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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.converters.Escher2Standard
 
getCanvasDefaultWidth() - Method in class edu.ucsd.sbrg.escher.converters.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.converters.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.converters.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.converters.SBGN2Escher
Extract id from either a Glyph or a Port.
getInferCompartmentBoundaries() - Method in class edu.ucsd.sbrg.escher.converters.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.converters.Escher2Standard
 
getLabelWidth() - Method in class edu.ucsd.sbrg.escher.converters.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.converters.Escher2SBML
 
getLayoutName() - Method in class edu.ucsd.sbrg.escher.converters.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.converters.Escher2SBML
 
getNodeLabelHeight() - Method in class edu.ucsd.sbrg.escher.converters.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.utilities.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.converters.Escher2Standard
 
getPrimaryNodeWidth() - Method in class edu.ucsd.sbrg.escher.converters.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.converters.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.converters.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.converters.Escher2SBML
 
glyphId2LabelMap - Variable in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
Glyph ids with their respective label.
glyphIds - Variable in class edu.ucsd.sbrg.escher.converters.SBGN2Escher
List of Glyph ids.
GROUP_IO - Static variable in interface edu.ucsd.sbrg.escher.utilities.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.utilities.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.utilities.EscherOptions
Here you can influence how elements in the layout are called or identified.
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