Package org.biopax.paxtools.converter.psi

Class PsiToBiopax3Converter

java.lang.Object

org.biopax.paxtools.converter.psi.PsiToBiopax3Converter

public class PsiToBiopax3Converter
extends Object

The PSIMI 2.5 to BioPAX Level3 converter.

Author:

Igor Rodchenkov (rodche)

Constructor Summary

Constructors

Constructor	Description
PsiToBiopax3Converter()	Constructor.
PsiToBiopax3Converter(String xmlBase)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	convert(InputStream inputStream, OutputStream outputStream, boolean forceInteractionToComplex)	Converts the PSI-MI inputStream into BioPAX outputStream.
void	convert(psidev.psi.mi.xml.model.EntrySet entrySet, OutputStream outputStream, boolean forceInteractionToComplex)	Converts the PSI interactions from the EntrySet and places into BioPAX output stream.
void	convertTab(InputStream inputStream, OutputStream outputStream, boolean forceInteractionToComplex)	Converts the PSI-MITAB inputStream into BioPAX outputStream.
String	getXmlBase()

Methods inherited from class java.lang.Object

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

Constructor Details

PsiToBiopax3Converter

public PsiToBiopax3Converter()

Constructor. Will use the default empty string xml:base.

PsiToBiopax3Converter

public PsiToBiopax3Converter(String xmlBase)

Constructor.

Parameters:

xmlBase - xml:base to be used when generating non-canonical BioPAX objects' URIs

Method Details

convert

public void convert(InputStream inputStream,
 OutputStream outputStream,
 boolean forceInteractionToComplex)
             throws IOException,
psidev.psi.mi.xml.PsimiXmlReaderException

Converts the PSI-MI inputStream into BioPAX outputStream. Streams will be closed by the converter. Warning: for very large models (about 1-2Gb if serialized), and when ByteArrayOutputStream is used, OutOfMemoryError might be thrown (increasing the "heap" RAM won't help; but using FileOutputStream will).

Parameters:

inputStream - PSI-MI

outputStream - BioPAX

forceInteractionToComplex - - always generate Complex instead of MolecularInteraction

Throws:

IOException - when an I/O error occur

psidev.psi.mi.xml.PsimiXmlReaderException - when an error in the PSI-MI parser happens

convertTab

public void convertTab(InputStream inputStream,
 OutputStream outputStream,
 boolean forceInteractionToComplex)
                throws IOException,
psidev.psi.mi.tab.PsimiTabException

Converts the PSI-MITAB inputStream into BioPAX outputStream. Streams will be closed by the converter.

Parameters:

inputStream - psi-mitab

outputStream - biopax

forceInteractionToComplex - - always generate Complex instead of MolecularInteraction

Throws:

IOException - when an I/O error occur

psidev.psi.mi.tab.PsimiTabException - when there's a problem within the PSI-MITAB parser

convert

public void convert(psidev.psi.mi.xml.model.EntrySet entrySet,
 OutputStream outputStream,
 boolean forceInteractionToComplex)

Converts the PSI interactions from the EntrySet and places into BioPAX output stream. Stream will be closed by the converter.

Parameters:

entrySet - PSI-MI entry set

outputStream - output stream for writing the BioPAX RDF/XML result

forceInteractionToComplex - true/false - whether to always generate Complex instead of MolecularInteraction

getXmlBase

public String getXmlBase()

Returns:

the xml:base, a namespace for the converter-generated BioPAX objects' URIs.