Index

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W

warn(String) - Method in class org.pathvisio.libgpml.debug.Logger

warn(String, Throwable) - Method in class org.pathvisio.libgpml.debug.Logger

warnEnabled - Variable in class org.pathvisio.libgpml.debug.Logger

warnings - Variable in class org.pathvisio.libgpml.io.AbstractPathwayModelFormat

WayPoint(double, double) - Constructor for class org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint

WayPoint(Point2D) - Constructor for class org.pathvisio.libgpml.model.connector.ConnectorShape.WayPoint

waypointNumbers - Variable in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape

waypoints - Variable in class org.pathvisio.libgpml.model.connector.AbstractConnector

wayPointsToCenter(ConnectorShape.WayPoint[], ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape

wayPointsToCenter(ConnectorShape.WayPoint[], ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape

Sets all waypoints to the center of the segments.

width - Variable in class org.pathvisio.libgpml.model.ShapedElement

WIDTH - org.pathvisio.libgpml.prop.StaticProperty

WIRE - org.pathvisio.libgpml.model.shape.ArrowShape.FillType

Wire fill-type, there is only an outline.

WorkerThreadOnly - Annotation Type in org.pathvisio.libgpml.debug

Indicates that this class or method should only be accessed by threads other than the Event Dispatch Thread

WP_DESCRIPTION - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract

In GPML2013a, Pathway description is written as a PathwayElement.Comment with source="WikiPathways-description".

writeAliasRef(Group, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes aliasRef property information for a data node.

writeAnchors(List<LineElement.Anchor>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes anchor LineElement.Anchor information.

writeAnchors(List<LineElement.Anchor>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes anchor LineElement.Anchor information.

writeAnnotationRefs(List<PathwayElement.AnnotationRef>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes annotation reference information for pathway or pathway element.

writeAnnotations(List<Annotation>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes annotation Annotation information.

writeArrowHeadType(ArrowHeadType, String, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes the arrowHead for point jdom element.

writeAuthors(List<Pathway.Author>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes author Pathway.Author information.

writeBiopax(PathwayModel, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes gpml:Biopax information openControlledVocabulary and PublicationXref.

writeBiopaxRefs(List<PathwayElement.CitationRef>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes BiopaxRef information from PathwayElement.getCitationRefs() for pathway or pathway element.

writeCitationRefs(List<PathwayElement.CitationRef>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes citation reference information for pathway or pathway element.

writeCitations(List<Citation>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes citation Citation information.

writeColor(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes color property information for shaped pathway elements.

writeComments(List<PathwayElement.Comment>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes comments PathwayElement.Comment information for pathway or pathway element.

writeComments(List<PathwayElement.Comment>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes comments PathwayElement.Comment information for pathway or pathway element.

writeDataNodes(List<DataNode>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes datanode DataNode information.

writeDataNodes(List<DataNode>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes datanode DataNode information.

writeDynamicProperties(Map<String, String>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes dynamic property information for pathway or pathway element.

writeElementId(String, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes elementId PathwayObject property information.

writeElementId(String, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes elementId PathwayObject property information.

writeElementInfo(PathwayElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes elementId, comment group {comment, dynamic property, annotationRef, citationRef) and evidenceRef PathwayElement information for datanodes, interactions, graphicalLines, labels, shapes, and group.

writeElementInfo(PathwayElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes elementId, comment group {comment, dynamic property, annotationRef, citationRef) and evidenceRef PathwayElement information for

writeElementRef(GraphLink.LinkableTo, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes elementRef property information.

writeEvidenceRefs(List<PathwayElement.EvidenceRef>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes evidence reference information for pathway or pathway element , ElementInfo#getEvidenceRefs.

writeEvidences(List<Evidence>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes evidence Evidence information.

writeFontProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes font property information, except color.

writeFontProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes font property information.

writeGraphicalLines(List<GraphicalLine>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes graphical line GraphicalLine information.

writeGraphicalLines(List<GraphicalLine>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes graphical line GraphicalLine information.

writeGroupRef(Group, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes groupRef property information.

writeGroupRef(Group, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes groupRef property information.

writeGroups(List<Group>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes group Group information.

writeGroups(List<Group>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes group Group information.

writeInfoBox(Pathway, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes the infobox x and y coordinate information.

writeInteractions(List<Interaction>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes interaction Interaction information.

writeInteractions(List<Interaction>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes interaction Interaction information.

writeLabels(List<Label>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes label Label information.

writeLabels(List<Label>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes label Label information.

writeLegend(Pathway, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes the legend x and y coordinate information.

writeLineDynamicProperties(Map<String, String>, LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes dynamic property information for LineElement.

writeLineElement(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes line element LineElement information for interactions or graphicalLines.

writeLineElement(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes line element LineElement information for interactions or graphicalLines.

writeLineStyleProperty(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes line style property information.

writeLineStyleProperty(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes line style property information.

writeOpenControlledVocabulary(PathwayModel, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes gpml:Biopax bp:OpenControlledVocabulary Annotation information.

writePathwayDynamicProperties(Pathway, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes dynamic property information for pathway or pathway element.

writePathwayInfo(PathwayModel, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes pathway object Pathway information to root element.

writePathwayInfo(PathwayModel, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes pathway object Pathway information and authors list to root element.

writePointElementRef(GraphLink.LinkableTo, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes point elementRef property information as GraphRef.

writePoints(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes point LineElement.LinePoint information.

writePoints(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes point LineElement.LinePoint information.

writePublicationXref(List<Citation>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes gpml:Biopax bp:PublicationXref Citation information.

writePublicationXrefInfo(String, String, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes Biopax PublicationXref information to PublicationXref element.

writer - Variable in class org.pathvisio.libgpml.model.GPMLFormat

writeRectProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes rect property information.

writeRectProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes rect property information.

writeShapedElement(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes shapedElement ShapedElement information for datanodes, labels, shapes, or groups.

writeShapedElement(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes shapedElement ShapedElement information for datanodes, labels, shapes, or groups.

writeShapedOrStateDynamicProperties(Map<String, String>, ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes dynamic property information for ShapedElement or DataNode.State pathway element.

writeShapes(List<Shape>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes shape Shape information.

writeShapes(List<Shape>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes shape Shape information.

writeShapeStyleProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes shape style property information, except borderColor, zOrder, and fillColor.

writeShapeStyleProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes shape style property information.

writeStates(List<DataNode.State>, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes state DataNode.State information.

writeStates(List<DataNode>, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes state DataNode.State information.

writeToXml(File, boolean) - Method in class org.pathvisio.libgpml.model.PathwayModel

Writes the JDOM document to the file specified

writeToXml(PathwayModel, File, boolean) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes the JDOM document to the file specified.

writeToXml(PathwayModel, File, boolean) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes the JDOM document to the file specified.

writeToXml(PathwayModel, File, boolean) - Method in class org.pathvisio.libgpml.model.GPMLFormat

Writes the JDOM document to the file specified

writeToXml(PathwayModel, File, boolean) - Method in interface org.pathvisio.libgpml.model.GPMLFormatWriter

Write pathway model to file.

writeToXml(PathwayModel, OutputStream, boolean) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes the JDOM Document document to the outputstream specified.

writeToXml(PathwayModel, OutputStream, boolean) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes the JDOM Document document to the outputstream specified.

writeToXml(PathwayModel, OutputStream, boolean) - Method in class org.pathvisio.libgpml.model.GPMLFormat

Writes the pathway model to output stream.

writeToXml(PathwayModel, OutputStream, boolean) - Method in interface org.pathvisio.libgpml.model.GPMLFormatWriter

Writes pathway model to outputstream.

writeUrl(String, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes url link information to new element.

writeXref(Xref, Element, boolean) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter

Writes xref Xref information to new element.

writeXref(Xref, Element, boolean) - Method in class org.pathvisio.libgpml.model.GPML2021Writer

Writes xref Xref information to new element.

A B C D E F G H I J L M N O P R S T U V W X Y Z
All Classes|All Packages