edu.msu.cme.rdp.classifier.comparison
Class ComparisonManager

java.lang.Object
  java.lang.Thread
      edu.msu.cme.rdp.classifier.comparison.ComparisonManager

All Implemented Interfaces:

java.lang.Runnable

public class ComparisonManager
extends java.lang.Thread

Nested Class Summary

(package private) class

ComparisonManager.Timer The timer will wake up and check the time set by jsp, if the time expired, which indicates the jsp page has been refreshed for a long time, abort the current seqmatch thread.

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

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

Field Summary

private static java.lang.String	ABORTED
private ComparisonBrowserBean	browserBean
private static ClassifierFactory	classifierFactory
private static java.lang.String	COMPLETED
private boolean	exceedLimit
private static java.lang.String	FAILED
private java.util.Date	lastCheckTime
private static java.lang.String	NOT_STARTED
private int	numOfDone
private static java.lang.String	RUNNING
private java.lang.String	s1Filename
private java.util.ArrayList	s1SeqList
private java.lang.String	s2Filename
private java.util.ArrayList	s2SeqList
private static java.lang.String	SAMPLE1
private static java.lang.String	SAMPLE2
private java.lang.String	status
private ComparisonManager.Timer	timer
private int	totalNumOfSequence

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

ComparisonManager(java.io.InputStream inputStream1, java.lang.String f1, java.io.InputStream inputStream2, java.lang.String f2)

Method Summary

ComparisonBrowserBean	getBrowserBean()
private java.util.Date	getLastCheckTime()
int	getProgress()
java.lang.String	getS1Filename()
java.lang.String	getS2Filename()
java.lang.String	getStatus()
boolean	isAborted()
boolean	isCompleted()
boolean	isRunning()
private TaxonTree	reconstructTree(ClassificationResult result, TaxonTree root, java.lang.String sample)
void	run()
void	setAbort(boolean a)
void	setCheckTime(int sec)
private void	setLastCheckTime(java.util.Date d)
private void	setStatus(java.lang.String s)
void	start()

Methods inherited from class java.lang.Thread

activeCount, checkAccess, 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, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

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

Field Detail

classifierFactory

private static ClassifierFactory classifierFactory

lastCheckTime

private java.util.Date lastCheckTime

timer

private ComparisonManager.Timer timer

totalNumOfSequence

private int totalNumOfSequence

exceedLimit

private boolean exceedLimit

numOfDone

private int numOfDone

browserBean

private ComparisonBrowserBean browserBean

s1SeqList

private java.util.ArrayList s1SeqList

s2SeqList

private java.util.ArrayList s2SeqList

s1Filename

private java.lang.String s1Filename

s2Filename

private java.lang.String s2Filename

SAMPLE1

private static final java.lang.String SAMPLE1

See Also:

Constant Field Values

SAMPLE2

private static final java.lang.String SAMPLE2

See Also:

Constant Field Values

COMPLETED

private static final java.lang.String COMPLETED

See Also:

Constant Field Values

NOT_STARTED

private static final java.lang.String NOT_STARTED

See Also:

Constant Field Values

RUNNING

private static final java.lang.String RUNNING

See Also:

Constant Field Values

ABORTED

private static final java.lang.String ABORTED

See Also:

Constant Field Values

FAILED

private static final java.lang.String FAILED

See Also:

Constant Field Values

status

private java.lang.String status

Constructor Detail

ComparisonManager

public ComparisonManager(java.io.InputStream inputStream1,
                         java.lang.String f1,
                         java.io.InputStream inputStream2,
                         java.lang.String f2)

Method Detail

start

public void start()

Overrides:

start in class java.lang.Thread

getS1Filename

public java.lang.String getS1Filename()

getS2Filename

public java.lang.String getS2Filename()

setStatus

private void setStatus(java.lang.String s)

getStatus

public java.lang.String getStatus()

setCheckTime

public void setCheckTime(int sec)

getLastCheckTime

private java.util.Date getLastCheckTime()

getProgress

public int getProgress()

isAborted

public boolean isAborted()

isCompleted

public boolean isCompleted()

isRunning

public boolean isRunning()

setAbort

public void setAbort(boolean a)

setLastCheckTime

private void setLastCheckTime(java.util.Date d)

run

public void run()

Specified by:

run in interface java.lang.Runnable

Overrides:

run in class java.lang.Thread

reconstructTree

private TaxonTree reconstructTree(ClassificationResult result,
                                  TaxonTree root,
                                  java.lang.String sample)

getBrowserBean

public ComparisonBrowserBean getBrowserBean()