fr.curie.BiNoM.pathways.wrappers
Class BioPAX

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

public class BioPAX
extends java.lang.Object

BioPAX wrapper with some utilities implemented

Author:

Andrei Zinovyev

Field Summary

static boolean	addBiopaxModelOntology not used
static java.lang.String	biopaxFileString Standard BioPAX v.2 prefix
com.hp.hpl.jena.ontology.OntModel	biopaxmodel BioPAX OWL as com.hp.hpl.jena.ontology.OntModel
static java.lang.String	biopaxString Standard BioPAX v.2 prefix
static java.lang.String	idName Some identifier for this BioPAX
static java.lang.String	importString Standard BioPAX v.2 prefix
com.hp.hpl.jena.rdf.model.Model	model BioPAX OWL as com.hp.hpl.jena.rdf.Model
static java.lang.String	modelnamespaceFileString not yet used
static java.lang.String	modelnamespaceString not yet used
com.hp.hpl.jena.ontology.Ontology	modelontology
static java.lang.String	namespaceFileString Standard BioPAX v.2 prefix
static java.lang.String	namespaceString Standard BioPAX v.2 prefix
com.hp.hpl.jena.ontology.Ontology	ontology com.hp.hpl.jena.ontology.Ontology object

Constructor Summary

BioPAX()

BioPAX(java.lang.String _biopaxString, java.lang.String _namespaceString, java.lang.String _modelnamespaceString)
Non-standard constructor with some prefixes

Method Summary

openControlledVocabulary	addGOTerm(java.lang.String id, java.lang.String name) Adds to OWL model an openControlledVocabulary term
openControlledVocabulary	getCompartment(java.lang.String name)
void	loadBioPAX(java.io.InputStream is) Loads BioPAX content from InputStream is
void	loadBioPAX(java.lang.String fn) Loads BioPAX content from file fn
void	loadBioPAXFromString(java.lang.String text) Loads BioPAX content from String
void	makeCompartments() Adds some standard compartments
static void	printDump(com.hp.hpl.jena.rdf.model.Model model) Prints the content of the BioPAX Model object as readable text
static void	saveToFile(java.lang.String fileName, com.hp.hpl.jena.rdf.model.Model model) Save Model object to file
static void	saveToFile(java.lang.String fileName, com.hp.hpl.jena.ontology.OntModel model) Save an OntModel object to file

Methods inherited from class java.lang.Object

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

Field Detail

biopaxString

public static java.lang.String biopaxString

Standard BioPAX v.2 prefix

biopaxFileString

public static java.lang.String biopaxFileString

Standard BioPAX v.2 prefix

namespaceString

public static java.lang.String namespaceString

Standard BioPAX v.2 prefix

namespaceFileString

public static java.lang.String namespaceFileString

Standard BioPAX v.2 prefix

importString

public static java.lang.String importString

Standard BioPAX v.2 prefix

modelnamespaceString

public static java.lang.String modelnamespaceString

not yet used

modelnamespaceFileString

public static java.lang.String modelnamespaceFileString

not yet used

idName

public static java.lang.String idName

Some identifier for this BioPAX

biopaxmodel

public com.hp.hpl.jena.ontology.OntModel biopaxmodel

BioPAX OWL as com.hp.hpl.jena.ontology.OntModel

model

public com.hp.hpl.jena.rdf.model.Model model

BioPAX OWL as com.hp.hpl.jena.rdf.Model

ontology

public com.hp.hpl.jena.ontology.Ontology ontology

com.hp.hpl.jena.ontology.Ontology object

modelontology

public com.hp.hpl.jena.ontology.Ontology modelontology

addBiopaxModelOntology

public static boolean addBiopaxModelOntology

not used

Constructor Detail

BioPAX

public BioPAX()

BioPAX

public BioPAX(java.lang.String _biopaxString,
              java.lang.String _namespaceString,
              java.lang.String _modelnamespaceString)

Non-standard constructor with some prefixes

Parameters:

_biopaxString -

_namespaceString -

_modelnamespaceString -

Method Detail

saveToFile

public static void saveToFile(java.lang.String fileName,
                              com.hp.hpl.jena.ontology.OntModel model)

Save an OntModel object to file

Parameters:

fileName -

model -

saveToFile

public static void saveToFile(java.lang.String fileName,
                              com.hp.hpl.jena.rdf.model.Model model)

Save Model object to file

Parameters:

fileName -

model -

printDump

public static void printDump(com.hp.hpl.jena.rdf.model.Model model)

Prints the content of the BioPAX Model object as readable text

addGOTerm

public openControlledVocabulary addGOTerm(java.lang.String id,
                                          java.lang.String name)
                                   throws java.lang.Exception

Adds to OWL model an openControlledVocabulary term

Parameters:

id - is the GO id

name - is the standard name for this id

Returns:

Throws:

java.lang.Exception

makeCompartments

public void makeCompartments()

Adds some standard compartments

getCompartment

public openControlledVocabulary getCompartment(java.lang.String name)

Parameters:

name -

Returns:

openControlledVocabulary term named name

loadBioPAX

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

Loads BioPAX content from file fn

Parameters:

fn -

Throws:

java.lang.Exception

loadBioPAX

public void loadBioPAX(java.io.InputStream is)
                throws java.lang.Exception

Loads BioPAX content from InputStream is

Parameters:

is -

Throws:

java.lang.Exception

loadBioPAXFromString

public void loadBioPAXFromString(java.lang.String text)
                          throws java.lang.Exception

Loads BioPAX content from String

Parameters:

text -

Throws:

java.lang.Exception