fr.curie.BiNoM.pathways
Class CytoscapeToBioPAXConverter

java.lang.Object
  fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter

public class CytoscapeToBioPAXConverter
extends java.lang.Object

Deprecated class. It was used before for exporting BioPAX interface, but now a more universal method is used (implemented in BioPAXUtilities)

Constructor Summary

CytoscapeToBioPAXConverter()

Method Summary

static BioPAX	convert(edu.rpi.cs.xgmml.GraphDocument graph, BioPAX biopax)
static void	filterIDs(BioPAX biopax, edu.rpi.cs.xgmml.GraphDocument gr)
static void	filterIDs(BioPAX biopax, java.util.Vector species, java.util.Vector reactions)
static void	filterPathwaySteps(BioPAX biopax, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap pathwayStepsRemove)
static java.lang.String	getControlledURI(control cntrl)
static void	removeConversion(conversion br, java.util.HashMap participants, java.util.HashMap allparticipants, java.util.Vector reactions, java.util.HashMap interactions, BioPAXToSBMLConverter b2s)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CytoscapeToBioPAXConverter

public CytoscapeToBioPAXConverter()

Method Detail

convert

public static BioPAX convert(edu.rpi.cs.xgmml.GraphDocument graph,
                             BioPAX biopax)
                      throws java.lang.Exception

Throws:

java.lang.Exception

filterIDs

public static void filterIDs(BioPAX biopax,
                             edu.rpi.cs.xgmml.GraphDocument gr)
                      throws java.lang.Exception

Throws:

java.lang.Exception

filterIDs

public static void filterIDs(BioPAX biopax,
                             java.util.Vector species,
                             java.util.Vector reactions)
                      throws java.lang.Exception

Throws:

java.lang.Exception

removeConversion

public static void removeConversion(conversion br,
                                    java.util.HashMap participants,
                                    java.util.HashMap allparticipants,
                                    java.util.Vector reactions,
                                    java.util.HashMap interactions,
                                    BioPAXToSBMLConverter b2s)
                             throws java.lang.Exception

Throws:

java.lang.Exception

getControlledURI

public static java.lang.String getControlledURI(control cntrl)
                                         throws java.lang.Exception

Throws:

java.lang.Exception

filterPathwaySteps

public static void filterPathwaySteps(BioPAX biopax,
                                      java.util.HashMap interactions,
                                      java.util.HashMap pathwaySteps,
                                      java.util.HashMap pathwayStepsRemove)
                               throws java.lang.Exception

Throws:

java.lang.Exception