org.biopax.paxtools.io
Class BioPAXIOHandlerAdapter

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

All Implemented Interfaces:

BioPAXIOHandler

Direct Known Subclasses:

SimpleIOHandler

public abstract class BioPAXIOHandlerAdapter
extends java.lang.Object
implements BioPAXIOHandler

Field Summary

protected static java.lang.String	bp
protected EditorMap	editorMap
protected BioPAXFactory	factory
protected BioPAXLevel	level
protected java.util.Map<java.lang.String,java.lang.String>	namespaces
protected static java.lang.String	owl
protected static java.lang.String	rdf
protected static java.lang.String	rdfs
protected static java.lang.String	xsd

Constructor Summary

BioPAXIOHandlerAdapter()

BioPAXIOHandlerAdapter(BioPAXFactory factory, BioPAXLevel level)

BioPAXIOHandlerAdapter(BioPAXLevel level)

Method Summary

protected void	bindValue(java.lang.String valueString, PropertyEditor editor, BioPAXElement bpe, Model model)
Model	convertFromMultipleOwlFiles(java.lang.String... files) This is experimental and is not not complete.
Model	convertFromOWL(java.io.InputStream in) Reads a BioPAX model from an OWL file input stream (in) and converts it to a model.
void	convertToOWL(Model model, java.io.OutputStream outputStream, java.lang.String... ids) Similar to BioPAXIOHandler#convertToOWL(org.biopax.paxtools .model.Model, Object), but extracts a sub-model, converts it into BioPAX (OWL) format, and writes it into the outputStream.
protected void	createAndAdd(Model model, java.lang.String id, java.lang.String localName)
protected abstract void	createAndBind(Model model)
void	fixReusedPEPs(boolean fixReusedPEPs) Enables (true) or disables (false) the fixing of reused peps.
EditorMap	getEditorMap()
BioPAXFactory	getFactory()
BioPAXLevel	getLevel()
protected PropertyEditor	getRDFCommentEditor(BioPAXElement bpe)
ReusedPEPHelper	getReusedPEPHelper()
protected abstract void	init(java.io.InputStream in)
boolean	isConvertingFromLevel1ToLevel2() This flag will allow reader to automatically convert level1 classes to corresponding level 2 classes.
boolean	isFixReusedPEPs() This option is only applicable two level 2 models.
boolean	isTreatNilAsNull() This flag will fix a common legacy bug from BioCyc where the "NIL" string was used for representing unknown values.
protected BioPAXElement	literalFixes(PropertyEditor editor, BioPAXElement bpe, Model model, java.lang.String value)
protected abstract java.util.Map<java.lang.String,java.lang.String>	readNameSpaces()
protected abstract void	resetEditorMap() Updates the member EditorMap for the new BioPAX level and factory (different implementations of EditorMap can be used in modules, e.g.
protected void	resetLevel(BioPAXLevel level, BioPAXFactory factory)
protected java.lang.Object	resourceFixes(BioPAXElement bpe, java.lang.Object value)
void	setConvertingFromLevel1ToLevel2(boolean convertingFromLevel1ToLevel2) This flag will allow reader to automatically convert level1 classes to corresponding level 2 classes.
void	setEditorMap(EditorMap editorMap)
void	setFactory(BioPAXFactory factory)
void	treatNilAsNull(boolean treatNILasNull) This flag will fix a common legacy bug from BioCyc where the "NIL" string was used for representing unknown values.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biopax.paxtools.io.BioPAXIOHandler

convertToOWL

Field Detail

level

protected BioPAXLevel level

factory

protected BioPAXFactory factory

editorMap

protected EditorMap editorMap

namespaces

protected java.util.Map<java.lang.String,java.lang.String> namespaces

rdf

protected static final java.lang.String rdf

See Also:

Constant Field Values

rdfs

protected static final java.lang.String rdfs

See Also:

Constant Field Values

bp

protected static java.lang.String bp

xsd

protected static final java.lang.String xsd

See Also:

Constant Field Values

owl

protected static final java.lang.String owl

See Also:

Constant Field Values

Constructor Detail

BioPAXIOHandlerAdapter

public BioPAXIOHandlerAdapter()

BioPAXIOHandlerAdapter

public BioPAXIOHandlerAdapter(BioPAXLevel level)

BioPAXIOHandlerAdapter

public BioPAXIOHandlerAdapter(BioPAXFactory factory,
                              BioPAXLevel level)

Method Detail

resetLevel

protected void resetLevel(BioPAXLevel level,
                          BioPAXFactory factory)

resetEditorMap

protected abstract void resetEditorMap()

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.)

fixReusedPEPs

public void fixReusedPEPs(boolean fixReusedPEPs)

Enables (true) or disables (false) the fixing of reused peps.

Specified by:

fixReusedPEPs in interface BioPAXIOHandler

Parameters:

fixReusedPEPs - true if fixing is desired

See Also:

fixReusedPEPs

treatNilAsNull

public void treatNilAsNull(boolean treatNILasNull)

Description copied from interface: BioPAXIOHandler

This flag will fix a common legacy bug from BioCyc where the "NIL" string was used for representing unknown values.

Specified by:

treatNilAsNull in interface BioPAXIOHandler

setConvertingFromLevel1ToLevel2

public void setConvertingFromLevel1ToLevel2(boolean convertingFromLevel1ToLevel2)

Description copied from interface: BioPAXIOHandler

This flag will allow reader to automatically convert level1 classes to corresponding level 2 classes.

Specified by:

setConvertingFromLevel1ToLevel2 in interface BioPAXIOHandler

isTreatNilAsNull

public boolean isTreatNilAsNull()

Description copied from interface: BioPAXIOHandler

This flag will fix a common legacy bug from BioCyc where the "NIL" string was used for representing unknown values.

Specified by:

isTreatNilAsNull in interface BioPAXIOHandler

Returns:

true if this option is enabled.

isConvertingFromLevel1ToLevel2

public boolean isConvertingFromLevel1ToLevel2()

Description copied from interface: BioPAXIOHandler

This flag will allow reader to automatically convert level1 classes to corresponding level 2 classes.

Specified by:

isConvertingFromLevel1ToLevel2 in interface BioPAXIOHandler

Returns:

true if this option is enabled.

isFixReusedPEPs

public boolean isFixReusedPEPs()

Description copied from interface: BioPAXIOHandler

This option is only applicable two level 2 models. When enabled it will replicate illegally reused pysicalEntityParticipants in Level2 files.

Specified by:

isFixReusedPEPs in interface BioPAXIOHandler

Returns:

true if this option is enabled.

getReusedPEPHelper

public ReusedPEPHelper getReusedPEPHelper()

getFactory

public BioPAXFactory getFactory()

Specified by:

getFactory in interface BioPAXIOHandler

Returns:

factory used for creating objects

setFactory

public void setFactory(BioPAXFactory factory)

Specified by:

setFactory in interface BioPAXIOHandler

Parameters:

factory - used for creating objects

getEditorMap

public EditorMap getEditorMap()

Specified by:

getEditorMap in interface BioPAXIOHandler

Returns:

EditorMap used for this handler.

setEditorMap

public void setEditorMap(EditorMap editorMap)

Specified by:

setEditorMap in interface BioPAXIOHandler

Parameters:

editorMap - used for this handler.

getLevel

public BioPAXLevel getLevel()

Specified by:

getLevel in interface BioPAXIOHandler

Returns:

The level of the model that is being read.

convertFromMultipleOwlFiles

public Model convertFromMultipleOwlFiles(java.lang.String... files)
                                  throws java.io.FileNotFoundException

This is experimental and is not not complete. Files have to be given in dependency order. i.e. a former file should not point to the latter. Use it at your own risk.

Specified by:

convertFromMultipleOwlFiles in interface BioPAXIOHandler

Parameters:

files - Dependency ordered biopax owl file names

Returns:

a merged model.

Throws:

java.io.FileNotFoundException - if any file can not be found

convertFromOWL

public Model convertFromOWL(java.io.InputStream in)

Reads a BioPAX model from an OWL file input stream (in) and converts it to a model.

Specified by:

convertFromOWL in interface BioPAXIOHandler

Parameters:

in - inputStream from which the model will be read

Returns:

an empty model in case of invalid input.

createAndAdd

protected void createAndAdd(Model model,
                            java.lang.String id,
                            java.lang.String localName)

init

protected abstract void init(java.io.InputStream in)

readNameSpaces

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

createAndBind

protected abstract void createAndBind(Model model)

literalFixes

protected BioPAXElement literalFixes(PropertyEditor editor,
                                     BioPAXElement bpe,
                                     Model model,
                                     java.lang.String value)

resourceFixes

protected java.lang.Object resourceFixes(BioPAXElement bpe,
                                         java.lang.Object value)

bindValue

protected void bindValue(java.lang.String valueString,
                         PropertyEditor editor,
                         BioPAXElement bpe,
                         Model model)

getRDFCommentEditor

protected PropertyEditor getRDFCommentEditor(BioPAXElement bpe)

convertToOWL

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

Similar to BioPAXIOHandler#convertToOWL(org.biopax.paxtools .model.Model, Object), but extracts a sub-model, converts it into BioPAX (OWL) format, and writes it into the outputStream. Saved data can be then read via BioPAXIOHandler interface (e.g., SimpleIOHandler).

Specified by:

convertToOWL in interface BioPAXIOHandler

Parameters:

model - model to be converted into OWL format

outputStream - output stream into which the output will be written

ids - the list of "root" element IDs to export (with all their properties/children altogether)

Throws:

java.io.IOException - in case of I/O problems