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

Class AbstractSimpleSampleTest

java.lang.Object

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

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

All Implemented Interfaces:

AozanTest, SampleTest

Direct Known Subclasses:

FastQScreenMappedExceptRefGenomeSampleTest, FastQScreenMappedPercentSampleTest, GenomeNamesSampleTest, PFClusterCountSampleTest, RawClusterCountSampleTest, RecoverablePFClusterCountSampleTest, RecoverableRawClusterCountSampleTest

public abstract class AbstractSimpleSampleTest
extends AbstractSampleTest

This class define a simple sample 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.
protected abstract String	getKey(int read, int readSample, int sampleId, int lane, boolean undetermined)	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 read, int readSample, int sampleId)	Do a test.
protected int	transformScore(int score, RunData data, int read, int readSample, int sampleId)	Transform the score.
protected Number	transformValue(Number value, RunData data, int read, int readSample, int sampleId)	Transform the value.

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

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

getKey

protected abstract String getKey(int read,
                                 int readSample,
                                 int sampleId,
                                 int lane,
                                 boolean undetermined)

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

Parameters:

read - index of the read

readSample - index of read without indexed reads

sampleId - the id of the sample

lane - sample lane

undetermined - true if the sample is an undetermined sample

Returns:

a String with the required key

transformValue

protected Number transformValue(Number value,
                                RunData data,
                                int read,
                                int readSample,
                                int sampleId)

Transform the value.

Parameters:

value - value to transform

data - run data

read - index of read

readSample - index of read without indexed reads

sampleId - the sample Id

Returns:

the transformed value

transformScore

protected int transformScore(int score,
                             RunData data,
                             int read,
                             int readSample,
                             int sampleId)

Transform the score.

Parameters:

score - value to transform

data - run data

read - index of read

readSample - index of read without indexed reads

sampleId - the sample id

Returns:

the transformed score

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 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

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