Class ReporterIonQuantification
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.quantification.Quantification
com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
- All Implemented Interfaces:
Serializable
public class ReporterIonQuantification extends Quantification
This class contains quantification parameters.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
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Nested Class Summary
Nested classes/interfaces inherited from class com.compomics.util.experiment.quantification.Quantification
Quantification.QuantificationMethod
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Field Summary
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Constructor Summary
Constructors Constructor Description ReporterIonQuantification()
Empty default constructorReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
Constructor for the reporter ion quantification. -
Method Summary
Modifier and Type Method Description void
assignSample(String reporterName, String sample)
Assign a sample to an ion referenced by its static index.ArrayList<String>
getControlSamples()
Returns the indexes of the samples labeled as control.static String
getDefaultReference(String experimentReference, String sampleReference, int replicateNumber)
Returns the default reference for an identification.NormalizationFactors
getNormalizationFactors()
Returns the normalization factors.String
getReporterIndex(String aSample)
This method returns the reporter ion name associated to the given sample.ReporterMethod
getReporterMethod()
Returns the reporter method used.String
getSample(String reporterIonName)
This method returns the sample associated to the given ion.Integer
getSampleIndex(String sampleReference)
Returns the sample index for the given sample.Set<String>
getSampleIndexes()
Returns a set containing the indexes of every sample.void
setControlSamples(ArrayList<String> controlSamples)
Sets the indexes of the samples labeled as control.void
setMethod(ReporterMethod reporterMethod)
Sets the reporter method used.void
setNormalizationFactors(NormalizationFactors normalizationFactors)
Sets the normalization factors.void
setSampleIndex(String sampleReference, Integer index)
Set the sample index for the given sample.Methods inherited from class com.compomics.util.experiment.quantification.Quantification
getMethodUsed, setMethodUsed
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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ReporterIonQuantification
public ReporterIonQuantification()Empty default constructor -
ReporterIonQuantification
Constructor for the reporter ion quantification.- Parameters:
methodUsed
- the method used for this quantification
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Method Details
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assignSample
Assign a sample to an ion referenced by its static index.- Parameters:
reporterName
- the name of the reporter ionsample
- the sample
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getSampleIndex
Returns the sample index for the given sample.- Parameters:
sampleReference
- the sample reference- Returns:
- the sample index for the given sample
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setSampleIndex
Set the sample index for the given sample.- Parameters:
sampleReference
- the sample referenceindex
- the index
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getSample
This method returns the sample associated to the given ion.- Parameters:
reporterIonName
- the static index of the reporter ion- Returns:
- the corresponding sample
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getReporterIndex
This method returns the reporter ion name associated to the given sample. Null if not found.- Parameters:
aSample
- the sample- Returns:
- the static index of the associated ion
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getReporterMethod
Returns the reporter method used.- Returns:
- the method used
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setMethod
Sets the reporter method used.- Parameters:
reporterMethod
- the reporter method used
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getDefaultReference
public static String getDefaultReference(String experimentReference, String sampleReference, int replicateNumber)Returns the default reference for an identification.- Parameters:
experimentReference
- the experiment referencesampleReference
- the sample referencereplicateNumber
- the replicate number- Returns:
- the default reference
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getControlSamples
Returns the indexes of the samples labeled as control.- Returns:
- the indexes of the samples labeled as control
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setControlSamples
Sets the indexes of the samples labeled as control.- Parameters:
controlSamples
- the indexes of the samples to label as control
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getSampleIndexes
Returns a set containing the indexes of every sample.- Returns:
- a set containing the indexes of every sample
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getNormalizationFactors
Returns the normalization factors.- Returns:
- the normalization factors
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setNormalizationFactors
Sets the normalization factors.- Parameters:
normalizationFactors
- the normalization factors
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