public class ReporterIonQuantification extends Quantification
Quantification.QuantificationMethod
methodUsed, modifiedPeptidesQuantification, peptideQuantification, proteinQuantification, psmIDentificationToQuantification
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(int reporterIndex,
Sample sample)
Assign a sample to an ion referenced by its static index.
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static java.lang.String |
getDefaultReference(java.lang.String experimentReference,
java.lang.String sampleReference,
int replicateNumber)
Returns the default reference for an identification.
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java.lang.Integer |
getReporterIndex(Sample aSample)
This method returns the ion associated to the given sample.
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ReporterMethod |
getReporterMethod()
returns the reporter method used.
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Sample |
getSample(int reporterIndex)
This method returns the sample associated to the given ion.
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void |
setMethod(ReporterMethod reporterMethod)
Sets the reporter method used.
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addPeptideQuantification, addProteinQuantification, addPsmQuantification, buildPeptidesAndProteinQuantifications, establishConnection, getMethodUsed, getModifiedPeptideQuantification, getPeptideMatch, getPeptideQuantification, getProteinMatch, getProteinQuantification, getPsmIDentificationToQuantification, getSpectrumMatch, getSpectrumMatches, setMatchChanged, setMethodUsed
addUrParam, getParameterKey, getUrParam
public ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
methodUsed
- the method used for this quantificationpublic void assignSample(int reporterIndex, Sample sample)
reporterIndex
- the index of the ionsample
- the samplepublic Sample getSample(int reporterIndex)
reporterIndex
- the static index of the reporter ionpublic java.lang.Integer getReporterIndex(Sample aSample)
aSample
- the samplepublic ReporterMethod getReporterMethod()
public void setMethod(ReporterMethod reporterMethod)
reporterMethod
- the reporter method usedpublic static java.lang.String getDefaultReference(java.lang.String experimentReference, java.lang.String sampleReference, int replicateNumber)
experimentReference
- the experiment referencesampleReference
- the sample referencereplicateNumber
- the replicate numberCopyright © 2013. All Rights Reserved.