fr.curie.BiNoM.pathways
Class BioPAXToCytoscapeConverter

java.lang.Object
  fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
      fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

public class BioPAXToCytoscapeConverter
extends BioPAXToSBMLConverter

Converts BioPAX (represented by BioPAX object) to XGMML (represented by GraphDocument object)

Nested Class Summary

static class	BioPAXToCytoscapeConverter.Graph Little auxillary container for BioPAX and GraphDocument object
static class	BioPAXToCytoscapeConverter.Option Set of conversion options

Nested classes/interfaces inherited from class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

BioPAXToSBMLConverter.BioPAXSpecies

Field Summary

static java.util.HashMap<java.lang.String,BioPAX>	biopax_map A map from BioPAX file key to static set of BioPAX objects
static int	FULL_INDEX_CONVERSION Mode of conversion: from BioPAX to full index (see BiNoM documentation)
static int	PATHWAY_STRUCTURE_CONVERSION Mode of conversion: from BioPAX to Pathway Structure BioPAX interface
static int	PROTEIN_PROTEIN_INTERACTION_CONVERSION Mode of conversion: from BioPAX to Protein-protein interaction BioPAX interface
static int	REACTION_NETWORK_CONVERSION Mode of conversion: from BioPAX to Reaction Network BioPAX interface

Fields inherited from class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

alwaysMentionCompartment, biopax, bioPAXreactions, bpnm, compartments, complexList, considerCompartmentNameRatherThanId, controls, dnaList, includedSpecies, independentSpecies, independentSpeciesIds, proteinList, reactions, rnaList, sbmlDoc, smallMoleculeList, species, useBiopaxModelOntology

Constructor Summary

BioPAXToCytoscapeConverter()

Method Summary

edu.rpi.cs.xgmml.GraphicNode	addInteractionNode(edu.rpi.cs.xgmml.GraphicGraph grf, interaction in, java.util.HashMap pathways, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap nodes) Adds a 'interaction' node to Pathway Structure interface
edu.rpi.cs.xgmml.GraphicNode	addPathwayNode(edu.rpi.cs.xgmml.GraphicGraph grf, pathway p, java.util.HashMap pathways, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap nodes, java.util.HashMap edges, BioPAXToCytoscapeConverter.Option option) Adds a pathway node to Pathway Structure interface
edu.rpi.cs.xgmml.GraphicNode	addPathwayStepNode(edu.rpi.cs.xgmml.GraphicGraph grf, pathwayStep ps, java.util.HashMap pathways, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap nodes, java.util.HashMap edges, BioPAXToCytoscapeConverter.Option option) Adds a 'pathway step' node to Pathway Structure interface
static BioPAXToCytoscapeConverter.Graph	convert(int algo, BioPAXToCytoscapeConverter b2c, java.lang.String name, BioPAXToCytoscapeConverter.Option option) Convert using BioPAXToCytoscapeConverter and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
static BioPAXToCytoscapeConverter.Graph	convert(int algo, java.io.InputStream is, java.lang.String name, BioPAXToCytoscapeConverter.Option option) Convert from InputStream and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
static BioPAXToCytoscapeConverter.Graph	convert(int algo, java.lang.String file, BioPAXToCytoscapeConverter.Option option) Convert from file (specified by path) and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
static BioPAXToCytoscapeConverter.Graph	convert(int algo, java.lang.String file, java.lang.String name, BioPAXToCytoscapeConverter.Option option) Convert using file name and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
static java.lang.String	getFileKey(java.lang.String file) key could be based on: filename + date + size or md5(filecontents);
edu.rpi.cs.xgmml.GraphDocument	getXGMMLGraph(java.lang.String name, org.sbml.x2001.ns.celldesigner.SbmlDocument sbml) Implementation of extracting Reaction Network interface (requires first conversion from BioPAX to SBML, from which the interface is converted).
edu.rpi.cs.xgmml.GraphDocument	getXGMMLPathwayGraph(java.lang.String name, BioPAX biopax, BioPAXToCytoscapeConverter.Option option) Implementation of extracting Pathway Structure interface (requires first conversion from BioPAX to SBML, from which the interface is converted).
edu.rpi.cs.xgmml.GraphDocument	getXGMMLProteinGraph(java.lang.String name, BioPAX biopax, BioPAXToCytoscapeConverter.Option option) Implementation of extracting Protein Interaction interface (requires first conversion from BioPAX to SBML, from which the interface is converted).

Methods inherited from class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

addControl, addConversionReaction, addIncludedParticipant, findIndependentSpecies, getAllCompartments, getTypeForParticipant, makeComment, makeLists, populateSbml

Methods inherited from class java.lang.Object

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

Field Detail

FULL_INDEX_CONVERSION

public static final int FULL_INDEX_CONVERSION

Mode of conversion: from BioPAX to full index (see BiNoM documentation)

See Also:

Constant Field Values

REACTION_NETWORK_CONVERSION

public static final int REACTION_NETWORK_CONVERSION

Mode of conversion: from BioPAX to Reaction Network BioPAX interface

See Also:

Constant Field Values

PATHWAY_STRUCTURE_CONVERSION

public static final int PATHWAY_STRUCTURE_CONVERSION

Mode of conversion: from BioPAX to Pathway Structure BioPAX interface

See Also:

Constant Field Values

PROTEIN_PROTEIN_INTERACTION_CONVERSION

public static final int PROTEIN_PROTEIN_INTERACTION_CONVERSION

Mode of conversion: from BioPAX to Protein-protein interaction BioPAX interface

See Also:

Constant Field Values

biopax_map

public static java.util.HashMap<java.lang.String,BioPAX> biopax_map

A map from BioPAX file key to static set of BioPAX objects

It is kept to accelerate BioPAX access in case of frequent calls

for import of the same file

Constructor Detail

BioPAXToCytoscapeConverter

public BioPAXToCytoscapeConverter()

Method Detail

convert

public static BioPAXToCytoscapeConverter.Graph convert(int algo,
                                                       java.io.InputStream is,
                                                       java.lang.String name,
                                                       BioPAXToCytoscapeConverter.Option option)
                                                throws java.lang.Exception

Convert from InputStream and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

Throws:

java.lang.Exception

convert

public static BioPAXToCytoscapeConverter.Graph convert(int algo,
                                                       BioPAXToCytoscapeConverter b2c,
                                                       java.lang.String name,
                                                       BioPAXToCytoscapeConverter.Option option)
                                                throws java.lang.Exception

Convert using BioPAXToCytoscapeConverter and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

Throws:

java.lang.Exception

getFileKey

public static java.lang.String getFileKey(java.lang.String file)

key could be based on: filename + date + size or md5(filecontents);

convert

public static BioPAXToCytoscapeConverter.Graph convert(int algo,
                                                       java.lang.String file,
                                                       java.lang.String name,
                                                       BioPAXToCytoscapeConverter.Option option)
                                                throws java.lang.Exception

Convert using file name and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

Throws:

java.lang.Exception

convert

public static BioPAXToCytoscapeConverter.Graph convert(int algo,
                                                       java.lang.String file,
                                                       BioPAXToCytoscapeConverter.Option option)
                                                throws java.lang.Exception

Convert from file (specified by path) and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

Throws:

java.lang.Exception

getXGMMLGraph

public edu.rpi.cs.xgmml.GraphDocument getXGMMLGraph(java.lang.String name,
                                                    org.sbml.x2001.ns.celldesigner.SbmlDocument sbml)
                                             throws java.lang.Exception

Implementation of extracting Reaction Network interface (requires first conversion from BioPAX to SBML, from which the interface is converted). Also nees biopaxReactions, independentSpeciesIds, species, controls maps valid (they are filled by BioPAXToSBMLConverter.populateSbml() parent method )

Throws:

java.lang.Exception

getXGMMLPathwayGraph

public edu.rpi.cs.xgmml.GraphDocument getXGMMLPathwayGraph(java.lang.String name,
                                                           BioPAX biopax,
                                                           BioPAXToCytoscapeConverter.Option option)
                                                    throws java.lang.Exception

Implementation of extracting Pathway Structure interface (requires first conversion from BioPAX to SBML, from which the interface is converted). Also nees biopaxReactions, independentSpeciesIds, species, controls and other maps valid (they are filled by BioPAXToSBMLConverter.populateSbml() parent method )

Throws:

java.lang.Exception

addPathwayNode

public edu.rpi.cs.xgmml.GraphicNode addPathwayNode(edu.rpi.cs.xgmml.GraphicGraph grf,
                                                   pathway p,
                                                   java.util.HashMap pathways,
                                                   java.util.HashMap interactions,
                                                   java.util.HashMap pathwaySteps,
                                                   java.util.HashMap nodes,
                                                   java.util.HashMap edges,
                                                   BioPAXToCytoscapeConverter.Option option)
                                            throws java.lang.Exception

Adds a pathway node to Pathway Structure interface

Throws:

java.lang.Exception

addPathwayStepNode

public edu.rpi.cs.xgmml.GraphicNode addPathwayStepNode(edu.rpi.cs.xgmml.GraphicGraph grf,
                                                       pathwayStep ps,
                                                       java.util.HashMap pathways,
                                                       java.util.HashMap interactions,
                                                       java.util.HashMap pathwaySteps,
                                                       java.util.HashMap nodes,
                                                       java.util.HashMap edges,
                                                       BioPAXToCytoscapeConverter.Option option)
                                                throws java.lang.Exception

Adds a 'pathway step' node to Pathway Structure interface

Throws:

java.lang.Exception

addInteractionNode

public edu.rpi.cs.xgmml.GraphicNode addInteractionNode(edu.rpi.cs.xgmml.GraphicGraph grf,
                                                       interaction in,
                                                       java.util.HashMap pathways,
                                                       java.util.HashMap interactions,
                                                       java.util.HashMap pathwaySteps,
                                                       java.util.HashMap nodes)
                                                throws java.lang.Exception

Adds a 'interaction' node to Pathway Structure interface

Throws:

java.lang.Exception

getXGMMLProteinGraph

public edu.rpi.cs.xgmml.GraphDocument getXGMMLProteinGraph(java.lang.String name,
                                                           BioPAX biopax,
                                                           BioPAXToCytoscapeConverter.Option option)
                                                    throws java.lang.Exception

Implementation of extracting Protein Interaction interface (requires first conversion from BioPAX to SBML, from which the interface is converted). Also nees biopaxReactions, independentSpeciesIds, species, controls and other maps valid (they are filled by BioPAXToSBMLConverter.populateSbml() parent method )

Throws:

java.lang.Exception