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

Class SamplesheetCollector

java.lang.Object

fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector

All Implemented Interfaces:

Collector

public class SamplesheetCollector
extends Object
implements Collector

This class define a Bcl2fastq samplesheet collector.

Since:

0.8

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static String	COLLECTOR_NAME	The collector name.
static String	SAMPLESHEET_DATA_PREFIX

Constructor Summary

Constructors

Constructor	Description
SamplesheetCollector()

Method Summary

Modifier and Type	Method	Description
void	clear()	Remove temporary files.
void	collect(RunData data)	Collect data.
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.
boolean	isSummaryCollector()	Test if the class is a summary collector.

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

SAMPLESHEET_DATA_PREFIX

public static final String SAMPLESHEET_DATA_PREFIX

See Also:

Constant Field Values

Constructor Detail

SamplesheetCollector

public SamplesheetCollector()

Method Detail

getName

public String getName()

Description copied from interface: Collector

Get the name of the collector.

Specified by:

getName in interface Collector

Returns:

the name of the collector

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

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

Parameters:

qc - QC object for the run

conf - the collector configuration

collect

public void collect(RunData data)
             throws AozanException

Description copied from interface: Collector

Collect data.

Specified by:

collect in interface Collector

Parameters:

data - result data object

Throws:

AozanException - if an error occurs while collecting data

clear

public void clear()

Description copied from interface: Collector

Remove temporary files.

Specified by:

clear in interface Collector

isSummaryCollector

public boolean isSummaryCollector()

Description copied from interface: Collector

Test if the class is a summary collector. A summary collector must be executed after all the other collectors.

Specified by:

isSummaryCollector in interface Collector

Returns:

true if the collector is a summary collector