public class CellDesignerExportTask
extends java.lang.Object
Constructor and Description |
---|
CellDesignerExportTask(java.io.File file,
CellDesignerExportToFileDialog.CellDesignerExportToFileOptions _options) |
Modifier and Type | Method and Description |
---|---|
static void |
addHypotheticalInfluences(SbmlDocument cd4,
boolean complexMutualInhibition,
boolean inhCatalysisReactant) |
static void |
addTransition(SbmlDocument cd4,
java.lang.String id,
java.lang.String type,
java.lang.String color,
java.lang.String species1,
java.lang.String alias1,
java.lang.String species2,
java.lang.String alias2) |
void |
applyCellDesignerOptions(SbmlDocument sbml,
CellDesignerExportToFileDialog.CellDesignerExportToFileOptions options) |
static void |
assignColorToAllReactions(SbmlDocument cd,
java.lang.String color) |
void |
assignCytoscapeColorsToReactions(SbmlDocument sbml,
CyNetwork network) |
void |
assignCytoscapeColorsToSpecies(SbmlDocument sbml,
CyNetwork network) |
void |
assignFontSizeToAllSpecies(SbmlDocument sbml,
float fontSize) |
static Pair |
calcAveragePair(java.util.Vector<Pair> ps) |
static void |
findSBMLSpeciesAndReactions(SbmlDocument sbml,
java.util.Vector species,
java.util.Vector speciesAliases,
java.util.Vector reactions,
java.util.Vector degraded) |
CyNetwork |
getCyNetwork() |
static Pair |
getReactionCenter(ReactionDocument.Reaction r,
java.util.HashMap<java.lang.String,Pair> aliasPositions) |
java.lang.String |
getTitle() |
void |
halt() |
boolean |
isColorChanged(CyNetwork network) |
static void |
modifyPositionOfSpecies(SbmlDocument cd,
GraphDocument gr) |
static void |
removeEditPoints(SbmlDocument cd1) |
static void |
RemoveNames(SbmlDocument sbml) |
static void |
RemoveResidueNames(SbmlDocument sbml) |
void |
run() |
static void |
ScaleSizes(SbmlDocument sbml,
float factor,
boolean onlyDistances) |
void |
setTaskMonitor(TaskMonitor taskMonitor) |
public CellDesignerExportTask(java.io.File file, CellDesignerExportToFileDialog.CellDesignerExportToFileOptions _options)
public void halt()
public void setTaskMonitor(TaskMonitor taskMonitor) throws java.lang.IllegalThreadStateException
java.lang.IllegalThreadStateException
public java.lang.String getTitle()
public CyNetwork getCyNetwork()
public void run()
public static void findSBMLSpeciesAndReactions(SbmlDocument sbml, java.util.Vector species, java.util.Vector speciesAliases, java.util.Vector reactions, java.util.Vector degraded)
public boolean isColorChanged(CyNetwork network)
public void assignCytoscapeColorsToSpecies(SbmlDocument sbml, CyNetwork network)
public void applyCellDesignerOptions(SbmlDocument sbml, CellDesignerExportToFileDialog.CellDesignerExportToFileOptions options)
public static void modifyPositionOfSpecies(SbmlDocument cd, GraphDocument gr)
public static void RemoveNames(SbmlDocument sbml)
public static void RemoveResidueNames(SbmlDocument sbml)
public static void ScaleSizes(SbmlDocument sbml, float factor, boolean onlyDistances)
public static void removeEditPoints(SbmlDocument cd1)
public static Pair getReactionCenter(ReactionDocument.Reaction r, java.util.HashMap<java.lang.String,Pair> aliasPositions)
public static void assignColorToAllReactions(SbmlDocument cd, java.lang.String color)
public void assignCytoscapeColorsToReactions(SbmlDocument sbml, CyNetwork network)
public void assignFontSizeToAllSpecies(SbmlDocument sbml, float fontSize)
public static void addHypotheticalInfluences(SbmlDocument cd4, boolean complexMutualInhibition, boolean inhCatalysisReactant)
public static void addTransition(SbmlDocument cd4, java.lang.String id, java.lang.String type, java.lang.String color, java.lang.String species1, java.lang.String alias1, java.lang.String species2, java.lang.String alias2)