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

Class UndeterminedIndexesCollector

java.lang.Object

fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector

fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector

All Implemented Interfaces:

Collector

public class UndeterminedIndexesCollector
extends AbstractFastqCollector

This class allow to collect information about the undetermined indices that can be recovered.

Since:

1.3

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static String	COLLECTOR_NAME	The collector name.
static String	RUN_DATA_PREFIX	Prefix for run data

Constructor Summary

Constructors

Constructor	Description
UndeterminedIndexesCollector()

Method Summary

Modifier and Type	Method	Description
protected fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread	collectSample(RunData data, FastqSample fastqSample, File reportDir, boolean runPE)	Collect data for a fastqSample.
void	configure(QC qc, CollectorConfiguration conf)	Configure the collector with the path of the run data.
List<String>	getCollectorsNamesRequiered()	Get the name of the collectors required to run this collector.
String	getName()	Get the name of the collector.
protected int	getThreadsNumber()	Return the number of thread that the collector can be used for execution.
protected boolean	isProcessAllReads()	Test if all reads (e.g.
protected boolean	isProcessStandardSamples()	Test if standard samples must be processed.
protected boolean	isProcessUndeterminedIndicesSamples()	Test if undetermined indices samples must be processed.

Methods inherited from class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector

clear, clearTemporaryFiles, collect, getFastqSamples, getTemporaryDir, isSummaryCollector, saveResultPart

Methods inherited from class java.lang.Object

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

Field Detail

COLLECTOR_NAME

public static final String COLLECTOR_NAME

The collector name.

See Also:

Constant Field Values

RUN_DATA_PREFIX

public static final String RUN_DATA_PREFIX

Prefix for run data

See Also:

Constant Field Values

Constructor Detail

UndeterminedIndexesCollector

public UndeterminedIndexesCollector()

Method Detail

getName

public String getName()

Description copied from interface: Collector

Get the name of the collector.

Returns:

the name of the collector

isProcessStandardSamples

protected boolean isProcessStandardSamples()

Description copied from class: AbstractFastqCollector

Test if standard samples must be processed.

Overrides:

isProcessStandardSamples in class AbstractFastqCollector

Returns:

true if standard samples must be processed

isProcessUndeterminedIndicesSamples

protected boolean isProcessUndeterminedIndicesSamples()

Description copied from class: AbstractFastqCollector

Test if undetermined indices samples must be processed.

Specified by:

isProcessUndeterminedIndicesSamples in class AbstractFastqCollector

Returns:

true if undetermined indices samples must be processed

isProcessAllReads

protected boolean isProcessAllReads()

Description copied from class: AbstractFastqCollector

Test if all reads (e.g. first end and second ends) must be processed or only one.

Overrides:

isProcessAllReads in class AbstractFastqCollector

Returns:

true if all reads must be processed

getCollectorsNamesRequiered

public List<String> getCollectorsNamesRequiered()

Description copied from interface: Collector

Get the name of the collectors required to run this collector.

Specified by:

getCollectorsNamesRequiered in interface Collector

Overrides:

getCollectorsNamesRequiered in class AbstractFastqCollector

Returns:

a list of String with the name of the required collectors

configure

public void configure(QC qc,
                      CollectorConfiguration conf)

Description copied from interface: Collector

Configure the collector with the path of the run data.

Specified by:

configure in interface Collector

Overrides:

configure in class AbstractFastqCollector

Parameters:

qc - QC object for the run

conf - the collector configuration

getThreadsNumber

protected int getThreadsNumber()

Description copied from class: AbstractFastqCollector

Return the number of thread that the collector can be used for execution.

Specified by:

getThreadsNumber in class AbstractFastqCollector

Returns:

number of thread

collectSample

protected fr.ens.biologie.genomique.aozan.collectors.AbstractFastqProcessThread collectSample(RunData data,
                                                                                              FastqSample fastqSample,
                                                                                              File reportDir,
                                                                                              boolean runPE)
                                                                                       throws AozanException

Description copied from class: AbstractFastqCollector

Collect data for a fastqSample.

Specified by:

collectSample in class AbstractFastqCollector

Parameters:

data - result data object

fastqSample - sample object

reportDir - the report dir

runPE - if is a PE run

Returns:

process thread instance

Throws:

AozanException - if an error occurs while execution