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

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

public class ProteinQuantification
extends ExperimentObject

This class models the quantification results for a protein match. User: Marc Date: Sep 1, 2010 Time: 3:31:25 PM

See Also:
Serialized Form

Constructor Summary
ProteinQuantification(String proteinKey)
          Constructor for the protein quantification
ProteinQuantification(String proteinKey, HashMap<String,PeptideQuantification> peptideQuantification)
          Constructor for the protein quantification
ProteinQuantification(String proteinKey, HashMap<String,PeptideQuantification> peptideQuantification, HashMap<Integer,Ratio> proteinRatios)
          Constructor for the protein quantification
 
Method Summary
 void addPeptideQuantification(PeptideQuantification newPeptideQuantification)
          Adds a new peptide quantification in the protein quantification
 String getKey()
          Returns the indexing key of the protein quantification
 HashMap<String,PeptideQuantification> getPeptideQuantification()
          Getter for the corresponding peptide quantification
 PeptideQuantification getPeptideQuantification(String index)
          Returns a specific peptide quantification
 HashMap<Integer,Ratio> getProteinRatios()
          Getter for the ratios
 void setProteinRatios(HashMap<Integer,Ratio> ratios)
          sets new protein 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

ProteinQuantification

public ProteinQuantification(String proteinKey)
Constructor for the protein quantification

Parameters:
proteinKey - the identified protein match key

ProteinQuantification

public ProteinQuantification(String proteinKey,
                             HashMap<String,PeptideQuantification> peptideQuantification)
Constructor for the protein quantification

Parameters:
proteinKey - the identified protein match key
peptideQuantification - the corresponding peptide quantification

ProteinQuantification

public ProteinQuantification(String proteinKey,
                             HashMap<String,PeptideQuantification> peptideQuantification,
                             HashMap<Integer,Ratio> proteinRatios)
Constructor for the protein quantification

Parameters:
proteinKey - the identified protein match key
proteinRatios - the estimated protein ratios
peptideQuantification - the corresponding peptide quantification
Method Detail

setProteinRatios

public void setProteinRatios(HashMap<Integer,Ratio> ratios)
sets new protein ratios

Parameters:
ratios - estimated protein ratios

getProteinRatios

public HashMap<Integer,Ratio> getProteinRatios()
Getter for the ratios

Returns:
the estimated ratios

getPeptideQuantification

public HashMap<String,PeptideQuantification> getPeptideQuantification()
Getter for the corresponding peptide quantification

Returns:
list of peptide quantification

getPeptideQuantification

public PeptideQuantification getPeptideQuantification(String index)
Returns a specific peptide quantification

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

addPeptideQuantification

public void addPeptideQuantification(PeptideQuantification newPeptideQuantification)
Adds a new peptide quantification in the protein quantification

Parameters:
newPeptideQuantification - the new peptide quantification

getKey

public String getKey()
Returns the indexing key of the protein quantification

Returns:
the indexing key of the protein quantification


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