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E

edu.ucsd.sbrg.escher - package edu.ucsd.sbrg.escher
 
edu.ucsd.sbrg.escher.converters - package edu.ucsd.sbrg.escher.converters
Provides converters for Escher JSON to community standards (SBGN, SBML) and vice-versa.
edu.ucsd.sbrg.escher.gui - package edu.ucsd.sbrg.escher.gui
Classes for the graphical user interface.
edu.ucsd.sbrg.escher.model - package edu.ucsd.sbrg.escher.model
Represents model classes for representation of Escher's components.
edu.ucsd.sbrg.escher.utilities - package edu.ucsd.sbrg.escher.utilities
Provides utility methods, e.g.
edu.ucsd.sbrg.math - package edu.ucsd.sbrg.math
 
edu.ucsd.sbrg.sbgn - package edu.ucsd.sbrg.sbgn
 
Element - Interface in edu.ucsd.sbrg.escher.model
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.Gene
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.Node
 
equals(Object) - Method in class edu.ucsd.sbrg.escher.model.Segment
 
equals(Object) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
Escher2SBGN - Class in edu.ucsd.sbrg.escher.converters
 
Escher2SBGN() - Constructor for class edu.ucsd.sbrg.escher.converters.Escher2SBGN
Default constructor.
Escher2SBML - Class in edu.ucsd.sbrg.escher.converters
This class takes an EscherMap as input and creates an SBMLDocument based on the information provided.
Escher2SBML() - Constructor for class edu.ucsd.sbrg.escher.converters.Escher2SBML
 
Escher2Standard<T> - Class in edu.ucsd.sbrg.escher.converters
 
Escher2Standard() - Constructor for class edu.ucsd.sbrg.escher.converters.Escher2Standard
 
ESCHER_NODE_LINK - Static variable in class edu.ucsd.sbrg.escher.converters.Escher2Standard
Used as a key for a mapping between data structures.
EscherBase - Interface in edu.ucsd.sbrg.escher.model
 
EscherCompartment - Class in edu.ucsd.sbrg.escher.model
 
EscherCompartment() - Constructor for class edu.ucsd.sbrg.escher.model.EscherCompartment
 
EscherCompartment(EscherCompartment) - Constructor for class edu.ucsd.sbrg.escher.model.EscherCompartment
 
EscherConverter - Class in edu.ucsd.sbrg.escher
 
EscherConverter(String...) - Constructor for class edu.ucsd.sbrg.escher.EscherConverter
Called by the main method.
EscherConverterUI - Class in edu.ucsd.sbrg.escher.gui
 
EscherConverterUI(AppConf) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
EscherConverterWorker<T> - Class in edu.ucsd.sbrg.escher.gui
 
EscherConverterWorker(EscherMap, Class<? extends T>, SBProperties) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherConverterWorker
 
EscherIOOptions - Interface in edu.ucsd.sbrg.escher.utilities
 
EscherKeywords - Enum in edu.ucsd.sbrg.escher.utilities
 
escherMap - Variable in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Output Escher map.
EscherMap - Class in edu.ucsd.sbrg.escher.model
 
EscherMap() - Constructor for class edu.ucsd.sbrg.escher.model.EscherMap
Default constructor.
EscherMap(EscherMap) - Constructor for class edu.ucsd.sbrg.escher.model.EscherMap
Copy constructor.
EscherMapDisplay - Class in edu.ucsd.sbrg.escher.gui
 
EscherMapDisplay(OpenedFile<EscherMap>, SBProperties) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherMapDisplay
 
escherMaps - Variable in class edu.ucsd.sbrg.escher.converters.SBML2Escher
List of escher maps converted from the layouts exported from the SBML document.
EscherOptions - Interface in edu.ucsd.sbrg.escher.utilities
These options influence how the output will be created and how the Escher maps are interpreted.
EscherOptions.InputFormat - Enum in edu.ucsd.sbrg.escher.utilities
Enumeration of allowable input file formats.
EscherOptions.OutputFormat - Enum in edu.ucsd.sbrg.escher.utilities
Enumeration of allowable output file formats.
EscherParser - Class in edu.ucsd.sbrg.escher.utilities
 
EscherParser() - Constructor for class edu.ucsd.sbrg.escher.utilities.EscherParser
 
EscherParserWorker - Class in edu.ucsd.sbrg.escher.gui
 
EscherParserWorker(Component, File...) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherParserWorker
 
EscherReaction - Class in edu.ucsd.sbrg.escher.model
Represents all properties of a reaction in an Escher map.
EscherReaction() - Constructor for class edu.ucsd.sbrg.escher.model.EscherReaction
Creates a new reaction object where all properties are initialized with null values.
EscherReaction(EscherReaction) - Constructor for class edu.ucsd.sbrg.escher.model.EscherReaction
 
EXTRACT_COBRA - Static variable in interface edu.ucsd.sbrg.escher.utilities.EscherOptions
Whether to extract CoBRA model, if FBC present on SBML file.
extractCobraModel(File) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Extracts CoBRA from SBMLDocument if it is FBC compliant.
extractCoefficient(Object) - Method in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
 
extractReactionId(Set<Map.Entry<String, List<String>>>) - Method in class edu.ucsd.sbrg.escher.converters.Escher2Standard
 
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