Class AbstractSimpleLaneTest
- java.lang.Object
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- fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest
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- fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest
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- 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
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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.
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods 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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface fr.ens.biologie.genomique.aozan.tests.AozanTest
getCollectorsNamesRequiered
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Constructor Detail
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AbstractSimpleLaneTest
protected AbstractSimpleLaneTest(String name, String description, String columnName)
Constructor that set the field of this abstract test.- Parameters:
name
- name of the testdescription
- description of the testcolumnName
- column name of the test
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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 testdescription
- description of the testcolumnName
- column name of the testunit
- unit of the test
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Method Detail
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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
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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 readindexedRead
- true if the read is indexedlane
- index of the lane- Returns:
- a String with the required key
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transformValue
protected Number transformValue(Number value, RunData data, int read, boolean indexedRead, int lane)
Transform the value.- Parameters:
value
- value to transformdata
- run dataread
- index of readlane
- lane indexindexedRead
- true if the read is indexed- Returns:
- the transformed value
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isValuePercent
protected boolean isValuePercent()
Test if the value is a percent.- Returns:
- true if the value is a percent
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getValueType
protected abstract Class<?> getValueType()
Get the type of the value.- Returns:
- a Class object with the type
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test
public TestResult test(RunData data, int read, boolean indexedRead, int lane)
Description copied from interface:LaneTest
Do a test.- Parameters:
data
- result objectread
- index of readindexedRead
- true if the read is an index readlane
- the index of the lane- Returns:
- a TestResult object with the result of the test
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testIndexedRead
protected boolean testIndexedRead()
Test if indexed read test must return a score >=0.- Returns:
- if indexed read must return a score
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