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.IdentificationMatch
          extended by com.compomics.util.experiment.identification.matches.PeptideMatch
All Implemented Interfaces:
Serializable, Cloneable

public class PeptideMatch
extends IdentificationMatch

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, String spectrumMatchKey)
          Constructor for the peptide match
 
Method Summary
 void addSpectrumMatch(String spectrumMatchKey)
          add a spectrum match
 String getKey()
          returns the key of a match
 String getMainMatchKey()
          method returns the key of the main match
 int getSpectrumCount()
          returns the number of spectra matched
 ArrayList<String> 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(String spectrumMatchKey)
          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, getParameterKey, 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,
                    String spectrumMatchKey)
Constructor for the peptide match

Parameters:
peptide - The matching peptide
spectrumMatchKey - The key of the main spectrum match
Method Detail

getKey

public String getKey()
Description copied from class: IdentificationMatch
returns the key of a match

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

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

getMainMatchKey

public String getMainMatchKey()
method returns the key of the main match

Returns:
the main match key

setMainMatch

public void setMainMatch(String spectrumMatchKey)
methods sets the main match

Parameters:
spectrumMatchKey - the key of the main match

getSpectrumMatches

public ArrayList<String> getSpectrumMatches()
returns all spectra matched

Returns:
all spectrum matches

addSpectrumMatch

public void addSpectrumMatch(String spectrumMatchKey)
add a spectrum match

Parameters:
spectrumMatchKey - a spectrum match

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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