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A

AbstractBox - Class in edu.ucsd.sbrg.escher.model
 
AbstractBox() - Constructor for class edu.ucsd.sbrg.escher.model.AbstractBox
 
AbstractBox(AbstractBox) - Constructor for class edu.ucsd.sbrg.escher.model.AbstractBox
 
AbstractEscherBase - Class in edu.ucsd.sbrg.escher.model
 
AbstractEscherBase() - Constructor for class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
AbstractEscherBase(AbstractEscherBase) - Constructor for class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
AbstractPosition - Class in edu.ucsd.sbrg.escher.model
 
AbstractPosition() - Constructor for class edu.ucsd.sbrg.escher.model.AbstractPosition
 
AbstractPosition(AbstractPosition) - Constructor for class edu.ucsd.sbrg.escher.model.AbstractPosition
 
AbstractPosition(Double, Double) - Constructor for class edu.ucsd.sbrg.escher.model.AbstractPosition
 
add(Point) - Method in class edu.ucsd.sbrg.escher.model.Point
 
addCanvasInfo(Bbox) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Add canvas info to the internal SBGN2Escher.escherMap field.
addCanvasInfo(Layout) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Create a Canvas instance from an SBML Layout.
addCompartment(EscherCompartment) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
addConnectedSegment(String, Segment) - Method in class edu.ucsd.sbrg.escher.model.Node
 
addConnectedSegment(String, String) - Method in class edu.ucsd.sbrg.escher.model.Node
 
addCopyrightToSplashScreen() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
addGene(Gene) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
addMetabolite(Metabolite) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
addMetaInfo() - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Add meta info about the map to the internal SBGN2Escher.escherMap field.
addNode(Node) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
addReaction(EscherReaction) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
addSegment(Segment) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
addTextLabel(TextLabel) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
addVersionNumberToSplashScreen() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
arc2GlyphMap - Variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Arcs' ids with their respective process (Glyph) nodes ids.

B

batchProcess(File, File, SBProperties) - Method in class edu.ucsd.sbrg.escher.EscherConverter
Convert files one by one by calling the EscherConverter.convert(File, File, SBProperties) recursively.
bezier(double, Point, Point, Point, Point) - Static method in class edu.ucsd.sbrg.math.Geometry
Gives the Beziér point at parameter t for the given definition and control points.
bezier(double, double, double, double, double, double, double, double, double) - Static method in class edu.ucsd.sbrg.math.Geometry
 
bezier(double, CubicCurve2D) - Static method in class edu.ucsd.sbrg.math.Geometry
 
Box - Interface in edu.ucsd.sbrg.escher.model
A base class for a box with height and width
bundle - Static variable in class edu.ucsd.sbrg.escher.converter.Escher2SBGN
Localization support.
bundle - Static variable in class edu.ucsd.sbrg.escher.converter.Escher2SBML
Localization support.
bundle - Static variable in class edu.ucsd.sbrg.escher.converter.Escher2Standard
Localization support.
bundle - Static variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Default values.
bundle - Static variable in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Default values,
bundle - Static variable in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
Localization support.
bundle - Static variable in class edu.ucsd.sbrg.escher.gui.EscherConverterWorker
Localization support.
bundle - Static variable in class edu.ucsd.sbrg.escher.gui.EscherParserWorker
Localization support.
bundle - Static variable in class edu.ucsd.sbrg.escher.model.EscherReaction
Localization support.
bundle - Static variable in interface edu.ucsd.sbrg.escher.util.EscherIOOptions
Localization support.
bundle - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
Localization support.
bundle - Static variable in class edu.ucsd.sbrg.escher.util.EscherParser
Deprecated.
Localization support.

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.util.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.util.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.util.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.util.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.util.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.converter.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.converter.Escher2SBGN
 
convert(EscherMap) - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
convert(EscherMap) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
convert(Sbgn) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Converts Sbgn document to EscherMap by iteratively creating nodes, reactions, etc.
convert(SBMLDocument) - Method in class edu.ucsd.sbrg.escher.converter.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.util.EscherParser
Deprecated.
 
createMetabolite(SpeciesReference) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Creates a Metabolite from a SpeciesReference.
createMidMarker(Glyph) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Create an Escher Node(mid-marker) from process Glyph.
createMidMarker(ReactionGlyph) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Creates a Node(mid-marker) from a ReactionGlyph.
createMultiMarker(Arc.Next) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Create an Escher Node(multi-marker) from Arc.Next.
createMultiMarkers(SpeciesReferenceGlyph) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Creates a list of Nodes(multi-markers) from a SpeciesReferenceGlyph.
createNode(Glyph) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Create an Escher Node(metabolite) from EPN Glyph.
createNode(SpeciesGlyph) - Method in class edu.ucsd.sbrg.escher.converter.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.converter.SBGN2Escher
Create an EscherReaction from an SBGN-ML Glyph.
createReaction(ReactionGlyph) - Method in class edu.ucsd.sbrg.escher.converter.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.converter.SBGN2Escher
Create a list of Segments from an SBGN-ML Arc.
createSegments(SpeciesReferenceGlyph, ReactionGlyph) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Creates a list of Segments from a SpeciesReferenceGlyph.
createTextLabel(Glyph) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Create a TextLabel from an SBGN-ML Glyph.
createTextLabel(TextGlyph) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Create a TextLabel from a TextGlyph.

D

defaultEscherSchema() - Static method in class edu.ucsd.sbrg.escher.util.Utils
Get the default Escher Schema (v1.0.0).
determineSpeciesReferenceRole(SpeciesReferenceGlyph, ReactionGlyph) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Finds out whether a SpeciesReferenceGlyph is a product, substrate or modifier.
document - Variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Input SBGN-ML document.
document - Variable in class edu.ucsd.sbrg.escher.converter.SBML2Escher
SBML document to extract escher maps from.
doInBackground() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterWorker
 
doInBackground() - Method in class edu.ucsd.sbrg.escher.gui.EscherParserWorker
 
doInBackground() - Method in class edu.ucsd.sbrg.escher.gui.SBGNWritingTask
 

E

edu.ucsd.sbrg.escher - package edu.ucsd.sbrg.escher
 
edu.ucsd.sbrg.escher.converter - package edu.ucsd.sbrg.escher.converter
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.util - package edu.ucsd.sbrg.escher.util
Provides utility methods, e.g. validation, Jackson mappers, command line options, etc.
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.converter
 
Escher2SBGN() - Constructor for class edu.ucsd.sbrg.escher.converter.Escher2SBGN
Default constructor.
Escher2SBML - Class in edu.ucsd.sbrg.escher.converter
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
 
Escher2Standard<T> - Class in edu.ucsd.sbrg.escher.converter
 
Escher2Standard() - Constructor for class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
ESCHER_NODE_LINK - Static variable in class edu.ucsd.sbrg.escher.converter.Escher2Standard
Used as a key for a mapping between data structures.
EscherBase - Interface in edu.ucsd.sbrg.escher.model
Base class for all Escher objects
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
Main class of the application.
EscherConverter(String...) - Constructor for class edu.ucsd.sbrg.escher.EscherConverter
Called by the main method.
EscherConverterUI - Class in edu.ucsd.sbrg.escher.gui
Main class of the User Interface of EscherConverter
EscherConverterUI(AppConf) - Constructor for class edu.ucsd.sbrg.escher.gui.EscherConverterUI
Starts the user interface.
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.util
Input and output options
EscherKeywords - Enum in edu.ucsd.sbrg.escher.util
 
escherMap - Variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Output Escher map.
EscherMap - Class in edu.ucsd.sbrg.escher.model
Includes all the elements of an EscherMap
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
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
 
escherMaps - Variable in class edu.ucsd.sbrg.escher.converter.SBML2Escher
List of escher maps converted from the layouts exported from the SBML document.
EscherOptions - Interface in edu.ucsd.sbrg.escher.util
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
Enumeration of allowable input file formats.
EscherOptions.OutputFormat - Enum in edu.ucsd.sbrg.escher.util
Enumeration of allowable output file formats.
EscherParser - Class in edu.ucsd.sbrg.escher.util
Deprecated.
This class has been replaced by the newer Jackson-based ObjectMapper. See EscherConverter.parseEscherJson(java.io.File) for details.
EscherParser() - Constructor for class edu.ucsd.sbrg.escher.util.EscherParser
Deprecated.
 
EscherParserWorker - Class in edu.ucsd.sbrg.escher.gui
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
Constructor
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.util.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. cobrapy must be present for this.
extractCoefficient(Object) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
 
extractReactionId(Set<Map.Entry<String, List<String>>>) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
Returns the reaction id of a set of segments, gives warning if multiple ones are used in segments

F

findIntersection(Shape, CubicCurve2D) - Static method in class edu.ucsd.sbrg.math.Geometry
Be careful, when using this method!!!
findMidmarker(EscherMap) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
FORMAT - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
The desired format for the conversion, e.g., SBML.

G

Gene - Class in edu.ucsd.sbrg.escher.model
 
Gene() - Constructor for class edu.ucsd.sbrg.escher.model.Gene
 
Gene(Gene) - Constructor for class edu.ucsd.sbrg.escher.model.Gene
 
Gene(String, String) - Constructor for class edu.ucsd.sbrg.escher.model.Gene
 
Geometry - Class in edu.ucsd.sbrg.math
 
Geometry() - Constructor for class edu.ucsd.sbrg.math.Geometry
 
getBasePoint1() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
getBasePoint2() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
getBigg2nodes() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getBigg2reactions() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getBiggId() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getBiggId() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getCanvas() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getCanvasDefaultHeight() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getCanvasDefaultWidth() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getCmdLineOptions() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getCoefficient() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
getCompartment(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getCompartment() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getCompartmentCount() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getConnectedSegments() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getConnectedSegments(String) - Method in class edu.ucsd.sbrg.escher.model.Node
 
getDefaultCompartmentId() - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
getDescription() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getFromNodeId() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
getGeneCount() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getGeneList() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getGeneReactionRule() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getGenes() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getGlyphIdFromPortId(String) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Get Glyph id from a Port or Glyph id.
getHeight() - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
getHeight() - Method in interface edu.ucsd.sbrg.escher.model.Box
 
getId() - Method in interface edu.ucsd.sbrg.escher.model.Element
 
getId() - Method in class edu.ucsd.sbrg.escher.model.EscherCompartment
 
getId() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getId() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getId() - Method in class edu.ucsd.sbrg.escher.model.Gene
 
getId() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
getId() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getId() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
getId() - Method in class edu.ucsd.sbrg.escher.model.TextLabel
 
getIdFromSourceOrTarget(Object) - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Extract id from either a Glyph or a Port.
getInferCompartmentBoundaries() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getInstitute() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getInteractiveOptions() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getLabelHeight() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getLabelWidth() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getLabelX() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getLabelX() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getLabelY() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getLabelY() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getLayoutId() - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
getLayoutName() - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
getLogPackages() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getMetabolite(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getMetaboliteCount() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getMetaboliteList() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getMetabolites() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
Gives you the mapping between BiGG ids and the metabolites with that BiGG id that participate in this reaction.
getMidmarker() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getName() - Method in class edu.ucsd.sbrg.escher.model.EscherCompartment
 
getName() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getName() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getName() - Method in class edu.ucsd.sbrg.escher.model.Gene
 
getName() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getNode(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getNodeDepth() - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
getNodeLabelHeight() - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
getNodeRefId() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
getNodes(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getNodes() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getNodes() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getNodesCount() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getObjectFactory() - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
getObjectMapper() - Static method in class edu.ucsd.sbrg.escher.util.Utils
Get the pre-configured ObjectMapper for (de)serialization.
getOpenedFile() - Method in class edu.ucsd.sbrg.escher.gui.EscherMapDisplay
 
getOrganization() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getPrimaryNodeHeight() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getPrimaryNodeWidth() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getProvider() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getReaction(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getReactionCount() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getReactionNodeRatio() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getReactions(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getReactions() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getReversibility() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getSBGNBase(String) - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
getSBMLDocument() - Method in class edu.ucsd.sbrg.escher.gui.EscherMapDisplay
 
getSchema() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getSecondaryNodeRatio() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
getSegment(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getSegmentCount() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getSegments() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
getText() - Method in class edu.ucsd.sbrg.escher.model.TextLabel
 
getTextLabel(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getTextLabelCount() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getTextLabels() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getToNodeId() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
getType() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getURL() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
getURLAboutMessage() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
getURLLicense() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
getURLlicenseFile() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getURLOnlineHelp() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
getURLOnlineUpdate() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getUserObject(String) - Method in class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
getUserObject(String) - Method in interface edu.ucsd.sbrg.escher.model.EscherBase
 
getVersionNumber() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getWidth() - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
getWidth() - Method in interface edu.ucsd.sbrg.escher.model.Box
 
getX() - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
getX() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getX() - Method in interface edu.ucsd.sbrg.escher.model.Position
 
getY() - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
getY() - Method in class edu.ucsd.sbrg.escher.model.Node
 
getY() - Method in interface edu.ucsd.sbrg.escher.model.Position
 
getYearOfProgramRelease() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getYearWhenProjectWasStarted() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
getZ() - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
glyphId2LabelMap - Variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Glyph ids with their respective label.
glyphIds - Variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
List of Glyph ids.
GROUP_IO - Static variable in interface edu.ucsd.sbrg.escher.util.EscherIOOptions
Definition of input and output data files as well as the format for the output.
GROUP_LAYOUT - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
The options in this group allow you to influence how large certain elements should be displayed.
GROUP_NAMING - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
Here you can influence how elements in the layout are called or identified.

H

hashCode() - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
hashCode() - Method in class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
hashCode() - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
hashCode() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
hashCode() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
hashCode() - Method in class edu.ucsd.sbrg.escher.model.Gene
 
hashCode() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
hashCode() - Method in class edu.ucsd.sbrg.escher.model.Node
 
hashCode() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
hashCode() - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
height - Variable in class edu.ucsd.sbrg.escher.model.AbstractBox
 

I

INFER_COMPARTMENT_BOUNDS - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
This converter can infer where the boundaries of compartments could be drawn.
initGUI(AppConf) - Method in class edu.ucsd.sbrg.escher.EscherConverter
 
INPUT - Static variable in interface edu.ucsd.sbrg.escher.util.EscherIOOptions
Specifies the JSON input file.
INTERMERIM_RESULTS - Static variable in class edu.ucsd.sbrg.escher.gui.EscherParserWorker
 
intersect(Set<Node>) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isMetabolite() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isMidmarker() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isMultimarker() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isPrimary() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetBasePoint1() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
isSetBasePoint2() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
isSetBiggId() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isSetBiggId() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetCanvas() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
isSetCoefficient() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
isSetCompartment() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetConnectedSegments() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetDescription() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
isSetFromNodeId() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
isSetGeneReactionRule() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isSetHeight() - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
isSetHeight() - Method in interface edu.ucsd.sbrg.escher.model.Box
 
isSetId() - Method in interface edu.ucsd.sbrg.escher.model.Element
 
isSetId() - Method in class edu.ucsd.sbrg.escher.model.EscherCompartment
 
isSetId() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
isSetId() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isSetId() - Method in class edu.ucsd.sbrg.escher.model.Gene
 
isSetId() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
isSetId() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetId() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
isSetId() - Method in class edu.ucsd.sbrg.escher.model.TextLabel
 
isSetIsPrimary() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetLabelX() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isSetLabelX() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetLabelY() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isSetLabelY() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetMidmarker() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isSetName() - Method in class edu.ucsd.sbrg.escher.model.EscherCompartment
 
isSetName() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
isSetName() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isSetName() - Method in class edu.ucsd.sbrg.escher.model.Gene
 
isSetName() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetNodeRefId() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
isSetPrimary() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetReversibility() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
isSetSchema() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
isSetText() - Method in class edu.ucsd.sbrg.escher.model.TextLabel
 
isSetToNodeId() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
isSetType() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetURL() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
isSetWidth() - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
isSetWidth() - Method in interface edu.ucsd.sbrg.escher.model.Box
 
isSetX() - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
isSetX() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetX() - Method in interface edu.ucsd.sbrg.escher.model.Position
 
isSetY() - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
isSetY() - Method in class edu.ucsd.sbrg.escher.model.Node
 
isSetY() - Method in interface edu.ucsd.sbrg.escher.model.Position
 

J

jsonSchemaSchema() - Static method in class edu.ucsd.sbrg.escher.util.Utils
Get the schema validation schema (meta-schema) file.

L

LABEL_HEIGHT - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
With this option you can specify the height of the bounding box of text labels.
LABEL_WIDTH - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
This option defines the width of bounding boxes for text labels.
LAYOUT_ID - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
In contrast to the name, this identifier does not have to be human-readable.
LAYOUT_NAME - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
This should be a human-readable name for the layout that is to be created.
layouts - Variable in class edu.ucsd.sbrg.escher.converter.SBML2Escher
List of layouts exported from the SBML document.

M

main(String[]) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Starts the program.
main(String[]) - Static method in class edu.ucsd.sbrg.math.Geometry
 
messages - Static variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Localization support.
messages - Static variable in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Localization support.
Metabolite - Class in edu.ucsd.sbrg.escher.model
 
Metabolite() - Constructor for class edu.ucsd.sbrg.escher.model.Metabolite
 
Metabolite(Metabolite) - Constructor for class edu.ucsd.sbrg.escher.model.Metabolite
Copy constructor
metaboliteIds - Variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
List of Metabolite ids.
midPoint(double, double) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
Calculates mid-point of two decimal values.

N

Node - Class in edu.ucsd.sbrg.escher.model
 
Node() - Constructor for class edu.ucsd.sbrg.escher.model.Node
 
Node(Node) - Constructor for class edu.ucsd.sbrg.escher.model.Node
 
Node.Type - Enum in edu.ucsd.sbrg.escher.model
The kinds of node.
NODE_DEPTH - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
The length of nodes along z-coordinate.
NODE_LABEL_HEIGHT - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
Node labels can have a size different from general labels in the graph.
nodes() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 

O

openFile(File...) - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
OUTPUT - Static variable in interface edu.ucsd.sbrg.escher.util.EscherIOOptions
The path to the file into which the output should be written.

P

parse(File) - Method in class edu.ucsd.sbrg.escher.util.EscherParser
Deprecated.
 
parse(InputStream, String) - Method in class edu.ucsd.sbrg.escher.util.EscherParser
Deprecated.
 
parseEscherJson(File) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Parses given JSON file into an EscherMap instance using Jackson.
parseEscherJson(InputStream) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Parses an InputStream that represents an Escher JSON file into an EscherMap instance using Jackson.
parseSBGNML(File, SBProperties) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
 
parseSBGNML(InputStream, SBProperties) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Parses an SBGNML input and calls a convert method to EscherMap.
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.converter.SBGN2Escher
Port ids with their respective Glyph ids.
Position - Interface in edu.ucsd.sbrg.escher.model
A base class for a position with x and y coordinates
postprocessMap() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
Post-processes EscherMap and populates internal helper fields.
preprocessDataStructure(EscherMap) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
Pre-processes every reaction in a data structure
preProcessSbgn() - Method in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Processes the input Sbgn document and populates internal helper fields.
primary_node_height - Variable in class edu.ucsd.sbrg.escher.converter.SBML2Escher
The height of primary nodes; in case bounding boxes have no dimensions
PRIMARY_NODE_HEIGHT - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
The primary node should be bigger than the secondary node.
primary_node_width - Variable in class edu.ucsd.sbrg.escher.converter.SBML2Escher
The width of primary nodes; in case bounding boxes have no dimensions
PRIMARY_NODE_WIDTH - Static variable in interface edu.ucsd.sbrg.escher.util.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.converter.SBGN2Escher
List of process (Glyph) ids.
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
 

R

REACTION_LABEL_HEIGHT - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
This option allows you to specify the height of labels for reactions.
REACTION_NODE_RATIO - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
This value is used as a conversion factor to determine the size of the reaction display box depending on the size of primary nodes.
reactionId - Variable in class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Generated reaction ids.
reactions() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
removeBasePoint1() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
removeBasePoint2() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
removeNode(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
Removes node from EscherMap.nodes.
removeSegment(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
resolveCompartmentCode(String) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
reverse(Segment) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
Inverses the given segment in place.

S

saveFileAs() - Method in class edu.ucsd.sbrg.escher.gui.EscherConverterUI
 
SBGN2Escher - Class in edu.ucsd.sbrg.escher.converter
Converter from SBML Layout Extension to Escher.
SBGN2Escher() - Constructor for class edu.ucsd.sbrg.escher.converter.SBGN2Escher
Default constructor.
SBGNbuilder - Class in edu.ucsd.sbrg.sbgn
A helper class that facilitates the creation of SBGN map objects.
SBGNbuilder() - Constructor for class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
SBGNbuilder.Language - Enum in edu.ucsd.sbrg.sbgn
Enumeration of SBGN languages.
SBGNWritingTask - Class in edu.ucsd.sbrg.escher.gui
Writes the Sbgn into a file
SBGNWritingTask(OpenedFile<Sbgn>) - Constructor for class edu.ucsd.sbrg.escher.gui.SBGNWritingTask
 
SBML2Escher - Class in edu.ucsd.sbrg.escher.converter
Converter from SBML Layout Extension to Escher.
SBML2Escher() - Constructor for class edu.ucsd.sbrg.escher.converter.SBML2Escher
Default constructor.
SBML_CONDITION - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
Helper constant for internal use.
SBMLLayoutViewPanel - Class in edu.ucsd.sbrg.escher.gui
The panel the SBML is displayed in.
SBMLLayoutViewPanel() - Constructor for class edu.ucsd.sbrg.escher.gui.SBMLLayoutViewPanel
 
SBMLLayoutViewPanel(Layout) - Constructor for class edu.ucsd.sbrg.escher.gui.SBMLLayoutViewPanel
 
scale(double) - Method in class edu.ucsd.sbrg.escher.model.Point
 
SECONDARY_NODE_RATIO - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
Similar to the reaction node ratio, the size of secondary nodes (width and height) is determined by dividing the corresponding values from the primary nodes by this value.
Segment - Class in edu.ucsd.sbrg.escher.model
 
Segment() - Constructor for class edu.ucsd.sbrg.escher.model.Segment
 
Segment(Segment) - Constructor for class edu.ucsd.sbrg.escher.model.Segment
 
segments() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setBasePoint1(Point) - Method in class edu.ucsd.sbrg.escher.model.Segment
 
setBasePoint2(Point) - Method in class edu.ucsd.sbrg.escher.model.Segment
 
setBiggId(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setBiggId(String) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setCanvas(Canvas) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setCanvasDefaultHeight(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setCanvasDefaultWidth(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setCoefficient(Double) - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
setConnectedSegments(Map<String, List<String>>) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setDefaultCompartmentId(String) - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
setDefaultCompartmentName(String) - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
setDescription(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setFromNodeId(String) - Method in class edu.ucsd.sbrg.escher.model.Segment
 
setGeneList(List<Gene>) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setGeneReactionRule(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setHeight(Double) - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
setHeight(Double) - Method in interface edu.ucsd.sbrg.escher.model.Box
 
setId(String) - Method in interface edu.ucsd.sbrg.escher.model.Element
 
setId(String) - Method in class edu.ucsd.sbrg.escher.model.EscherCompartment
 
setId(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setId(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setId(String) - Method in class edu.ucsd.sbrg.escher.model.Gene
 
setId(String) - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
setId(String) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setId(String) - Method in class edu.ucsd.sbrg.escher.model.Segment
 
setId(String) - Method in class edu.ucsd.sbrg.escher.model.TextLabel
 
setInferCompartmentBoundaries(boolean) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setLabelHeight(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setLabelWidth(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setLabelX(Double) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setLabelX(Double) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setLabelY(Double) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setLabelY(Double) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setLayoutId(String) - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
setLayoutName(String) - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
setMetaboliteList(List<Metabolite>) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setMidmarker(Node) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setName(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setName(String) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setName(String) - Method in class edu.ucsd.sbrg.escher.model.Gene
 
setName(String) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setNodeDepth(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
setNodeHeight(double) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
 
setNodeLabelHeight(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
setNodeRefId(String) - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
setNodes(Map<String, Node>) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setNodeWidth(double) - Method in class edu.ucsd.sbrg.escher.converter.SBML2Escher
 
setPrimary(Boolean) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setPrimaryNodeHeight(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setPrimaryNodeWidth(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setReactionNodeRatio(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setReactions(Map<String, EscherReaction>) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setReversibility(Boolean) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setSBMLLayout(Layout) - Method in class edu.ucsd.sbrg.escher.gui.SBMLLayoutViewPanel
Draws a given layout, using the SysBio library
setSchema(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setSecondaryNodeRatio(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
setSegments(Map<String, Segment>) - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
setText(String) - Method in class edu.ucsd.sbrg.escher.model.TextLabel
 
setTextLabels(Map<String, TextLabel>) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setToNodeId(String) - Method in class edu.ucsd.sbrg.escher.model.Segment
 
setType(Node.Type) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setURL(String) - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
setWidth(Double) - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
setWidth(Double) - Method in interface edu.ucsd.sbrg.escher.model.Box
 
setX(Double) - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
setX(Double) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setX(Double) - Method in interface edu.ucsd.sbrg.escher.model.Position
 
setY(Double) - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
setY(Double) - Method in class edu.ucsd.sbrg.escher.model.Node
 
setY(Double) - Method in interface edu.ucsd.sbrg.escher.model.Position
 
setZ(double) - Method in class edu.ucsd.sbrg.escher.converter.Escher2SBML
 
showsGUI() - Method in class edu.ucsd.sbrg.escher.EscherConverter
 

T

TextLabel - Class in edu.ucsd.sbrg.escher.model
 
TextLabel() - Constructor for class edu.ucsd.sbrg.escher.model.TextLabel
 
TextLabel(TextLabel) - Constructor for class edu.ucsd.sbrg.escher.model.TextLabel
 
textLabels() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
toDouble(Double) - Static method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 
toString() - Method in class edu.ucsd.sbrg.escher.converter.Escher2Standard
 
toString() - Method in class edu.ucsd.sbrg.escher.model.AbstractBox
 
toString() - Method in class edu.ucsd.sbrg.escher.model.AbstractPosition
 
toString() - Method in class edu.ucsd.sbrg.escher.model.EscherMap
 
toString() - Method in class edu.ucsd.sbrg.escher.model.EscherReaction
 
toString() - Method in class edu.ucsd.sbrg.escher.model.Gene
 
toString() - Method in class edu.ucsd.sbrg.escher.model.Metabolite
 
toString() - Method in class edu.ucsd.sbrg.escher.model.Node
 
toString() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
toString() - Method in class edu.ucsd.sbrg.escher.model.TextLabel
 
toString() - Method in enum edu.ucsd.sbrg.sbgn.SBGNbuilder.Language
 
toString() - Method in class edu.ucsd.sbrg.sbgn.SBGNbuilder
 

U

unsetFromNodeId() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
unsetToNodeId() - Method in class edu.ucsd.sbrg.escher.model.Segment
 
userObjectEntrySet() - Method in class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
userObjectEntrySet() - Method in interface edu.ucsd.sbrg.escher.model.EscherBase
 
userObjectKeys() - Method in class edu.ucsd.sbrg.escher.model.AbstractEscherBase
 
userObjectKeys() - Method in interface edu.ucsd.sbrg.escher.model.EscherBase
 
Utils - Class in edu.ucsd.sbrg.escher.util
Utility methods.
Utils() - Constructor for class edu.ucsd.sbrg.escher.util.Utils
 

V

validateEscher(File) - Method in class edu.ucsd.sbrg.escher.util.Validator
Validates an Escher JSON file.
validateSbgnml(File) - Method in class edu.ucsd.sbrg.escher.util.Validator
Validates an SBGN-ML XML file.
validateSbmlLE(File) - Method in class edu.ucsd.sbrg.escher.util.Validator
Validates an SBGN-ML XML file.
Validator - Class in edu.ucsd.sbrg.escher.util
Validator for input files.
Validator() - Constructor for class edu.ucsd.sbrg.escher.util.Validator
Default constructor.
Validator(JsonNode) - Constructor for class edu.ucsd.sbrg.escher.util.Validator
Constructor.
valueOf(String) - Static method in enum edu.ucsd.sbrg.escher.model.Node.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.ucsd.sbrg.escher.util.EscherKeywords
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.ucsd.sbrg.escher.util.EscherOptions.InputFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.ucsd.sbrg.escher.util.EscherOptions.OutputFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.ucsd.sbrg.sbgn.SBGNbuilder.Language
Returns the enum constant of this type with the specified name.
values() - Static method in enum edu.ucsd.sbrg.escher.model.Node.Type
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
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
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
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
Returns an array containing the constants of this enum type, in the order they are declared.

W

width - Variable in class edu.ucsd.sbrg.escher.model.AbstractBox
 
writeEscherJson(EscherMap, File) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Serializes an EscherMap instance to JSON and writes to output file.
writeEscherJson(List<EscherMap>, File) - Static method in class edu.ucsd.sbrg.escher.EscherConverter
Serializes a List to JSON and writes to output directory.

X

x - Variable in class edu.ucsd.sbrg.escher.model.AbstractPosition
 

Y

y - Variable in class edu.ucsd.sbrg.escher.model.AbstractPosition
 

Z

Z - Static variable in interface edu.ucsd.sbrg.escher.util.EscherOptions
The position on the z-axis where the entire two-dimensional graph should be drawn.
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