- saveFileAs() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
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- SBGN2Escher - Class in edu.ucsd.sbrg.escher.converters
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Converter from SBML Layout Extension to Escher.
- SBGN2Escher() - Constructor for class edu.ucsd.sbrg.escher.converters.SBGN2Escher
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Default constructor.
- SBGNbuilder - Class in edu.ucsd.sbrg.sbgn
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A helper class that facilitates the creation of SBGN map objects.
- SBGNbuilder() - Constructor for class edu.ucsd.sbrg.sbgn.SBGNbuilder
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- SBGNbuilder.Language - Enum in edu.ucsd.sbrg.sbgn
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Enumeration of SBGN languages.
- SBGNWritingTask - Class in edu.ucsd.sbrg.escher.gui
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- SBGNWritingTask(OpenedFile<Sbgn>) - Constructor for class edu.ucsd.sbrg.escher.gui.SBGNWritingTask
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- SBML2Escher - Class in edu.ucsd.sbrg.escher.converters
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Converter from SBML Layout Extension to Escher.
- SBML2Escher() - Constructor for class edu.ucsd.sbrg.escher.converters.SBML2Escher
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Default constructor.
- SBML_CONDITION - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
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Helper constant for internal use.
- SBMLLayoutViewPanel - Class in edu.ucsd.sbrg.escher.gui
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- SBMLLayoutViewPanel() - Constructor for class edu.ucsd.sbrg.escher.gui.SBMLLayoutViewPanel
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- SBMLLayoutViewPanel(Layout) - Constructor for class edu.ucsd.sbrg.escher.gui.SBMLLayoutViewPanel
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- scale(double) - Method in class edu.ucsd.sbrg.escher.model.Point
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- SECONDARY_NODE_RATIO - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
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Similar to the reaction node ratio, the size of secondary nodes (width
and height) is determined by dividing the corresponding values from the
primary nodes by this value.
- Segment - Class in edu.ucsd.sbrg.escher.model
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- Segment() - Constructor for class edu.ucsd.sbrg.escher.model.Segment
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- Segment(Segment) - Constructor for class edu.ucsd.sbrg.escher.model.Segment
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- segments() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setBasePoint1(Point) - Method in class edu.ucsd.sbrg.escher.model.Segment
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- setBasePoint2(Point) - Method in class edu.ucsd.sbrg.escher.model.Segment
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- setBiggId(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setBiggId(String) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setCanvas(Canvas) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setCanvasDefaultHeight(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setCanvasDefaultWidth(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setCoefficient(Double) - Method in class edu.ucsd.sbrg.escher.model.Metabolite
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- setConnectedSegments(Map<String, List<String>>) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setDefaultCompartmentId(String) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBML
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- setDefaultCompartmentName(String) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBML
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- setDescription(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setFromNodeId(String) - Method in class edu.ucsd.sbrg.escher.model.Segment
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- setGeneList(List<Gene>) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setGeneReactionRule(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setHeight(Double) - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
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- setHeight(Double) - Method in interface edu.ucsd.sbrg.escher.model.Box
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- setId(String) - Method in interface edu.ucsd.sbrg.escher.model.Element
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- setId(String) - Method in class edu.ucsd.sbrg.escher.model.EscherCompartment
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- setId(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setId(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setId(String) - Method in class edu.ucsd.sbrg.escher.model.Gene
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- setId(String) - Method in class edu.ucsd.sbrg.escher.model.Metabolite
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- setId(String) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setId(String) - Method in class edu.ucsd.sbrg.escher.model.Segment
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- setId(String) - Method in class edu.ucsd.sbrg.escher.model.TextLabel
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- setInferCompartmentBoundaries(boolean) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setLabelHeight(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setLabelWidth(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setLabelX(Double) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setLabelX(Double) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setLabelY(Double) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setLabelY(Double) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setLayoutId(String) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBML
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- setLayoutName(String) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBML
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- setMetaboliteList(List<Metabolite>) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setMidmarker(Node) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setName(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setName(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setName(String) - Method in class edu.ucsd.sbrg.escher.model.Gene
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- setName(String) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setNodeDepth(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBML
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- setNodeLabelHeight(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBML
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- setNodeRefId(String) - Method in class edu.ucsd.sbrg.escher.model.Metabolite
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- setNodes(Map<String, Node>) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setPrimary(Boolean) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setPrimaryNodeHeight(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setPrimaryNodeWidth(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setReactionNodeRatio(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setReactions(Map<String, EscherReaction>) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setReversibility(Boolean) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setSchema(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setSecondaryNodeRatio(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
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- setSegments(Map<String, Segment>) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- setText(String) - Method in class edu.ucsd.sbrg.escher.model.TextLabel
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- setTextLabels(Map<String, TextLabel>) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setToNodeId(String) - Method in class edu.ucsd.sbrg.escher.model.Segment
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- setType(Node.Type) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setURL(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- setWidth(Double) - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
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- setWidth(Double) - Method in interface edu.ucsd.sbrg.escher.model.Box
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- setX(Double) - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
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- setX(Double) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setX(Double) - Method in interface edu.ucsd.sbrg.escher.model.Position
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- setY(Double) - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
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- setY(Double) - Method in class edu.ucsd.sbrg.escher.model.Node
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- setY(Double) - Method in interface edu.ucsd.sbrg.escher.model.Position
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- setZ(double) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBML
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- showsGUI() - Method in class edu.ucsd.sbrg.escher.EscherConverter
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