org.biopax.paxtools.io
Class SimpleIOHandler

java.lang.Object
  org.biopax.paxtools.io.BioPAXIOHandlerAdapter
      org.biopax.paxtools.io.SimpleIOHandler

All Implemented Interfaces:

BioPAXIOHandler

public class SimpleIOHandler
extends BioPAXIOHandlerAdapter

Simple BioPAX reader/writer.

Nested Class Summary

class

SimpleIOHandler.Triple

Field Summary

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

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

Constructor Summary

SimpleIOHandler()

SimpleIOHandler(BioPAXFactory factory, BioPAXLevel level)

SimpleIOHandler(BioPAXLevel level)

Method Summary

void	convertToOWL(Model model, java.io.OutputStream outputStream) Converts a model into BioPAX (OWL) format, and writes it into the outputStream.
protected void	createAndBind(Model model)
java.lang.String	getId()
java.lang.String	getXmlStreamInfo() This may be required for external applications to access the specific information (e.g., location) when reporting XML exceptions.
protected void	init(java.io.InputStream in)
void	mergeDuplicates(boolean mergeDuplicates)
void	normalizeNameSpaces(boolean normalizeNameSpaces)
protected java.util.Map<java.lang.String,java.lang.String>	readNameSpaces()
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.
void	writeObject(java.io.Writer out, BioPAXElement bean) Writes the XML representation of individual BioPAX element that is BioPAX-like but only for display or debug purpose (incomplete).

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

bindValue, convertFromMultipleOwlFiles, convertFromOWL, convertToOWL, createAndAdd, fixReusedPEPs, getEditorMap, getFactory, getLevel, getRDFCommentEditor, getReusedPEPHelper, isConvertingFromLevel1ToLevel2, isFixReusedPEPs, isTreatNilAsNull, literalFixes, 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

SimpleIOHandler

public SimpleIOHandler()

SimpleIOHandler

public SimpleIOHandler(BioPAXLevel level)

SimpleIOHandler

public SimpleIOHandler(BioPAXFactory factory,
                       BioPAXLevel level)

Method Detail

mergeDuplicates

public void mergeDuplicates(boolean mergeDuplicates)

resetEditorMap

protected final 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

getXmlStreamInfo

public java.lang.String getXmlStreamInfo()

This may be required for external applications to access the specific information (e.g., location) when reporting XML exceptions.

Returns:

init

protected void init(java.io.InputStream in)

Specified by:

init in class BioPAXIOHandlerAdapter

readNameSpaces

protected java.util.Map<java.lang.String,java.lang.String> readNameSpaces()

Specified by:

readNameSpaces in class BioPAXIOHandlerAdapter

createAndBind

protected void createAndBind(Model model)

Specified by:

createAndBind in class BioPAXIOHandlerAdapter

getId

public java.lang.String getId()

convertToOWL

public void convertToOWL(Model model,
                         java.io.OutputStream outputStream)

Converts a model into BioPAX (OWL) format, and writes it into the outputStream. Saved data can be then read via BioPAXIOHandler interface (e.g., SimpleIOHandler). Note: When the model is incomplete (i.e., contains elements that refer externals, dangling BioPAX elements) and is exported by this method, it works; however one will find corresponding object properties set to NULL later, after converting such data back to Model.

Parameters:

model - model to be converted into OWL format

outputStream - output stream into which the output will be written

Throws:

BioPaxIOException - in case of I/O problems

writeObject

public void writeObject(java.io.Writer out,
                        BioPAXElement bean)
                 throws java.io.IOException

Writes the XML representation of individual BioPAX element that is BioPAX-like but only for display or debug purpose (incomplete). Note: use BioPAXIOHandler#convertToOWL(org.biopax.paxtools .model.Model, Object) instead if you have a model and want to save and later restore it.

Parameters:

out -

bean -

Throws:

java.io.IOException

normalizeNameSpaces

public void normalizeNameSpaces(boolean normalizeNameSpaces)