org.biojava.bio.structure.align.client
Class FarmJobRunnable

java.lang.Object
  org.biojava.bio.structure.align.client.FarmJobRunnable

All Implemented Interfaces:

java.lang.Runnable

public class FarmJobRunnable
extends java.lang.Object
implements java.lang.Runnable

Contains the single thread for a job that can run multiple alignments.

Author:

Andreas Prlic

Field Summary

protected AtomCache

cache

Constructor Summary

FarmJobRunnable(FarmJobParameters params)

Method Summary

void	addAlignmentProgressListener(AlignmentProgressListener listener)
java.lang.String	alignPair(java.lang.String name1, java.lang.String name2)
java.lang.String	alignPair(java.lang.String name1, java.lang.String name2, java.lang.String algorithmName)
void	clearListeners()
protected PdbPairsMessage	getAlignmentPairsFromServer() talk to centralized server and fetch all alignments to run.
protected static java.lang.String	getRandomUsername()
boolean	isWaitForAlignments()
static void	log(java.lang.String message)
void	run()
protected void	sendResultsToServer(java.util.List<java.lang.String> results)
void	setWaitForAlignments(boolean waitForAlignments)
void	terminate() Send signal to terminate calculations

Methods inherited from class java.lang.Object

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

Field Detail

cache

protected AtomCache cache

Constructor Detail

FarmJobRunnable

public FarmJobRunnable(FarmJobParameters params)

Method Detail

addAlignmentProgressListener

public void addAlignmentProgressListener(AlignmentProgressListener listener)

clearListeners

public void clearListeners()

getRandomUsername

protected static java.lang.String getRandomUsername()

log

public static void log(java.lang.String message)

run

public void run()

Specified by:

run in interface java.lang.Runnable

alignPair

public java.lang.String alignPair(java.lang.String name1,
                                  java.lang.String name2)
                           throws StructureException,
                                  java.io.IOException

Throws:

StructureException

java.io.IOException

alignPair

public java.lang.String alignPair(java.lang.String name1,
                                  java.lang.String name2,
                                  java.lang.String algorithmName)
                           throws StructureException,
                                  java.io.IOException

Throws:

StructureException

java.io.IOException

getAlignmentPairsFromServer

protected PdbPairsMessage getAlignmentPairsFromServer()

talk to centralized server and fetch all alignments to run.

Returns:

a list of pairs to align.

sendResultsToServer

protected void sendResultsToServer(java.util.List<java.lang.String> results)

terminate

public void terminate()

Send signal to terminate calculations

isWaitForAlignments

public boolean isWaitForAlignments()

setWaitForAlignments

public void setWaitForAlignments(boolean waitForAlignments)