Package fr.ens.biologie.genomique.aozan.tests

Interface AozanTest

All Known Subinterfaces:

GlobalTest, LaneTest, PooledSampleTest, ProjectTest, SampleTest

All Known Implementing Classes:

AbstractFastQCSampleTest, AbstractGlobalTest, AbstractLaneTest, AbstractPooledSampleTest, AbstractProjectTest, AbstractSampleTest, AbstractSimpleGlobalTest, AbstractSimpleLaneTest, AbstractSimpleProjectTest, AbstractSimpleSampleTest, AbstractSimpleSampleTest, BaseCountGlobalTest, BasePFMeanQualityScoreSampleTest, ClusterDensityGlobalTest, ClusterDensityLaneTest, ClusterDensityPFGlobalTest, ClusterDensityPFLaneTest, ClusterRecoveryReportSampleTest, Cycle100ErrorRateLaneTest, Cycle20IntensityPercentLaneTest, Cycle35ErrorRateLaneTest, Cycle75ErrorRateLaneTest, CycleCountGlobalTest, DensityLaneTest, ErrorRateGlobalTest, ErrorRateLaneTest, FastQCAdapterContentSampleTest, FastQCBasicStatsSampleTest, FastQCDuplicationLevelSampleTest, FastQCKmerContentSampleTest, FastQCNContentSampleTest, FastQCOverrepresentedSequencesSampleTest, FastQCPerBaseQualityScoresSampleTest, FastQCPerBaseSequenceContentSampleTest, FastQCPerSequenceGCContentSampleTest, FastQCPerSequenceQualityScoresSampleTest, FastQCPerTileSequenceQualitySampleTest, FastQCSequenceLengthDistributionSampleTest, FastQScreenMappedExceptRefGenomeSampleTest, FastQScreenMappedExceptRefPercentPooledSampleTest, FastQScreenMappedPercentPooledSampleTest, FastQScreenMappedPercentSampleTest, FastQScreenReportPooledSampleTest, FastQScreenReportProjectTest, FastQScreenReportSampleTest, FastQScreenSampleOvercontaminationCountPooledSampleTest, FastQScreenSampleOvercontaminationCountProjectTest, FirstCycleIntensityLaneTest, GenomeNamesPooledSampleTest, GenomeNamesProjectTest, GenomeNamesSampleTest, InLanePercentSampleTest, InProjectPercentPooledSampleTest, InRunPercentPooledSampleTest, IsIndexedPooledSampleTest, IsIndexedProjectTest, LaneCountGlobalTest, LaneCountPooledSampleTest, LaneCountProjectTest, LoadingConcentrationPercentGlobalTest, MaxPFClusterCountPooledSampleTest, MaxPFClusterCountProjectTest, MaxRawClusterCountPooledSampleTest, MaxRawClusterCountProjectTest, MeanPFClusterCountGlobalTest, MeanPhiXRawClusterCountGlobalTest, MeanRawClusterCountGlobalTest, MedianPFClusterCountGlobalTest, MedianPhiXRawClusterCountGlobalTest, MedianRawClusterCountGlobalTest, MinPFClusterCountPooledSampleTest, MinPFClusterCountProjectTest, MinRawClusterCountPooledSampleTest, MinRawClusterCountProjectTest, MultiQCReportProjectTest, NonIndexedBaseCountGlobalTest, OccupancyPercentGlobalTest, OccupancyPercentLaneTest, PFBaseMeanQualityScorePooledSampleTest, PFClusterCountGlobalTest, PFClusterCountLaneTest, PFClusterCountPooledSampleTest, PFClusterCountProjectTest, PFClusterCountSampleTest, PFClusterPercentGlobalTest, PFClusterPercentLaneTest, PFClusterRecoveryCountPooledSampleTest, PFClusterSDGlobalTest, PFPercentPooledSampleTest, PFPercentSampleTest, PhasingPrephasingPercentLaneTest, PhiXAlignPercentGlobalTest, PhiXAlignPercentLaneTest, PhiXRawClusterCountGlobalTest, PhiXRawClusterCountLaneTest, PhiXRawClusterSDGlobalTest, ProjectCountGlobalTest, Q30PercentGlobalTest, Q30PercentLaneTest, Q30PercentPooledSampleTest, Q30PercentSampleTest, RawClusterCountGlobalTest, RawClusterCountLaneTest, RawClusterCountPooledSampleTest, RawClusterCountProjectTest, RawClusterCountSampleTest, RawClusterRecoveryCountPooledSampleTest, RawClusterSDGlobalTest, RecoverablePFClusterCountSampleTest, RecoverablePFClusterPercentPooledSampleTest, RecoverablePFClusterPercentProjectTest, RecoverablePFClusterPercentSampleTest, RecoverableRawClusterCountSampleTest, RecoverableRawClusterPercentPooledSampleTest, RecoverableRawClusterPercentProjectTest, RecoverableRawClusterPercentSampleTest, SampleCountGlobalTest, SampleCountPooledSampleTest, SampleCountProjectTest, SampleInPoolCountPooledSampleTest, UndeterminedClusterPercentGlobalTest, YieldLaneTest, YieldPFLaneTest

public interface AozanTest

This interface define an Aozan QC test.

Since:

0.8

Author:

Laurent Jourdren

Method Summary

Modifier and Type	Method	Description
List<AozanTest>	configure(TestConfiguration conf)	Configure the test.
List<String>	getCollectorsNamesRequiered()	Get the name of the collectors required for the test.
String	getColumnName()	Get the column name of the test in the QC result file.
String	getDescription()	Get the description of the test.
String	getName()	Get the name of the test.
String	getUnit()	Get the unit of the result of the test.
void	init()	Initialize the test.

Method Detail

getName

String getName()

Get the name of the test.

Returns:

the name of the test

getDescription

String getDescription()

Get the description of the test.

Returns:

the description of the test

getColumnName

String getColumnName()

Get the column name of the test in the QC result file.

Returns:

the coloumn name of the test

getUnit

String getUnit()

Get the unit of the result of the test.

Returns:

the unit of the result of the test

getCollectorsNamesRequiered

List<String> getCollectorsNamesRequiered()

Get the name of the collectors required for the test.

Returns:

a list of String with the name of the required collectors

configure

List<AozanTest> configure(TestConfiguration conf)
                   throws AozanException

Configure the test.

Parameters:

conf - the test configuration

Returns:

list of Aozan tests

Throws:

AozanException

init

void init()
   throws AozanException

Initialize the test.

Throws:

AozanException - if an error occurs while initialize the test.