org.biopax.paxtools.io

Interface BioPAXIOHandler

All Known Implementing Classes:

BioPAXIOHandlerAdapter, JenaIOHandler, SimpleIOHandler

public interface BioPAXIOHandler

This interface defines IO related operations that can be performed on BioPAX models.

Method Summary

Modifier and Type	Method and Description
Model	convertFromMultipleOwlFiles(String... files) This method will read multiple OWL document and will merge them into an in memory BioPAX model.
Model	convertFromOWL(InputStream in) This method will read the OWL document given by the input stream and will convert it into an in memory BioPAX model.
void	convertToOWL(Model model, OutputStream outputStream) This method will write the model to the output stream.
void	convertToOWL(Model model, OutputStream outputStream, String... ids) This method will "excise" a new model from the given model that contains the objects with given ids and their dependents.
void	fixReusedPEPs(boolean fixReusedPEPs) This option is only applicable two level 2 models.
EditorMap	getEditorMap()
BioPAXFactory	getFactory()
BioPAXLevel	getLevel()
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.
void	setConvertingFromLevel1ToLevel2(boolean convertingFromLevel1ToLevel2) Deprecated. BioPAX Level 1 exports are obsolete (anyway, L1 input is always converted to L2 automatically).
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.

Method Detail

fixReusedPEPs

void fixReusedPEPs(boolean fixReusedPEPs)

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

Parameters:

fixReusedPEPs - true or false

treatNilAsNull

void treatNilAsNull(boolean treatNILasNull)

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

Parameters:

treatNILasNull - true or false

convertFromOWL

Model convertFromOWL(InputStream in)

This method will read the OWL document given by the input stream and will convert it into an in memory BioPAX model.

Parameters:

in - a BioPAX data input stream (RDF/XML format)

Returns:

new BioPAX object Model

convertFromMultipleOwlFiles

Model convertFromMultipleOwlFiles(String... files)
                           throws FileNotFoundException

This method will read multiple OWL document and will merge them into an in memory BioPAX model.

Parameters:

files - input BioPAX files (RDF/XML)

Returns:

new BioPAX object model

Throws:

FileNotFoundException - when a file does not exist.

convertToOWL

void convertToOWL(Model model,
                  OutputStream outputStream)

This method will write the model to the output stream. Default encoding is RDF/XML.

Parameters:

model - a BioPAX model

outputStream - output stream

setConvertingFromLevel1ToLevel2

void setConvertingFromLevel1ToLevel2(boolean convertingFromLevel1ToLevel2)

Deprecated. BioPAX Level 1 exports are obsolete (anyway, L1 input is always converted to L2 automatically).

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

Parameters:

convertingFromLevel1ToLevel2 - true/false, whether actual BioPAX data is of Level1

isTreatNilAsNull

boolean isTreatNilAsNull()

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

Returns:

true if this option is enabled.

isConvertingFromLevel1ToLevel2

boolean isConvertingFromLevel1ToLevel2()

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

Returns:

true if this option is enabled (e.g. auto-enabled if Level1 data were detected).

isFixReusedPEPs

boolean isFixReusedPEPs()

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

Returns:

true if this option is enabled.

getFactory

BioPAXFactory getFactory()

Returns:

the factory that is used to create new BioPAX POJOs during a BioPAXIOHandler operation.

setFactory

void setFactory(BioPAXFactory factory)

Parameters:

factory - used for creating objects

getEditorMap

EditorMap getEditorMap()

Returns:

EditorMap used for this handler.

setEditorMap

void setEditorMap(EditorMap editorMap)

Parameters:

editorMap - used for this handler.

getLevel

BioPAXLevel getLevel()

Returns:

The level of the model that is being read.

convertToOWL

void convertToOWL(Model model,
                  OutputStream outputStream,
                  String... ids)

This method will "excise" a new model from the given model that contains the objects with given ids and their dependents.

Parameters:

model - BioPAX object model to be exported to the output stream as RDF/XML

outputStream - the stream

ids - optional list of absolute URIs of BioPAX objects - roots/seeds for extracting a sub-model to be exported