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.

Author:
Marc Vaudel
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class com.compomics.util.experiment.identification.IdentificationMatch
IdentificationMatch.MatchType
 
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()
          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.
 IdentificationMatch.MatchType getType()
          Returns the type of match.
 void setMainMatch(String spectrumMatchKey)
          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()
Returns the key of the main match.

Returns:
the main match key

setMainMatch

public void setMainMatch(String spectrumMatchKey)
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

getType

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

Specified by:
getType in class IdentificationMatch
Returns:
the type of match


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