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S

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