Uses of Class
org.pathvisio.libgpml.model.PathwayModel

Packages that use PathwayModel

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

Uses of PathwayModel in org.pathvisio.libgpml.io

Methods in org.pathvisio.libgpml.io that return PathwayModel

Modifier and Type	Method	Description
PathwayModel	PathwayModelImporter.doImport(java.io.File file)	Imports the pathway model from given file.

Methods in org.pathvisio.libgpml.io with parameters of type PathwayModel

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

Uses of PathwayModel in org.pathvisio.libgpml.model

Fields in org.pathvisio.libgpml.model declared as PathwayModel

Modifier and Type	Field	Description
(package private) PathwayModel	Test.data
private PathwayModel	TestAlias.p
private PathwayModel	TestAnchor.p
private PathwayModel	TestAnnotation.p
private PathwayModel	TestCitation.p
private PathwayModel	TestCopy.p
private PathwayModel	TestElementId.p
private PathwayModel	TestEvidence.p
(package private) PathwayModel	TestGraph.p
private PathwayModel	TestGraphLink.p
(package private) PathwayModel	TestGroup.p
(package private) PathwayModel	TestGroupNested.p
private PathwayModel	TestLinePoint.p
private PathwayModel	TestReferenceable.p
private PathwayModel	TestState.p
protected PathwayModel	PathwayObject.pathwayModel

Methods in org.pathvisio.libgpml.model that return PathwayModel

Modifier and Type	Method	Description
PathwayModel	PathwayModel.clone()	Clones this pathway model.
PathwayModel	GPMLFormat.doImport(java.io.File file)
PathwayModel	Drawable.getPathwayModel()	Returns the pathway model of this pathway element.
PathwayModel	PathwayObject.getPathwayModel()	Returns the pathway model for this pathway element.

Methods in org.pathvisio.libgpml.model with parameters of type PathwayModel

Modifier and Type	Method	Description
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)
static java.util.Set<GraphLink.LinkableFrom>	GraphLink.getReferences(GraphLink.LinkableTo elementRef, PathwayModel pathwayModel)	Return a list of GraphLink.LinkableFrom LineElement.LinePoint(s) referring to a certain GraphLink.LinkableTo pathway element or anchor.
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 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	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.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	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.
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
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	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	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	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.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 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	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.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 static void	GPMLFormatAbstract.refreshLineElements(PathwayModel pathwayModel)	Refreshes line elements.
protected void	PathwayObject.setPathwayModel(PathwayModel pathwayModel)	Sets the pathway model of this pathway element to the given pathway model.
protected void	DataNode.setPathwayModelTo(PathwayModel pathwayModel)	Sets the pathway model for this pathway element.
protected void	DataNode.State.setPathwayModelTo(PathwayModel pathwayModel)	Sets the pathway model for this pathway element.
protected void	LineElement.GenericPoint.setPathwayModelTo(PathwayModel pathwayModel)	Sets the pathway model for this line point or anchor.
protected void	LineElement.setPathwayModelTo(PathwayModel pathwayModel)	Sets the pathway model for this pathway element.
protected void	PathwayObject.setPathwayModelTo(PathwayModel pathwayModel)	Sets the pathway model for this pathway element.
void	PathwayModel.transferStatusFlagListeners(PathwayModel dest)	Transfer statusflag listeners from one pathway to another.
protected void	GPMLFormatAbstract.updateGroups(PathwayModel pathwayModel)	Removes group from pathwayModel if empty.
protected void	GPML2013aWriter.writeBiopax(PathwayModel pathwayModel, org.jdom2.Element root)	Writes gpml:Biopax information openControlledVocabulary and PublicationXref.
protected void	GPML2013aWriter.writeOpenControlledVocabulary(PathwayModel pathwayModel, org.jdom2.Element bp)	Writes gpml:Biopax bp:OpenControlledVocabulary Annotation information.
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.
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.