum org.pathvisio.libgpml.model.type.HAlignType: Returns String.
getName() - Method in class org.pathvisio.libgpml.model.type.LineStyleType: Returns the name key for this LineStyleType.
getName() - Method in class org.pathvisio.libgpml.model.type.ShapeType: Returns the name key for this ShapeType.
getName() - Method in class org.pathvisio.libgpml.model.type.StateType: Returns the name key for this StateType.
getName() - Method in enum org.pathvisio.libgpml.model.type.VAlignType: Returns String.
getName() - Method in interface org.pathvisio.libgpml.prop.Property: Returns the name of property, used e.g.
getName() - Method in enum org.pathvisio.libgpml.prop.StaticProperty: inheritDoc
getNames() - Static method in class org.pathvisio.libgpml.model.type.AnchorShapeType: Returns the names of all registered AnchorTypes as a String array.
getNames() - Static method in class org.pathvisio.libgpml.model.type.AnnotationType: Returns the names of all registered AnnotationTypes as a String array.
getNames() - Static method in class org.pathvisio.libgpml.model.type.ArrowHeadType: Returns the names of all registered ArrowHeadTypes as a list.
getNames() - Static method in class org.pathvisio.libgpml.model.type.ConnectorType: Returns the names of all registered ConnectorTypes as a String array.
getNames() - Static method in class org.pathvisio.libgpml.model.type.DataNodeType: Returns the names of all registered DataNodeTypes as a String array.
getNames() - Static method in class org.pathvisio.libgpml.model.type.GroupType: Returns the names of all registered GroupTypes as a list.
getNames() - Static method in enum org.pathvisio.libgpml.model.type.HAlignType: Returns String values as an array.
getNames() - Static method in class org.pathvisio.libgpml.model.type.LineStyleType: Returns the names of all registered LineStyleTypes as a String array.
getNames() - Static method in class org.pathvisio.libgpml.model.type.ShapeType: Returns the names of all registered ShapeTypes as a list.
getNames() - Static method in class org.pathvisio.libgpml.model.type.StateType: Returns the names of all registered StateTypes as an array.
getNames() - Static method in enum org.pathvisio.libgpml.model.type.VAlignType: Returns String values as an array.
getNewElement() - Method in class org.pathvisio.libgpml.model.CopyElement: Returns the new pathway element.
getNewStatus() - Method in class org.pathvisio.libgpml.model.PathwayModel.StatusFlagEvent
getNrLines(String) - Static method in class org.pathvisio.libgpml.util.FileUtils: Determines the number of lines in the given file.
getNrSegments(ConnectorRestrictions) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
getNrSegments(ConnectorRestrictions) - Method in class org.pathvisio.libgpml.model.connector.FreeConnectorShape: Returns the number of segments given connector restrictions.
getNrWaypoints(int, int, int) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
getObjectType() - Method in class org.pathvisio.libgpml.model.Annotation: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.Citation: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.DataNode: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the object type of this pathway element.
getObjectType() - Method in interface org.pathvisio.libgpml.model.Drawable: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.Evidence: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.GraphicalLine: Returns the object type of this pathway element.
getObjectType() - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableTo: Returns the object type of the pathway object.
getObjectType() - Method in class org.pathvisio.libgpml.model.Group: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.Interaction: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.Label: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the object type of this pathway element.
getObjectType() - Method in class org.pathvisio.libgpml.model.PathwayObject: Returns the object type of the pathway object.
getObjectType() - Method in class org.pathvisio.libgpml.model.Shape: Returns the object type of this pathway element.
getOppositeAxis(int) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
getOppositeSide(int) - Method in class org.pathvisio.libgpml.model.LineElement: Returns the opposite for a SIDE_* constant (e.g.
getOrder() - Method in class org.pathvisio.libgpml.model.Pathway.Author: Returns the authorship order of this author.
getOrder() - Method in enum org.pathvisio.libgpml.prop.StaticProperty
getOrganism() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the organism of this pathway.
getOS() - Static method in class org.pathvisio.libgpml.util.Utils: Returns the OS.
getPathway() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the pathway object containing metadata, e.g.
getPathwayElements() - Method in class org.pathvisio.libgpml.model.Group: Returns the list of pathway element members of the group.
getPathwayElements() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns all pathway elements for the pathway model (pathway, dataNodes, interactions, graphicalLines, labels, shapes, and groups).
getPathwayModel() - Method in interface org.pathvisio.libgpml.model.Drawable: Returns the pathway model of this pathway element.
getPathwayModel() - Method in class org.pathvisio.libgpml.model.PathwayObject: Returns the pathway model for this pathway element.
getPathwayObject(String) - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns Pathway Object for the given String elementId key.
getPathwayObjects() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns all pathway objects for the pathway model.
getPluggableShape(ShapeCatalog.Internal) - Static method in class org.pathvisio.libgpml.model.shape.ShapeCatalog: Internal, Only for general shape types that can be described as a path.
getPoints2D() - Method in class org.pathvisio.libgpml.model.LineElement: converts all points from MPoint to Point2D
getPosition() - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Returns the proportional distance of an anchor along the line it belongs to, between 0 and 1.
getProperty(String) - Static method in class org.pathvisio.libgpml.prop.PropertyManager: Gets the property matching the given ID.
getPropertyEx(Object) - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns property of given key.
getPropertyEx(Object) - Method in class org.pathvisio.libgpml.model.PathwayObject: Returns static property of given key.
getPropertyKeys() - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns keys of available static properties and dynamic properties as an object list
getPropertyKeys() - Method in class org.pathvisio.libgpml.model.PathwayObject: Returns keys of available static properties and dynamic properties as an object list.
getPropertyType(String) - Static method in class org.pathvisio.libgpml.prop.PropertyManager: Gets the property type matching the given ID.
getReaderForNamespace(Namespace) - Static method in class org.pathvisio.libgpml.model.GPMLFormat: Returns GPML reader given namespace.
getReceptor() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
getReceptorSquare() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
getReferences(GraphLink.LinkableTo, PathwayModel) - Static method in class org.pathvisio.libgpml.model.GraphLink: Return a list of GraphLink.LinkableFrom LineElement.LinePoint(s) referring to a certain GraphLink.LinkableTo pathway element or anchor.
getReferringLinkableFroms(GraphLink.LinkableTo) - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns all GraphLink.LinkableFrom LineElement.LinePoint that refer to a GraphLink.LinkableTo pathway element or anchor.
getRegularPolygon(int, double, double) - Static method in class org.pathvisio.libgpml.model.shape.ShapeCatalog: Returns regular polygon shape given number of sides, width, and height.
getRelX() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the relative x coordinate.
getRelX() - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableFrom: Returns the relative x coordinate.
getRelX() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns the relative x coordinate.
getRelY() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the relative y coordinate.
getRelY() - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableFrom: Returns the relative y coordinate.
getRelY() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns the relative y coordinate.
getRootQName() - Method in class org.pathvisio.libgpml.util.RootElementFinder.RootElementHandler
getRootUri() - Method in class org.pathvisio.libgpml.util.RootElementFinder.RootElementHandler
getRootUri(File) - Static method in class org.pathvisio.libgpml.util.RootElementFinder: Returns root URI.
getRotatedBounds() - Method in class org.pathvisio.libgpml.model.Group: Iterates over all group elements to find the TOTAL rectangular bounds, taking into account rotation of the nested elements.
getRotatedBounds() - Method in interface org.pathvisio.libgpml.model.Groupable: Returns the rectangular bounds of the object after rotation is applied.
getRotatedBounds() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the rectangular bounds of this line pathway elements.
getRotatedBounds() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the rectangular bounds of this shaped pathway element after rotation is applied.
getRotation() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the rotation of this shaped pathway element.
getRRound() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
getSchemaFile() - Method in class org.pathvisio.libgpml.model.GPMLFormatAbstract: Returns the GPML schema file.
getSchemaFile() - Method in interface org.pathvisio.libgpml.model.GPMLFormatVersion: Returns the GPML schema file.
getSegmentAxis(int) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
getSegmentDirection(int) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
getSegments() - Method in class org.pathvisio.libgpml.model.connector.AbstractConnector: Returns the segments of the connector shape as an array.
getSegments() - Method in interface org.pathvisio.libgpml.model.connector.ConnectorShape: Get the individual segments of the path
getShape() - Method in class org.pathvisio.libgpml.model.connector.AbstractConnector: Returns the connector shape.
getShape() - Method in interface org.pathvisio.libgpml.model.connector.ConnectorShape: Returns the Shape that represents the connector path.
getShape() - Method in class org.pathvisio.libgpml.model.shape.AnchorShape
getShape() - Method in class org.pathvisio.libgpml.model.shape.ArrowShape
getShape(double, double) - Method in class org.pathvisio.libgpml.model.shape.AbstractShape
getShape(double, double) - Method in interface org.pathvisio.libgpml.model.shape.IShape
getShape(double, double) - Method in class org.pathvisio.libgpml.model.type.ShapeType: Returns the shape resized given width and height.
getShapedElements() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns all shaped pathway elements for the pathway model (dataNodes, states, labels, shapes, and groups).
getShapedElementsExclStates() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns all shaped pathway elements for the pathway model (dataNodes, labels, shapes, and groups).
getShapes() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the list of shape pathway elements.
getShapeType() - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Returns the visual representation of an anchor, e.g., none, square.
getShapeType() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the visual appearance of a two dimensional object, e.g.
getSide(double, double) - Static method in class org.pathvisio.libgpml.model.LineElement
getSide(double, double, double, double) - Static method in class org.pathvisio.libgpml.model.LineElement: Get the side of the given pathway element to which the x and y coordinates connect
getSource() - Method in class org.pathvisio.libgpml.model.Citation: Returns source for this citation (for GPML2013a Biopax).
getSource() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the source of this pathway, e.g.
getSource() - Method in class org.pathvisio.libgpml.model.PathwayElement.Comment: Returns the source of this Comment.
getSourceElement() - Method in class org.pathvisio.libgpml.model.CopyElement: Returns source pathway element.
getSourceFile() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the xml file containing the Gpml/mapp pathway currently displayed
getStartArrowHeadType() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the arrowHead property of the start point.
getStartElementRef() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the elementRef of the end point.
getStartLinePoint() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the start (first) point of points list.
getStartLinePointX() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the x coordinate of the start point.
getStartLinePointY() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the y coordinate of the start point.
getStartPoint2D() - Method in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: Returns the start point to which the connector must connect
getStartPoint2D() - Method in class org.pathvisio.libgpml.model.LineElement: converts start point from MPoint to Point2D
getStartSide() - Method in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: Returns the side of the object to which the start of the connector connects
getStartSide() - Method in class org.pathvisio.libgpml.model.LineElement: Calculate on which side of a PathwayElement (SIDE_NORTH, SIDE_EAST, SIDE_SOUTH or SIDE_WEST) the start of this line is connected to.
getStates() - Method in class org.pathvisio.libgpml.model.DataNode
getStateXrefs() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns the Xref of all States of all DataNodes in this pathway as a List.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.DataNode: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.Group: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.Interaction: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.Label: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.LineElement: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.Pathway
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.PathwayObject: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.Shape: Returns static property value for given key.
getStaticProperty(StaticProperty) - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns static property value for given key.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.DataNode: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.Group: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.Interaction: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.Label: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.LineElement: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.Pathway: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.PathwayElement: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.PathwayObject: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.Shape: Returns all static properties for this pathway object.
getStaticPropertyKeys() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns all static properties for this pathway object.
getStream() - Method in class org.pathvisio.libgpml.debug.Logger
getTag() - Method in enum org.pathvisio.libgpml.model.type.ObjectType: Returns the GPML tag corresponding to this object type, can also function as a human-readable description.
getTagMapping(String) - Static method in enum org.pathvisio.libgpml.model.type.ObjectType: Return the ObjectType that corresponds to a certain tag.
getTBar() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry: Returns inhibition (Tbar) arrowhead shape.
getTextColor() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the color of text for this shaped pathway element..
getTextLabel() - Method in class org.pathvisio.libgpml.model.DataNode: Returns the text of this datanode.
getTextLabel() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the text of of this state.
getTextLabel() - Method in class org.pathvisio.libgpml.model.Group: Returns the text of of this group.
getTextLabel() - Method in class org.pathvisio.libgpml.model.Label: Returns the text of of the label.
getTextLabel() - Method in class org.pathvisio.libgpml.model.Shape: Returns the text of of the shape.
getTextLabel() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns text label for shaped pathway elements.
getTitle() - Method in class org.pathvisio.libgpml.model.Citation: Returns source for this citation (for GPML2013a Biopax).
getTitle() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the title or name of this pathway.
getTop() - Method in interface org.pathvisio.libgpml.model.Groupable: Returns the top y coordinate of the bounding box around (start, end) this pathway element.
getTop() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the top y coordinate of the bounding box around (start, end) this line pathway element.
getTop() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the top y coordinate of the bounding box around (start, end) this shaped pathway element.
getTopPathwayElement() - Method in class org.pathvisio.libgpml.model.PathwayElement.InfoRef: Returns the top target pathway element PathwayElement for a PathwayElement.AnnotationRef, PathwayElement.CitationRef, or PathwayElement.EvidenceRef.
getTotalLength(ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.SegmentedConnector: Returns the sum of the lengths of the segments
getTranscriptionTranslation() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry: Returns transcription-translation arrowhead shape.
getType() - Method in class org.pathvisio.libgpml.model.Annotation: Returns the type of this annotation.
getType() - Method in class org.pathvisio.libgpml.model.DataNode: Returns the type of this datanode.
getType() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the type of this state.
getType() - Method in class org.pathvisio.libgpml.model.Group: Returns GroupType.
getType() - Method in class org.pathvisio.libgpml.model.PathwayModelEvent: Returns the type.
getType() - Method in interface org.pathvisio.libgpml.prop.Property: Returns the data type for this property.
getType() - Method in enum org.pathvisio.libgpml.prop.StaticProperty: Used to be type() which returned StaticPropertyType
getUniqueElementId() - Method in class org.pathvisio.libgpml.model.PathwayModel: Returns a unique elementId.
getUniqueId(Set<String>) - Static method in class org.pathvisio.libgpml.model.PathwayModel: Randomly generates a new unique ID, based on strings of hex digits (0..9 or a..f) given a set of existing IDs.
getUrlLink() - Method in class org.pathvisio.libgpml.model.Annotation: Returns the url link for a web address.
getUrlLink() - Method in class org.pathvisio.libgpml.model.Citation: Returns the url link for a web address.
getUrlLink() - Method in class org.pathvisio.libgpml.model.Evidence: Returns the url link for a web address.
getUsername() - Method in class org.pathvisio.libgpml.model.Pathway.Author: Returns the username of this author.
getVAlign() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the vertical alignment of displayed text, e.g., Top, Middle, Bottom.
getValue() - Method in class org.pathvisio.libgpml.model.Annotation: Returns the name, term, or text of this annotation.
getValue() - Method in class org.pathvisio.libgpml.model.Evidence: Returns the name, term, or text of this evidence.
getValues() - Static method in class org.pathvisio.libgpml.model.type.AnchorShapeType: Returns the anchor type values of all AnchorTypes as a list.
getValues() - Static method in class org.pathvisio.libgpml.model.type.AnnotationType: Returns the annotation type values of all AnnotationTypes as a list.
getValues() - Static method in class org.pathvisio.libgpml.model.type.ArrowHeadType: Returns the arrow head type values of all ArrowHeadTypes as a list.
getValues() - Static method in class org.pathvisio.libgpml.model.type.ConnectorType: Returns the connector type values of all ConnectorTypes as a list.
getValues() - Static method in class org.pathvisio.libgpml.model.type.DataNodeType: Returns the data node type values of all DataNodeTypes as a list.
getValues() - Static method in class org.pathvisio.libgpml.model.type.GroupType: Returns the group type values of all GroupTypes as a list.
getValues() - Static method in class org.pathvisio.libgpml.model.type.LineStyleType: Returns the line style type values of all LineStyleType as an array.
getValues() - Static method in class org.pathvisio.libgpml.model.type.ShapeType: Returns the data node type values of all ShapeTypes as a list.
getValues() - Static method in class org.pathvisio.libgpml.model.type.StateType: Returns the state type values of all StateTypes as an array.
getVersion() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the version of this pathway.
getVisibleNames() - Static method in class org.pathvisio.libgpml.model.type.ArrowHeadType: Returns an array of visible arrowheads name.
getVisibleNames() - Static method in class org.pathvisio.libgpml.model.type.ShapeType: Returns the names of visible registered ShapeTypes as a list.
getVisibleValues() - Static method in class org.pathvisio.libgpml.model.type.ArrowHeadType: Returns an array of visible arrowheads values.
getVisibleValues() - Static method in class org.pathvisio.libgpml.model.type.ShapeType: Returns the data node type values of visible ShapeTypes as a list.
getWarnings() - Method in class org.pathvisio.libgpml.io.AbstractPathwayModelFormat
getWarnings() - Method in interface org.pathvisio.libgpml.io.PathwayModelIO: After import or export, this can be used to check if there are any warnings
getWayPointPreferences() - Method in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: Returns the preferred waypoints, to which the connector must draw it's path.
getWayPointPreferences() - Method in class org.pathvisio.libgpml.model.LineElement: Get the preferred waypoints, to which the connector must draw it's path.
getWayPoints() - Method in class org.pathvisio.libgpml.model.connector.AbstractConnector: Returns the waypoints of the connector shape as an array.
getWayPoints() - Method in interface org.pathvisio.libgpml.model.connector.ConnectorShape: Get the waypoints through which the connector passes
getWidth() - Method in interface org.pathvisio.libgpml.model.Groupable: Calculates and returns the width of the bounding box around (start, end) this pathway element.
getWidth() - Method in class org.pathvisio.libgpml.model.LineElement: Calculates and returns the width of the bounding box around (start, end) this line pathway element.
getWidth() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the width of this shaped pathway element.
getX() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns x coordinate value.
getXref() - Method in class org.pathvisio.libgpml.model.Annotation: Returns the Annotation Xref.
getXref() - Method in class org.pathvisio.libgpml.model.Citation: Returns this Citation Xref.
getXref() - Method in class org.pathvisio.libgpml.model.DataNode: Returns the Xref for this datanode.
getXref() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the Xref for this state.
getXref() - Method in class org.pathvisio.libgpml.model.Evidence: Returns this evidence Xref.
getXref() - Method in class org.pathvisio.libgpml.model.Group: Returns the Xref for the group.
getXref() - Method in class org.pathvisio.libgpml.model.Interaction: Returns the Xref for this interaction.
getXref() - Method in class org.pathvisio.libgpml.model.Pathway.Author: Returns the Xref for the author.
getXref() - Method in class org.pathvisio.libgpml.model.Pathway: Returns the Xref for this pathway.
getXref() - Method in interface org.pathvisio.libgpml.model.Xrefable: Returns the Xref for this pathway element.
getXrefDataSource(String) - Static method in class org.pathvisio.libgpml.util.XrefUtils: Returns DataSource object from given string.
getXrefDataSourceStr(DataSource) - Static method in class org.pathvisio.libgpml.util.XrefUtils: Returns string for data source given DataSource.
getXrefDataSourceStrGPML2013a(DataSource) - Static method in class org.pathvisio.libgpml.util.XrefUtils: Returns string for data source given DataSource for GPML2013a format.
getY() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns y coordinate value.
getYear() - Method in class org.pathvisio.libgpml.model.Citation: Returns year for this citation (for GPML2013a Biopax).
getZOrder() - Method in class org.pathvisio.libgpml.model.DataNode.State: Returns the z-order of this pathway element.
getZOrder() - Method in interface org.pathvisio.libgpml.model.Drawable: Returns the z-order of this pathway element.
getZOrder() - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Returns the z-order of this pathway element.
getZOrder() - Method in class org.pathvisio.libgpml.model.LineElement: Returns the z-order of this pathway element.
getZOrder() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns the z-order of this pathway element.
getZOrder() - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the z-order of this pathway element.
gmmlObjectModified(PathwayModelEvent) - Method in class org.pathvisio.libgpml.model.Test
gmmlObjectModified(PathwayObjectEvent) - Method in interface org.pathvisio.libgpml.model.PathwayObjectListener: Notifies of pathway object changes.
gmmlObjectModified(PathwayObjectEvent) - Method in class org.pathvisio.libgpml.model.Test
GOLGI_APPARATUS - org.pathvisio.libgpml.model.shape.ShapeCatalog.Internal
GOLGI_APPARATUS - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
GPML2013a - Static variable in class org.pathvisio.libgpml.model.GPMLFormat
GPML2013A_KEY_SET - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: This Set stores the deprecated GPML2013a properties.
GPML2013aFormatAbstract - Class in org.pathvisio.libgpml.model: Abstract class for GPML2013a format.
GPML2013aFormatAbstract(String, Namespace) - Constructor for class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Constructor for GPML2013aFormat Abstract.
GPML2013aFormatAbstract.AttributeInfo - Class in org.pathvisio.libgpml.model: Name of resource containing the gpml schema definition.
GPML2013aReader - Class in org.pathvisio.libgpml.model: This class reads a PathwayModel from an input source (GPML 2013a).
GPML2013aReader(String, Namespace) - Constructor for class org.pathvisio.libgpml.model.GPML2013aReader: GPML2013aReader.readFromRoot(org.pathvisio.libgpml.model.PathwayModel, org.jdom2.Element)
GPML2013aREADER - Static variable in class org.pathvisio.libgpml.model.GPML2013aReader
GPML2013aReader.PublicationXref - Class in org.pathvisio.libgpml.model: Local class to help with reading gpml:Biopax:bp:PublicationXref.
GPML2013aWriter - Class in org.pathvisio.libgpml.model: This class writes a PathwayModel to an output (GPML 2013a).
GPML2013aWriter(String, Namespace) - Constructor for class org.pathvisio.libgpml.model.GPML2013aWriter: Constructor for GPML2013aWriter.
GPML2013aWRITER - Static variable in class org.pathvisio.libgpml.model.GPML2013aWriter
GPML2021 - Static variable in class org.pathvisio.libgpml.model.GPMLFormat
GPML2021FormatAbstract - Class in org.pathvisio.libgpml.model: Read / write GPML files.
GPML2021FormatAbstract(String, Namespace) - Constructor for class org.pathvisio.libgpml.model.GPML2021FormatAbstract: Constructor for GPML2021Format Abstract.
GPML2021Reader - Class in org.pathvisio.libgpml.model: This class reads a PathwayModel from an input source (GPML 2021).
GPML2021Reader(String, Namespace) - Constructor for class org.pathvisio.libgpml.model.GPML2021Reader: Constructor for GPML reader.
GPML2021READER - Static variable in class org.pathvisio.libgpml.model.GPML2021Reader
GPML2021Writer - Class in org.pathvisio.libgpml.model: This class writes a PathwayModel to an output (GPML 2021).
GPML2021Writer(String, Namespace) - Constructor for class org.pathvisio.libgpml.model.GPML2021Writer: Constructor for GPML writer.
GPML2021WRITER - Static variable in class org.pathvisio.libgpml.model.GPML2021Writer
GPMLFormat - Class in org.pathvisio.libgpml.model: Class responsible for interaction with Gpml format.
GPMLFormat(GPMLFormatWriter) - Constructor for class org.pathvisio.libgpml.model.GPMLFormat: Instantiates a GpmlFormat.
GPMLFormatAbstract - Class in org.pathvisio.libgpml.model: Abstract class for GPML format.
GPMLFormatAbstract(String, Namespace) - Constructor for class org.pathvisio.libgpml.model.GPMLFormatAbstract: Constructor for GPML2013aFormat Abstract.
GPMLFormatReader - Interface in org.pathvisio.libgpml.model: Interface for GPML reading.
GPMLFormatVersion - Interface in org.pathvisio.libgpml.model: Interface for GPML format versions.
GPMLFormatWriter - Interface in org.pathvisio.libgpml.model: Interface for GPML writing.
GraphicalLine - Class in org.pathvisio.libgpml.model: This class stores information for GraphicalLine pathway element.
GraphicalLine() - Constructor for class org.pathvisio.libgpml.model.GraphicalLine: Instantiates a GraphicalLine pathway element given all possible parameters.
graphicalLines - Variable in class org.pathvisio.libgpml.model.PathwayModel
GRAPHLINE - org.pathvisio.libgpml.model.type.ObjectType: A connector pathway element without semantic meaning.
GraphLink - Class in org.pathvisio.libgpml.model: This class only contains static methods and should not be instantiated.
GraphLink() - Constructor for class org.pathvisio.libgpml.model.GraphLink
GraphLink.LinkableFrom - Interface in org.pathvisio.libgpml.model: Classes which want to refer *to* a GraphLink.LinkableTo PathwayElement must implement this interface.
GraphLink.LinkableTo - Interface in org.pathvisio.libgpml.model: PathwayElements which can be referred to must implement this interface.
Group - Class in org.pathvisio.libgpml.model: This class stores all information relevant to a Group pathway element.
Group(GroupType) - Constructor for class org.pathvisio.libgpml.model.Group: Instantiates a Group given all required parameters.
Group(GroupType, Xref) - Constructor for class org.pathvisio.libgpml.model.Group: Instantiates a Group given all required parameters and xref.
GROUP - org.pathvisio.libgpml.model.type.ObjectType: A pathway element grouping of other pathway elements.
GROUP - Static variable in class org.pathvisio.libgpml.model.type.GroupType
Groupable - Interface in org.pathvisio.libgpml.model: Interface for classes which can belong in a Group.
groupRef - Variable in class org.pathvisio.libgpml.model.LineElement
groupRef - Variable in class org.pathvisio.libgpml.model.ShapedElement
GROUPREF - org.pathvisio.libgpml.prop.StaticProperty
groups - Variable in class org.pathvisio.libgpml.model.PathwayModel
GroupType - Class in org.pathvisio.libgpml.model.type: This class contains extensible enum for Group type property.
GroupType(String) - Constructor for class org.pathvisio.libgpml.model.type.GroupType: The constructor is private.
GROUPTYPE - org.pathvisio.libgpml.prop.StaticProperty
GROUPTYPE - org.pathvisio.libgpml.prop.StaticPropertyType
GROUPTYPE_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract

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