D-Index

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D

d - Variable in class org.pathvisio.libgpml.model.TestAlias
d1 - Variable in class org.pathvisio.libgpml.model.TestAnnotation
d1 - Variable in class org.pathvisio.libgpml.model.TestCitation
d1 - Variable in class org.pathvisio.libgpml.model.TestEvidence
d1 - Variable in class org.pathvisio.libgpml.model.TestGroup
d1 - Variable in class org.pathvisio.libgpml.model.TestGroupNested
d1 - Variable in class org.pathvisio.libgpml.model.TestReferenceable
d1 - Variable in class org.pathvisio.libgpml.model.TestState
d2 - Variable in class org.pathvisio.libgpml.model.TestGroup
d2 - Variable in class org.pathvisio.libgpml.model.TestGroupNested
d3 - Variable in class org.pathvisio.libgpml.model.TestGroup
d3 - Variable in class org.pathvisio.libgpml.model.TestGroupNested
DASHED - Static variable in class org.pathvisio.libgpml.model.type.LineStyleType
data - Variable in class org.pathvisio.libgpml.model.Test
DataNode - Class in org.pathvisio.libgpml.model: This class stores information for a DataNode pathway element.
DataNode(String, DataNodeType) - Constructor for class org.pathvisio.libgpml.model.DataNode: Instantiates a DataNode given all required parameters.
DataNode(String, DataNodeType, Xref, Group) - Constructor for class org.pathvisio.libgpml.model.DataNode: Instantiates a DataNode given all possible parameters.
DATANODE - org.pathvisio.libgpml.model.type.ObjectType: A data node pathway element denotes a biological entity that forms a node in a pathway.
DataNode.State - Class in org.pathvisio.libgpml.model: This class stores all information relevant to a State pathway element.
dataNodes - Variable in class org.pathvisio.libgpml.model.PathwayModel
DataNodeType - Class in org.pathvisio.libgpml.model.type: This class contains extensible enum for DataNode type property.
DataNodeType(String) - Constructor for class org.pathvisio.libgpml.model.type.DataNodeType: The constructor is private.
DATANODETYPE - org.pathvisio.libgpml.prop.StaticProperty
DATANODETYPE - org.pathvisio.libgpml.prop.StaticPropertyType
DATANODETYPE_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract
DATASOURCE - org.pathvisio.libgpml.prop.StaticPropertyType
debug(String) - Method in class org.pathvisio.libgpml.debug.Logger
debugEnabled - Variable in class org.pathvisio.libgpml.debug.Logger
DebugIterator(DebugList<E>) - Constructor for class org.pathvisio.libgpml.debug.DebugList.DebugIterator
DebugIterator(DebugList<E>, int) - Constructor for class org.pathvisio.libgpml.debug.DebugList.DebugIterator
DebugList<E> - Class in org.pathvisio.libgpml.debug: This is a List that helps in the search for ConcurrentModification problems.
DebugList() - Constructor for class org.pathvisio.libgpml.debug.DebugList
DebugList.DebugIterator<E> - Class in org.pathvisio.libgpml.debug: An iterator to go with the DebugList.
def - Variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract.AttributeInfo: default value for the attribute
DEFAULT_M_MARGIN - Static variable in class org.pathvisio.libgpml.model.Group: Default margins for group bounding-box in GPML2013a.
DEFAULT_SHAPE - Static variable in class org.pathvisio.libgpml.model.shape.ShapeRegistry
defaultAnchor - Static variable in class org.pathvisio.libgpml.model.shape.ShapeRegistry
defaultArrow - Static variable in class org.pathvisio.libgpml.model.shape.ShapeRegistry
defaultShape - Static variable in class org.pathvisio.libgpml.model.shape.ShapeRegistry
DEGRADATION - org.pathvisio.libgpml.model.shape.ShapeCatalog.Internal
DEGRADATION - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
delegate - Variable in class org.pathvisio.libgpml.debug.DebugList.DebugIterator
delegate - Variable in class org.pathvisio.libgpml.debug.DebugList
DELETED - Static variable in class org.pathvisio.libgpml.model.PathwayModelEvent
DEPRECATED_MAP - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: This Map maps deprecated String to the new ShapeType when reading GPML2013a GPML2013aReader.readShapeStyleProperty(org.pathvisio.libgpml.model.ShapedElement, org.jdom2.Element).
description - Variable in class org.pathvisio.libgpml.model.Pathway
DESCRIPTION - org.pathvisio.libgpml.prop.StaticProperty
DESCRIPTION - org.pathvisio.libgpml.prop.StaticPropertyType
DIRECTED - Static variable in class org.pathvisio.libgpml.model.type.ArrowHeadType
DIRECTED_LIST - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
direction(LinAlg.Point, LinAlg.Point) - Static method in class org.pathvisio.libgpml.util.LinAlg: negative: ccw positive: cw
DIRECTION - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
disallowLinks - Variable in class org.pathvisio.libgpml.model.type.AnchorShapeType
DISEASE - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
distance(LinAlg.Point, LinAlg.Point) - Static method in class org.pathvisio.libgpml.util.LinAlg
DNA - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
DNA_ICON - org.pathvisio.libgpml.model.shape.ShapeCatalog.Internal
DNA_ICON - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
doExport(File, PathwayModel) - Method in interface org.pathvisio.libgpml.io.PathwayModelExporter: Exports the given pathway to the file
doExport(File, PathwayModel) - Method in class org.pathvisio.libgpml.model.GPMLFormat
doExport(File, PathwayModel, int) - Method in interface org.pathvisio.libgpml.io.PathwayModelExporter: Exports the given pathway to the file
doExport(File, PathwayModel, int) - Method in class org.pathvisio.libgpml.model.GPMLFormat
doImport(File) - Method in interface org.pathvisio.libgpml.io.PathwayModelImporter: Imports the pathway model from given file.
doImport(File) - Method in class org.pathvisio.libgpml.model.GPMLFormat
dontFireEvents(int) - Method in class org.pathvisio.libgpml.model.PathwayObject: Sets noFire to the given integer.
dot(LinAlg.Point, LinAlg.Point) - Static method in class org.pathvisio.libgpml.util.LinAlg
DOUBLE - org.pathvisio.libgpml.prop.StaticPropertyType
DOUBLE - Static variable in class org.pathvisio.libgpml.model.type.LineStyleType
DOUBLE_LINE_KEY - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: In GPML2013a, Double LineStyleType, Cellular Component Shape Types, and State rotation were stored as a dynamic properties using the following String keys.
downloadFile(URL, File) - Static method in class org.pathvisio.libgpml.util.FileUtils: Downloads a remote file given by an URL to the given local file
Drawable - Interface in org.pathvisio.libgpml.model: Interface for classes which can be drawn a pathway model canvas.
dynamicProperties - Variable in class org.pathvisio.libgpml.model.PathwayElement: Map for storing dynamic properties.

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