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

Class StatisticsCollector

java.lang.Object

fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector

All Implemented Interfaces:

Collector

Direct Known Subclasses:

ProjectStatisticsCollector, SampleStatisticsCollector

public abstract class StatisticsCollector
extends Object
implements Collector

The class define a abstract statistics collector.

Since:

2.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
StatisticsCollector()

Method Summary

Modifier and Type	Method	Description
protected void	addFastqScreenReport(int projectId, int sampleId, List<File> reportFiles)	Add a FastqScreen report.
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.
abstract Map<Integer,EntityStat>	extractEntityStats(RunData data)	Extract entity stats.
abstract String	getCollectorPrefix()	Gets the collector prefix.
List<String>	getCollectorsNamesRequiered()	Get the name of the collectors required to run this collector.
double	getContaminationThreshold()	Gets the contamination threshold.
File	getReportDirectory()	Gets the report directory.
abstract boolean	isProjectStatisticsCollector()	Checks if is project statistics collector.
abstract boolean	isSampleStatisticsCollector()	Checks if is sample statistics 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

Methods inherited from interface fr.ens.biologie.genomique.aozan.collectors.Collector

getName

Constructor Detail

StatisticsCollector

public StatisticsCollector()

Method Detail

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

clear

public void clear()

Description copied from interface: Collector

Remove temporary files.

Specified by:

clear in interface Collector

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

addFastqScreenReport

protected void addFastqScreenReport(int projectId,
                                    int sampleId,
                                    List<File> reportFiles)

Add a FastqScreen report.

Parameters:

projectId - the projectId

sampleId - the sampleId

reportFiles - the list of report file

extractEntityStats

public abstract Map<Integer,EntityStat> extractEntityStats(RunData data)
                                                          throws AozanException

Extract entity stats.

Parameters:

data - the data

Returns:

the list

Throws:

AozanException - the aozan exception

isSampleStatisticsCollector

public abstract boolean isSampleStatisticsCollector()

Checks if is sample statistics collector.

Returns:

true, if is sample statistics collector

isProjectStatisticsCollector

public abstract boolean isProjectStatisticsCollector()

Checks if is project statistics collector.

Returns:

true, if is project statistics collector

getCollectorPrefix

public abstract String getCollectorPrefix()

Gets the collector prefix.

Returns:

the collector prefix

getReportDirectory

public File getReportDirectory()

Gets the report directory.

Returns:

the report directory

getContaminationThreshold

public double getContaminationThreshold()

Gets the contamination threshold.

Returns:

the contamination threshold

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