org.biopax.paxtools.io.jena

Class JenaIOHandler

java.lang.Object

org.biopax.paxtools.io.BioPAXIOHandlerAdapter

org.biopax.paxtools.io.jena.JenaIOHandler

All Implemented Interfaces:

BioPAXIOHandler

public final class JenaIOHandler
extends BioPAXIOHandlerAdapter

Provides I/O support for BioPAX models presented in OWL format using the com.hp.hpl.jena package.

Field Summary

Fields inherited from class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

base, bp, editorMap, factory, level, namespaces, owl, rdf, rdfs, xsd

Constructor Summary

Constructors

Constructor and Description
JenaIOHandler() If set to true, "error-mode: strict" option will be passed to Jena reader.
JenaIOHandler(BioPAXFactory factory, BioPAXLevel level)
JenaIOHandler(BioPAXLevel level)

Method Summary

Modifier and Type	Method and Description
void	convertToOWL(Model model, OutputStream outputStream) Writes a model in OWL format using the an output stream.
protected void	createAndBind(Model model) This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.
protected void	init(InputStream in) This method provides a hook for the implementers of this abstract class to perform the initial reading from the input stream.
com.hp.hpl.jena.ontology.OntModel	readJenaModel(InputStream in)
protected Map<String,String>	readNameSpaces() This method provides a hook for the implementers of this abstract class to set the namespaces of the model.
protected void	resetEditorMap() Updates the member EditorMap for the new BioPAX level and factory (different implementations of EditorMap can be used in modules, e.g.

Methods inherited from class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

bindValue, convertFromMultipleOwlFiles, convertFromOWL, convertToOWL, createAndAdd, fixReusedPEPs, getEditorMap, getFactory, getLevel, getRDFCommentEditor, getReusedPEPHelper, isConvertingFromLevel1ToLevel2, isFixReusedPEPs, isTreatNilAsNull, L1ToL2Fixes, reset, resetLevel, resourceFixes, setConvertingFromLevel1ToLevel2, setEditorMap, setFactory, treatNilAsNull

Methods inherited from class java.lang.Object

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

Constructor Detail

JenaIOHandler

public JenaIOHandler()

If set to true, "error-mode: strict" option will be passed to Jena reader.

JenaIOHandler

public JenaIOHandler(BioPAXLevel level)

JenaIOHandler

public JenaIOHandler(BioPAXFactory factory,
                     BioPAXLevel level)

Method Detail

resetEditorMap

protected void resetEditorMap()

Description copied from class: BioPAXIOHandlerAdapter

Updates the member EditorMap for the new BioPAX level and factory (different implementations of EditorMap can be used in modules, e.g. SimpleEditorMap and JenaEditorMap.)

Specified by:

resetEditorMap in class BioPAXIOHandlerAdapter

init

protected void init(InputStream in)

Description copied from class: BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to perform the initial reading from the input stream.

Specified by:

init in class BioPAXIOHandlerAdapter

Parameters:

in - BioPAX RDF/XML input stream

readNameSpaces

protected Map<String,String> readNameSpaces()

Description copied from class: BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to set the namespaces of the model.

Specified by:

readNameSpaces in class BioPAXIOHandlerAdapter

Returns:

a map of namespaces.

createAndBind

protected void createAndBind(Model model)

Description copied from class: BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.

Specified by:

createAndBind in class BioPAXIOHandlerAdapter

Parameters:

model - to be populated

convertToOWL

public void convertToOWL(Model model,
                         OutputStream outputStream)

Writes a model in OWL format using the an output stream.

Parameters:

model - model to be converted into OWL format

outputStream - output stream to which the model will be written

readJenaModel

public com.hp.hpl.jena.ontology.OntModel readJenaModel(InputStream in)