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

Class ClusterDensityLaneTest

java.lang.Object

fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest

fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest

fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityLaneTest

All Implemented Interfaces:

AozanTest, LaneTest

public class ClusterDensityLaneTest
extends AbstractSimpleLaneTest

This class define a lane test on cluster density.

Since:

0.8

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
ClusterDensityLaneTest()	Public constructor.

Method Summary

Modifier and Type	Method	Description
List<String>	getCollectorsNamesRequiered()	Get the name of the collectors required for the test.
protected String	getKey(int read, boolean indexedRead, int lane)	Get the the key in the RunData object for the value to test.
protected Class<?>	getValueType()	Get the type of the value.
protected Number	transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)	Transform the value.

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest

configure, isValuePercent, test, testIndexedRead

Methods inherited from class fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest

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

ClusterDensityLaneTest

public ClusterDensityLaneTest()

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

getKey

protected String getKey(int read,
                        boolean indexedRead,
                        int lane)

Description copied from class: AbstractSimpleLaneTest

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

Specified by:

getKey in class AbstractSimpleLaneTest

Parameters:

read - index of the read

indexedRead - true if the read is indexed

lane - index of the lane

Returns:

a String with the required key

getValueType

protected Class<?> getValueType()

Description copied from class: AbstractSimpleLaneTest

Get the type of the value.

Specified by:

getValueType in class AbstractSimpleLaneTest

Returns:

a Class object with the type

transformValue

protected Number transformValue(Number value,
                                RunData data,
                                int read,
                                boolean indexedRead,
                                int lane)

Description copied from class: AbstractSimpleLaneTest

Transform the value.

Overrides:

transformValue in class AbstractSimpleLaneTest

Parameters:

value - value to transform

data - run data

read - index of read

indexedRead - true if the read is indexed

lane - lane index

Returns:

the transformed value