public class ReporterIonQuantification extends Quantification
Quantification.QuantificationMethod
methodUsed
Constructor and Description |
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ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
Constructor for the reporter ion quantification.
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Modifier and Type | Method and Description |
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void |
assignSample(String reporterName,
Sample sample)
Assign a sample to an ion referenced by its static index.
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ArrayList<String> |
getControlSamples()
Returns the indexes of the samples labeled as control.
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static String |
getDefaultReference(String experimentReference,
String sampleReference,
int replicateNumber)
Returns the default reference for an identification.
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NormalizationFactors |
getNormalizationFactors()
Returns the normalization factors.
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String |
getReporterIndex(Sample aSample)
This method returns the reporter ion name associated to the given sample.
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ReporterMethod |
getReporterMethod()
Returns the reporter method used.
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Sample |
getSample(String reporterIonName)
This method returns the sample associated to the given ion.
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Set<String> |
getSampleIndexes()
Returns a set containing the indexes of every sample.
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void |
setControlSamples(ArrayList<String> controlSamples)
Sets the indexes of the samples labeled as control.
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void |
setMethod(ReporterMethod reporterMethod)
Sets the reporter method used.
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void |
setNormalizationFactors(NormalizationFactors normalizationFactors)
Sets the normalization factors.
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getMethodUsed, setMethodUsed
addUrParam, getParameterKey, getUrParam
public ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
methodUsed
- the method used for this quantificationpublic void assignSample(String reporterName, Sample sample)
reporterName
- the name of the reporter ionsample
- the samplepublic Sample getSample(String reporterIonName)
reporterIonName
- the static index of the reporter ionpublic String getReporterIndex(Sample aSample)
aSample
- the samplepublic ReporterMethod getReporterMethod()
public void setMethod(ReporterMethod reporterMethod)
reporterMethod
- the reporter method usedpublic static String getDefaultReference(String experimentReference, String sampleReference, int replicateNumber)
experimentReference
- the experiment referencesampleReference
- the sample referencereplicateNumber
- the replicate numberpublic ArrayList<String> getControlSamples()
public void setControlSamples(ArrayList<String> controlSamples)
controlSamples
- the indexes of the samples to label as controlpublic Set<String> getSampleIndexes()
public NormalizationFactors getNormalizationFactors()
public void setNormalizationFactors(NormalizationFactors normalizationFactors)
normalizationFactors
- the normalization factorsCopyright © 2016. All rights reserved.