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

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

public class PeptideQuantification
extends ExperimentObject

This class models quantification at the peptide level.

Author:
Marc Vaudel
See Also:
Serialized Form

Constructor Summary
PeptideQuantification(java.lang.String peptideKey)
          Constructor for the peptide quantification
PeptideQuantification(java.lang.String peptideKey, java.util.HashMap<java.lang.String,PsmQuantification> psmQuantification)
          Constructor for the peptide quantification
PeptideQuantification(java.lang.String peptideKey, java.util.HashMap<java.lang.String,PsmQuantification> psmQuantification, java.util.HashMap<java.lang.Integer,Ratio> ratios)
          Constructor for the peptide quantification
 
Method Summary
 void addPsmQuantification(PsmQuantification newPsmQuantification)
          Adds a new psm quantification in the psm quantification map
 java.lang.String getKey()
          Returns the key of the peptide quantification
 PsmQuantification getPsm(java.lang.String index)
          returns a specific psm quantification
 java.util.HashMap<java.lang.String,PsmQuantification> getPsmQuantification()
          Getter for the corresponding spectrum quantification
 java.util.HashMap<java.lang.Integer,Ratio> getRatios()
          Getter for the peptide ratios
 void setPeptideRatios(java.util.HashMap<java.lang.Integer,Ratio> ratios)
          sets new peptide ratios
 
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

PeptideQuantification

public PeptideQuantification(java.lang.String peptideKey)
Constructor for the peptide quantification

Parameters:
peptideKey - the key of the identification peptide match

PeptideQuantification

public PeptideQuantification(java.lang.String peptideKey,
                             java.util.HashMap<java.lang.String,PsmQuantification> psmQuantification)
Constructor for the peptide quantification

Parameters:
peptideKey - the key of the identification peptide match
psmQuantification - the corresponding spectrum quantification

PeptideQuantification

public PeptideQuantification(java.lang.String peptideKey,
                             java.util.HashMap<java.lang.String,PsmQuantification> psmQuantification,
                             java.util.HashMap<java.lang.Integer,Ratio> ratios)
Constructor for the peptide quantification

Parameters:
peptideKey - the identification peptide match
psmQuantification - the corresponding spectrum quantification
ratios - the estimated ratios
Method Detail

setPeptideRatios

public void setPeptideRatios(java.util.HashMap<java.lang.Integer,Ratio> ratios)
sets new peptide ratios

Parameters:
ratios - the new peptide ratios

getRatios

public java.util.HashMap<java.lang.Integer,Ratio> getRatios()
Getter for the peptide ratios

Returns:
the peptide ratios

getPsmQuantification

public java.util.HashMap<java.lang.String,PsmQuantification> getPsmQuantification()
Getter for the corresponding spectrum quantification

Returns:
List of spectrum quantification

getPsm

public PsmQuantification getPsm(java.lang.String index)
returns a specific psm quantification

Parameters:
index - the index of the quantification
Returns:
the desired psm

addPsmQuantification

public void addPsmQuantification(PsmQuantification newPsmQuantification)
Adds a new psm quantification in the psm quantification map

Parameters:
newPsmQuantification - the new psm quantification

getKey

public java.lang.String getKey()
Returns the key of the peptide quantification

Returns:
the key of the peptide quantification


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