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

Class AbstractSimpleSampleTest

java.lang.Object

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

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

All Implemented Interfaces:

AozanTest, PooledSampleTest

Direct Known Subclasses:

FastQScreenMappedExceptRefPercentPooledSampleTest, FastQScreenMappedPercentPooledSampleTest, GenomeNamesPooledSampleTest, IsIndexedPooledSampleTest, LaneCountPooledSampleTest, MaxPFClusterCountPooledSampleTest, MaxRawClusterCountPooledSampleTest, MinPFClusterCountPooledSampleTest, MinRawClusterCountPooledSampleTest, PFClusterCountPooledSampleTest, PFClusterRecoveryCountPooledSampleTest, RawClusterCountPooledSampleTest, RawClusterRecoveryCountPooledSampleTest, SampleCountPooledSampleTest

public abstract class AbstractSimpleSampleTest
extends AbstractPooledSampleTest

This class define a simple lane test.

Since:

0.8

Author:

Laurent Jourdren

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
List<AozanTest>	configure(TestConfiguration conf)	Configure the test.
ScoreInterval	getInterval()
protected abstract String	getKey(int pooledSampleId)	Get the the key in the RunData object for the value to test.
protected abstract 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.
protected boolean	testIndexedRead()	Test if indexed read test must return a score >=0.
protected Number	transformValue(Number value, RunData data)	Transform the value.

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

Methods inherited from interface fr.ens.biologie.genomique.aozan.tests.AozanTest

getCollectorsNamesRequiered

Constructor Detail

AbstractSimpleSampleTest

protected AbstractSimpleSampleTest(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

AbstractSimpleSampleTest

protected AbstractSimpleSampleTest(String name,
                                   String description,
                                   String columnName,
                                   String unit)

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

unit - unit of the test

Method Detail

configure

public List<AozanTest> configure(TestConfiguration conf)
                          throws AozanException

Description copied from interface: AozanTest

Configure the test.

Parameters:

conf - the test configuration

Returns:

list of Aozan tests

Throws:

AozanException

getKey

protected abstract String getKey(int pooledSampleId)

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

Parameters:

pooledSampleId - the pooled sample Id

Returns:

a String with the required key

transformValue

protected Number transformValue(Number value,
                                RunData data)

Transform the value.

Parameters:

value - value to transform

data - run data

Returns:

the transformed value

isValuePercent

protected boolean isValuePercent()

Test if the value is a percent.

Returns:

true if the value is a percent

getValueType

protected abstract Class<?> getValueType()

Get the type of the value.

Returns:

a Class object with the type

test

public TestResult test(RunData data,
                       int pooledSampleId)

Description copied from interface: PooledSampleTest

Do a test.

Parameters:

data - result object

pooledSampleId - pooled sample Id

Returns:

a TestResult object with the result of the test

testIndexedRead

protected boolean testIndexedRead()

Test if indexed read test must return a score >=0.

Returns:

if indexed read must return a score

getInterval

public ScoreInterval getInterval()