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

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

public class ProteinMatch
extends ExperimentObject

This class models a protein match.

Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:59:02 AM

See Also:
Serialized Form

Constructor Summary
ProteinMatch()
          Constructor for the protein match
ProteinMatch(PeptideMatch peptideMatch)
          Constructor for the protein match
ProteinMatch(Protein protein)
          Constructor for the protein match
 
Method Summary
 void addPeptideMatch(PeptideMatch peptideMatch)
          add a subordinated peptide match
 void addTheoreticProtein(Protein protein)
          setter for the matching protein
 boolean contains(Protein aProtein)
          Returns a boolean indicating whether a protein was found in this protein match
 boolean contains(ProteinMatch proteinMatch)
          Returns a boolean indicating whether the protein match contains another set of theoretic proteins.
 ProteinMatch getComplementMatch(ProteinMatch proteinMatch)
          returns a proteinMatch complementary to the protein match given Example: if the protein match was identified on proteins A, B and C; if the given match was identified on A; the method returns a protein match with B and C.
 String getKey()
          Returns the index of the protein match
 Protein getMainMatch()
          Returns the main match after protein inference
 int getNProteins()
          Returns the number of proteins for this match
 int getPeptideCount()
          Returns the number of peptides found
 HashMap<String,PeptideMatch> getPeptideMatches()
          getter for the peptide matches
static String getProteinMatchKey(Peptide peptide)
          Convenience method which returns the protein key of a peptide
 int getSpectrumCount()
          method to get the spectrum count for this protein match
 Protein getTheoreticProtein(String accession)
          getter for the matching protein
 Set<String> getTheoreticProteinsAccessions()
          Returns the accessions of the possible theoretic proteins
 boolean isDecoy()
          methods indicates if the protein match is a decoy one
 void setMainMatch(Protein mainMatch)
          Sets the main protein after protein inference
 
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

ProteinMatch

public ProteinMatch()
Constructor for the protein match


ProteinMatch

public ProteinMatch(Protein protein)
Constructor for the protein match

Parameters:
protein - the matching protein

ProteinMatch

public ProteinMatch(PeptideMatch peptideMatch)
Constructor for the protein match

Parameters:
peptideMatch - The corresponding peptide matches
Method Detail

getTheoreticProtein

public Protein getTheoreticProtein(String accession)
getter for the matching protein

Returns:
the matching protein

getTheoreticProteinsAccessions

public Set<String> getTheoreticProteinsAccessions()
Returns the accessions of the possible theoretic proteins

Returns:
the accessions of the possible theoretic proteins

addTheoreticProtein

public void addTheoreticProtein(Protein protein)
setter for the matching protein

Parameters:
protein - the matching protein

getMainMatch

public Protein getMainMatch()
Returns the main match after protein inference

Returns:
the main match after protein inference

setMainMatch

public void setMainMatch(Protein mainMatch)
Sets the main protein after protein inference

Parameters:
mainMatch - the main match

getPeptideMatches

public HashMap<String,PeptideMatch> getPeptideMatches()
getter for the peptide matches

Returns:
subordinated peptide matches

addPeptideMatch

public void addPeptideMatch(PeptideMatch peptideMatch)
add a subordinated peptide match

Parameters:
peptideMatch - a peptide match

getSpectrumCount

public int getSpectrumCount()
method to get the spectrum count for this protein match

Returns:
the spectrum count for this protein match

getPeptideCount

public int getPeptideCount()
Returns the number of peptides found

Returns:
the number of peptides found

isDecoy

public boolean isDecoy()
methods indicates if the protein match is a decoy one

Returns:
boolean indicating if the protein match is a decoy one

getKey

public String getKey()
Returns the index of the protein match

Returns:
the index of the protein match

getProteinMatchKey

public static String getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key of a peptide

Parameters:
peptide - the considered peptide
Returns:
the protein match key

getNProteins

public int getNProteins()
Returns the number of proteins for this match

Returns:
the number of proteins for this match

contains

public boolean contains(ProteinMatch proteinMatch)
Returns a boolean indicating whether the protein match contains another set of theoretic proteins.

Parameters:
proteinMatch - another protein match
Returns:
a boolean indicating whether the protein match contains another set of theoretic proteins

contains

public boolean contains(Protein aProtein)
Returns a boolean indicating whether a protein was found in this protein match

Parameters:
aProtein - the inspected protein
Returns:
a boolean indicating whether a protein was found in this protein match

getComplementMatch

public ProteinMatch getComplementMatch(ProteinMatch proteinMatch)
                                throws Exception
returns a proteinMatch complementary to the protein match given Example: if the protein match was identified on proteins A, B and C; if the given match was identified on A; the method returns a protein match with B and C.

Parameters:
proteinMatch - the given protein match
Returns:
a proteinMatch complementary to the protein match given
Throws:
Exception - Exception thrown when two spectrum matches from the same search engine are attached to the same spectrum


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