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

Class AbstractSimpleLaneTest

java.lang.Object

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

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

All Implemented Interfaces:

AozanTest, LaneTest

Direct Known Subclasses:

ClusterDensityLaneTest, ClusterDensityPFLaneTest, Cycle100ErrorRateLaneTest, Cycle20IntensityPercentLaneTest, Cycle35ErrorRateLaneTest, Cycle75ErrorRateLaneTest, DensityLaneTest, ErrorRateLaneTest, FirstCycleIntensityLaneTest, OccupancyPercentLaneTest, PFClusterCountLaneTest, RawClusterCountLaneTest, YieldLaneTest, YieldPFLaneTest

public abstract class AbstractSimpleLaneTest
extends AbstractLaneTest

This class define a simple lane test.

Since:

0.8

Author:

Laurent Jourdren

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractSimpleLaneTest(String name, String description, String columnName)	Constructor that set the field of this abstract test.
protected	AbstractSimpleLaneTest(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, boolean indexedRead, int lane)	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, boolean indexedRead, int lane)	Do a test.
protected boolean	testIndexedRead()	Test if indexed read test must return a score >=0.
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.AbstractLaneTest

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

AbstractSimpleLaneTest

protected AbstractSimpleLaneTest(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

AbstractSimpleLaneTest

protected AbstractSimpleLaneTest(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 read,
                                 boolean indexedRead,
                                 int lane)

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

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

transformValue

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

Transform the value.

Parameters:

value - value to transform

data - run data

read - index of read

lane - lane index

indexedRead - true if the read is indexed

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 read,
                       boolean indexedRead,
                       int lane)

Description copied from interface: LaneTest

Do a test.

Parameters:

data - result object

read - index of read

indexedRead - true if the read is an index read

lane - the index of the lane

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