- 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
-