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C

Canvas - Class in edu.ucsd.sbrg.escher.model
 
Canvas() - Constructor for class edu.ucsd.sbrg.escher.model.Canvas
 
Canvas(Canvas) - Constructor for class edu.ucsd.sbrg.escher.model.Canvas
 
CANVAS_DEFAULT_HEIGHT - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
Just as in the case of the width of the canvas, this value needs to be specified for cases where the JSON input file lacks an explicit specification of the canvas height.
CANVAS_DEFAULT_WIDTH - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
This value is used when no width has been defined for the canvas.
clone() - Method in class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
clone() - Method in class edu.ucsd.sbrg.escher.model.Canvas
 
clone() - Method in class edu.ucsd.sbrg.escher.model.EscherCompartment
 
clone() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
clone() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
clone() - Method in class edu.ucsd.sbrg.escher.model.Gene
 
clone() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
clone() - Method in class edu.ucsd.sbrg.escher.model.Node
 
clone() - Method in class edu.ucsd.sbrg.escher.model.Point
 
clone() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
clone() - Method in class edu.ucsd.sbrg.escher.model.TextLabel
 
closeFile() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
COMBINE - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
Whether to combine layouts of an SBML file, if more than one.
commandLineMode(AppConf) - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
COMPARTMENT_ID - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
A compartment needs to have a unique identifier, which needs to be a machine-readable Sting that must start with a letter or underscore and can only contain ASCII characters.
COMPARTMENT_NAME - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
With this option it is possible to define a name for the default compartment can be that needs to be generated for the conversion to SBML.
compartments() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
compCode - Static variable in class edu.ucsd.sbrg.escher.converters.Escher2Standard
Compartment codes.
configure(Escher2Standard<T>, SBProperties) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
This configures the generic Escher2Standard and sets the common layout options.
contains(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
convert(EscherMap) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBGN
 
convert(EscherMap) - Method in class edu.ucsd.sbrg.escher.converters.Escher2SBML
 
convert(EscherMap) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
 
convert(Sbgn) - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Converts Sbgn document to EscherMap by iteratively creating nodes, reactions, etc.
convert(SBMLDocument) - Method in class edu.ucsd.sbrg.escher.converters.SBML2Escher
Converts an SBMLDocument to a list of EscherMaps by iteratively creating nodes, reactions, etc.
convert(EscherMap, Class<? extends T>, SBProperties) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Generic method which converts the given EscherMap instance to the specified generic parameter format, by calling the corresponding converter.
convert(Sbgn, SBProperties) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Calls SBGN-ML to Escher converter.
convert(SBMLDocument, SBProperties) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Calls SBML Layout Extension to Escher converter.
convert(File, Class<? extends T>, SBProperties) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Converts given JSON input to given output format.
convert(File, File, SBProperties) - Method in class edu.ucsd.sbrg.escher.EscherConverter
convert(Point2D) - Static method in class edu.ucsd.sbrg.math.Geometry
 
convert(Point) - Static method in class edu.ucsd.sbrg.math.Geometry
 
createArc(String, SBGNBase, SBGNBase, SBGNProperties.ArcType) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createArcEnd(double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createArcNext(double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createArcStart(double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createBbox(double, double, double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createBbox(Double, Double, Double, Double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, SBGNProperties.GlyphType) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, SBGNProperties.GlyphType, Bbox) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, SBGNProperties.GlyphType, Bbox, boolean) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, SBGNProperties.GlyphType, Bbox, SBGNProperties.GlyphOrientation) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, SBGNProperties.GlyphType, Bbox, SBGNProperties.GlyphOrientation, boolean) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, SBGNProperties.GlyphType, double, double, double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, SBGNProperties.GlyphType, double, double, double, double, boolean) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, SBGNProperties.GlyphType, double, double, double, double, SBGNProperties.GlyphOrientation) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, String, SBGNProperties.GlyphType) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, String, SBGNProperties.GlyphType, Bbox) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyph(String, String, SBGNProperties.GlyphType, double, double, double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyphCallout(double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createGlyphCallout(Point) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createJToolBar() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
createLabel(String) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createLabel(String, Bbox) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createLabel(String, double, double, double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createMainComponent() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
createMap(SBGNbuilder.Language) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createMap(SBGNbuilder.Language, Bbox) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createMap(SBGNbuilder.Language, double, double, double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createMapId(File) - Static method in class edu.ucsd.sbrg.escher.utilities.EscherParser
 
createMetabolite(SpeciesReference) - Method in class edu.ucsd.sbrg.escher.converters.SBML2Escher
Creates a Metabolite from a SpeciesReference.
createMidMarker(Glyph) - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Create an Escher Node(mid-marker) from process Glyph.
createMidMarker(ReactionGlyph) - Method in class edu.ucsd.sbrg.escher.converters.SBML2Escher
Creates a Node(mid-marker) from a ReactionGlyph.
createMultiMarker(Arc.Next) - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Create an Escher Node(multi-marker) from Arc.Next.
createMultiMarkers(SpeciesReferenceGlyph) - Method in class edu.ucsd.sbrg.escher.converters.SBML2Escher
Creates a list of Nodes(multi-markers) from a SpeciesReferenceGlyph.
createNode(Glyph) - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Create an Escher Node(metabolite) from EPN Glyph.
createNode(SpeciesGlyph) - Method in class edu.ucsd.sbrg.escher.converters.SBML2Escher
Creates a Node(metabolite) from a SpeciesGlyph.
createNotes(String) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createPoint(double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createPort(String, double, double) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createReaction(Glyph) - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Create an EscherReaction from an SBGN-ML Glyph.
createReaction(ReactionGlyph) - Method in class edu.ucsd.sbrg.escher.converters.SBML2Escher
Creates an EscherReaction from a ReactionGlyph.
createSbgn() - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
createSegments(Arc) - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Create a list of Segments from an SBGN-ML Arc.
createSegments(SpeciesReferenceGlyph, ReactionGlyph) - Method in class edu.ucsd.sbrg.escher.converters.SBML2Escher
Creates a list of Segments from a SpeciesReferenceGlyph.
createTextLabel(Glyph) - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Create a TextLabel from an SBGN-ML Glyph.
createTextLabel(TextGlyph) - Method in class edu.ucsd.sbrg.escher.converters.SBML2Escher
Create a TextLabel from a TextGlyph.
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