S-Index

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S

s - Variable in class org.pathvisio.libgpml.debug.Logger
s1 - Variable in class org.pathvisio.libgpml.model.TestCopy
SARCOPLASMIC_RETICULUM - org.pathvisio.libgpml.model.shape.ShapeCatalog.Internal
SARCOPLASMIC_RETICULUM - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
schemaType - Variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract.AttributeInfo: xsd validated type.
Segment(Point2D, Point2D) - Constructor for class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment
SEGMENT_OFFSET - Static variable in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
SEGMENTED - Static variable in class org.pathvisio.libgpml.model.type.ConnectorType
SegmentedConnector - Class in org.pathvisio.libgpml.model.connector: Base class for segmented connectors.
SegmentedConnector() - Constructor for class org.pathvisio.libgpml.model.connector.SegmentedConnector
segments - Variable in class org.pathvisio.libgpml.model.connector.AbstractConnector
set(int, E) - Method in class org.pathvisio.libgpml.debug.DebugList
set(E) - Method in class org.pathvisio.libgpml.debug.DebugList.DebugIterator
setAliasRef(Group) - Method in class org.pathvisio.libgpml.model.DataNode: Sets the group aliasRef to which this data node refers to as an alias.
setAnnotatable(Referenceable.Annotatable) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Sets the target pathway, pathway element, or citationRef Referenceable.Annotatable for this annotationRef.
setAnnotatableTo(Referenceable.Annotatable) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Sets the target pathway element or citationRef Referenceable.Annotatable for this annotationRef.
setAnnotation(Annotation) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Sets the source annotation for this annotationRef.
setAnnotationTo(Annotation) - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Sets the source annotation for this annotationRef.
setAttr(String, String, Element, String) - Method in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Sets a certain attribute value, performs a basic check for some types, and throws an exception if trying to set an invalid value.
setAuthors(List<String>) - Method in class org.pathvisio.libgpml.model.Citation: Sets list of authors for this citation (for GPML2013a Biopax).
setBackgroundColor(Color) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the background color of this pathway.
setBoardHeight(double) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the board height.
setBoardWidth(double) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the board width.
setBorderColor(Color) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the border color of this shaped pathway element.
setBorderStyle(LineStyleType) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the visual appearance of a border, e.g.
setBorderWidth(double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the pixel value for the border of this shaped pathway element.
setCenterX(double) - Method in interface org.pathvisio.libgpml.model.Groupable: Sets the x position of the center of the pathway element.
setCenterX(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the x position of the center of the line.
setCenterX(double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the center x coordinate for this shaped pathway element.
setCenterY(double) - Method in interface org.pathvisio.libgpml.model.Groupable: Sets the y position of the center of the pathway element.
setCenterY(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the y position of the center of the line.
setCenterY(double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the center y coordinate for this shaped pathway element.
setCitable(Referenceable.Citable) - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Sets the target pathway, pathway element, or annotationRef Referenceable.Citable to which the annotationRef belongs.
setCitableTo(Referenceable.Citable) - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Sets the target pathway, pathway element, or annotationRef Referenceable.Citable for this annotationRef.
setCitation(Citation) - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Sets the source citation for this citationRef.
setCitationTo(Citation) - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Sets the source citation for this citationRef.
setComments(List<PathwayElement.Comment>) - Method in class org.pathvisio.libgpml.model.PathwayElement: Sets comments to the given comments list.
setCommentText(String) - Method in class org.pathvisio.libgpml.model.PathwayElement.Comment: Sets the text of this Comment.
setConnectorType(ConnectorType) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the value of the connectorType property.
setDescription(String) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the description of this pathway.
setDest(String) - Method in class org.pathvisio.libgpml.debug.Logger: If dest is "STDERR" or "STDOUT", the standard error / output are used.
setDynamicProperty(String, String) - Method in class org.pathvisio.libgpml.model.PathwayElement: Sets a dynamic property.
setElementId(String) - Method in class org.pathvisio.libgpml.model.PathwayObject: Sets the elementId of the pathway element.
setElementRef(GraphLink.LinkableTo) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Sets the pathway element to which the point refers to.
setEndArrowHeadType(ArrowHeadType) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the arrow head type of the end point.
setEndElementRef(GraphLink.LinkableTo) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the elementRef for the end point.
setEndLinePoint(LineElement.LinePoint) - Method in class org.pathvisio.libgpml.model.LineElement: Sets end linePoint coordinates to the coordinates of the given linePoint.
setEndLinePointX(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the x coordinate of the end point.
setEndLinePointY(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the y coordinate of the end point.
setEvidence(Evidence) - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef: Sets the source evidence for this evidenceRef.
setEvidenceable(Referenceable.Evidenceable) - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef: Sets the target pathway, pathway element, or evidenceRef Referenceable.Evidenceable to which the evidenceRef belongs.
setEvidenceableTo(Referenceable.Evidenceable) - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef: Sets the target pathway, pathway element, or evidenceRef Referenceable.Evidenceable for this evidenceRef.
setEvidenceTo(Evidence) - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef: Sets the source evidence for this evidenceRef.
setFillColor(Color) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the color used to paint the area of this shaped pathway element, not including its border.
setFontDecoration(boolean) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the typographic style for underline or normal.
setFontName(String) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the name of the set of printable text characters to be used for visualization, e.g., Arial.
setFontSize(double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets point value for the size of the font.
setFontStrikethru(boolean) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the typographic style for strikethru or normal.
setFontStyle(boolean) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the typographic style applied to displayed text, e.g.
setFontWeight(boolean) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the thickness of the font used, a bold font would have more weight.
setGeneratedElementId() - Method in class org.pathvisio.libgpml.model.PathwayObject: Sets the elementId to generated elementId from pathwayModel.
setGroupGraphicsProperty(Group, GroupType) - Method in class org.pathvisio.libgpml.model.GPML2013aReader: Reads and sets graphics properties for Group.
setGroupRef(Group) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the parent group for this pathway element.
setGroupRef(Group) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the parent group for this pathway element.
setGroupRefTo(Group) - Method in class org.pathvisio.libgpml.model.DataNode.State: Do not allow groupRef to be set for this state.
setGroupRefTo(Group) - Method in interface org.pathvisio.libgpml.model.Groupable: Verifies if given parent group is new and valid.
setGroupRefTo(Group) - Method in class org.pathvisio.libgpml.model.LineElement: Verifies if given parent group is new and valid.
setGroupRefTo(Group) - Method in class org.pathvisio.libgpml.model.ShapedElement: Verifies if given parent group is new and valid.
setHAlign(HAlignType) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the horizontal alignment of displayed text, e.g., Left, Center, Right.
setHasRef(boolean) - Method in class org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref: Sets hasRef to true if at least one gpml:CommentGroup:BiopaxRef which refers to this gpml:Biopax:PublicationXref, false otherwise.
setHeight(double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the height of this shaped pathway element.
setHidden(boolean) - Method in enum org.pathvisio.libgpml.prop.StaticProperty
setHref(String) - Method in class org.pathvisio.libgpml.model.Label: Sets the hyperlink for this Label.
setLeft(double) - Method in interface org.pathvisio.libgpml.model.Groupable: Sets the position of the left side of the rectangular bounds of the pathway element.
setLeft(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the position of the left side of the rectangular bounds of the line
setLeft(double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the center x coordinate given the left x coordinate of the bounding box around (start, end) this shaped pathway element.
setLicense(String) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the license of this pathway.
setLineColor(Color) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the color of a line.
setLinePoints(List<LineElement.LinePoint>) - Method in class org.pathvisio.libgpml.model.LineElement: Sets linePoints to the given list of LinePoints.
setLineStyle(LineStyleType) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the visual appearance of a line, e.g.
setLineWidth(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the pixel value for the width of a line.
setLogLevel(boolean, boolean, boolean, boolean, boolean, boolean) - Method in class org.pathvisio.libgpml.debug.Logger: get/set log level to a certain level.
setMEnd(Point2D) - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment
setMStart(Point2D) - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment
setName(String) - Method in class org.pathvisio.libgpml.model.Pathway.Author: Sets the name of this author.
setNewElement(PathwayElement) - Method in class org.pathvisio.libgpml.model.CopyElement: Sets the new pathway element.
setNewPathway(Pathway) - Method in class org.pathvisio.libgpml.model.PathwayModel: Sets new pathway after to PathwayModel.removeOldPathway(org.pathvisio.libgpml.model.Pathway), both called by PathwayModel.replacePathway(org.pathvisio.libgpml.model.Pathway).
setOf(T) - Static method in class org.pathvisio.libgpml.util.Utils: Creates a new Set of the given value(s)
setOrder(int) - Method in class org.pathvisio.libgpml.model.Pathway.Author: Sets the authorship order of this author.
setOrganism(String) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the organism of this pathway.
setPathwayModel(PathwayModel) - Method in class org.pathvisio.libgpml.model.PathwayObject: Sets the pathway model of this pathway element to the given pathway model.
setPathwayModelTo(PathwayModel) - Method in class org.pathvisio.libgpml.model.DataNode: Sets the pathway model for this pathway element.
setPathwayModelTo(PathwayModel) - Method in class org.pathvisio.libgpml.model.DataNode.State: Sets the pathway model for this pathway element.
setPathwayModelTo(PathwayModel) - Method in class org.pathvisio.libgpml.model.LineElement.GenericPoint: Sets the pathway model for this line point or anchor.
setPathwayModelTo(PathwayModel) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the pathway model for this pathway element.
setPathwayModelTo(PathwayModel) - Method in class org.pathvisio.libgpml.model.PathwayObject: Sets the pathway model for this pathway element.
setPosition(double) - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Sets the proportional distance of an anchor along the line it belongs to, between 0 and 1.
setPropertyEx(Object, Object) - Method in class org.pathvisio.libgpml.model.PathwayElement: Sets dynamic or static properties at the same time.
setPropertyEx(Object, Object) - Method in class org.pathvisio.libgpml.model.PathwayObject: Sets properties.
setRelativePosition(double, double) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Sets X, Y, relX and relY for this point.
setRelX(double) - Method in class org.pathvisio.libgpml.model.DataNode.State: Sets the relative x coordinate.
setRelX(double) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Sets the relative x coordinate.
setRelY(double) - Method in class org.pathvisio.libgpml.model.DataNode.State: Sets the relative y coordinate.
setRelY(double) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Sets the relative y coordinate.
setRotation(Double) - Method in class org.pathvisio.libgpml.model.Group: Rotation is not allowed for Groups and will always be set to 0 (default).
setRotation(Double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the rotation of this shaped pathway element.
setSegments(ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.AbstractConnector: Sets the segment cache that will be returned by AbstractConnector.getSegments().
setShape(Shape) - Method in class org.pathvisio.libgpml.model.connector.AbstractConnector: Sets the shape cache that will be returned by AbstractConnector.getShape().
setShapeType(IShape) - Method in class org.pathvisio.libgpml.model.ShapedElement: Returns the visual appearance of a two dimensional object, e.g.
setShapeType(AnchorShapeType) - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Sets the shapeType for given anchor pathway element.
setSource(String) - Method in class org.pathvisio.libgpml.model.Citation: Sets source for this citation (for GPML2013a Biopax).
setSource(String) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the source of this pathway, e.g.
setSource(String) - Method in class org.pathvisio.libgpml.model.PathwayElement.Comment: Sets the source of this Comment.
setSourceElement(PathwayElement) - Method in class org.pathvisio.libgpml.model.CopyElement: Sets source pathway element.
setSourceFile(File) - Method in class org.pathvisio.libgpml.model.PathwayModel
setStartArrowHeadType(ArrowHeadType) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the arrow head type of the start point.
setStartElementRef(GraphLink.LinkableTo) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the elementRef for the start point.
setStartLinePoint(LineElement.LinePoint) - Method in class org.pathvisio.libgpml.model.LineElement: Sets start linePoint coordinates to the coordinates of the given linePoint.
setStartLinePointX(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the x coordinate of the start point.
setStartLinePointY(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the y coordinate of the start point.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.DataNode: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.DataNode.State: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.Group: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.Interaction: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.Label: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.LineElement: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.Pathway: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.PathwayElement: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.PathwayObject: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.Shape: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStaticProperty(StaticProperty, Object) - Method in class org.pathvisio.libgpml.model.ShapedElement: This works so that o.setNotes(x) is the equivalent of o.setProperty("Notes", x); Value may be null in some cases, e.g.
setStream(PrintStream) - Method in class org.pathvisio.libgpml.debug.Logger
setTextColor(Color) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the color of text for this shaped pathway element.
setTextLabel(String) - Method in class org.pathvisio.libgpml.model.DataNode: Sets the text of this shaped pathway element.
setTextLabel(String) - Method in class org.pathvisio.libgpml.model.DataNode.State: Sets the text of of this shaped pathway element.
setTextLabel(String) - Method in class org.pathvisio.libgpml.model.Group: Sets the text of this shaped pathway element.
setTextLabel(String) - Method in class org.pathvisio.libgpml.model.Label: Sets the text of this shaped pathway element.
setTextLabel(String) - Method in class org.pathvisio.libgpml.model.Shape: Sets the text of this shaped pathway element.
setTextLabel(String) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets text label for this shaped pathway elements.
setTitle(String) - Method in class org.pathvisio.libgpml.model.Citation: Sets source for this citation (for GPML2013a Biopax).
setTitle(String) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the title or name of this pathway.
setTop(double) - Method in interface org.pathvisio.libgpml.model.Groupable: Sets the position of the top side of the rectangular bounds of the pathway element.
setTop(double) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the position of the top side of the rectangular bounds of the line
setTop(double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the center y coordinate given the top y coordinate of the bounding box around (start, end) this shaped pathway element.
setType(AnnotationType) - Method in class org.pathvisio.libgpml.model.Annotation: Sets the type of this annotation.
setType(DataNodeType) - Method in class org.pathvisio.libgpml.model.DataNode: Sets the type of this datanode, e.g.
setType(GroupType) - Method in class org.pathvisio.libgpml.model.Group: Sets GroupType to the given groupType.
setType(StateType) - Method in class org.pathvisio.libgpml.model.DataNode.State: Sets the type of this state.
setUp() - Method in class org.pathvisio.libgpml.debug.TestDebug
setUp() - Method in class org.pathvisio.libgpml.model.Test
setUp() - Method in class org.pathvisio.libgpml.model.TestAlias
setUp() - Method in class org.pathvisio.libgpml.model.TestAnchor: Creates and adds anchor to line, line to pathwayModel.
setUp() - Method in class org.pathvisio.libgpml.model.TestAnnotation: Two annotationRefs (same annotation) added to a data node.
setUp() - Method in class org.pathvisio.libgpml.model.TestCitation: Two annotationRefs (same annotation) added to a data node.
setUp() - Method in class org.pathvisio.libgpml.model.TestCopy
setUp() - Method in class org.pathvisio.libgpml.model.TestElementId
setUp() - Method in class org.pathvisio.libgpml.model.TestEvidence: Two annotationRefs (same annotation) added to a data node.
setUp() - Method in class org.pathvisio.libgpml.model.TestGraph
setUp() - Method in class org.pathvisio.libgpml.model.TestGraphLink
setUp() - Method in class org.pathvisio.libgpml.model.TestGroup: Creates and adds anchor to line, line to pathwayModel.
setUp() - Method in class org.pathvisio.libgpml.model.TestGroupNested: Creates and adds anchor to line, line to pathwayModel.
setUp() - Method in class org.pathvisio.libgpml.model.TestLinePoint: Creates and adds anchor to line, line to pathwayModel.
setUp() - Method in class org.pathvisio.libgpml.model.TestReferenceable
setUp() - Method in class org.pathvisio.libgpml.model.TestState
setUrlLink(String) - Method in class org.pathvisio.libgpml.model.Annotation: Sets the url link for a web address.
setUrlLink(String) - Method in class org.pathvisio.libgpml.model.Citation: Sets the url link for a web address.
setUrlLink(String) - Method in class org.pathvisio.libgpml.model.Evidence: Sets the url link for a web address.
setUsername(String) - Method in class org.pathvisio.libgpml.model.Pathway.Author: Sets the username of this author.
setVAlign(VAlignType) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the vertical alignment of displayed text, e.g., Top, Middle, Bottom.
setValue(String) - Method in class org.pathvisio.libgpml.model.Annotation: Sets the name, term, or text of this annotation.
setValue(String) - Method in class org.pathvisio.libgpml.model.Evidence: Sets the name, term, or text of this evidence.
setVersion(String) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the version of this pathway.
setWayPoints(ConnectorShape.WayPoint[]) - Method in class org.pathvisio.libgpml.model.connector.AbstractConnector: Sets the waypoints cache that will be returned by AbstractConnector.getWayPoints().
setWidth(double) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the width of this shaped pathway element.
setX(double) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Sets x coordinate to given value.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.Annotation: Sets the Xref for this annotation.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.Citation: Sets the Xref for this citation.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.DataNode: Sets the Xref for this datanode.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.DataNode.State: Sets the Xref for this state.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.Evidence: Sets the Xref for this evidence.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.Group: Sets the Xref for this group.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.Interaction: Sets the Xref for this interaction.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.Pathway.Author: Sets the Xref for the author.
setXref(Xref) - Method in class org.pathvisio.libgpml.model.Pathway: Sets the Xref for this pathway.
setXref(Xref) - Method in interface org.pathvisio.libgpml.model.Xrefable: Sets the Xref for this pathway element.
setY(double) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Sets y coordinate to given value.
setYear(String) - Method in class org.pathvisio.libgpml.model.Citation: Sets year for this citation (for GPML2013a Biopax).
setZOrder(int) - Method in class org.pathvisio.libgpml.model.DataNode.State: Do nothing.
setZOrder(int) - Method in interface org.pathvisio.libgpml.model.Drawable: Sets the z-order of this pathway element.
setZOrder(int) - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Do nothing.
setZOrder(int) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Do nothing.
setZOrder(int) - Method in class org.pathvisio.libgpml.model.LineElement: Sets the z-order of this pathway element.
setZOrder(int) - Method in class org.pathvisio.libgpml.model.ShapedElement: Sets the z-order of this pathway element.
sh - Variable in class org.pathvisio.libgpml.model.shape.AbstractShape
shape - Variable in class org.pathvisio.libgpml.model.connector.AbstractConnector
shape - Variable in class org.pathvisio.libgpml.model.LineElement
shape - Variable in class org.pathvisio.libgpml.model.shape.AnchorShape
shape - Variable in class org.pathvisio.libgpml.model.shape.ArrowShape
shape - Variable in class org.pathvisio.libgpml.model.type.ShapeType
Shape - Class in org.pathvisio.libgpml.model: This class stores all information relevant to a Shape pathway element.
Shape() - Constructor for class org.pathvisio.libgpml.model.Shape: Instantiates a Shape pathway element.
SHAPE - org.pathvisio.libgpml.model.type.ObjectType: A graphical pathway element with or without a text label.
ShapeCatalog - Class in org.pathvisio.libgpml.model.shape: This class defines some shapes.
ShapeCatalog() - Constructor for class org.pathvisio.libgpml.model.shape.ShapeCatalog
ShapeCatalog.Internal - Enum in org.pathvisio.libgpml.model.shape: these constants are internal, only for the switch statement below.
ShapedElement - Class in org.pathvisio.libgpml.model: This class stores information for shaped pathway element DataNode, DataNode.State, Label, Shape, and Group.
ShapedElement() - Constructor for class org.pathvisio.libgpml.model.ShapedElement: Instantiates a shaped pathway element.
shapeMap - Static variable in class org.pathvisio.libgpml.model.shape.ShapeRegistry
ShapeRegistry - Class in org.pathvisio.libgpml.model.shape: The Shape registry stores all arrow heads and shapes at this moment the shape registry initializes itself, by calling registerShape() on BasicShapes, GenMAPPShapes and MIMShapes.
ShapeRegistry() - Constructor for class org.pathvisio.libgpml.model.shape.ShapeRegistry
shapes - Static variable in class org.pathvisio.libgpml.model.connector.ConnectorShapeFactory
shapes - Variable in class org.pathvisio.libgpml.model.PathwayModel
shapeType - Variable in class org.pathvisio.libgpml.model.LineElement.Anchor
shapeType - Variable in class org.pathvisio.libgpml.model.ShapedElement
ShapeType - Class in org.pathvisio.libgpml.model.type: This enum class contains extensible enum for Shape type property.
ShapeType(String, Shape) - Constructor for class org.pathvisio.libgpml.model.type.ShapeType: The constructor is private.
ShapeType(String, Shape, boolean, boolean) - Constructor for class org.pathvisio.libgpml.model.type.ShapeType: The constructor is private.
SHAPETYPE - org.pathvisio.libgpml.prop.StaticProperty
SHAPETYPE - org.pathvisio.libgpml.prop.StaticPropertyType
SHAPETYPE_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract
SHAPETYPE_MAP - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
SHAPETYPE_TO_CAMELCASE - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: This BidiMapis used for mapping ShapeType Strings to their new camelCase spelling for reading and writing GPML2013a.
SIDE_EAST - Static variable in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: line is connected to a PathwayElement on it's EAST side.
SIDE_NORTH - Static variable in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: line is connected to a PathwayElement on it's NORTH side.
SIDE_SOUTH - Static variable in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: line is connected to a PathwayElement on it's SOUTH side.
SIDE_WEST - Static variable in interface org.pathvisio.libgpml.model.connector.ConnectorRestrictions: line is connected to a PathwayElement on it's WEST side.
SITE - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
SITEGRPID - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
SITEGRPID_DB - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
size() - Method in class org.pathvisio.libgpml.debug.DebugList
SOLID - Static variable in class org.pathvisio.libgpml.model.type.LineStyleType
source - Variable in class org.pathvisio.libgpml.model.Citation
source - Variable in class org.pathvisio.libgpml.model.Pathway
source - Variable in class org.pathvisio.libgpml.model.PathwayElement.Comment
SOURCE - org.pathvisio.libgpml.prop.StaticProperty
sourceElement - Variable in class org.pathvisio.libgpml.model.CopyElement
sourceFile - Variable in class org.pathvisio.libgpml.model.PathwayModel
SQUARE - Static variable in class org.pathvisio.libgpml.model.type.AnchorShapeType
st1 - Variable in class org.pathvisio.libgpml.model.TestState
st2 - Variable in class org.pathvisio.libgpml.model.TestState
st3 - Variable in class org.pathvisio.libgpml.model.TestState
start - Variable in class org.pathvisio.libgpml.debug.StopWatch
start - Variable in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment
start - Variable in class org.pathvisio.libgpml.model.TestGraph
start() - Method in class org.pathvisio.libgpml.debug.StopWatch
startArrowHeadType - Variable in class org.pathvisio.libgpml.model.LineElement
STARTARROWHEADTYPE - org.pathvisio.libgpml.prop.StaticProperty
startElement(String, String, String, Attributes) - Method in class org.pathvisio.libgpml.util.RootElementFinder.RootElementHandler
STARTELEMENTREF - org.pathvisio.libgpml.prop.StaticProperty
STARTX - org.pathvisio.libgpml.prop.StaticProperty
STARTY - org.pathvisio.libgpml.prop.StaticProperty
State(String, StateType, double, double) - Constructor for class org.pathvisio.libgpml.model.DataNode.State: Instantiates a State pathway element given all possible parameters except xref.
State(String, StateType, double, double, Xref) - Constructor for class org.pathvisio.libgpml.model.DataNode.State: Instantiates a State pathway element given all possible parameters.
STATE - org.pathvisio.libgpml.model.type.ObjectType: A state pathway element represents a specific state of the biological entity.
STATE_DIRECTION_MAP - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Map for DataNode.State phosphosite PathwayElement.Comment direction character to Annotation and Xref information.
STATE_PTM_MAP - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: This Map for DataNode.State phosphosite PathwayElement.Comment maps PTM character to Annotation and Xref information.
STATE_REF_LIST - Variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: This Set contains known phosphosite related annotation types for DataNode.State phosphosite PathwayElement.Comment in GPML2013a.
STATE_ROTATION - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
states - Variable in class org.pathvisio.libgpml.model.DataNode
StateType - Class in org.pathvisio.libgpml.model.type: This class contains extensible enum for state types.
StateType(String) - Constructor for class org.pathvisio.libgpml.model.type.StateType: The constructor is private.
STATETYPE - org.pathvisio.libgpml.prop.StaticProperty
STATETYPE - org.pathvisio.libgpml.prop.StaticPropertyType
STATETYPE_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract
StaticProperty - Enum in org.pathvisio.libgpml.prop: Static properties for ObjectTypes, linked in PathwayObject.
StaticProperty(String, String, StaticPropertyType, int) - Constructor for enum org.pathvisio.libgpml.prop.StaticProperty
StaticProperty(String, String, StaticPropertyType, int, boolean, boolean, boolean) - Constructor for enum org.pathvisio.libgpml.prop.StaticProperty
StaticPropertyType - Enum in org.pathvisio.libgpml.prop: The properties in StaticProperty define properties of different types, all the possible types are defined here.
StaticPropertyType() - Constructor for enum org.pathvisio.libgpml.prop.StaticPropertyType
statusFlagChanged(PathwayModel.StatusFlagEvent) - Method in interface org.pathvisio.libgpml.model.PathwayModel.StatusFlagListener
StatusFlagEvent(boolean) - Constructor for class org.pathvisio.libgpml.model.PathwayModel.StatusFlagEvent
statusFlagListeners - Variable in class org.pathvisio.libgpml.model.PathwayModel
STIMULATION - Static variable in class org.pathvisio.libgpml.model.type.ArrowHeadType
STIMULATION_LIST - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
stop() - Method in class org.pathvisio.libgpml.debug.StopWatch
stopToLog(String) - Method in class org.pathvisio.libgpml.debug.StopWatch
StopWatch - Class in org.pathvisio.libgpml.debug: A simple helper class for speed optimizations.
StopWatch() - Constructor for class org.pathvisio.libgpml.debug.StopWatch
STRAIGHT - Static variable in class org.pathvisio.libgpml.model.type.ConnectorType
StraightConnectorShape - Class in org.pathvisio.libgpml.model.connector: Implements a straight connector Shape, i.e.
StraightConnectorShape() - Constructor for class org.pathvisio.libgpml.model.connector.StraightConnectorShape
STRING - org.pathvisio.libgpml.prop.StaticPropertyType
stringEquals(String, String) - Static method in class org.pathvisio.libgpml.util.Utils: Compares two Strings, returning true if they are equal.
stringNullEqualsEmpty(String, String) - Static method in class org.pathvisio.libgpml.util.Utils: Compares two Strings, returning true if they are equal.
stringToColor(String) - Static method in class org.pathvisio.libgpml.util.ColorUtils: Converts a (gpml) string containing either a named color, e.g.
stringToInputStream(String) - Static method in class org.pathvisio.libgpml.util.Utils: Converts a string to input stream.
subList(int, int) - Method in class org.pathvisio.libgpml.debug.DebugList
subtract(LinAlg.Point) - Method in class org.pathvisio.libgpml.util.LinAlg.Point
summary() - Method in class org.pathvisio.libgpml.model.PathwayModel: Prints a summary of this pathway model.
summary(PathwayObject) - Static method in class org.pathvisio.libgpml.util.Utils: Returns string summary information for a pathway object.
summaryHelper(PathwayObject, StringBuilder, StaticProperty, String) - Static method in class org.pathvisio.libgpml.util.Utils: append a property to the summary

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