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

Class FastQScreenMappedExceptRefPercentPooledSampleTest

java.lang.Object

fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest

fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest

fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest

All Implemented Interfaces:

AozanTest, PooledSampleTest

public class FastQScreenMappedExceptRefPercentPooledSampleTest
extends AbstractSimpleSampleTest

The class adds in the qc report html one result from fastqScreen for each sample, after compile replicat data. It print the percent of reads which mapped on at least one genomes except the genome sample.

Since:

2.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
FastQScreenMappedExceptRefPercentPooledSampleTest()	Public constructor.

Method Summary

Modifier and Type	Method	Description
List<String>	getCollectorsNamesRequiered()	Get the name of the collectors required for the test.
String	getKey(int pooledSampleId)	Get the the key in the RunData object for the value to test.
String	getSampleKey(int sampleId)	Get the the key in the RunData object for the value to test.
protected Class<?>	getValueType()	Get the type of the value.
protected boolean	isValuePercent()	Test if the value is a percent.
TestResult	test(RunData data, int pooledSampleId)	Do a test.

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest

configure, getInterval, testIndexedRead, transformValue

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest

getColumnName, getDescription, getName, getUnit, init

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FastQScreenMappedExceptRefPercentPooledSampleTest

public FastQScreenMappedExceptRefPercentPooledSampleTest()

Public constructor.

Method Detail

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

test

public TestResult test(RunData data,
                       int pooledSampleId)

Description copied from interface: PooledSampleTest

Do a test.

Specified by:

test in interface PooledSampleTest

Overrides:

test in class AbstractSimpleSampleTest

Parameters:

data - result object

pooledSampleId - pooled sample Id

Returns:

a TestResult object with the result of the test

getKey

public String getKey(int pooledSampleId)

Description copied from class: AbstractSimpleSampleTest

Get the the key in the RunData object for the value to test.

Specified by:

getKey in class AbstractSimpleSampleTest

Parameters:

pooledSampleId - the pooled sample Id

Returns:

a String with the required key

getSampleKey

public String getSampleKey(int sampleId)

Get the the key in the RunData object for the value to test.

Parameters:

sampleId - the sample Id

Returns:

a String with the required key

isValuePercent

protected boolean isValuePercent()

Description copied from class: AbstractSimpleSampleTest

Test if the value is a percent.

Overrides:

isValuePercent in class AbstractSimpleSampleTest

Returns:

true if the value is a percent

getValueType

protected Class<?> getValueType()

Description copied from class: AbstractSimpleSampleTest

Get the type of the value.

Specified by:

getValueType in class AbstractSimpleSampleTest

Returns:

a Class object with the type