fr.curie.BiNoM.pathways.utils
Class BioPAXUtilities

java.lang.Object
  fr.curie.BiNoM.pathways.utils.BioPAXUtilities

public class BioPAXUtilities
extends java.lang.Object

Set of utilities for manipulating com.hp.hpl.jena.rdf.model.Model objects

Author:

Andrei Zinovyev

Constructor Summary

BioPAXUtilities()

Method Summary

static void	copyURIwithAllLinks(java.lang.String namespace, java.lang.String uri, com.hp.hpl.jena.rdf.model.Model modelfrom, com.hp.hpl.jena.rdf.model.Model modelto) Extract a part of model which is necessary to define a things with uri
static com.hp.hpl.jena.ontology.OntModel	extractFromModel(com.hp.hpl.jena.rdf.model.Model source, Graph graph)
static com.hp.hpl.jena.ontology.OntModel	extractFromModel(com.hp.hpl.jena.rdf.model.Model source, edu.rpi.cs.xgmml.GraphDocument graph)
static com.hp.hpl.jena.ontology.OntModel	extractFromModel(com.hp.hpl.jena.rdf.model.Model source, edu.rpi.cs.xgmml.GraphDocument graph, java.lang.String namespace, java.lang.String importString)
static com.hp.hpl.jena.ontology.OntModel	extractFromModel(com.hp.hpl.jena.rdf.model.Model source, Graph graph, java.lang.String namespace, java.lang.String importString) From all elements in graph BIOPAX_URI attribute values are used to extract a part of the source
static com.hp.hpl.jena.ontology.OntModel	extractFromModel(com.hp.hpl.jena.rdf.model.Model source, java.util.Vector ids, java.lang.String namespace, java.lang.String importString)
static com.hp.hpl.jena.rdf.model.Model	extractURIwithAllLinks(com.hp.hpl.jena.rdf.model.Model source, java.util.Vector uris, java.lang.String namespace, java.lang.String importString) Extract a part of model which is necessary to define all things with uris
static java.lang.String	getDefaultNsPrefix(com.hp.hpl.jena.rdf.model.Model source)
static com.hp.hpl.jena.rdf.model.Model	loadModel(java.lang.String fn, java.lang.String namespaceString, java.lang.String importString) Load the OWL model from file
static com.hp.hpl.jena.rdf.model.Model	makeCopy(com.hp.hpl.jena.rdf.model.Model source, java.lang.String namespaceString, java.lang.String importString) Clones the source Model
static int	numberOfStatements(com.hp.hpl.jena.rdf.model.Model source)
static int	numberOfStatements(com.ibm.adtech.jastor.Thing thing)
static void	saveModel(com.hp.hpl.jena.rdf.model.Model model, java.lang.String fn)
static void	saveModel(com.hp.hpl.jena.rdf.model.Model model, java.lang.String fn, java.lang.String biopaxString) Save OWL model to the file

Methods inherited from class java.lang.Object

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

Constructor Detail

BioPAXUtilities

public BioPAXUtilities()

Method Detail

numberOfStatements

public static int numberOfStatements(com.ibm.adtech.jastor.Thing thing)

Parameters:

thing -

Returns:

Number of statements describing the thing

numberOfStatements

public static int numberOfStatements(com.hp.hpl.jena.rdf.model.Model source)

extractURIwithAllLinks

public static com.hp.hpl.jena.rdf.model.Model extractURIwithAllLinks(com.hp.hpl.jena.rdf.model.Model source,
                                                                     java.util.Vector uris,
                                                                     java.lang.String namespace,
                                                                     java.lang.String importString)
                                                              throws java.lang.Exception

Extract a part of model which is necessary to define all things with uris

Parameters:

source -

uris -

namespace -

importString -

Returns:

Throws:

java.lang.Exception

copyURIwithAllLinks

public static void copyURIwithAllLinks(java.lang.String namespace,
                                       java.lang.String uri,
                                       com.hp.hpl.jena.rdf.model.Model modelfrom,
                                       com.hp.hpl.jena.rdf.model.Model modelto)
                                throws java.lang.Exception

Extract a part of model which is necessary to define a things with uri

Parameters:

namespace -

uri -

modelfrom -

modelto -

Throws:

java.lang.Exception

saveModel

public static void saveModel(com.hp.hpl.jena.rdf.model.Model model,
                             java.lang.String fn,
                             java.lang.String biopaxString)
                      throws java.lang.Exception

Save OWL model to the file

Parameters:

model -

fn -

biopaxString -

Throws:

java.lang.Exception

saveModel

public static void saveModel(com.hp.hpl.jena.rdf.model.Model model,
                             java.lang.String fn)
                      throws java.lang.Exception

Throws:

java.lang.Exception

loadModel

public static com.hp.hpl.jena.rdf.model.Model loadModel(java.lang.String fn,
                                                        java.lang.String namespaceString,
                                                        java.lang.String importString)
                                                 throws java.lang.Exception

Load the OWL model from file

Parameters:

fn -

namespaceString -

importString -

Returns:

Throws:

java.lang.Exception

makeCopy

public static com.hp.hpl.jena.rdf.model.Model makeCopy(com.hp.hpl.jena.rdf.model.Model source,
                                                       java.lang.String namespaceString,
                                                       java.lang.String importString)

Clones the source Model

Parameters:

source -

namespaceString -

importString -

Returns:

extractFromModel

public static com.hp.hpl.jena.ontology.OntModel extractFromModel(com.hp.hpl.jena.rdf.model.Model source,
                                                                 Graph graph,
                                                                 java.lang.String namespace,
                                                                 java.lang.String importString)
                                                          throws java.lang.Exception

From all elements in graph BIOPAX_URI attribute values are used to extract a part of the source

Parameters:

source -

graph -

namespace -

importString -

Returns:

Throws:

java.lang.Exception

extractFromModel

public static com.hp.hpl.jena.ontology.OntModel extractFromModel(com.hp.hpl.jena.rdf.model.Model source,
                                                                 Graph graph)
                                                          throws java.lang.Exception

Throws:

java.lang.Exception

extractFromModel

public static com.hp.hpl.jena.ontology.OntModel extractFromModel(com.hp.hpl.jena.rdf.model.Model source,
                                                                 java.util.Vector ids,
                                                                 java.lang.String namespace,
                                                                 java.lang.String importString)
                                                          throws java.lang.Exception

Throws:

java.lang.Exception

extractFromModel

public static com.hp.hpl.jena.ontology.OntModel extractFromModel(com.hp.hpl.jena.rdf.model.Model source,
                                                                 edu.rpi.cs.xgmml.GraphDocument graph,
                                                                 java.lang.String namespace,
                                                                 java.lang.String importString)
                                                          throws java.lang.Exception

Throws:

java.lang.Exception

extractFromModel

public static com.hp.hpl.jena.ontology.OntModel extractFromModel(com.hp.hpl.jena.rdf.model.Model source,
                                                                 edu.rpi.cs.xgmml.GraphDocument graph)
                                                          throws java.lang.Exception

Throws:

java.lang.Exception

getDefaultNsPrefix

public static java.lang.String getDefaultNsPrefix(com.hp.hpl.jena.rdf.model.Model source)