Package fr.ens.biologie.genomique.aozan.collectors

Class UndeterminedIndexesProcessThread

java.lang.Object

fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesProcessThread

All Implemented Interfaces:

Runnable

public class UndeterminedIndexesProcessThread
extends Object

This class allow to process the undetermined fastq file of a lane to extract indices that can be recovered.

Since:

1.3

Author:

Laurent Jourdren, Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
UndeterminedIndexesProcessThread(RunData data, FastqSample fastqSample, File reportDir, File undeterminedIndexedXSLFile)	Constructor.

Method Summary

Modifier and Type	Method	Description
Throwable	getException()	Get the exception generated by the call to processSequences in the run() method.
FastqSample	getFastqSample()	Return the fastqSample which represent a sample to treat.
RunData	getResults()	Get the results of the analysis.
boolean	isSuccess()	Test if the call to run method was a success.
protected void	logThreadEnd(String duration)
protected void	logThreadStart()
static int	mismatches(String a, String b)	Get the number of mismatches of two string of the same length.
protected void	process()
protected void	processResults()	Process results after the end of the thread.
void	run()
protected void	setException(Throwable exception)	Set the exception if occurs.
protected void	setSuccess(boolean success)	Set if the process has been successful.

Methods inherited from class java.lang.Object

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

Constructor Detail

UndeterminedIndexesProcessThread

public UndeterminedIndexesProcessThread(RunData data,
                                        FastqSample fastqSample,
                                        File reportDir,
                                        File undeterminedIndexedXSLFile)
                                 throws AozanException

Constructor.

Parameters:

data - run data instance

fastqSample - sample to process

reportDir - output report directory

undeterminedIndexedXSLFile - xsl file use to create report html

Throws:

AozanException - if sample cannot be processed

Method Detail

logThreadStart

protected void logThreadStart()

process

protected void process()
                throws AozanException

Throws:

AozanException

logThreadEnd

protected void logThreadEnd(String duration)

processResults

protected void processResults()
                       throws AozanException

Process results after the end of the thread.

Throws:

AozanException - if an error occurs while generate report

mismatches

public static final int mismatches(String a,
                                   String b)

Get the number of mismatches of two string of the same length.

Parameters:

a - the first string

b - the second string

Returns:

the number of mismatches

run

public void run()

Specified by:

run in interface Runnable

getResults

public RunData getResults()

Get the results of the analysis.

Returns:

a RunData object with only the result of the thread

getException

public Throwable getException()

Get the exception generated by the call to processSequences in the run() method.

Returns:

a exception object or null if no Exception has been thrown

isSuccess

public boolean isSuccess()

Test if the call to run method was a success.

Returns:

true if the call to run method was a success

getFastqSample

public FastqSample getFastqSample()

Return the fastqSample which represent a sample to treat.

Returns:

fastqSample, object which represent a sample to treat

setException

protected void setException(Throwable exception)

Set the exception if occurs.

Parameters:

exception - the exception

setSuccess

protected void setSuccess(boolean success)

Set if the process has been successful.

Parameters:

success - the success result