- edu.ucsd.sbrg.escher - package edu.ucsd.sbrg.escher
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- edu.ucsd.sbrg.escher.converter - package edu.ucsd.sbrg.escher.converter
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Provides converters for Escher JSON to community standards (SBGN, SBML) and vice-versa.
- edu.ucsd.sbrg.escher.gui - package edu.ucsd.sbrg.escher.gui
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Classes for the graphical user interface.
- edu.ucsd.sbrg.escher.model - package edu.ucsd.sbrg.escher.model
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Represents model classes for representation of Escher's components.
- edu.ucsd.sbrg.escher.util - package edu.ucsd.sbrg.escher.util
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Provides utility methods, e.g. validation, Jackson mappers, command line options, etc.
- edu.ucsd.sbrg.math - package edu.ucsd.sbrg.math
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- edu.ucsd.sbrg.sbgn - package edu.ucsd.sbrg.sbgn
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- Element - Interface in edu.ucsd.sbrg.escher.model
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.AbstractEscherBase
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.Gene
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.Metabolite
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.Node
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- equals(Object) - Method in class edu.ucsd.sbrg.escher.model.Segment
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- equals(Object) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
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- Escher2SBGN - Class in edu.ucsd.sbrg.escher.converter
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- Escher2SBGN() - Constructor for class edu.ucsd.sbrg.escher.converter.Escher2SBGN
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Default constructor.
- Escher2SBML - Class in edu.ucsd.sbrg.escher.converter
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This class takes an
EscherMap
as input and creates an
SBMLDocument
based on the information provided.
- Escher2SBML() - Constructor for class edu.ucsd.sbrg.escher.converter.Escher2SBML
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- Escher2Standard<T> - Class in edu.ucsd.sbrg.escher.converter
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- Escher2Standard() - Constructor for class edu.ucsd.sbrg.escher.converter.Escher2Standard
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- ESCHER_NODE_LINK - Static variable in class edu.ucsd.sbrg.escher.converter.Escher2Standard
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Used as a key for a mapping between data structures.
- EscherBase - Interface in edu.ucsd.sbrg.escher.model
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Base class for all Escher objects
- EscherCompartment - Class in edu.ucsd.sbrg.escher.model
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- EscherCompartment() - Constructor for class edu.ucsd.sbrg.escher.model.EscherCompartment
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- EscherCompartment(EscherCompartment) - Constructor for class edu.ucsd.sbrg.escher.model.EscherCompartment
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- EscherConverter - Class in edu.ucsd.sbrg.escher
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Main class of the application.
- EscherConverter(String...) - Constructor for class edu.ucsd.sbrg.escher.EscherConverter
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Called by the main method.
- EscherConverterUI - Class in edu.ucsd.sbrg.escher.gui
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Main class of the User Interface of EscherConverter
- EscherConverterUI(AppConf) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherConverterUI
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Starts the user interface.
- EscherConverterWorker<T> - Class in edu.ucsd.sbrg.escher.gui
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- EscherConverterWorker(EscherMap, Class<? extends T>, SBProperties) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherConverterWorker
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- EscherIOOptions - Interface in edu.ucsd.sbrg.escher.util
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Input and output options
- EscherKeywords - Enum in edu.ucsd.sbrg.escher.util
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- escherMap - Variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
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Output Escher map.
- EscherMap - Class in edu.ucsd.sbrg.escher.model
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Includes all the elements of an EscherMap
- EscherMap() - Constructor for class edu.ucsd.sbrg.escher.model.EscherMap
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Default constructor.
- EscherMap(EscherMap) - Constructor for class edu.ucsd.sbrg.escher.model.EscherMap
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Copy constructor.
- EscherMapDisplay - Class in edu.ucsd.sbrg.escher.gui
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An EscherMap needs first be converted into an SBMLDocument
which can then be displayed
- EscherMapDisplay(OpenedFile<EscherMap>, SBProperties) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherMapDisplay
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- escherMaps - Variable in class edu.ucsd.sbrg.escher.converter.SBML2Escher
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List of escher maps converted from the layouts exported from the SBML document.
- EscherOptions - Interface in edu.ucsd.sbrg.escher.util
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These options influence how the output will be created and how the Escher
maps are interpreted.
- EscherOptions.InputFormat - Enum in edu.ucsd.sbrg.escher.util
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Enumeration of allowable input file formats.
- EscherOptions.OutputFormat - Enum in edu.ucsd.sbrg.escher.util
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Enumeration of allowable output file formats.
- EscherParser - Class in edu.ucsd.sbrg.escher.util
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- EscherParser() - Constructor for class edu.ucsd.sbrg.escher.util.EscherParser
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Deprecated.
- EscherParserWorker - Class in edu.ucsd.sbrg.escher.gui
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Handles by which parser a given file should be parsed depending on the format and calls convert function on it.
- EscherParserWorker(Component, File...) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherParserWorker
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Constructor
- EscherReaction - Class in edu.ucsd.sbrg.escher.model
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Represents all properties of a reaction in an Escher map.
- EscherReaction() - Constructor for class edu.ucsd.sbrg.escher.model.EscherReaction
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Creates a new reaction object where all properties are initialized with
null
values.
- EscherReaction(EscherReaction) - Constructor for class edu.ucsd.sbrg.escher.model.EscherReaction
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- EXTRACT_COBRA - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
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Whether to extract CoBRA model, if FBC present on SBML file.
- extractCobraModel(File) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
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Extracts CoBRA from SBMLDocument
if it is FBC compliant. cobrapy must be present for
this.
- extractCoefficient(Object) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
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- extractReactionId(Set<Map.Entry<String, List<String>>>) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
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Returns the reaction id of a set of segments, gives warning if multiple ones are used in segments
- validateEscher(File) - Method in class edu.ucsd.sbrg.escher.util.Validator
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Validates an Escher JSON file.
- validateSbgnml(File) - Method in class edu.ucsd.sbrg.escher.util.Validator
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Validates an SBGN-ML XML file.
- validateSbmlLE(File) - Method in class edu.ucsd.sbrg.escher.util.Validator
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Validates an SBGN-ML XML file.
- Validator - Class in edu.ucsd.sbrg.escher.util
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Validator for input files.
- Validator() - Constructor for class edu.ucsd.sbrg.escher.util.Validator
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Default constructor.
- Validator(JsonNode) - Constructor for class edu.ucsd.sbrg.escher.util.Validator
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Constructor.
- valueOf(String) - Static method in enum edu.ucsd.sbrg.escher.model.Node.Type
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum edu.ucsd.sbrg.escher.util.EscherKeywords
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum edu.ucsd.sbrg.escher.util.EscherOptions.InputFormat
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum edu.ucsd.sbrg.escher.util.EscherOptions.OutputFormat
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Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum edu.ucsd.sbrg.sbgn.SBGNbuilder.Language
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Returns the enum constant of this type with the specified name.
- values() - Static method in enum edu.ucsd.sbrg.escher.model.Node.Type
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Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum edu.ucsd.sbrg.escher.util.EscherKeywords
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Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum edu.ucsd.sbrg.escher.util.EscherOptions.InputFormat
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Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum edu.ucsd.sbrg.escher.util.EscherOptions.OutputFormat
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Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum edu.ucsd.sbrg.sbgn.SBGNbuilder.Language
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Returns an array containing the constants of this enum type, in
the order they are declared.