fr.curie.BiNoM.pathways
Class CellDesignerToBioPAXConverter

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

public class CellDesignerToBioPAXConverter
extends java.lang.Object

Implementation of converter from CellDesigner 3.* file to BioPAX

Field Summary

static boolean	alwaysMentionCompartment Check to include compartment label in the name
BioPAX	biopax The result of the conversion
java.util.HashMap	cellDesignerTerms Map from CellDesigner terms (strings) to OpenControlledVocabulary objects
java.util.HashMap	compartmentHash Map from compartment ids to CompartmentDocument.Compartment objects
java.util.Vector	complexes_list List of CellDesigner CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias objects
java.lang.String	filename Name of CellDesigner file
java.util.Vector	proteins List of CellDesigner CelldesignerProteinDocument.CelldesignerProtein objects
java.util.HashMap	pubmedrefsHash Map from Pubmed ids to publicationXref objects
java.util.Vector	reactions List of CellDesigner ReactionDocument.Reaction objects
org.sbml.x2001.ns.celldesigner.SbmlDocument	sbml Java xml-beans mapping of CellDesigner file
java.util.Vector	species List of CellDesigner SpeciesDocument.Species objects
static boolean	useBiopaxModelOntology not used

Constructor Summary

CellDesignerToBioPAXConverter()

Method Summary

void	addPublicationXrefsToEntity(entity ent, java.util.Vector v)
BioPAX	convert() The main conversion function to be used from outside
static java.lang.String	correctName(java.lang.String name) Eliminates spaces, stars, dashes from the string
void	createCellDesignerTerms() Encodes a list of standard terms (protein modification types (GOs) and influence types) by controlledVocabulary terms
physicalEntityParticipant	createEntityParticipantForSpecies(java.lang.String id, java.util.Vector species, java.util.Vector complexes_list, java.util.HashMap physEntities, org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml, BioPAX biopax, java.lang.String rId) Converts physicalEntity participant for a reaction rId
java.util.Vector	extractPubMedReferenceFromComment(java.lang.String comment) Extracts pubmed ids from a string in the form PMID: xxxxxx and creates publicationXref list
static java.util.HashMap	getCompartmentHash(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml) Creates the map of compartments
static org.sbml.x2001.ns.celldesigner.CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias	getComplexById(java.util.Vector complexes, java.lang.String id)
static java.util.Vector	getComplexes(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml) Creates the list of complexes
static java.util.Vector	getGenes(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml) Creates the list of genes
static org.sbml.x2001.ns.celldesigner.CelldesignerProteinDocument.CelldesignerProtein	getProteinById(java.util.Vector proteins, java.lang.String pid)
static java.util.Vector	getProteins(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml) Creates the list of proteins
static org.sbml.x2001.ns.celldesigner.ReactionDocument.Reaction	getReactionById(java.util.Vector reactions, java.lang.String id)
static java.util.Vector	getReactions(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml) Creates the list of reactions
static java.util.Vector	getSpecies(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml) Creates the list of species
static org.sbml.x2001.ns.celldesigner.SpeciesDocument.Species	getSpeciesById(java.util.Vector species, java.lang.String id)
static boolean	isRealReaction(org.sbml.x2001.ns.celldesigner.ReactionDocument.Reaction r, org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml) Returns true if the reaction r describes real interaction (not influence on a phenotype, for example)
BioPAX	populateModel() The converter itself

Methods inherited from class java.lang.Object

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

Field Detail

alwaysMentionCompartment

public static boolean alwaysMentionCompartment

Check to include compartment label in the name

useBiopaxModelOntology

public static boolean useBiopaxModelOntology

not used

species

public java.util.Vector species

List of CellDesigner SpeciesDocument.Species objects

reactions

public java.util.Vector reactions

List of CellDesigner ReactionDocument.Reaction objects

complexes_list

public java.util.Vector complexes_list

List of CellDesigner CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias objects

proteins

public java.util.Vector proteins

List of CellDesigner CelldesignerProteinDocument.CelldesignerProtein objects

filename

public java.lang.String filename

Name of CellDesigner file

sbml

public org.sbml.x2001.ns.celldesigner.SbmlDocument sbml

Java xml-beans mapping of CellDesigner file

biopax

public BioPAX biopax

The result of the conversion

compartmentHash

public java.util.HashMap compartmentHash

Map from compartment ids to CompartmentDocument.Compartment objects

pubmedrefsHash

public java.util.HashMap pubmedrefsHash

Map from Pubmed ids to publicationXref objects

cellDesignerTerms

public java.util.HashMap cellDesignerTerms

Map from CellDesigner terms (strings) to OpenControlledVocabulary objects

Constructor Detail

CellDesignerToBioPAXConverter

public CellDesignerToBioPAXConverter()

Method Detail

convert

public BioPAX convert()

The main conversion function to be used from outside

populateModel

public BioPAX populateModel()

The converter itself

getProteins

public static java.util.Vector getProteins(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)

Creates the list of proteins

getGenes

public static java.util.Vector getGenes(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)

Creates the list of genes

getProteinById

public static org.sbml.x2001.ns.celldesigner.CelldesignerProteinDocument.CelldesignerProtein getProteinById(java.util.Vector proteins,
                                                                                                            java.lang.String pid)

getReactions

public static java.util.Vector getReactions(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)

Creates the list of reactions

getReactionById

public static org.sbml.x2001.ns.celldesigner.ReactionDocument.Reaction getReactionById(java.util.Vector reactions,
                                                                                       java.lang.String id)

getSpecies

public static java.util.Vector getSpecies(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)

Creates the list of species

getSpeciesById

public static org.sbml.x2001.ns.celldesigner.SpeciesDocument.Species getSpeciesById(java.util.Vector species,
                                                                                    java.lang.String id)

getComplexes

public static java.util.Vector getComplexes(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)

Creates the list of complexes

getComplexById

public static org.sbml.x2001.ns.celldesigner.CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias getComplexById(java.util.Vector complexes,
                                                                                                                                    java.lang.String id)

getCompartmentHash

public static java.util.HashMap getCompartmentHash(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)

Creates the map of compartments

createEntityParticipantForSpecies

public physicalEntityParticipant createEntityParticipantForSpecies(java.lang.String id,
                                                                   java.util.Vector species,
                                                                   java.util.Vector complexes_list,
                                                                   java.util.HashMap physEntities,
                                                                   org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml,
                                                                   BioPAX biopax,
                                                                   java.lang.String rId)

Converts physicalEntity participant for a reaction rId

extractPubMedReferenceFromComment

public java.util.Vector extractPubMedReferenceFromComment(java.lang.String comment)

Extracts pubmed ids from a string in the form PMID: xxxxxx and creates publicationXref list

addPublicationXrefsToEntity

public void addPublicationXrefsToEntity(entity ent,
                                        java.util.Vector v)

correctName

public static java.lang.String correctName(java.lang.String name)

Eliminates spaces, stars, dashes from the string

createCellDesignerTerms

public void createCellDesignerTerms()

Encodes a list of standard terms (protein modification types (GOs) and influence types) by controlledVocabulary terms

isRealReaction

public static boolean isRealReaction(org.sbml.x2001.ns.celldesigner.ReactionDocument.Reaction r,
                                     org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)

Returns true if the reaction r describes real interaction (not influence on a phenotype, for example)