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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.quantification.Quantification
com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
public class ReporterIonQuantification
This class will contain quantification results.
Nested Class Summary |
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Nested classes/interfaces inherited from class com.compomics.util.experiment.quantification.Quantification |
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Quantification.QuantificationMethod |
Field Summary |
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Fields inherited from class com.compomics.util.experiment.quantification.Quantification |
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methodUsed, modifiedPeptidesQuantification, peptideQuantification, proteinQuantification, psmIDentificationToQuantification |
Constructor Summary | |
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ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
Constructor for the reporter ion quantification. |
Method Summary | |
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void |
assignSample(int reporterIndex,
Sample sample)
Assign a sample to an ion referenced by its static index. |
static String |
getDefaultReference(String experimentReference,
String sampleReference,
int replicateNumber)
Returns the default reference for an identification. |
Integer |
getReporterIndex(Sample aSample)
This method returns the ion associated to the given sample. |
ReporterMethod |
getReporterMethod()
returns the reporter method used. |
Sample |
getSample(int reporterIndex)
This method returns the sample associated to the given ion. |
void |
setMethod(ReporterMethod reporterMethod)
Sets the reporter method used. |
Methods inherited from class com.compomics.util.experiment.quantification.Quantification |
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addPeptideQuantification, addProteinQuantification, addPsmQuantification, buildPeptidesAndProteinQuantifications, establishConnection, getMethodUsed, getModifiedPeptideQuantification, getPeptideMatch, getPeptideQuantification, getProteinMatch, getProteinQuantification, getPsmIDentificationToQuantification, getSpectrumMatch, getSpectrumMatches, setMatchChanged, setMethodUsed |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
methodUsed
- the method used for this quantificationMethod Detail |
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public 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 ion
public Integer getReporterIndex(Sample aSample)
aSample
- the sample
public 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 number
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