org.mskcc.psibiopax.converter
Class PSIMIBioPAXConverter

java.lang.Object
  org.mskcc.psibiopax.converter.PSIMIBioPAXConverter

All Implemented Interfaces:

PSIMIConverter

public class PSIMIBioPAXConverter
extends java.lang.Object
implements PSIMIConverter

The converter class. 1 - Unmarshalls PSI data. 2 - Creates a set of EntryMapper threads, each of which is mapping a single PSI Entry object. 3 - Creates a BioPAXMarshaller class to aggregate and marshall the data.

Author:

Benjamin Gross

Field Summary

protected boolean

conversionIsComplete Ref to boolean which indicates conversion is complete.

Constructor Summary

PSIMIBioPAXConverter(BioPAXLevel bpLevel)
Constructor.

Method Summary

boolean	convert(psidev.psi.mi.xml.model.EntrySet entrySet, java.io.OutputStream outputStream) Converts the psi data in the EntrySet and places into outputstream.
boolean	convert(java.io.InputStream inputStream, java.io.OutputStream outputStream) Converts the psi data in inputStream and places into outputStream.

Methods inherited from class java.lang.Object

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

Field Detail

conversionIsComplete

protected boolean conversionIsComplete

Ref to boolean which indicates conversion is complete.

Constructor Detail

PSIMIBioPAXConverter

public PSIMIBioPAXConverter(BioPAXLevel bpLevel)

Constructor.

Parameters:

bpLevel - BioPAXLevel

Method Detail

convert

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

Converts the psi data in inputStream and places into outputStream. Streams will be closed by the converter.

Specified by:

convert in interface PSIMIConverter

Parameters:

inputStream - InputStream

outputStream - OutputStream

Returns:

boolean

Throws:

java.io.IOException

psidev.psi.mi.xml.PsimiXmlReaderException

convert

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

Converts the psi data in the EntrySet and places into outputstream. Stream will be closed by the converter.

Specified by:

convert in interface PSIMIConverter

Parameters:

entrySet - EntrySet

outputStream - OutputStream

Returns:

boolean

Throws:

psidev.psi.mi.xml.PsimiXmlReaderException