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

Class AbstractFastQCSampleTest

java.lang.Object

fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest

fr.ens.biologie.genomique.aozan.tests.sample.AbstractFastQCSampleTest

All Implemented Interfaces:

AozanTest, SampleTest

Direct Known Subclasses:

FastQCAdapterContentSampleTest, FastQCBasicStatsSampleTest, FastQCDuplicationLevelSampleTest, FastQCKmerContentSampleTest, FastQCNContentSampleTest, FastQCOverrepresentedSequencesSampleTest, FastQCPerBaseQualityScoresSampleTest, FastQCPerBaseSequenceContentSampleTest, FastQCPerSequenceGCContentSampleTest, FastQCPerSequenceQualityScoresSampleTest, FastQCPerTileSequenceQualitySampleTest, FastQCSequenceLengthDistributionSampleTest

public abstract class AbstractFastQCSampleTest
extends AbstractSampleTest

This class define an abstract FastQC test.

Since:

0.8

Author:

Laurent Jourdren

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractFastQCSampleTest(String name, String description, String columnName)	Constructor that set the field of this abstract test.

Method Summary

Modifier and Type	Method	Description
List<String>	getCollectorsNamesRequiered()	Get the name of the collectors required for the test.
protected abstract int	getHTMLAnchorIndex()	Get the anchor index of for the module in FastQC HTML report.
protected abstract String	getQCModuleName()	Get the name of the FastQC module.
TestResult	test(RunData data, int read, int readSample, int sampleId)	Do a test.

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest

getColumnName, getDescription, getName, getUnit, init

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.tests.AozanTest

configure

Constructor Detail

AbstractFastQCSampleTest

protected AbstractFastQCSampleTest(String name,
                                   String description,
                                   String columnName)

Constructor that set the field of this abstract test.

Parameters:

name - name of the test

description - description of the test

columnName - column name of the test

Method Detail

test

public TestResult test(RunData data,
                       int read,
                       int readSample,
                       int sampleId)

Description copied from interface: SampleTest

Do a test.

Parameters:

data - result object

read - index of read

readSample - index of read without indexed reads

sampleId - the sample id of the sample to test.

Returns:

a TestResult object with the result of the test

getCollectorsNamesRequiered

public List<String> getCollectorsNamesRequiered()

Description copied from interface: AozanTest

Get the name of the collectors required for the test.

Returns:

a list of String with the name of the required collectors

getQCModuleName

protected abstract String getQCModuleName()

Get the name of the FastQC module.

Returns:

the name of the FastQC module

getHTMLAnchorIndex

protected abstract int getHTMLAnchorIndex()

Get the anchor index of for the module in FastQC HTML report.

Returns:

the position anchor