com.compomics.util.experiment.quantification.matches
Class PsmQuantification

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.quantification.QuantificationMatch
          extended by com.compomics.util.experiment.quantification.matches.PsmQuantification
All Implemented Interfaces:
Serializable, Cloneable

public class PsmQuantification
extends QuantificationMatch

This class models the quantification of a spectrum.

Author:
Marc Vaudel
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class com.compomics.util.experiment.quantification.QuantificationMatch
QuantificationMatch.MatchType
 
Field Summary
 
Fields inherited from class com.compomics.util.experiment.quantification.QuantificationMatch
ratios
 
Constructor Summary
PsmQuantification(String spectrumKey, String spectrumMatchKey)
          Constructor for a spectrumQuantification
 
Method Summary
 void addIonMatch(int reporterIndex, IonMatch match)
          Method to add a match between a peak and a reporter ion
 HashMap<Integer,Double> getDeisotopedIntensities()
          returns the deisotoped intensities
 String getKey()
          Returns the key of a match.
 double getReferenceIntensity()
          Returns the reference intensity used to estimate the ratios
 HashMap<Integer,IonMatch> getReporterMatches()
          Getter for the reporter matches
 String getSpectrumMatchKey()
          Getter for the key of the spectrum match
 QuantificationMatch.MatchType getType()
          Returns the type of a match
 void setDeisotopedIntensities(HashMap<Integer,Double> deisotopedIntensities)
          Sets the deisotoped intensities
 void setReferenceIntensity(double referenceIntensity)
          Sets the reference intensity used to estimate the ratios
 
Methods inherited from class com.compomics.util.experiment.quantification.QuantificationMatch
addRatio, getRatios, setRatios
 
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

PsmQuantification

public PsmQuantification(String spectrumKey,
                         String spectrumMatchKey)
Constructor for a spectrumQuantification

Parameters:
spectrumKey - the corresponding spectrum key
spectrumMatchKey - the corresponding spectrum match key
Method Detail

addIonMatch

public void addIonMatch(int reporterIndex,
                        IonMatch match)
Method to add a match between a peak and a reporter ion

Parameters:
reporterIndex - static index of the reporter ion
match - The corresponding ion match

getKey

public String getKey()
Description copied from class: QuantificationMatch
Returns the key of a match.

Specified by:
getKey in class QuantificationMatch
Returns:
the key of a match

getSpectrumMatchKey

public String getSpectrumMatchKey()
Getter for the key of the spectrum match

Returns:
the key of the spectrum match

getReporterMatches

public HashMap<Integer,IonMatch> getReporterMatches()
Getter for the reporter matches

Returns:
matches between reporters and peaks

getDeisotopedIntensities

public HashMap<Integer,Double> getDeisotopedIntensities()
returns the deisotoped intensities

Returns:
the deisotoped intensities

setDeisotopedIntensities

public void setDeisotopedIntensities(HashMap<Integer,Double> deisotopedIntensities)
Sets the deisotoped intensities

Parameters:
deisotopedIntensities - the deisotoped intensities

getReferenceIntensity

public double getReferenceIntensity()
Returns the reference intensity used to estimate the ratios

Returns:
the reference intensity used to estimate the ratios

setReferenceIntensity

public void setReferenceIntensity(double referenceIntensity)
Sets the reference intensity used to estimate the ratios

Parameters:
referenceIntensity - the reference intensity used to estimate the ratios

getType

public QuantificationMatch.MatchType getType()
Description copied from class: QuantificationMatch
Returns the type of a match

Specified by:
getType in class QuantificationMatch
Returns:
the type of a match


Copyright © 2012. All Rights Reserved.