- 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.