com.compomics.util.experiment.identification.matches
Class PeptideMatch

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

public class PeptideMatch
extends ExperimentObject

This class models a peptide match.

Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:58:46 AM

See Also:
Serialized Form

Constructor Summary
PeptideMatch()
          constructor for the peptide match
PeptideMatch(Peptide peptide)
          Constructor for the peptide match
PeptideMatch(Peptide peptide, SpectrumMatch spectrumMatch)
          Constructor for the peptide match
 
Method Summary
 void addSpectrumMatch(SpectrumMatch spectrumMatch)
          add a spectrum match
 void addSpectrumMatches(HashMap<String,SpectrumMatch> newMatches)
          add spectrum matches
 String getKey()
          Convenience method to index peptideMatches on the peptide id
 SpectrumMatch getMainMatch()
          method returns the main match
 String getMainSpectrumKey()
          methods which returns the key of the main spectrum matched
 int getSpectrumCount()
          returns the number of spectra matched
 HashMap<String,SpectrumMatch> getSpectrumMatches()
          returns all spectra matched
 Peptide getTheoreticPeptide()
          getter for the theoretic peptide
 boolean isDecoy()
          inspects whether the peptide match is a decoy hit
 void setMainMatch(SpectrumMatch spectrumMatch)
          methods sets the main match
 void setTheoreticPeptide(Peptide theoreticPeptide)
          setter for the theoretic peptide
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PeptideMatch

public PeptideMatch()
constructor for the peptide match


PeptideMatch

public PeptideMatch(Peptide peptide)
Constructor for the peptide match

Parameters:
peptide - the matching peptide

PeptideMatch

public PeptideMatch(Peptide peptide,
                    SpectrumMatch spectrumMatch)
Constructor for the peptide match

Parameters:
peptide - The matching peptide
spectrumMatch - The main spectrum match
Method Detail

getKey

public String getKey()
Convenience method to index peptideMatches on the peptide id

Returns:
the peptideMatch id

getTheoreticPeptide

public Peptide getTheoreticPeptide()
getter for the theoretic peptide

Returns:
the theoretic peptide

setTheoreticPeptide

public void setTheoreticPeptide(Peptide theoreticPeptide)
setter for the theoretic peptide

Parameters:
theoreticPeptide - a theoretic peptide

getMainMatch

public SpectrumMatch getMainMatch()
method returns the main match

Returns:
the main match

setMainMatch

public void setMainMatch(SpectrumMatch spectrumMatch)
methods sets the main match

Parameters:
spectrumMatch - the main match

getMainSpectrumKey

public String getMainSpectrumKey()
methods which returns the key of the main spectrum matched

Returns:
key of the main spectrum matched

getSpectrumMatches

public HashMap<String,SpectrumMatch> getSpectrumMatches()
returns all spectra matched

Returns:
all spectrum matches

addSpectrumMatch

public void addSpectrumMatch(SpectrumMatch spectrumMatch)
add a spectrum match

Parameters:
spectrumMatch - a spectrum match

addSpectrumMatches

public void addSpectrumMatches(HashMap<String,SpectrumMatch> newMatches)
add spectrum matches

Parameters:
newMatches - matched spectra

getSpectrumCount

public int getSpectrumCount()
returns the number of spectra matched

Returns:
spectrum count

isDecoy

public boolean isDecoy()
inspects whether the peptide match is a decoy hit

Returns:
true if the peptide match is a decoy hit


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