T-Index

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T

tag - Variable in enum org.pathvisio.libgpml.model.type.ObjectType
tag - Variable in enum org.pathvisio.libgpml.prop.StaticProperty
tag() - Method in enum org.pathvisio.libgpml.prop.StaticProperty
TAG_MAP - Static variable in enum org.pathvisio.libgpml.model.type.ObjectType
tagMapping - Static variable in enum org.pathvisio.libgpml.prop.StaticProperty
TAIL - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
TAXONOMY - Static variable in class org.pathvisio.libgpml.model.type.AnnotationType
TBAR_GAP - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
TBARHEIGHT - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
TBARWIDTH - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
terminate() - Method in class org.pathvisio.libgpml.model.Annotation: Terminates this annotation.
terminate() - Method in class org.pathvisio.libgpml.model.Citation: Terminates this citation.
terminate() - Method in class org.pathvisio.libgpml.model.DataNode.State: Terminates this state and removes all links and references.
terminate() - Method in class org.pathvisio.libgpml.model.DataNode: Terminates this data node and removes all links and references.
terminate() - Method in class org.pathvisio.libgpml.model.Evidence: Terminates this evidence.
terminate() - Method in class org.pathvisio.libgpml.model.Group: Terminates this group and removes all references and links.
terminate() - Method in class org.pathvisio.libgpml.model.Label: Terminates this label and removes all links and references.
terminate() - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Terminates this anchor and removes all links and references.
terminate() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Terminates this line point and removes all links and references.
terminate() - Method in class org.pathvisio.libgpml.model.LineElement: Terminates this LineElement.
terminate() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Terminates this annotationRef.
terminate() - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Terminates this citationRef.
terminate() - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef: Terminates this evidenceRef.
terminate() - Method in class org.pathvisio.libgpml.model.PathwayElement: Terminates this pathway element.
terminate() - Method in class org.pathvisio.libgpml.model.PathwayObject: Terminates this pathway element.
terminate() - Method in class org.pathvisio.libgpml.model.Shape: Terminates this shape and removes all links and references.
terminate() - Method in class org.pathvisio.libgpml.model.ShapedElement: Terminates this pathway element.
Test - Class in org.pathvisio.libgpml.model: Tests for libgpml model classes.
Test() - Constructor for class org.pathvisio.libgpml.model.Test
test1() - Method in class org.pathvisio.libgpml.debug.TestDebug
TestAlias - Class in org.pathvisio.libgpml.model: Tests for aliasRef of DataNode.
TestAlias() - Constructor for class org.pathvisio.libgpml.model.TestAlias
TestAnchor - Class in org.pathvisio.libgpml.model: Test for LineElement.Anchor.
TestAnchor() - Constructor for class org.pathvisio.libgpml.model.TestAnchor
TestAnnotation - Class in org.pathvisio.libgpml.model: Tests for Annotation class.
TestAnnotation() - Constructor for class org.pathvisio.libgpml.model.TestAnnotation
testBridgeDb() - Method in class org.pathvisio.libgpml.util.TestXrefUtils
testCheckSetUp() - Method in class org.pathvisio.libgpml.model.TestReferenceable
TestCitation - Class in org.pathvisio.libgpml.model: For testing Citation methods
TestCitation() - Constructor for class org.pathvisio.libgpml.model.TestCitation
testClonePathway() - Method in class org.pathvisio.libgpml.model.TestCopy
testColor() - Method in class org.pathvisio.libgpml.model.Test
TestColorUtils - Class in org.pathvisio.libgpml.util: Tests for ColorUtils class.
TestColorUtils() - Constructor for class org.pathvisio.libgpml.util.TestColorUtils
TestCopy - Class in org.pathvisio.libgpml.model: Test for Clone methods.
TestCopy() - Constructor for class org.pathvisio.libgpml.model.TestCopy
testCopyDataNode() - Method in class org.pathvisio.libgpml.model.TestCopy
testCopyGraphicalLine() - Method in class org.pathvisio.libgpml.model.TestCopy
testCopyInteraction() - Method in class org.pathvisio.libgpml.model.TestCopy
testCopyLabel() - Method in class org.pathvisio.libgpml.model.TestCopy
testCopyShape() - Method in class org.pathvisio.libgpml.model.TestCopy
testDataNode() - Method in class org.pathvisio.libgpml.model.TestElementId
testDataNodeType() - Static method in class org.pathvisio.libgpml.model.type.TestDataNodeType: For testing data node type features.
TestDataNodeType - Class in org.pathvisio.libgpml.model.type: Test for extensible enum class.
TestDataNodeType() - Constructor for class org.pathvisio.libgpml.model.type.TestDataNodeType
TestDebug - Class in org.pathvisio.libgpml.debug: Tests for debug.
TestDebug() - Constructor for class org.pathvisio.libgpml.debug.TestDebug
testDuplicateAnnotation() - Method in class org.pathvisio.libgpml.model.TestAnnotation: Tests for when annotation with duplicate information is added to pathway model.
testDuplicateCitation() - Method in class org.pathvisio.libgpml.model.TestCitation: Tests for when annotation with duplicate information is added to pathway model.
testDuplicateEvidence() - Method in class org.pathvisio.libgpml.model.TestEvidence: Tests for when annotation with duplicate information is added to pathway model.
TestElementId - Class in org.pathvisio.libgpml.model: Tests for elementId.
TestElementId() - Constructor for class org.pathvisio.libgpml.model.TestElementId
testEquivalentXrefs() - Method in class org.pathvisio.libgpml.util.TestXrefUtils: Tests the method for checking if Xrefs are equal
TestEvidence - Class in org.pathvisio.libgpml.model: For testing Evidence methods
TestEvidence() - Constructor for class org.pathvisio.libgpml.model.TestEvidence
testFields() - Method in class org.pathvisio.libgpml.model.Test
TestGraph - Class in org.pathvisio.libgpml.model: Test graph properties of a pathway model.
TestGraph() - Constructor for class org.pathvisio.libgpml.model.TestGraph
testGraphicalLine() - Method in class org.pathvisio.libgpml.model.TestElementId
TestGraphLink - Class in org.pathvisio.libgpml.model: For testing methods for elementRef:
TestGraphLink() - Constructor for class org.pathvisio.libgpml.model.TestGraphLink
testGroup() - Method in class org.pathvisio.libgpml.model.TestElementId
TestGroup - Class in org.pathvisio.libgpml.model: Test for Group.
TestGroup() - Constructor for class org.pathvisio.libgpml.model.TestGroup
TestGroupNested - Class in org.pathvisio.libgpml.model: Tests for nested Group(s).
TestGroupNested() - Constructor for class org.pathvisio.libgpml.model.TestGroupNested
testGroupRectPropertyCalculation() - Method in class org.pathvisio.libgpml.util.TestGroupRectPropertyUtils
TestGroupRectPropertyUtils - Class in org.pathvisio.libgpml.util: Tests for GroupRectPropertyUtils class, the utility class for finding group bounds.
TestGroupRectPropertyUtils() - Constructor for class org.pathvisio.libgpml.util.TestGroupRectPropertyUtils
testGroupType() - Static method in class org.pathvisio.libgpml.model.type.TestDataNodeType: For testing group type features.
testHexToColorToHex() - Method in class org.pathvisio.libgpml.util.TestColorUtils
testInteraction() - Method in class org.pathvisio.libgpml.model.TestElementId
testLabel() - Method in class org.pathvisio.libgpml.model.TestElementId
testLineCoordinates() - Method in class org.pathvisio.libgpml.model.connector.TestSegmentedConnector: test conversion to / from line coordinates
TestLinePoint - Class in org.pathvisio.libgpml.model: Test for LineElement.LinePoint.
TestLinePoint() - Constructor for class org.pathvisio.libgpml.model.TestLinePoint
testLinkToAnchor() - Method in class org.pathvisio.libgpml.model.TestGraphLink: Test linking of start of interaction i to anchor of interaction i2.
testLinkToShapedElement() - Method in class org.pathvisio.libgpml.model.TestGraphLink: Tests linking of interaction i to datanodes d and d2.
testMappInfo() - Method in class org.pathvisio.libgpml.model.Test: Test that there is one and only one Pathway object
testParent() - Method in class org.pathvisio.libgpml.model.Test
testRef() - Method in class org.pathvisio.libgpml.model.Test: Test graphRef's and graphId's
testRef2() - Method in class org.pathvisio.libgpml.model.Test
TestReferenceable - Class in org.pathvisio.libgpml.model: Tests for Referenceable:
TestReferenceable() - Constructor for class org.pathvisio.libgpml.model.TestReferenceable
testRelative() - Method in class org.pathvisio.libgpml.model.TestGraph: test that the isRelative() method on mPoint properly reflects the fact that that the mPoint is linked to an object or not.
testRemove() - Method in class org.pathvisio.libgpml.model.TestGraph: test that, if a line points to a node, and the node is removed, the line is properly unlinked.
testRemoveAlias() - Method in class org.pathvisio.libgpml.model.TestAlias
testRemoveAnchor() - Method in class org.pathvisio.libgpml.model.TestAnchor: Tests removing anchor.
testRemoveAnnotation() - Method in class org.pathvisio.libgpml.model.TestAnnotation: Tests for removing annotation.
testRemoveAnnotation() - Method in class org.pathvisio.libgpml.model.TestReferenceable
testRemoveAnnotationRef() - Method in class org.pathvisio.libgpml.model.TestReferenceable
testRemoveCitation() - Method in class org.pathvisio.libgpml.model.TestCitation: Tests for removing annotation.
testRemoveDataNode() - Method in class org.pathvisio.libgpml.model.TestGroup
testRemoveDataNode() - Method in class org.pathvisio.libgpml.model.TestGroupNested
testRemoveDataNode() - Method in class org.pathvisio.libgpml.model.TestReferenceable
testRemoveDataNode() - Method in class org.pathvisio.libgpml.model.TestState: Tests removing a data node and its effect on states.
testRemoveDataNode2() - Method in class org.pathvisio.libgpml.model.TestGroupNested
testRemoveDataNodeFromGroup() - Method in class org.pathvisio.libgpml.model.TestGroup
testRemoveDataNodeFromGroup() - Method in class org.pathvisio.libgpml.model.TestGroupNested
testRemoveEvidence() - Method in class org.pathvisio.libgpml.model.TestEvidence: Tests for removing annotation.
testRemoveGroup() - Method in class org.pathvisio.libgpml.model.TestAlias
testRemoveGroup() - Method in class org.pathvisio.libgpml.model.TestGroup
testRemoveGroup() - Method in class org.pathvisio.libgpml.model.TestGroupNested
testRemoveLine() - Method in class org.pathvisio.libgpml.model.TestAnchor: Tests removing line and thus anchor.
testRemoveLine() - Method in class org.pathvisio.libgpml.model.TestLinePoint: Tests removing line and thus anchor.
testRemoveState() - Method in class org.pathvisio.libgpml.model.TestState: Tests removing a state.
TestSegmentedConnector - Class in org.pathvisio.libgpml.model.connector: Test for segmented connector.
TestSegmentedConnector() - Constructor for class org.pathvisio.libgpml.model.connector.TestSegmentedConnector
testSetLinePoints() - Method in class org.pathvisio.libgpml.model.TestLinePoint: Tests calling setLinePoints() before adding line to pathway model.
testShape() - Method in class org.pathvisio.libgpml.model.TestElementId
TestState - Class in org.pathvisio.libgpml.model: Test for DataNode.State.
TestState() - Constructor for class org.pathvisio.libgpml.model.TestState
testStringToColor() - Method in class org.pathvisio.libgpml.util.TestColorUtils
testSwitchGroup() - Method in class org.pathvisio.libgpml.model.TestGroup
testSwitchGroup() - Method in class org.pathvisio.libgpml.model.TestGroupNested
TestTemporary - Class in org.pathvisio.libgpml.model: Test for random things.
TestTemporary() - Constructor for class org.pathvisio.libgpml.model.TestTemporary
testThis() - Static method in class org.pathvisio.libgpml.model.TestTemporary: Temporary place for testing various methods.
testTransparency() - Method in class org.pathvisio.libgpml.util.TestColorUtils
testUngroup() - Method in class org.pathvisio.libgpml.model.TestGroup: Check that when a line points to the group, it stays at the same position when the group disappears.
testWriteGPML2021() - Method in class org.pathvisio.libgpml.model.TestAlias
testWriteGPML2021() - Method in class org.pathvisio.libgpml.model.TestGroupNested
testWrongFormat() - Method in class org.pathvisio.libgpml.model.Test
testXRefEquals() - Method in class org.pathvisio.libgpml.model.Test: test that Xref and XrefWithSymbol obey the equals contract
TestXrefUtils - Class in org.pathvisio.libgpml.util: Tests for XrefUtils class.
TestXrefUtils() - Constructor for class org.pathvisio.libgpml.util.TestXrefUtils
textColor - Variable in class org.pathvisio.libgpml.model.ShapedElement
TEXTCOLOR - org.pathvisio.libgpml.prop.StaticProperty
TEXTCOLOR_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract
textLabel - Variable in class org.pathvisio.libgpml.model.DataNode.State
textLabel - Variable in class org.pathvisio.libgpml.model.DataNode
textLabel - Variable in class org.pathvisio.libgpml.model.Group
textLabel - Variable in class org.pathvisio.libgpml.model.Label
textLabel - Variable in class org.pathvisio.libgpml.model.Shape
TEXTLABEL - org.pathvisio.libgpml.prop.StaticProperty
ThreadSafe - Annotation Type in org.pathvisio.libgpml.debug: Use this annotation to indicate that this method is Thread-safe, i.e.
title - Variable in class org.pathvisio.libgpml.model.Citation: Optional attributes for GPML2013a Biopax
title - Variable in class org.pathvisio.libgpml.model.Pathway
TITLE - org.pathvisio.libgpml.prop.StaticProperty
toAbsoluteCoordinate(Point2D) - Method in interface org.pathvisio.libgpml.model.Drawable: Converts a point to pathway coordinates (relative to the pathway).
toAbsoluteCoordinate(Point2D) - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableTo: Converts a point to pathway coordinates (relative to the pathway)
toAbsoluteCoordinate(Point2D) - Method in interface org.pathvisio.libgpml.model.Groupable: Converts a point to pathway coordinates (relative to the pathway).
toAbsoluteCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Returns the absolute coordinate as a Point2D.
toAbsoluteCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns the absolute coordinate as a Point2D.
toAbsoluteCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.LineElement
toAbsoluteCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.ShapedElement: Converts a point to pathway coordinates (relative to the pathway).
toArray() - Method in class org.pathvisio.libgpml.debug.DebugList
toArray(T[]) - Method in class org.pathvisio.libgpml.debug.DebugList
toCamelCase(String) - Method in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: Converts shapeType String to UpperCamelCase convention.
toLineCoordinate(Point2D) - Method in interface org.pathvisio.libgpml.model.connector.ConnectorShape: Translates a 2-dimensional view coordinate to a 1-dimensional line coordinate.
toLineCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.connector.SegmentedConnector: Translates a 2-dimensional view coordinate to a 1-dimensional line coordinate.
toLineCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.connector.StraightConnectorShape: Translates a 2-dimensional view coordinate to a 1-dimensional line coordinate.
toLineCoordinates(LinAlg.Point, LinAlg.Point, LinAlg.Point) - Static method in class org.pathvisio.libgpml.util.LinAlg: Convert a 2-D point to 1-D line coordinates (relative position on the line, range {0,1})
TOP - org.pathvisio.libgpml.model.type.VAlignType
toPoint2D() - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns this line point as a Point2D.
toPoint2D() - Method in class org.pathvisio.libgpml.util.LinAlg.Point
toRelativeCoordinate(Point2D) - Method in interface org.pathvisio.libgpml.model.Drawable: Converts a point to shape coordinates (relative to the bounds of the LinkableTo)
toRelativeCoordinate(Point2D) - Method in interface org.pathvisio.libgpml.model.GraphLink.LinkableTo: Converts a point to shape coordinates (relative to the bounds of the LinkableTo).
toRelativeCoordinate(Point2D) - Method in interface org.pathvisio.libgpml.model.Groupable: Converts a point to shape coordinates (relative to the bounds of the object)
toRelativeCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.LineElement.Anchor: Returns the relative coordinate as a Point2D.
toRelativeCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.LineElement.LinePoint: Returns the relative coordinate as a Point2D.
toRelativeCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.LineElement
toRelativeCoordinate(Point2D) - Method in class org.pathvisio.libgpml.model.ShapedElement: Converts a point to shape coordinates (relative to the bounds of the shape).
toString() - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment
toString() - Method in class org.pathvisio.libgpml.model.Group: Writes this group out as a string.
toString() - Method in class org.pathvisio.libgpml.model.Pathway.Author: Writes author out as a string.
toString() - Method in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef: Writes annotationRef out as a string.
toString() - Method in class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Writes citationRef out as a string.
toString() - Method in class org.pathvisio.libgpml.model.PathwayElement.Comment: Writes comment out as a string.
toString() - Method in class org.pathvisio.libgpml.model.PathwayElement.EvidenceRef: Writes evidenceRef out as string.
toString() - Method in class org.pathvisio.libgpml.model.shape.AbstractShape: Returns String name of this shape.
toString() - Method in class org.pathvisio.libgpml.model.type.AnchorShapeType: Returns a string representation of this AnchorShapeType.
toString() - Method in class org.pathvisio.libgpml.model.type.AnnotationType: Returns a string representation of this AnnotationType.
toString() - Method in class org.pathvisio.libgpml.model.type.ArrowHeadType: Returns a string representation of this ArrowHeadType.
toString() - Method in class org.pathvisio.libgpml.model.type.ConnectorType: Returns a string representation of this ConnectorType.
toString() - Method in class org.pathvisio.libgpml.model.type.DataNodeType: Returns a string representation of this DataNodeType.
toString() - Method in class org.pathvisio.libgpml.model.type.GroupType: Returns a string representation of this GroupType.
toString() - Method in enum org.pathvisio.libgpml.model.type.HAlignType: Returns a string representation of this HAlignType.
toString() - Method in class org.pathvisio.libgpml.model.type.LineStyleType: Returns a string representation of this LineStyleType.
toString() - Method in class org.pathvisio.libgpml.model.type.ShapeType: Returns a string representation of this ShapeType.
toString() - Method in class org.pathvisio.libgpml.model.type.StateType: Returns a string representation of this StateType.
toString() - Method in enum org.pathvisio.libgpml.model.type.VAlignType: Returns a string representation of this VAlignType.
toString() - Method in class org.pathvisio.libgpml.util.LinAlg.Point
trace(String) - Method in class org.pathvisio.libgpml.debug.Logger
traceEnabled - Variable in class org.pathvisio.libgpml.debug.Logger
TRANSCRIPTION_TRANSLATION - Static variable in class org.pathvisio.libgpml.model.type.ArrowHeadType
TRANSCRIPTION_TRANSLATION_LIST - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
transferStatusFlagListeners(PathwayModel) - Method in class org.pathvisio.libgpml.model.PathwayModel: Transfer statusflag listeners from one pathway to another.
TRANSLOCATION - Static variable in class org.pathvisio.libgpml.model.type.ArrowHeadType
TRANSLOCATION_LIST - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
TRANSPARENT - Static variable in class org.pathvisio.libgpml.model.type.GroupType
TRIANGLE - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
type - Variable in class org.pathvisio.libgpml.model.Annotation
type - Variable in class org.pathvisio.libgpml.model.DataNode.State
type - Variable in class org.pathvisio.libgpml.model.DataNode
type - Variable in class org.pathvisio.libgpml.model.Group
type - Variable in class org.pathvisio.libgpml.model.PathwayModelEvent
type - Variable in enum org.pathvisio.libgpml.prop.StaticProperty

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