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)
protected void	init(InputStream in)
com.hp.hpl.jena.ontology.OntModel	readJenaModel(InputStream in)
protected Map<String,String>	readNameSpaces()
protected void	resetEditorMap()

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()

Specified by:

resetEditorMap in class BioPAXIOHandlerAdapter

init

protected void init(InputStream in)

Specified by:

init in class BioPAXIOHandlerAdapter

readNameSpaces

protected Map<String,String> readNameSpaces()

Specified by:

readNameSpaces in class BioPAXIOHandlerAdapter

createAndBind

protected void createAndBind(Model model)

Specified by:

createAndBind in class BioPAXIOHandlerAdapter

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)