org.mskcc.psibiopax.converter
Class EntryMapper

java.lang.Object
  java.lang.Thread
      org.mskcc.psibiopax.converter.EntryMapper

All Implemented Interfaces:

java.lang.Runnable

public class EntryMapper
extends java.lang.Thread

A thread class which processes an entry in a psi xml doc. This class returns a paxtools model to a BioPAXMarshaller, whose ref is passed during object construction.

Author:

Benjamin Gross

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

static java.lang.String

RDF_ID_PREFIX rdf id prefix.

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

EntryMapper(BioPAXMapper bpMapper, BioPAXMarshaller biopaxMarshaller, psidev.psi.mi.xml.model.Entry entry)
Constructor.

EntryMapper(BioPAXMapper bpMapper, BioPAXMarshaller biopaxMarshaller, psidev.psi.mi.xml.model.Entry entry, long seed)
Constructor.

Method Summary

void	run() Our implementation of run.

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

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

Field Detail

RDF_ID_PREFIX

public static final java.lang.String RDF_ID_PREFIX

rdf id prefix.

See Also:

Constant Field Values

Constructor Detail

EntryMapper

public EntryMapper(BioPAXMapper bpMapper,
                   BioPAXMarshaller biopaxMarshaller,
                   psidev.psi.mi.xml.model.Entry entry)

Constructor.

Parameters:

bpMapper - BioPAXMapper

biopaxMarshaller - BioPAXMarshaller

entry - EntrySet.Entry

EntryMapper

public EntryMapper(BioPAXMapper bpMapper,
                   BioPAXMarshaller biopaxMarshaller,
                   psidev.psi.mi.xml.model.Entry entry,
                   long seed)

Constructor.

Parameters:

bpMapper - BioPAXMapper

biopaxMarshaller - BioPAXMarshaller

entry - EntrySet.Entry

seed - long

Method Detail

run

public void run()

Our implementation of run.

Specified by:

run in interface java.lang.Runnable

Overrides:

run in class java.lang.Thread