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P

parse(File) - Method in class edu.ucsd.sbrg.escher.utilities.EscherParser
 
parse(InputStream, String) - Method in class edu.ucsd.sbrg.escher.utilities.EscherParser
 
parseEscherJson(File) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Parses given JSON file into an EscherMap instance using Jackson.
Point - Class in edu.ucsd.sbrg.escher.model
 
Point() - Constructor for class edu.ucsd.sbrg.escher.model.Point
 
Point(Double, Double) - Constructor for class edu.ucsd.sbrg.escher.model.Point
 
Point(Point) - Constructor for class edu.ucsd.sbrg.escher.model.Point
 
port2GlyphMap - Variable in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Port ids with their respective Glyph ids.
Position - Interface in edu.ucsd.sbrg.escher.model
 
preprocessDataStructure(EscherMap) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
 
preProcessSbgn() - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Processes the input Sbgn document and populates internal helper fields.
PRIMARY_NODE_HEIGHT - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
The primary node should be bigger than the secondary node.
PRIMARY_NODE_WIDTH - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
Escher maps distinguish between primary and secondary nodes.
process(List<OpenedFile<EscherMap>>) - Method in class edu.ucsd.sbrg.escher.gui.EscherParserWorker
 
processIds - Variable in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
List of process (Glyph) ids.
processMap() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
Post-processes EscherMap and populates internal helper fields.
propertyChange(PropertyChangeEvent) - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
putUserObject(String, T) - Method in class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
putUserObject(String, T) - Method in interface edu.ucsd.sbrg.escher.model.EscherBase
 
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