public class BioPAXToCytoscapeConverter extends BioPAXToSBMLConverter
Converts BioPAX (represented by BioPAX object) to XGMML (represented by GraphDocument object)
Modifier and Type | Class and Description |
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static class |
BioPAXToCytoscapeConverter.Graph
Little auxiliary container for BioPAX and GraphDocument object
|
static class |
BioPAXToCytoscapeConverter.Option
Set of conversion options
|
BioPAXToSBMLConverter.BioPAXSpecies
Modifier and Type | Field and Description |
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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 |
INTERACTION_CONVERSION
Mode of conversion: from BioPAX to Protein-protein interaction BioPAX interface
|
static int |
PATHWAY_STRUCTURE_CONVERSION
Mode of conversion: from BioPAX to Pathway Structure BioPAX interface
|
java.util.Vector<java.lang.String> |
pathwaysAdded |
static int |
REACTION_NETWORK_CONVERSION
Mode of conversion: from BioPAX to Reaction Network BioPAX interface
|
alwaysMentionCompartment, biopax, bioPAXreactions, bpnm, compartments, complexList, considerCompartmentNameRatherThanId, controls, dnaList, dnaRegionList, includedSpecies, independentSpecies, independentSpeciesIds, proteinList, reactions, rnaList, rnaRegionList, sbmlDoc, smallMoleculeList, species, useBiopaxModelOntology
Constructor and Description |
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BioPAXToCytoscapeConverter() |
Modifier and Type | Method and Description |
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void |
addComplexComponentConnections(Complex cm,
java.util.HashMap<java.lang.String,PhysicalEntity> proteins,
java.util.HashMap<java.lang.String,PhysicalEntity> complexes,
java.util.HashMap nodes,
java.util.HashMap edges,
GraphicGraph grf,
GraphicNode n) |
GraphicNode |
addInteractionNode(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
|
GraphicNode |
addPathwayNode(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
|
GraphicNode |
addPathwayStepNode(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
|
java.lang.String |
getEntityType(PhysicalEntity p) |
static java.lang.String |
getFileKey(java.lang.String file)
key could be based on: filename + date + size
or md5(filecontents);
|
GraphDocument |
getXGMMLGraph(java.lang.String name,
SbmlDocument sbml)
Implementation of extracting Reaction Network interface
(requires first conversion from BioPAX to SBML,
from which the interface is converted).
|
GraphDocument |
getXGMMLInteractionGraph(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).
|
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).
|
addControl, addConversionReaction, addIncludedParticipant, addInteractionReaction, addModifierToReaction, findIndependentSpecies, getAllCompartments, getTypeForParticipant, makeComment, makeLists, populateSbml
public static final int FULL_INDEX_CONVERSION
public static final int REACTION_NETWORK_CONVERSION
public static final int PATHWAY_STRUCTURE_CONVERSION
public static final int INTERACTION_CONVERSION
public java.util.Vector<java.lang.String> pathwaysAdded
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
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
java.lang.Exception
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
java.lang.Exception
public static java.lang.String getFileKey(java.lang.String file)
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
java.lang.Exception
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
java.lang.Exception
public GraphDocument getXGMMLGraph(java.lang.String name, 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 )
java.lang.Exception
public 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 )
java.lang.Exception
public GraphicNode addPathwayNode(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
java.lang.Exception
public GraphicNode addPathwayStepNode(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
java.lang.Exception
public GraphicNode addInteractionNode(GraphicGraph grf, Interaction in, java.util.HashMap pathways, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap nodes) throws java.lang.Exception
java.lang.Exception
public GraphDocument getXGMMLInteractionGraph(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 need biopaxReactions, independentSpeciesIds, species, controls and other maps valid (they are filled by BioPAXToSBMLConverter.populateSbml() parent method )
java.lang.Exception
public void addComplexComponentConnections(Complex cm, java.util.HashMap<java.lang.String,PhysicalEntity> proteins, java.util.HashMap<java.lang.String,PhysicalEntity> complexes, java.util.HashMap nodes, java.util.HashMap edges, GraphicGraph grf, GraphicNode n) throws java.lang.Exception
java.lang.Exception
public java.lang.String getEntityType(PhysicalEntity p)