ubic.erminej

Class Analyzer

java.lang.Object

java.lang.Thread

ubic.erminej.Analyzer

All Implemented Interfaces:

Runnable

public class Analyzer
extends Thread

Version:

$Id: Analyzer.java,v 1.1 2013/05/20 04:22:35 paul Exp $

Author:

pavlidis

Nested Class Summary

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

Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.apache.commons.logging.Log	log

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor and Description
Analyzer(SettingsHolder settings, StatusViewer messenger, GeneAnnotations geneAnnots)
Analyzer(SettingsHolder settings, StatusViewer messenger, GeneAnnotations geneAnnots, String loadFile) For loading an analysis from a file.

Method Summary

Methods

Modifier and Type	Method and Description
Collection<GeneSetPvalRun>	doAnalysis()
Collection<GeneSetPvalRun>	getLatestResults() Blocks until results are returned.
boolean	isFinishedNormally()
boolean	isStop()
boolean	isWasError()
Collection<GeneSetPvalRun>	loadAnalysis() Load from a file, which can contain more than one set.
void	run()
void	stopRunning(boolean s)

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

log

protected static final org.apache.commons.logging.Log log

Constructor Detail

Analyzer

public Analyzer(SettingsHolder settings,
        StatusViewer messenger,
        GeneAnnotations geneAnnots)

Parameters:

csframe -

settings -

messenger -

geneAnnots -

rawDataSets -

geneScoreSets -

Analyzer

public Analyzer(SettingsHolder settings,
        StatusViewer messenger,
        GeneAnnotations geneAnnots,
        String loadFile)

For loading an analysis from a file.

Parameters:

csframe -

settings -

messenger -

geneAnnots -

rawDataSets -

geneScoreSets -

loadFile -

Method Detail

getLatestResults

public Collection<GeneSetPvalRun> getLatestResults()
                                            throws IllegalStateException

Blocks until results are returned.

Returns:

Throws:

IllegalStateException

isFinishedNormally

public boolean isFinishedNormally()

Returns:

Returns the finishedNormally.

isStop

public boolean isStop()

Returns:

isWasError

public boolean isWasError()

Returns:

Returns the wasError.

loadAnalysis

public Collection<GeneSetPvalRun> loadAnalysis()
                                        throws Exception

Load from a file, which can contain more than one set.

Returns:

Throws:

IOException

Exception

run

public void run()

Specified by:

run in interface Runnable

Overrides:

run in class Thread

stopRunning

public void stopRunning(boolean s)

Parameters:

finished -

doAnalysis

public Collection<GeneSetPvalRun> doAnalysis()

Parameters:

results -

Returns:

Throws:

IOException