C-Index

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C

c - Variable in class org.pathvisio.libgpml.model.TestCopy
c1 - Variable in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape.CurvedSegment
c1 - Variable in class org.pathvisio.libgpml.model.TestReferenceable
c2 - Variable in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape.CurvedSegment
calculateAdjustedShape(double, double) - Method in class org.pathvisio.libgpml.model.connector.AbstractConnector: Calculates shape from the width of the line endings.
calculateAdjustedShape(double, double) - Method in interface org.pathvisio.libgpml.model.connector.ConnectorShape: Calculates shape from the width of the line endings.
calculateCurve(int) - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape: Calculates the bezier curve, using NRSTEP segments for each curvedSegment.
calculateCurvedSegments(ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape: Based on the given elbow segments, calculate a new segment and control points for each bezier curve.
calculateNewEndPoint(double) - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment: The coordinates of the new end point if the length of the segment is reduced by the parameter.
calculateNewStartPoint(double) - Method in class org.pathvisio.libgpml.model.connector.ConnectorShape.Segment: The coordinates of the new start point if the length of the segment is reduced by the parameter.
calculateSegments(ConnectorRestrictions, ConnectorShape.WayPoint[]) - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape: Also calculates curvedSegments and curve.
calculateSegments(ConnectorRestrictions, ConnectorShape.WayPoint[]) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
calculateSegments(ConnectorRestrictions, ConnectorShape.WayPoint[]) - Method in class org.pathvisio.libgpml.model.connector.FreeConnectorShape: Calculates segments given restrictions and waypoints.
calculateShape() - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape: Calculates shape from the width of the line endings.
calculateShape() - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape: Calculates shape from the width of the line endings.
calculateShape(ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.AbstractConnector: Calculates shape from the width of the line endings.
calculateShape(ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape: Calculates shapes from the width of the line endings.
calculateShape(ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.SegmentedConnector: Calculates shape from the width of the line endings.
calculateShape(ConnectorShape.Segment[]) - Method in class org.pathvisio.libgpml.model.connector.StraightConnectorShape: Calculates shape from the width of the line endings.
calculateWayPoint(Point2D, Point2D, int, int) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
calculateWayPoints(ConnectorRestrictions) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
CATALYSIS - Static variable in class org.pathvisio.libgpml.model.type.ArrowHeadType
CATALYSIS_DIAM - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
CATALYSIS_GAP - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
CATALYSIS_GAP_HEIGHT - Static variable in class org.pathvisio.libgpml.model.shape.ArrowShapeRegistry
CATALYSIS_LIST - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
cause - Variable in class org.pathvisio.libgpml.debug.DebugList
CELL - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
CELL_CMPNT_KEY - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
CELL_CMPNT_MAP - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract: This cellular component Map maps ShapeTypes.
CELL_ICON - org.pathvisio.libgpml.model.shape.ShapeCatalog.Internal
CELL_ICON - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
CELL_NODE - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
CENTER - org.pathvisio.libgpml.model.type.HAlignType
centerX - Variable in class org.pathvisio.libgpml.model.ShapedElement
CENTERX - org.pathvisio.libgpml.prop.StaticProperty
centerY - Variable in class org.pathvisio.libgpml.model.ShapedElement
CENTERY - org.pathvisio.libgpml.prop.StaticProperty
changed - Variable in class org.pathvisio.libgpml.model.PathwayModel
checkMBoardSize(PathwayObject) - Method in class org.pathvisio.libgpml.model.PathwayModel: Checks whether the board size is still large enough for the given PathwayElement and increases the size if not
childModified(PathwayObjectEvent) - Method in class org.pathvisio.libgpml.model.PathwayModel: Used by children of this Pathway to notify the parent of modifications.
CIRCLE - Static variable in class org.pathvisio.libgpml.model.type.AnchorShapeType
citable - Variable in class org.pathvisio.libgpml.model.PathwayElement.CitationRef
citation - Variable in class org.pathvisio.libgpml.model.PathwayElement.CitationRef
Citation - Class in org.pathvisio.libgpml.model: This class stores information for a Citation.
Citation(Xref, String) - Constructor for class org.pathvisio.libgpml.model.Citation: Instantiates a Citation pathway element given all possible parameters.
CITATION - org.pathvisio.libgpml.model.type.ObjectType: A reference to a source of information.
CitationRef(Citation) - Constructor for class org.pathvisio.libgpml.model.PathwayElement.CitationRef: Instantiates an CitationRef given source Citation and initializes annotationRefs lists.
CITATIONREF - org.pathvisio.libgpml.prop.StaticProperty
CITATIONREF - org.pathvisio.libgpml.prop.StaticPropertyType
citationRefs - Variable in class org.pathvisio.libgpml.model.Citation: citationRefs with this citation as source
citationRefs - Variable in class org.pathvisio.libgpml.model.PathwayElement.AnnotationRef
citationRefs - Variable in class org.pathvisio.libgpml.model.PathwayElement
citations - Variable in class org.pathvisio.libgpml.model.PathwayModel
clear() - Method in class org.pathvisio.libgpml.debug.DebugList
clearChangedFlag() - Method in class org.pathvisio.libgpml.model.PathwayModel: ClearChangedFlag should be called after when the current pathway is known to be the same as the one on disk.
clearWarnings() - Method in class org.pathvisio.libgpml.io.AbstractPathwayModelFormat
clone() - Method in class org.pathvisio.libgpml.model.Pathway.Author: Clones this author.
clone() - Method in class org.pathvisio.libgpml.model.PathwayElement.Comment: Clones this comment.
clone() - Method in class org.pathvisio.libgpml.model.PathwayModel: Clones this pathway model.
clone() - Method in class org.pathvisio.libgpml.util.LinAlg.Point
CLOSED - org.pathvisio.libgpml.model.shape.ArrowShape.FillType: Closed fill-type, where both the outline and the body are colored with the line color.
collection2String(Collection<?>, String, String) - Static method in class org.pathvisio.libgpml.util.Utils: Converts a list to a string.
COLOR - org.pathvisio.libgpml.prop.StaticPropertyType
colorMap - Static variable in class org.pathvisio.libgpml.util.ColorUtils: Mapping of string gpml:ColorType (older versions of gpml) to a hexBinary String.
colorToHex(Color, boolean) - Static method in class org.pathvisio.libgpml.util.ColorUtils: Converts a Color object to a hexBinary string.
ColorUtils - Class in org.pathvisio.libgpml.util: This utils class contains methods for converting Color to hexBinary or color name String, and vice versa.
ColorUtils() - Constructor for class org.pathvisio.libgpml.util.ColorUtils
Comment(String, String) - Constructor for class org.pathvisio.libgpml.model.PathwayElement.Comment: Instantiates a Comment with commentText and source.
COMMENT - org.pathvisio.libgpml.prop.StaticProperty
COMMENT - org.pathvisio.libgpml.prop.StaticPropertyType
comments - Variable in class org.pathvisio.libgpml.model.PathwayElement
commentText - Variable in class org.pathvisio.libgpml.model.PathwayElement.Comment
compareTo(AnchorShapeType) - Method in class org.pathvisio.libgpml.model.type.AnchorShapeType: Compares string representations of given AnchorType lexicographically.
compareTo(ConnectorType) - Method in class org.pathvisio.libgpml.model.type.ConnectorType: Compares string representations of given ConnectorType lexicographically.
compareTo(GroupType) - Method in class org.pathvisio.libgpml.model.type.GroupType: Compares string representations of given GroupType lexicographically.
COMPLEX - Static variable in class org.pathvisio.libgpml.model.type.DataNodeType
COMPLEX - Static variable in class org.pathvisio.libgpml.model.type.GroupType
COMPLEX_M_MARGIN - Static variable in class org.pathvisio.libgpml.model.Group
ConnectorRestrictions - Interface in org.pathvisio.libgpml.model.connector: Methods to provide restrictions for the connector path
ConnectorShape - Interface in org.pathvisio.libgpml.model.connector: Implement this to provide a line shape for connectors.
ConnectorShape.Segment - Class in org.pathvisio.libgpml.model.connector: A single segment of the connector path.
ConnectorShape.WayPoint - Class in org.pathvisio.libgpml.model.connector: The class for a waypoint, a point through which the connector passes.
ConnectorShapeFactory - Class in org.pathvisio.libgpml.model.connector: Constructs connector shapes.
ConnectorShapeFactory() - Constructor for class org.pathvisio.libgpml.model.connector.ConnectorShapeFactory
connectorType - Variable in class org.pathvisio.libgpml.model.LineElement
ConnectorType - Class in org.pathvisio.libgpml.model.type: This class contains extensible enum for different connectorType property.
ConnectorType(String) - Constructor for class org.pathvisio.libgpml.model.type.ConnectorType: The constructor is private.
CONNECTORTYPE - org.pathvisio.libgpml.prop.StaticProperty
CONNECTORTYPE - org.pathvisio.libgpml.prop.StaticPropertyType
CONNECTORTYPE_DEFAULT - Static variable in class org.pathvisio.libgpml.model.GPML2021FormatAbstract
contains(Object) - Method in class org.pathvisio.libgpml.debug.DebugList
containsAll(Collection<?>) - Method in class org.pathvisio.libgpml.debug.DebugList
containsCaseInsensitive(String, List<String>) - Static method in class org.pathvisio.libgpml.util.Utils: Case insensitive contains method for List.
CONVERSION - Static variable in class org.pathvisio.libgpml.model.type.ArrowHeadType
CONVERSION_LIST - Static variable in class org.pathvisio.libgpml.model.GPML2013aFormatAbstract
ConverterException - Exception in org.pathvisio.libgpml.io: Exception that occurs during import, export, save or load of a pathway model.
ConverterException(Exception) - Constructor for exception org.pathvisio.libgpml.io.ConverterException
ConverterException(String) - Constructor for exception org.pathvisio.libgpml.io.ConverterException
convertStateCommentToRefs(DataNode.State, Set<String>) - Method in class org.pathvisio.libgpml.model.GPML2013aReader: This method is used to handle DataNode.State PathwayElement.Comment which were manually added to encode phosphosite information.
convertStateRefToComments(DataNode.State, Element) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter: This method handles converting DataNode.State phosphosite PathwayElement.AnnotationRef and Xref information back to PathwayElement.Comment for writing to GPML2013a.
coordinateChange - Variable in class org.pathvisio.libgpml.model.PathwayObjectEvent
coordinatesChanged() - Method in class org.pathvisio.libgpml.model.DataNode.State: Updates coordinates, called by PathwayModel.childModified(org.pathvisio.libgpml.model.PathwayObjectEvent)
copy() - Method in class org.pathvisio.libgpml.model.DataNode: Copies this pathway element.
copy() - Method in class org.pathvisio.libgpml.model.DataNode.State: Copies this pathway element.
copy() - Method in class org.pathvisio.libgpml.model.GraphicalLine: Copies this pathway element.
copy() - Method in class org.pathvisio.libgpml.model.Group: Copies this pathway element.
copy() - Method in class org.pathvisio.libgpml.model.Interaction: Copies this pathway element.
copy() - Method in class org.pathvisio.libgpml.model.Label: Copies this pathway element.
copy() - Method in class org.pathvisio.libgpml.model.Pathway: Copy Object.
copy() - Method in class org.pathvisio.libgpml.model.PathwayElement: Copies this pathway element.
copy() - Method in class org.pathvisio.libgpml.model.Shape: Copies this pathway element.
copyAnnotationRefs(List<PathwayElement.AnnotationRef>) - Method in class org.pathvisio.libgpml.model.PathwayElement: Copies annotationRefs and nested citationRefs and evidenceRefs if applicable.
copyCitationRefs(List<PathwayElement.CitationRef>) - Method in class org.pathvisio.libgpml.model.PathwayElement: Copies citationsRefs and nested annotationRefs if applicable.
CopyElement - Class in org.pathvisio.libgpml.model: This class stores information for copied PathwayElement.
CopyElement(PathwayElement, PathwayElement) - Constructor for class org.pathvisio.libgpml.model.CopyElement: Instantiates a CopyElement which holds references to a new pathway element and the original source element it was copied from.
copyEvidenceRefs(List<PathwayElement.EvidenceRef>) - Method in class org.pathvisio.libgpml.model.PathwayElement: Copies evidenceRefs.
copyRef() - Method in class org.pathvisio.libgpml.model.Annotation: Copies this annotation.
copyRef() - Method in class org.pathvisio.libgpml.model.Citation: Copies this citation.
copyRef() - Method in class org.pathvisio.libgpml.model.Evidence: Copies this evidence.
copyReferencesFrom(PathwayElement) - Method in class org.pathvisio.libgpml.model.DataNode: Copies references from the given source data node, including state references.
copyReferencesFrom(PathwayElement) - Method in class org.pathvisio.libgpml.model.PathwayElement: Copies references from the given source pathway element.
copyValuesFrom(Annotation) - Method in class org.pathvisio.libgpml.model.Annotation: Copies values from the given source pathway element.
copyValuesFrom(Citation) - Method in class org.pathvisio.libgpml.model.Citation: Copies values from the given source pathway element.
copyValuesFrom(DataNode) - Method in class org.pathvisio.libgpml.model.DataNode: Copies values from the given source pathway element.
copyValuesFrom(DataNode.State) - Method in class org.pathvisio.libgpml.model.DataNode.State: Copies values from the given source pathway element.
copyValuesFrom(DataNode.State) - Method in class org.pathvisio.libgpml.model.GraphicalLine: Copies values from the given source pathway element.
copyValuesFrom(Evidence) - Method in class org.pathvisio.libgpml.model.Evidence: Copies values from the given source pathway element.
copyValuesFrom(Group) - Method in class org.pathvisio.libgpml.model.Group: Copies values from the given source pathway element.
copyValuesFrom(Interaction) - Method in class org.pathvisio.libgpml.model.Interaction: Copies values from the given source pathway element.
copyValuesFrom(Label) - Method in class org.pathvisio.libgpml.model.Label: Copies values from the given source pathway element.
copyValuesFrom(LineElement) - Method in class org.pathvisio.libgpml.model.LineElement: Copies values from the given source pathway element.
copyValuesFrom(Pathway) - Method in class org.pathvisio.libgpml.model.Pathway: Note: doesn't change parent, only fields Used by UndoAction.
copyValuesFrom(PathwayElement) - Method in class org.pathvisio.libgpml.model.PathwayElement: Copies values from the given source pathway element.
copyValuesFrom(Shape) - Method in class org.pathvisio.libgpml.model.Shape: Copies values from the given source pathway element.
copyValuesFrom(ShapedElement) - Method in class org.pathvisio.libgpml.model.ShapedElement: Copies values from the given source pathway element.
CORONAVIRUS_ICON - org.pathvisio.libgpml.model.shape.ShapeCatalog.Internal
CORONAVIRUS_ICON - Static variable in class org.pathvisio.libgpml.model.type.ShapeType
cr - Variable in class org.pathvisio.libgpml.model.TestCopy
cr1 - Variable in class org.pathvisio.libgpml.model.TestReferenceable
cr2 - Variable in class org.pathvisio.libgpml.model.TestReferenceable
createAllPropertiesEvent(PathwayObject) - Static method in class org.pathvisio.libgpml.model.PathwayObjectEvent: Creates an all properties event.
createConnectorShape(String) - Static method in class org.pathvisio.libgpml.model.connector.ConnectorShapeFactory: Creates an instance of a the implementor of ConnectorShape identified by the given name.
createCoordinatePropertyEvent(PathwayObject) - Static method in class org.pathvisio.libgpml.model.PathwayObjectEvent: Creates a coordinate property event.
createJdom(PathwayModel) - Method in class org.pathvisio.libgpml.model.GPML2013aWriter: Creates and returns the JDOM document Document written from given pathwayModel PathwayModel data.
createJdom(PathwayModel) - Method in class org.pathvisio.libgpml.model.GPML2021Writer: Creates and returns the JDOM document Document written from given pathwayModel PathwayModel data.
createJdom(PathwayModel) - Method in class org.pathvisio.libgpml.model.GPMLFormat
createJdom(PathwayModel) - Method in interface org.pathvisio.libgpml.model.GPMLFormatWriter: Creates a Jdom document from pathway model.
createSinglePropertyEvent(PathwayObject, Object) - Static method in class org.pathvisio.libgpml.model.PathwayObjectEvent: Creates a single property event.
createStraightSegment(Point2D, Point2D, int) - Method in class org.pathvisio.libgpml.model.connector.ElbowConnectorShape
createXref(String, String) - Static method in class org.pathvisio.libgpml.util.XrefUtils: Instantiates an Xref given String identifier and dataSource.
createXref(String, DataSource) - Static method in class org.pathvisio.libgpml.util.XrefUtils: Instantiates an Xref given String identifier and DataSource dataSource.
CURVED - Static variable in class org.pathvisio.libgpml.model.type.ConnectorType
CurvedConnectorShape - Class in org.pathvisio.libgpml.model.connector: Implements a curved connector that draws curved lines between the segments.
CurvedConnectorShape() - Constructor for class org.pathvisio.libgpml.model.connector.CurvedConnectorShape
CurvedConnectorShape.CurvedSegment - Class in org.pathvisio.libgpml.model.connector: Segment for curved connector, also stores bezier control points
CurvedSegment(Point2D, Point2D, Point2D, Point2D) - Constructor for class org.pathvisio.libgpml.model.connector.CurvedConnectorShape.CurvedSegment: Constructor for a curved segment.
curvedSegments - Variable in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape
curveHigh - Variable in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape
curveLow - Variable in class org.pathvisio.libgpml.model.connector.CurvedConnectorShape

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