com.compomics.util.experiment.quantification.reporterion
Class ReporterIonQuantification

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.quantification.Quantification
          extended by com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
All Implemented Interfaces:
Serializable, Cloneable

public class ReporterIonQuantification
extends Quantification

This class will contain quantification results.

Author:
Marc Vaudel
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class com.compomics.util.experiment.quantification.Quantification
Quantification.QuantificationMethod
 
Field Summary
 
Fields inherited from class com.compomics.util.experiment.quantification.Quantification
methodUsed, modifiedPeptidesQuantification, peptideQuantification, proteinQuantification, psmIDentificationToQuantification
 
Constructor Summary
ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
          Constructor for the reporter ion quantification.
 
Method Summary
 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
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
addUrParam, getParameterKey, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ReporterIonQuantification

public ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
Constructor for the reporter ion quantification.

Parameters:
methodUsed - the method used for this quantification
Method Detail

assignSample

public void assignSample(int reporterIndex,
                         Sample sample)
Assign a sample to an ion referenced by its static index.

Parameters:
reporterIndex - the index of the ion
sample - the sample

getSample

public Sample getSample(int reporterIndex)
This method returns the sample associated to the given ion.

Parameters:
reporterIndex - the static index of the reporter ion
Returns:
the corresponding sample

getReporterIndex

public Integer getReporterIndex(Sample aSample)
This method returns the ion associated to the given sample.

Parameters:
aSample - the sample
Returns:
the static index of the associated ion

getReporterMethod

public ReporterMethod getReporterMethod()
returns the reporter method used.

Returns:
the method used

setMethod

public void setMethod(ReporterMethod reporterMethod)
Sets the reporter method used.

Parameters:
reporterMethod - the reporter method used

getDefaultReference

public static String getDefaultReference(String experimentReference,
                                         String sampleReference,
                                         int replicateNumber)
Returns the default reference for an identification.

Parameters:
experimentReference - the experiment reference
sampleReference - the sample reference
replicateNumber - the replicate number
Returns:
the default reference


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