fr.curie.BiNoM.pathways.wrappers
Class Transpath

java.lang.Object
  fr.curie.BiNoM.pathways.wrappers.Transpath

public class Transpath
extends java.lang.Object

Experimental converter from Transpath to BioPAX

Author:

Andrei Zinovyev

Field Summary

java.util.HashMap	annotationHash
com.biobaseInternational.NetworkDocument	annotations
BioPAX	biopax
java.util.HashMap	entities
static int	MOLECULAR_EVIDENCE
java.util.HashMap	moleculeHash
com.biobaseInternational.NetworkDocument	network
static int	PATHWAY_STEP
static int	SEMANTIC
java.util.Vector	speciesFilter
int	typeOfReactionExtraction

Constructor Summary

Transpath()

Method Summary

void	addAccno(entity ent, java.lang.String accno)
void	addAccnoAnnotate(entity ent, java.lang.String accno)
void	AddModificationToComplexComponent(sequenceParticipant sp, com.biobaseInternational.MoleculeDocument.Molecule complex, com.biobaseInternational.MoleculeDocument.Molecule component)
void	AddModificationToParticipant(sequenceParticipant sp, com.biobaseInternational.MoleculeDocument.Molecule mol)
void	addPublication(entity ent, com.biobaseInternational.ItemDocument.Item it)
void	addReferencesToReaction(com.biobaseInternational.ReactionDocument.Reaction r, biochemicalReaction br)
void	addSynonym(entity ent, java.lang.String syn)
void	associateWithSpecies(physicalEntity ent, java.lang.String species)
void	createAccessionTable(java.lang.String fn)
static java.util.Vector	extractModificationsFromName(java.lang.String name)
java.lang.String	getXLink(com.biobaseInternational.ItemDocument.Item it, java.lang.String attr)
void	initializeModel()
void	loadFromFile(java.lang.String fn)
void	populateModel()

Methods inherited from class java.lang.Object

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

Field Detail

network

public com.biobaseInternational.NetworkDocument network

annotations

public com.biobaseInternational.NetworkDocument annotations

annotationHash

public java.util.HashMap annotationHash

biopax

public BioPAX biopax

entities

public java.util.HashMap entities

moleculeHash

public java.util.HashMap moleculeHash

speciesFilter

public java.util.Vector speciesFilter

typeOfReactionExtraction

public int typeOfReactionExtraction

MOLECULAR_EVIDENCE

public static int MOLECULAR_EVIDENCE

PATHWAY_STEP

public static int PATHWAY_STEP

SEMANTIC

public static int SEMANTIC

Constructor Detail

Transpath

public Transpath()

Method Detail

loadFromFile

public void loadFromFile(java.lang.String fn)
                  throws java.lang.Exception

Throws:

java.lang.Exception

initializeModel

public void initializeModel()

populateModel

public void populateModel()
                   throws java.lang.Exception

Throws:

java.lang.Exception

associateWithSpecies

public void associateWithSpecies(physicalEntity ent,
                                 java.lang.String species)
                          throws java.lang.Exception

Throws:

java.lang.Exception

addAccno

public void addAccno(entity ent,
                     java.lang.String accno)
              throws java.lang.Exception

Throws:

java.lang.Exception

addAccnoAnnotate

public void addAccnoAnnotate(entity ent,
                             java.lang.String accno)
                      throws java.lang.Exception

Throws:

java.lang.Exception

addSynonym

public void addSynonym(entity ent,
                       java.lang.String syn)
                throws java.lang.Exception

Throws:

java.lang.Exception

addPublication

public void addPublication(entity ent,
                           com.biobaseInternational.ItemDocument.Item it)
                    throws java.lang.Exception

Throws:

java.lang.Exception

getXLink

public java.lang.String getXLink(com.biobaseInternational.ItemDocument.Item it,
                                 java.lang.String attr)
                          throws java.lang.Exception

Throws:

java.lang.Exception

AddModificationToComplexComponent

public void AddModificationToComplexComponent(sequenceParticipant sp,
                                              com.biobaseInternational.MoleculeDocument.Molecule complex,
                                              com.biobaseInternational.MoleculeDocument.Molecule component)
                                       throws java.lang.Exception

Throws:

java.lang.Exception

AddModificationToParticipant

public void AddModificationToParticipant(sequenceParticipant sp,
                                         com.biobaseInternational.MoleculeDocument.Molecule mol)
                                  throws java.lang.Exception

Throws:

java.lang.Exception

extractModificationsFromName

public static java.util.Vector extractModificationsFromName(java.lang.String name)

createAccessionTable

public void createAccessionTable(java.lang.String fn)
                          throws java.lang.Exception

Throws:

java.lang.Exception

addReferencesToReaction

public void addReferencesToReaction(com.biobaseInternational.ReactionDocument.Reaction r,
                                    biochemicalReaction br)
                             throws java.lang.Exception

Throws:

java.lang.Exception