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. User: Marc Date: Sep 1, 2010 Time: 1:42:21 PM

See Also:
Serialized Form

Field Summary
 
Fields inherited from class com.compomics.util.experiment.quantification.Quantification
automatedMemoryManagement, cacheSize, EXTENTION, inMemory, loadedMatches, loadedMatchesMap, longKeys, methodUsed, modifiedMatches, peptideQuantification, proteinQuantification, psmIDentificationToQuantification, serializationDirectory, urParameters
 
Constructor Summary
ReporterIonQuantification(int 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
 int getReferenceLabel()
          Returns the reference label indexed by the corresponding reporter ion
 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
 void setReferenceLabel(int referenceLabel)
          Sets the reference label indexed by the corresponding reporter ion index
 
Methods inherited from class com.compomics.util.experiment.quantification.Quantification
addPeptideQuantification, addProteinQuantification, addPsmQuantification, addQuantificationParameter, buildPeptidesAndProteinQuantifications, emptyCache, getCacheSize, getFileName, getMethodUsed, getPeptideMatch, getPeptideQuantification, getProteinMatch, getProteinQuantification, getPsmIDentificationToQuantification, getQuantificationParameter, getSerializationDirectory, getSpectrumMatch, getSpectrumMatches, isAutomatedMemoryManagement, isInMemory, memoryCheck, removeQuantification, save, setAutomatedMemoryManagement, setCacheSize, setInMemory, setMatchChanged, setMethodUsed, setSerializationDirectory, updateCache
 
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(int 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

getReferenceLabel

public int getReferenceLabel()
Returns the reference label indexed by the corresponding reporter ion

Returns:
the index of the reporter ion corresponding to the reference label

setReferenceLabel

public void setReferenceLabel(int referenceLabel)
Sets the reference label indexed by the corresponding reporter ion index

Parameters:
referenceLabel - the index of the reporter ion corresponding to the reference label


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