Uses of Class
org.pathvisio.libgpml.io.ConverterException

Packages that use ConverterException

Package	Description
org.pathvisio.libgpml.io	Import and export classes
org.pathvisio.libgpml.model	Classes representing the pathway "model".

Uses of ConverterException in org.pathvisio.libgpml.io

Methods in org.pathvisio.libgpml.io that throw ConverterException

Modifier and Type	Method	Description
void	PathwayModelExporter.doExport(java.io.File file, PathwayModel pathwayModel)	Exports the given pathway to the file
void	PathwayModelExporter.doExport(java.io.File file, PathwayModel pathwayModel, int zoom)	Exports the given pathway to the file
PathwayModel	PathwayModelImporter.doImport(java.io.File file)	Imports the pathway model from given file.

Uses of ConverterException in org.pathvisio.libgpml.model

Methods in org.pathvisio.libgpml.model that throw ConverterException

Modifier and Type	Method	Description
protected void	GPML2013aReader.convertStateCommentToRefs(DataNode.State state, java.util.Set<java.lang.String> elementIdSet)	This method is used to handle DataNode.State PathwayElement.Comment which were manually added to encode phosphosite information.
protected void	GPML2013aWriter.convertStateRefToComments(DataNode.State state, org.jdom2.Element st)	This method handles converting DataNode.State phosphosite PathwayElement.AnnotationRef and Xref information back to PathwayElement.Comment for writing to GPML2013a.
org.jdom2.Document	GPML2013aWriter.createJdom(PathwayModel pathwayModel)	Creates and returns the JDOM document Document written from given pathwayModel PathwayModel data.
org.jdom2.Document	GPML2021Writer.createJdom(PathwayModel pathwayModel)	Creates and returns the JDOM document Document written from given pathwayModel PathwayModel data.
org.jdom2.Document	GPMLFormat.createJdom(PathwayModel data)
org.jdom2.Document	GPMLFormatWriter.createJdom(PathwayModel pathwayModel)	Creates a Jdom document from pathway model.
void	GPMLFormat.doExport(java.io.File file, PathwayModel pathwayModel)
void	GPMLFormat.doExport(java.io.File file, PathwayModel pathwayModel, int zoom)
PathwayModel	GPMLFormat.doImport(java.io.File file)
protected java.lang.String	GPML2013aFormatAbstract.fromCamelCase(java.lang.String str)	Converts shapeType String from UpperCamelCase convention back to its original appearance in GPML2013a.
protected java.lang.String	GPML2013aFormatAbstract.getArrowHeadTypeStr(ArrowHeadType arrowHead)	Returns the prioritized GPML2013a arrowHead type string for given GPML2021 Interaction Panel arrow head type.
protected java.lang.String	GPML2013aFormatAbstract.getAttr(java.lang.String tag, java.lang.String name, org.jdom2.Element el)	Gets a certain attribute value, and replaces it with a suitable default under certain conditions.
protected ArrowHeadType	GPML2013aFormatAbstract.getInteractionPanelType(java.lang.String arrowHeadStr)	Returns the GPML2021 Interaction Panel arrow head type for given GPML2013a arrowHead type string.
protected void	GPML2013aReader.readAnchors(LineElement lineElement, org.jdom2.Element gfx, java.util.Set<java.lang.String> elementIdSet)	Reads anchor LineElement.Anchor information for line element from element.
protected void	GPML2021Reader.readAnchors(LineElement lineElement, org.jdom2.Element wyps)	Reads anchor LineElement.Anchor information for line element from jdom element.
protected void	GPML2021Reader.readAnnotationRefs(PathwayModel pathwayModel, Referenceable.Annotatable annotatable, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads Annotation and PathwayElement.AnnotationRef information for an Referenceable.Annotatable.
protected ArrowHeadType	GPML2013aReader.readArrowHeadType(org.jdom2.Element pt, java.lang.String base)	Returns the arrowHead for give jdom point element.
protected void	GPML2021Reader.readAuthors(Pathway pathway, org.jdom2.Element root)	Reads author Pathway.Author information for pathway from root element.
protected void	GPML2021Reader.readCitationRefs(PathwayModel pathwayModel, Referenceable.Citable citable, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads Citation and PathwayElement.CitationRef information for a Referenceable.Citable.
protected void	GPML2013aReader.readCommentGroup(PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads comment group (comment, biopaxref/citationRef, dynamic property) for pathway element from jdom element.
protected void	GPML2021Reader.readCommentGroup(PathwayModel pathwayModel, PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads comment group (comment, dynamic property, annotationRef, citationRef, evidenceRef) information for PathwayElement from jdom element.
protected void	GPML2013aReader.readComments(PathwayElement pathwayElement, org.jdom2.Element e)	Reads comment PathwayElement.Comment information for pathway element from jdom element.
protected void	GPML2021Reader.readComments(PathwayElement pathwayElement, org.jdom2.Element e)	Reads comment PathwayElement.Comment information for pathway element from jdom element.
protected void	GPML2013aReader.readDataNodes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads data node DataNode information for pathway model from root element.
protected void	GPML2021Reader.readDataNodes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads data node DataNode information for pathway model from root element.
protected void	GPML2013aReader.readDynamicProperties(PathwayElement pathwayElement, org.jdom2.Element root)	Reads gpml:Attribute or dynamic property information for PathwayElement from jdom element.
protected void	GPML2021Reader.readDynamicProperties(PathwayElement pathwayElement, org.jdom2.Element e)	Reads dynamic property PathwayElement.setDynamicProperty(java.lang.String, java.lang.String) information for pathway element from jdom element.
protected java.lang.String	GPML2013aReader.readElementId(java.lang.String tag, org.jdom2.Element e, java.util.Set<java.lang.String> elementIdSet)	Returns elementId read for given Element.
protected void	GPML2021Reader.readEvidenceRefs(PathwayModel pathwayModel, Referenceable.Evidenceable evidenceable, org.jdom2.Element e, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads Evidence and PathwayElement.EvidenceRef information for an Referenceable.Evidenceable.
protected void	GPML2013aReader.readFontProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads font property information.
protected void	GPML2021Reader.readFontProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads font property information.
void	GPML2013aReader.readFromRoot(PathwayModel pathwayModel, org.jdom2.Element root)	Reads information from root element of Jdom document Document to the pathway model PathwayModel.
void	GPML2021Reader.readFromRoot(PathwayModel pathwayModel, org.jdom2.Element root)	Reads information from root element of Jdom document Document to the pathway model PathwayModel.
void	GPMLFormatReader.readFromRoot(PathwayModel pathwayModel, org.jdom2.Element root)	Reads pathway model from root element.
static void	GPMLFormat.readFromXml(PathwayModel pathwayModel, java.io.File file, boolean validate)	Reads the JDOM document from the file specified
static void	GPMLFormat.readFromXml(PathwayModel pathwayModel, java.io.InputStream in, boolean validate)	Reads the JDOM document from the string specified
static void	GPMLFormat.readFromXml(PathwayModel pathwayModel, java.io.Reader in, boolean validate)	Reads the JDOM document from the string specified
void	PathwayModel.readFromXml(java.io.File file, boolean validate)
void	PathwayModel.readFromXml(java.io.InputStream in, boolean validate)
void	PathwayModel.readFromXml(java.io.Reader in, boolean validate)
private static void	GPMLFormat.readFromXmlImpl(PathwayModel pathwayModel, org.xml.sax.InputSource is, boolean validate)	Reads a pathway model from given input source.
protected void	GPML2013aReader.readGraphicalLines(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads graphical line GraphicalLine information for pathway model from root element.
protected void	GPML2021Reader.readGraphicalLines(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads graphical line GraphicalLine information for pathway model from root element.
protected void	GPML2013aReader.readGroupGroupRef(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads groupRef property ShapedElement.setGroupRef(org.pathvisio.libgpml.model.Group) information of group pathway element.
protected void	GPML2013aReader.readGroupRef(ShapedElement shapedElement, org.jdom2.Element se, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads and sets groupRef for given (shaped) pathway element and jdom Element.
protected void	GPML2021Reader.readGroupRef(PathwayModel pathwayModel, ShapedElement shapedElement, org.jdom2.Element e)	Reads groupRef information for DataNode, Label, and Shape.
protected void	GPML2013aReader.readGroups(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<java.lang.String,Group> graphIdToGroup)	Reads group Group information for pathway model from root element.
protected void	GPML2021Reader.readGroups(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads group Group information for pathway model from root element.
protected void	GPML2021Reader.readInfoMap(org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads and maps ref (Annotation, Citation, and Evidence) elementId id to the corresponding jdom element in Map refIdToJdomElement, to assist other reading methods: GPML2021Reader.readAnnotationRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Annotatable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>), GPML2021Reader.readCitationRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Citable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>), and GPML2021Reader.readEvidenceRefs(org.pathvisio.libgpml.model.PathwayModel, org.pathvisio.libgpml.model.Referenceable.Evidenceable, org.jdom2.Element, java.util.Map<java.lang.String, org.jdom2.Element>).
protected void	GPML2013aReader.readInteractions(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads interaction Interaction information for pathway model from root element.
protected void	GPML2021Reader.readInteractions(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads interaction Interaction information for pathway model from root element.
protected void	GPML2013aReader.readLabels(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads label Label information for pathway model from root element.
protected void	GPML2021Reader.readLabels(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads label Label information for pathway model from root element.
protected void	GPML2013aReader.readLineElement(LineElement lineElement, org.jdom2.Element ln, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads line element LineElement information for interaction or graphical line from jdom element.
protected void	GPML2021Reader.readLineElement(PathwayModel pathwayModel, LineElement lineElement, org.jdom2.Element ln, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads line element LineElement information for interaction or graphical line from jdom element.
protected void	GPML2013aReader.readLineStyleProperty(LineElement lineElement, org.jdom2.Element gfx)	Reads line style property information.
protected void	GPML2021Reader.readLineStyleProperty(LineElement lineElement, org.jdom2.Element gfx)	Reads line style property information.
protected void	GPML2013aReader.readOpenControlledVocabulary(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet)	Reads gpml:Biopax bp:OpenControlledVocabulary information to Annotation for pathway model from root element.
protected Pathway	GPML2013aReader.readPathway(Pathway pathway, org.jdom2.Element root)	Reads pathway information from root element.
protected Pathway	GPML2021Reader.readPathway(Pathway pathway, org.jdom2.Element root)	Reads pathway information from jdom root element.
protected void	GPML2013aReader.readPointElementRefs(PathwayModel pathwayModel, java.util.Map<java.lang.String,Group> graphIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads LineElement.LinePoint elementRefs.
protected void	GPML2021Reader.readPointElementRefs(PathwayModel pathwayModel, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads elementRef LineElement.LinePoint.setElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo) for pathway model points.
protected void	GPML2013aReader.readPoints(LineElement lineElement, org.jdom2.Element ln, java.util.Set<java.lang.String> elementIdSet, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads points LineElement.LinePoint for pathway model line pathway elements.
protected void	GPML2021Reader.readPoints(LineElement lineElement, org.jdom2.Element wyps, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads point LineElement.LinePoint information for line element.
protected java.lang.String	GPML2013aReader.readPublicationXrefInfo(java.util.List<org.jdom2.Element> pubxfElements)	Reads Biopax PublicationXref information from PublicationXref children elements.
protected void	GPML2013aReader.readPublicationXrefMap(org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads gpml:Biopax:bp:PublicationXref and maps "id" to GPML2013aReader.PublicationXref in idToPublicationXref.
protected void	GPML2013aReader.readPublicationXrefs(PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads gpml:Biopax:bp:PublicationXref and BiopaxRef information for pathway element from jdom element.
protected void	GPML2013aReader.readRectProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads rect property information.
protected void	GPML2021Reader.readRectProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads rect property information.
protected void	GPML2013aReader.readShapedElement(ShapedElement shapedElement, org.jdom2.Element se, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads shaped pathway element ShapedElement information: graphics and comment group (comments, biopaxRefs (equivalent to citationRefs), and dynamic properties).
protected void	GPML2021Reader.readShapedElement(PathwayModel pathwayModel, ShapedElement shapedElement, org.jdom2.Element se, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads common properties for shaped pathway elements ShapedElement.
protected void	GPML2013aReader.readShapes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads shape Shape information for pathway model from root element.
protected void	GPML2021Reader.readShapes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads shape Shape information for pathway model from root element.
protected void	GPML2013aReader.readShapeStyleProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads shape style property information.
protected void	GPML2021Reader.readShapeStyleProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Reads shape style property information.
protected void	GPML2013aReader.readStates(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads state DataNode.State information for pathway model from root element.
protected void	GPML2021Reader.readStates(PathwayModel pathwayModel, DataNode dataNode, org.jdom2.Element dn, java.util.Map<java.lang.String,org.jdom2.Element> refIdToJdomElement)	Reads state DataNode.State information for data node from element.
protected java.lang.String	GPML2021Reader.readUrl(org.jdom2.Element e)	Reads Url link information from element.
protected org.bridgedb.Xref	GPML2013aReader.readXref(org.jdom2.Element e)	Reads xref Xref information from element.
protected org.bridgedb.Xref	GPML2021Reader.readXref(org.jdom2.Element e)	Reads xref Xref information from jdom element.
protected static void	GPMLFormatAbstract.refreshLineElements(PathwayModel pathwayModel)	Refreshes line elements.
protected void	GPML2013aFormatAbstract.setAttr(java.lang.String tag, java.lang.String name, org.jdom2.Element el, java.lang.String value)	Sets a certain attribute value, performs a basic check for some types, and throws an exception if trying to set an invalid value.
protected void	GPML2013aReader.setGroupGraphicsProperty(Group group, GroupType type)	Reads and sets graphics properties for Group.
void	TestAlias.testWriteGPML2021()
void	TestGroupNested.testWriteGPML2021()
protected java.lang.String	GPML2013aFormatAbstract.toCamelCase(java.lang.String str)	Converts shapeType String to UpperCamelCase convention.
protected void	GPMLFormatAbstract.updateGroups(PathwayModel pathwayModel)	Removes group from pathwayModel if empty.
void	GPMLFormatAbstract.validateDocument(org.jdom2.Document doc)	Validates a JDOM document against the xml-schema definition specified by 'xsdFile.'
void	GPMLFormatVersion.validateDocument(org.jdom2.Document doc)	Validates a JDOM document against the xml-schema definition specified by 'xsdFile'
protected void	GPML2013aWriter.writeAnchors(java.util.List<LineElement.Anchor> anchors, org.jdom2.Element gfx)	Writes anchor LineElement.Anchor information.
protected void	GPML2021Writer.writeAnchors(java.util.List<LineElement.Anchor> anchors, org.jdom2.Element wyps)	Writes anchor LineElement.Anchor information.
protected void	GPML2021Writer.writeAnnotationRefs(java.util.List<PathwayElement.AnnotationRef> annotationRefs, org.jdom2.Element e)	Writes annotation reference information for pathway or pathway element.
protected void	GPML2021Writer.writeAnnotations(java.util.List<Annotation> annotations, org.jdom2.Element root)	Writes annotation Annotation information.
protected void	GPML2013aWriter.writeArrowHeadType(ArrowHeadType arrowHead, java.lang.String base, org.jdom2.Element pt)	Writes the arrowHead for point jdom element.
protected void	GPML2021Writer.writeAuthors(java.util.List<Pathway.Author> authors, org.jdom2.Element root)	Writes author Pathway.Author information.
protected void	GPML2013aWriter.writeBiopax(PathwayModel pathwayModel, org.jdom2.Element root)	Writes gpml:Biopax information openControlledVocabulary and PublicationXref.
protected void	GPML2013aWriter.writeBiopaxRefs(java.util.List<PathwayElement.CitationRef> citationRefs, org.jdom2.Element e)	Writes BiopaxRef information from PathwayElement.getCitationRefs() for pathway or pathway element.
protected void	GPML2021Writer.writeCitationRefs(java.util.List<PathwayElement.CitationRef> citationRefs, org.jdom2.Element e)	Writes citation reference information for pathway or pathway element.
protected void	GPML2021Writer.writeCitations(java.util.List<Citation> citations, org.jdom2.Element root)	Writes citation Citation information.
protected void	GPML2013aWriter.writeColor(ShapedElement shapedElement, org.jdom2.Element gfx)	Writes color property information for shaped pathway elements.
protected void	GPML2013aWriter.writeComments(java.util.List<PathwayElement.Comment> comments, org.jdom2.Element e)	Writes comments PathwayElement.Comment information for pathway or pathway element.
protected void	GPML2021Writer.writeComments(java.util.List<PathwayElement.Comment> comments, org.jdom2.Element e)	Writes comments PathwayElement.Comment information for pathway or pathway element.
protected void	GPML2013aWriter.writeDataNodes(java.util.List<DataNode> dataNodes, org.jdom2.Element root)	Writes datanode DataNode information.
protected void	GPML2021Writer.writeDataNodes(java.util.List<DataNode> dataNodes, org.jdom2.Element root)	Writes datanode DataNode information.
protected void	GPML2021Writer.writeDynamicProperties(java.util.Map<java.lang.String,java.lang.String> dynamicProperties, org.jdom2.Element e)	Writes dynamic property information for pathway or pathway element.
protected void	GPML2013aWriter.writeElementInfo(PathwayElement elementInfo, org.jdom2.Element e)	Writes elementId, comment group {comment, dynamic property, annotationRef, citationRef) and evidenceRef PathwayElement information for datanodes, interactions, graphicalLines, labels, shapes, and group.
protected void	GPML2021Writer.writeElementInfo(PathwayElement elementInfo, org.jdom2.Element e)	Writes elementId, comment group {comment, dynamic property, annotationRef, citationRef) and evidenceRef PathwayElement information for
protected void	GPML2021Writer.writeEvidenceRefs(java.util.List<PathwayElement.EvidenceRef> evidenceRefs, org.jdom2.Element e)	Writes evidence reference information for pathway or pathway element , ElementInfo#getEvidenceRefs.
protected void	GPML2021Writer.writeEvidences(java.util.List<Evidence> evidences, org.jdom2.Element root)	Writes evidence Evidence information.
protected void	GPML2013aWriter.writeFontProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Writes font property information, except color.
protected void	GPML2021Writer.writeFontProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Writes font property information.
protected void	GPML2013aWriter.writeGraphicalLines(java.util.List<GraphicalLine> graphicalLines, org.jdom2.Element root)	Writes graphical line GraphicalLine information.
protected void	GPML2021Writer.writeGraphicalLines(java.util.List<GraphicalLine> graphicalLines, org.jdom2.Element root)	Writes graphical line GraphicalLine information.
protected void	GPML2013aWriter.writeGroups(java.util.List<Group> groups, org.jdom2.Element root)	Writes group Group information.
protected void	GPML2021Writer.writeGroups(java.util.List<Group> groups, org.jdom2.Element root)	Writes group Group information.
protected void	GPML2013aWriter.writeInteractions(java.util.List<Interaction> interactions, org.jdom2.Element root)	Writes interaction Interaction information.
protected void	GPML2021Writer.writeInteractions(java.util.List<Interaction> interactions, org.jdom2.Element root)	Writes interaction Interaction information.
protected void	GPML2013aWriter.writeLabels(java.util.List<Label> labels, org.jdom2.Element root)	Writes label Label information.
protected void	GPML2021Writer.writeLabels(java.util.List<Label> labels, org.jdom2.Element root)	Writes label Label information.
protected void	GPML2013aWriter.writeLineDynamicProperties(java.util.Map<java.lang.String,java.lang.String> dynamicProperties, LineElement lineElement, org.jdom2.Element ln)	Writes dynamic property information for LineElement.
protected void	GPML2013aWriter.writeLineElement(LineElement lineElement, org.jdom2.Element ln)	Writes line element LineElement information for interactions or graphicalLines.
protected void	GPML2021Writer.writeLineElement(LineElement lineElement, org.jdom2.Element ln)	Writes line element LineElement information for interactions or graphicalLines.
protected void	GPML2013aWriter.writeLineStyleProperty(LineElement lineElement, org.jdom2.Element gfx)	Writes line style property information.
protected void	GPML2021Writer.writeLineStyleProperty(LineElement lineElement, org.jdom2.Element gfx)	Writes line style property information.
protected void	GPML2013aWriter.writeOpenControlledVocabulary(PathwayModel pathwayModel, org.jdom2.Element bp)	Writes gpml:Biopax bp:OpenControlledVocabulary Annotation information.
protected void	GPML2013aWriter.writePathwayDynamicProperties(Pathway pathway, org.jdom2.Element root)	Writes dynamic property information for pathway or pathway element.
protected void	GPML2013aWriter.writePathwayInfo(PathwayModel pathwayModel, org.jdom2.Element root)	Writes pathway object Pathway information to root element.
protected void	GPML2021Writer.writePathwayInfo(PathwayModel pathwayModel, org.jdom2.Element root)	Writes pathway object Pathway information and authors list to root element.
protected void	GPML2013aWriter.writePoints(LineElement lineElement, org.jdom2.Element gfx)	Writes point LineElement.LinePoint information.
protected void	GPML2021Writer.writePoints(LineElement lineElement, org.jdom2.Element wyps)	Writes point LineElement.LinePoint information.
protected void	GPML2013aWriter.writePublicationXref(java.util.List<Citation> citations, org.jdom2.Element bp)	Writes gpml:Biopax bp:PublicationXref Citation information.
protected void	GPML2013aWriter.writePublicationXrefInfo(java.lang.String propertyValue, java.lang.String elementName, org.jdom2.Element pubxf)	Writes Biopax PublicationXref information to PublicationXref element.
protected void	GPML2013aWriter.writeRectProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Writes rect property information.
protected void	GPML2021Writer.writeRectProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Writes rect property information.
protected void	GPML2013aWriter.writeShapedElement(ShapedElement shapedElement, org.jdom2.Element se)	Writes shapedElement ShapedElement information for datanodes, labels, shapes, or groups.
protected void	GPML2021Writer.writeShapedElement(ShapedElement shapedElement, org.jdom2.Element se)	Writes shapedElement ShapedElement information for datanodes, labels, shapes, or groups.
protected void	GPML2013aWriter.writeShapedOrStateDynamicProperties(java.util.Map<java.lang.String,java.lang.String> dynamicProperties, ShapedElement shapedElement, org.jdom2.Element se)	Writes dynamic property information for ShapedElement or DataNode.State pathway element.
protected void	GPML2013aWriter.writeShapes(java.util.List<Shape> shapes, org.jdom2.Element root)	Writes shape Shape information.
protected void	GPML2021Writer.writeShapes(java.util.List<Shape> shapes, org.jdom2.Element root)	Writes shape Shape information.
protected void	GPML2013aWriter.writeShapeStyleProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Writes shape style property information, except borderColor, zOrder, and fillColor.
protected void	GPML2021Writer.writeShapeStyleProperty(ShapedElement shapedElement, org.jdom2.Element gfx)	Writes shape style property information.
protected void	GPML2013aWriter.writeStates(java.util.List<DataNode> dataNodes, org.jdom2.Element root)	Writes state DataNode.State information.
protected void	GPML2021Writer.writeStates(java.util.List<DataNode.State> states, org.jdom2.Element dn)	Writes state DataNode.State information.
void	GPML2013aWriter.writeToXml(PathwayModel pathwayModel, java.io.File file, boolean validate)	Writes the JDOM document to the file specified.
void	GPML2013aWriter.writeToXml(PathwayModel pathwayModel, java.io.OutputStream output, boolean validate)	Writes the JDOM Document document to the outputstream specified.
void	GPML2021Writer.writeToXml(PathwayModel pathwayModel, java.io.File file, boolean validate)	Writes the JDOM document to the file specified.
void	GPML2021Writer.writeToXml(PathwayModel pathwayModel, java.io.OutputStream output, boolean validate)	Writes the JDOM Document document to the outputstream specified.
void	GPMLFormat.writeToXml(PathwayModel pathwayModel, java.io.File file, boolean validate)	Writes the JDOM document to the file specified
void	GPMLFormat.writeToXml(PathwayModel pathwayModel, java.io.OutputStream out, boolean validate)	Writes the pathway model to output stream.
void	GPMLFormatWriter.writeToXml(PathwayModel pathwayModel, java.io.File file, boolean validate)	Write pathway model to file.
void	GPMLFormatWriter.writeToXml(PathwayModel pathwayModel, java.io.OutputStream out, boolean validate)	Writes pathway model to outputstream.
void	PathwayModel.writeToXml(java.io.File file, boolean validate)	Writes the JDOM document to the file specified
protected void	GPML2013aWriter.writeXref(org.bridgedb.Xref xref, org.jdom2.Element e, boolean required)	Writes xref Xref information to new element.