fr.ens.transcriptome.doelan.tests
Class FeatureFlagTest

java.lang.Object
  extended byfr.ens.transcriptome.nividic.platform.workflow.Algorithm
      extended byfr.ens.transcriptome.doelan.algorithms.QualityTest
          extended byfr.ens.transcriptome.doelan.algorithms.QualityUnitTest
              extended byfr.ens.transcriptome.doelan.tests.FeatureFlagTest
All Implemented Interfaces:
fr.ens.transcriptome.nividic.platform.module.Module, fr.ens.transcriptome.nividic.platform.workflow.WorkflowListener
Direct Known Subclasses:
AbsentSpotTest, BadFeatureTest, NotFoundFeatureTest

public abstract class FeatureFlagTest
extends QualityUnitTest
implements fr.ens.transcriptome.nividic.platform.module.Module

This class defines a test for not found spot flag.

Author:
Laurent Jourdren

Field Summary
 
Fields inherited from class fr.ens.transcriptome.doelan.algorithms.QualityTest
CONFIGURE_TEST_EVENT, GLOBAL_TEST_INIT_EVENT, RESULT_EVENT
 
Constructor Summary
FeatureFlagTest()
          Public constructor.
 
Method Summary
abstract  fr.ens.transcriptome.nividic.platform.module.AboutModule aboutModule()
          Get the description of the module.
protected  fr.ens.transcriptome.nividic.util.parameter.Parameters defineParameters()
          Set the parameters of the element.
protected abstract  double getDefaultThreshold()
           
protected abstract  java.lang.String getFlagFilerType()
           
protected abstract  int getFlagFilterValue()
           
 QualityUnitTestResult test(fr.ens.transcriptome.nividic.om.BioAssay bioassay, fr.ens.transcriptome.nividic.om.BioAssay arrayList, fr.ens.transcriptome.nividic.util.parameter.Parameters parameters)
          Test the quality of the bioassay.
 
Methods inherited from class fr.ens.transcriptome.doelan.algorithms.QualityUnitTest
doIt, isAddable, isDeletable, isModifiable, isShowable, isUniqueInstance
 
Methods inherited from class fr.ens.transcriptome.nividic.platform.workflow.Algorithm
addListener, getId, getInstanceId, getLogger, getParameters, in, init, isPause, isStop, out, removeListener, sendEvent, terminate, workflowNewException, workflowStateChanged
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FeatureFlagTest

public FeatureFlagTest()
                throws fr.ens.transcriptome.nividic.platform.PlatformException
Public constructor.

Throws:
fr.ens.transcriptome.nividic.platform.PlatformException - If the name or the version of the element is null .
Method Detail

aboutModule

public abstract fr.ens.transcriptome.nividic.platform.module.AboutModule aboutModule()
Get the description of the module.

Specified by:
aboutModule in interface fr.ens.transcriptome.nividic.platform.module.Module
Returns:
The description of the module

defineParameters

protected fr.ens.transcriptome.nividic.util.parameter.Parameters defineParameters()
Set the parameters of the element.

Returns:
The defaults parameters to set.

getFlagFilterValue

protected abstract int getFlagFilterValue()

getFlagFilerType

protected abstract java.lang.String getFlagFilerType()

getDefaultThreshold

protected abstract double getDefaultThreshold()

test

public QualityUnitTestResult test(fr.ens.transcriptome.nividic.om.BioAssay bioassay,
                                  fr.ens.transcriptome.nividic.om.BioAssay arrayList,
                                  fr.ens.transcriptome.nividic.util.parameter.Parameters parameters)
                           throws fr.ens.transcriptome.nividic.platform.PlatformException
Test the quality of the bioassay.

Specified by:
test in class QualityUnitTest
Parameters:
bioassay - BioAssay to test
arrayList - The array list
parameters - parameters of the test
Returns:
A QualityObjectResultTest Object
Throws:
fr.ens.transcriptome.nividic.platform.PlatformException - if an error occurs while executing the test.


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