Index

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All Classes|All Packages

R

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

In GPML2013a, specific Namespace are defined for Biopax elements.

RDF_NAMESPACE - Static variable in class org.pathvisio.libgpml.model.GPMLFormatAbstract

In GPML2013a, specific Namespace are defined for Biopax elements.

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

RDF_STRING - Static variable in class org.pathvisio.libgpml.model.GPMLFormatAbstract

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

RDFS_NAMESPACE - Static variable in class org.pathvisio.libgpml.model.GPMLFormatAbstract

readAllElementIds(Element, Set<String>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads elementIds (GraphIds in GPML2013a) of root element and adds to elementIdSet.

readAnchors(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads anchor LineElement.Anchor information for line element from jdom element.

readAnchors(LineElement, Element, Set<String>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads anchor LineElement.Anchor information for line element from element.

readAnnotationRefs(PathwayModel, Referenceable.Annotatable, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads Annotation and PathwayElement.AnnotationRef information for an Referenceable.Annotatable.

readArrowHeadType(Element, String) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Returns the arrowHead for give jdom point element.

readAuthors(Pathway, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads author Pathway.Author information for pathway from root element.

readCitationRefs(PathwayModel, Referenceable.Citable, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads Citation and PathwayElement.CitationRef information for a Referenceable.Citable.

readCommentGroup(PathwayElement, Element, Map<String, GPML2013aReader.PublicationXref>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads comment group (comment, biopaxref/citationRef, dynamic property) for pathway element from jdom element.

readCommentGroup(PathwayModel, PathwayElement, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads comment group (comment, dynamic property, annotationRef, citationRef, evidenceRef) information for PathwayElement from jdom element.

readComments(PathwayElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads comment PathwayElement.Comment information for pathway element from jdom element.

readComments(PathwayElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads comment PathwayElement.Comment information for pathway element from jdom element.

readDataNodes(PathwayModel, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads data node DataNode information for pathway model from root element.

readDataNodes(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads data node DataNode information for pathway model from root element.

readDynamicProperties(PathwayElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads gpml:Attribute or dynamic property information for PathwayElement from jdom element.

readDynamicProperties(PathwayElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads dynamic property PathwayElement.setDynamicProperty(java.lang.String, java.lang.String) information for pathway element from jdom element.

readElementId(String, Element, Set<String>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Returns elementId read for given Element.

readEvidenceRefs(PathwayModel, Referenceable.Evidenceable, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads Evidence and PathwayElement.EvidenceRef information for an Referenceable.Evidenceable.

readFontProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads font property information.

readFontProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads font property information.

readFromRoot(PathwayModel, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads information from root element of Jdom document Document to the pathway model PathwayModel.

readFromRoot(PathwayModel, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads information from root element of Jdom document Document to the pathway model PathwayModel.

readFromRoot(PathwayModel, Element) - Method in interface org.pathvisio.libgpml.model.GPMLFormatReader

Reads pathway model from root element.

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

readFromXml(InputStream, boolean) - Method in class org.pathvisio.libgpml.model.PathwayModel

readFromXml(Reader, boolean) - Method in class org.pathvisio.libgpml.model.PathwayModel

readFromXml(PathwayModel, File, boolean) - Static method in class org.pathvisio.libgpml.model.GPMLFormat

Reads the JDOM document from the file specified

readFromXml(PathwayModel, InputStream, boolean) - Static method in class org.pathvisio.libgpml.model.GPMLFormat

Reads the JDOM document from the string specified

readFromXml(PathwayModel, Reader, boolean) - Static method in class org.pathvisio.libgpml.model.GPMLFormat

Reads the JDOM document from the string specified

readFromXmlImpl(PathwayModel, InputSource, boolean) - Static method in class org.pathvisio.libgpml.model.GPMLFormat

Reads a pathway model from given input source.

readGraphicalLines(PathwayModel, Element, Map<String, Element>, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads graphical line GraphicalLine information for pathway model from root element.

readGraphicalLines(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads graphical line GraphicalLine information for pathway model from root element.

readGroupGroupRef(PathwayModel, Element, Map<String, Group>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads groupRef property ShapedElement.setGroupRef(org.pathvisio.libgpml.model.Group) information of group pathway element.

readGroupRef(PathwayModel, ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads groupRef information for DataNode, Label, and Shape.

readGroupRef(ShapedElement, Element, Map<String, Group>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads and sets groupRef for given (shaped) pathway element and jdom Element.

readGroups(PathwayModel, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads group Group information for pathway model from root element.

readGroups(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>, Map<String, Group>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads group Group information for pathway model from root element.

readInfoBox(Pathway, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads the infobox x and y coordinate information.

readInfoMap(Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

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>).

readInteractions(PathwayModel, Element, Map<String, Element>, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads interaction Interaction information for pathway model from root element.

readInteractions(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads interaction Interaction information for pathway model from root element.

readLabels(PathwayModel, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads label Label information for pathway model from root element.

readLabels(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads label Label information for pathway model from root element.

readLegend(Pathway, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads the Legend CenterX and CenterY to pathway dynamic properties PathwayElement.setDynamicProperty(java.lang.String, java.lang.String) .

readLineElement(LineElement, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads line element LineElement information for interaction or graphical line from jdom element.

readLineElement(PathwayModel, LineElement, Element, Map<String, Element>, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads line element LineElement information for interaction or graphical line from jdom element.

readLineStyleProperty(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads line style property information.

readLineStyleProperty(LineElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads line style property information.

readOpenControlledVocabulary(PathwayModel, Element, Set<String>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads gpml:Biopax bp:OpenControlledVocabulary information to Annotation for pathway model from root element.

readPathway(Pathway, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads pathway information from root element.

readPathway(Pathway, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads pathway information from jdom root element.

readPointElementRefs(PathwayModel, Map<String, Group>, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads LineElement.LinePoint elementRefs.

readPointElementRefs(PathwayModel, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads elementRef LineElement.LinePoint.setElementRef(org.pathvisio.libgpml.model.GraphLink.LinkableTo) for pathway model points.

readPoints(LineElement, Element, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads point LineElement.LinePoint information for line element.

readPoints(LineElement, Element, Set<String>, Map<Element, LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads points LineElement.LinePoint for pathway model line pathway elements.

readPublicationXrefInfo(List<Element>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads Biopax PublicationXref information from PublicationXref children elements.

readPublicationXrefMap(Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads gpml:Biopax:bp:PublicationXref and maps "id" to GPML2013aReader.PublicationXref in idToPublicationXref.

readPublicationXrefs(PathwayElement, Element, Map<String, GPML2013aReader.PublicationXref>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads gpml:Biopax:bp:PublicationXref and BiopaxRef information for pathway element from jdom element.

readRectProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads rect property information.

readRectProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads rect property information.

readShapedElement(PathwayModel, ShapedElement, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads common properties for shaped pathway elements ShapedElement.

readShapedElement(ShapedElement, Element, Map<String, GPML2013aReader.PublicationXref>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads shaped pathway element ShapedElement information: graphics and comment group (comments, biopaxRefs (equivalent to citationRefs), and dynamic properties).

readShapes(PathwayModel, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads shape Shape information for pathway model from root element.

readShapes(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>, Map<String, Group>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads shape Shape information for pathway model from root element.

readShapeStyleProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads shape style property information.

readShapeStyleProperty(ShapedElement, Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads shape style property information.

readStates(PathwayModel, Element, Set<String>, Map<String, GPML2013aReader.PublicationXref>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads state DataNode.State information for pathway model from root element.

readStates(PathwayModel, DataNode, Element, Map<String, Element>) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads state DataNode.State information for data node from element.

readUrl(Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads Url link information from element.

readXref(Element) - Method in class org.pathvisio.libgpml.model.GPML2013aReader

Reads xref Xref information from element.

readXref(Element) - Method in class org.pathvisio.libgpml.model.GPML2021Reader

Reads xref Xref information from jdom element.

recalculateShape(ConnectorRestrictions) - Method in interface org.pathvisio.libgpml.model.connector.ConnectorShape

Forces the connector to redraw it's path.

recalculateShape(ConnectorRestrictions) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape

Forces the connector to redraw it's path.

recalculateShape(ConnectorRestrictions) - Method in class org.pathvisio.libgpml.model.connector.FreeConnectorShape

Forces the connector to redraw it's path.

recalculateShape(ConnectorRestrictions) - Method in class org.pathvisio.libgpml.model.connector.StraightConnectorShape

Forces the connector to redraw it's path.

received - Variable in class org.pathvisio.libgpml.model.Test

receivedElementEvents - Variable in class org.pathvisio.libgpml.model.Test

RECEPHEIGHT - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry

RECEPWIDTH - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry

rectangle - Static variable in class org.pathvisio.libgpml.model.type.ShapeType

RECTANGLE - Static variable in class org.pathvisio.libgpml.model.type.ShapeType

refeeChanged() - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableFrom

Called whenever the object being referred to changes coordinates.

refeeChanged() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint

Called whenever the object being referred to has changed.

Referenceable - Interface in org.pathvisio.libgpml.model

Interface for Referenceable.Annotatable, Referenceable.Citable, and Referenceable.Evidenceable.

Referenceable.Annotatable - Interface in org.pathvisio.libgpml.model

Interface for classes which can hold a List of PathwayElement.AnnotationRef.

Referenceable.Citable - Interface in org.pathvisio.libgpml.model

Interface for classes which can hold a List of PathwayElement.CitationRef.

Referenceable.Evidenceable - Interface in org.pathvisio.libgpml.model

Interface for classes which can hold a List of PathwayElement.EvidenceRef.

refreshLineElements(PathwayModel) - Static method in class org.pathvisio.libgpml.model.GPMLFormatAbstract

Refreshes line elements.

register(String) - Static method in class org.pathvisio.libgpml.model.type.AnchorShapeType

Returns an AnchorType from a given string identifier name.

register(String) - Static method in class org.pathvisio.libgpml.model.type.AnnotationType

Returns an AnnotationType from a given string identifier name.

register(String) - Static method in class org.pathvisio.libgpml.model.type.ArrowHeadType

Returns a ArrowHeadType from a given string identifier name.

register(String) - Static method in class org.pathvisio.libgpml.model.type.ConnectorType

Returns a ConnectorType from a given name.

register(String) - Static method in class org.pathvisio.libgpml.model.type.DataNodeType

Returns a DataNodeType from a given string identifier name.

register(String) - Static method in class org.pathvisio.libgpml.model.type.GroupType

Returns a GroupType from a given string identifier name.

register(String) - Static method in class org.pathvisio.libgpml.model.type.LineStyleType

Returns a LineStyleType from a given string identifier name.

register(String) - Static method in class org.pathvisio.libgpml.model.type.StateType

Returns a StateType from a given string identifier name.

register(String, Shape) - Static method in class org.pathvisio.libgpml.model.type.ShapeType

Returns a ShapeType from a given string identifier name.

registerAnchor(String, Shape) - Static method in class org.pathvisio.libgpml.model.shape.ShapeRegistry

Registers an anchor shape.

registerArrow(String, Shape, ArrowShape.FillType) - Static method in class org.pathvisio.libgpml.model.shape.ShapeRegistry

Registers an arrow shape (without lineEndingLength parameter).

registerArrow(String, Shape, ArrowShape.FillType, int) - Static method in class org.pathvisio.libgpml.model.shape.ShapeRegistry

Registers an arrow shape.

registerProperty(Property) - Static method in class org.pathvisio.libgpml.prop.PropertyManager

Registers a property.

registerPropertyType(PropertyType) - Static method in class org.pathvisio.libgpml.prop.PropertyManager

Registers a property type.

registerShape(String, Class<? extends ConnectorShape>) - Static method in class org.pathvisio.libgpml.model.connector.ConnectorShapeFactory

registerShape(IShape) - Static method in class org.pathvisio.libgpml.model.shape.ShapeRegistry

Registers the given IShape.

registerShapes() - Static method in class org.pathvisio.libgpml.model.shape.AnchorShapeRegistry

registerShapes() - Static method in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry

registerShapes() - Static method in class org.pathvisio.libgpml.model.shape.ShapeCatalog

relX - Variable in class org.pathvisio.libgpml.model.DataNode.State

relX - Variable in class org.pathvisio.libgpml.model.LineElement.LinePoint

RELX - org.pathvisio.libgpml.prop.StaticProperty

relY - Variable in class org.pathvisio.libgpml.model.DataNode.State

relY - Variable in class org.pathvisio.libgpml.model.LineElement.LinePoint

RELY - org.pathvisio.libgpml.prop.StaticProperty

remove() - Method in class org.pathvisio.libgpml.debug.DebugList.DebugIterator

remove(int) - Method in class org.pathvisio.libgpml.debug.DebugList

remove(Object) - Method in class org.pathvisio.libgpml.debug.DebugList

remove(PathwayObject) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes a PathwayObject from this Pathway.

removeAliasRef(Group) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the mapping of given elementRef key from the elementRefToDataNode hash map.

removeAll(Collection<?>) - Method in class org.pathvisio.libgpml.debug.DebugList

removeAnchor(LineElement.Anchor) - Method in class org.pathvisio.libgpml.model.LineElement

Removes given anchor from the anchors list.

removeAnchors() - Method in class org.pathvisio.libgpml.model.LineElement

Removes all anchors from the anchors list.

removeAnnotation(Annotation) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes given annotation from annotations list and elementIdToPathwayObject map.

removeAnnotationRef(PathwayElement.AnnotationRef) - Method in class org.pathvisio.libgpml.model.Annotation

Removes the given annotationRef from annotationRefs list of this annotation.

removeAnnotationRef(PathwayElement.AnnotationRef) - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef

Removes given annotationRef from annotationRefs list.

removeAnnotationRef(PathwayElement.AnnotationRef) - Method in class org.pathvisio.libgpml.model.PathwayElement

Removes given annotationRef from annotationRefs list.

removeAnnotationRef(PathwayElement.AnnotationRef) - Method in interface org.pathvisio.libgpml.model.Referenceable.Annotatable

Removes given annotationRef from annotationRefs list.

removeAnnotationRefs() - Method in class org.pathvisio.libgpml.model.Annotation

Removes all annotationRefs from annotationRefs list.

removeAnnotationRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef

Removes all annotationRefs from annotationRefs list.

removeAnnotationRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement

Removes all annotationRefs from annotationRefs list.

removeAnnotationRefs() - Method in interface org.pathvisio.libgpml.model.Referenceable.Annotatable

Removes all annotationRefs from annotationRefs list.

removeAuthor(Pathway.Author) - Method in class org.pathvisio.libgpml.model.Pathway

Removes the given author from authors list.

removeCitation(Citation) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes given citation from citations list and elementIdToPathwayObject map.

removeCitationRef(PathwayElement.CitationRef) - Method in class org.pathvisio.libgpml.model.Citation

Removes the given citationRef from citationRefs list of the citation.

removeCitationRef(PathwayElement.CitationRef) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef

Removes given citationRef from citationRefs list.

removeCitationRef(PathwayElement.CitationRef) - Method in class org.pathvisio.libgpml.model.PathwayElement

Removes given citationRef from citationRefs list.

removeCitationRef(PathwayElement.CitationRef) - Method in interface org.pathvisio.libgpml.model.Referenceable.Citable

Removes given citationRef from citationRefs list.

removeCitationRefs() - Method in class org.pathvisio.libgpml.model.Citation

Removes all citationRefs from citationRefs list.

removeCitationRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef

Removes all citationRef from citationRefs list.

removeCitationRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement

Removes all citationRef from citationRefs list.

removeCitationRefs() - Method in interface org.pathvisio.libgpml.model.Referenceable.Citable

Removes all citationRefs from citationRefs list.

removeComment(PathwayElement.Comment) - Method in class org.pathvisio.libgpml.model.PathwayElement

Removes given comment from comments list.

removeDataNode(DataNode) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the given dataNode from dataNodes list and elementIdToPathwayObject map.

removeElementId(String) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the mapping of given elementId key from the elementIdToPathwayObject hash map.

removeElementRef(GraphLink.LinkableTo, GraphLink.LinkableFrom) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes a linePoint linked to a elementRef.

removeEvidence(Evidence) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes given evidence from evidences list and elementIdToPathwayObject map.

removeEvidenceRef(PathwayElement.EvidenceRef) - Method in class org.pathvisio.libgpml.model.Evidence

Removes the given evidenceRef from evidenceRefs list of this evidence.

removeEvidenceRef(PathwayElement.EvidenceRef) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef

Removes given evidenceRef from evidenceRefs list.

removeEvidenceRef(PathwayElement.EvidenceRef) - Method in class org.pathvisio.libgpml.model.PathwayElement

Removes given evidenceRef from evidenceRefs list.

removeEvidenceRef(PathwayElement.EvidenceRef) - Method in interface org.pathvisio.libgpml.model.Referenceable.Evidenceable

Removes given evidenceRef from evidenceRefs list.

removeEvidenceRefs() - Method in class org.pathvisio.libgpml.model.Evidence

Removes all evidenceRefs from evidenceRefs list.

removeEvidenceRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef

Removes all evidenceRefs from evidenceRefs list.

removeEvidenceRefs() - Method in class org.pathvisio.libgpml.model.PathwayElement

Removes all evidenceRefs from evidenceRefs list.

removeEvidenceRefs() - Method in interface org.pathvisio.libgpml.model.Referenceable.Evidenceable

Removes all evidenceRefs from evidenceRefs list.

removeExtension(String) - Static method in class org.pathvisio.libgpml.util.FileUtils

Removes the file extension (everything from the last occurence of '.')

removeGraphicalLine(GraphicalLine) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the given graphicalLine from graphicalLines list and elementIdToPathwayObject map..

removeGroup(Group) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the given group from groups list and elementIdToPathwayObject map.

removeInteraction(Interaction) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the given interaction from interactions list and elementIdToPathwayObject map..

removeLabel(Label) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the given label from labels list and elementIdToPathwayObject map.

removeLinePoints(List<LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.LineElement

Removes all points from the given line points list.

removeListener(PathwayModelListener) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes listener from this pathway model.

removeListener(PathwayObjectListener) - Method in class org.pathvisio.libgpml.model.PathwayObject

Removes pathway object listener.

removeOldPathway(Pathway) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes old pathway prior to PathwayModel.setNewPathway(org.pathvisio.libgpml.model.Pathway), both called by PathwayModel.replacePathway(org.pathvisio.libgpml.model.Pathway).

removePathwayElement(Groupable) - Method in class org.pathvisio.libgpml.model.Group

Removes the given pathway element from pathwayElements list of the group.

removePathwayElements() - Method in class org.pathvisio.libgpml.model.Group

Removes all pathway elements from the pathwayElements list.

removePathwayObject(PathwayObject) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the given pathway object from pathway model and elementIdToPathwayObject map.

removeShape(Shape) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes the given shape from shapes list and elementIdToPathwayObject map.

removeState(DataNode.State) - Method in class org.pathvisio.libgpml.model.DataNode

Removes given state from states list.

removeStates() - Method in class org.pathvisio.libgpml.model.DataNode

Removes all states from states list.

removeStatusFlagListener(PathwayModel.StatusFlagListener) - Method in class org.pathvisio.libgpml.model.PathwayModel

Removes a status flag listener

replaceExtension(File, String) - Static method in class org.pathvisio.libgpml.util.FileUtils

Replaces file extension with something else.

replacePathway(Pathway) - Method in class org.pathvisio.libgpml.model.PathwayModel

Replaces the Pathway, calls PathwayModel.removeOldPathway(org.pathvisio.libgpml.model.Pathway) and then PathwayModel.setNewPathway(org.pathvisio.libgpml.model.Pathway).

resetWayPointPreferences() - Method in class org.pathvisio.libgpml.model.LineElement

RESIZED - Static variable in class org.pathvisio.libgpml.model.PathwayModelEvent

retainAll(Collection<?>) - Method in class org.pathvisio.libgpml.debug.DebugList

RIGHT - org.pathvisio.libgpml.model.type.HAlignType

RNA - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType

RNA_ICON - org.pathvisio.libgpml.model.shape.ShapeCatalog.Internal

RNA_ICON - Static variable in class org.pathvisio.libgpml.model.type.ShapeType

RootElementFinder - Class in org.pathvisio.libgpml.util

This is similar to com.sun.xml.internal.ws.message.RootElementSniffer, perhaps can be re-used.

RootElementFinder() - Constructor for class org.pathvisio.libgpml.util.RootElementFinder

RootElementFinder.RootElementHandler - Class in org.pathvisio.libgpml.util

Root element handler class.

RootElementHandler() - Constructor for class org.pathvisio.libgpml.util.RootElementFinder.RootElementHandler

rootQName - Variable in class org.pathvisio.libgpml.util.RootElementFinder.RootElementHandler

rootUri - Variable in class org.pathvisio.libgpml.util.RootElementFinder.RootElementHandler

rotate(LinAlg.Point, double) - Static method in class org.pathvisio.libgpml.util.LinAlg

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

ROTATION - org.pathvisio.libgpml.prop.StaticProperty

ROTATION - org.pathvisio.libgpml.prop.StaticPropertyType

ROUNDED_RECTANGLE - Static variable in class org.pathvisio.libgpml.model.type.ShapeType

RRDIAM - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry

running - Variable in class org.pathvisio.libgpml.debug.StopWatch

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