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

Class SampleStatisticsCollector

java.lang.Object

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

fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector

All Implemented Interfaces:

Collector

public class SampleStatisticsCollector
extends StatisticsCollector

The class define a statistic collector on sample's data to build a project summary table in qc report.

Since:

2.0

Author:

Sandrine Perrin

Field Summary

Fields

Modifier and Type	Field	Description
static String	COLLECTOR_NAME	Collector name.
static String	COLLECTOR_PREFIX	Collector prefix for updating rundata
static String	UNDETERMINED_SAMPLE

Constructor Summary

Constructors

Constructor	Description
SampleStatisticsCollector()

Method Summary

Modifier and Type	Method	Description
Map<Integer,EntityStat>	extractEntityStats(RunData data)	Extract entity stats.
String	getCollectorPrefix()	Gets the collector prefix.
String	getName()	Get the name of the collector.
boolean	isProjectStatisticsCollector()	Checks if is project statistics collector.
boolean	isSampleStatisticsCollector()	Checks if is sample statistics collector.

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

addFastqScreenReport, clear, collect, configure, getCollectorsNamesRequiered, getContaminationThreshold, getReportDirectory, isSummaryCollector

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

Collector name.

See Also:

Constant Field Values

COLLECTOR_PREFIX

public static final String COLLECTOR_PREFIX

Collector prefix for updating rundata

See Also:

Constant Field Values

UNDETERMINED_SAMPLE

public static final String UNDETERMINED_SAMPLE

See Also:

Constant Field Values

Constructor Detail

SampleStatisticsCollector

public SampleStatisticsCollector()

Method Detail

getName

public String getName()

Description copied from interface: Collector

Get the name of the collector.

Returns:

the name of the collector

getCollectorPrefix

public String getCollectorPrefix()

Description copied from class: StatisticsCollector

Gets the collector prefix.

Specified by:

getCollectorPrefix in class StatisticsCollector

Returns:

the collector prefix

isSampleStatisticsCollector

public boolean isSampleStatisticsCollector()

Description copied from class: StatisticsCollector

Checks if is sample statistics collector.

Specified by:

isSampleStatisticsCollector in class StatisticsCollector

Returns:

true, if is sample statistics collector

isProjectStatisticsCollector

public boolean isProjectStatisticsCollector()

Description copied from class: StatisticsCollector

Checks if is project statistics collector.

Specified by:

isProjectStatisticsCollector in class StatisticsCollector

Returns:

true, if is project statistics collector

extractEntityStats

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

Description copied from class: StatisticsCollector

Extract entity stats.

Specified by:

extractEntityStats in class StatisticsCollector

Parameters:

data - the data

Returns:

the list

Throws:

AozanException - the aozan exception