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.Match
          extended by com.compomics.util.experiment.identification.matches.ProteinMatch
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class ProteinMatch
extends Match

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(Peptide peptide)
          Constructor for the protein match
ProteinMatch(java.lang.String proteinAccession)
          Constructor for the protein match
 
Method Summary
 void addPeptideMatch(java.lang.String peptideMatchKey)
          add a subordinated peptide match
 void addTheoreticProtein(java.lang.String proteinAccession)
          setter for the matching protein
 boolean contains(ProteinMatch proteinMatch)
          Returns a boolean indicating whether the protein match contains another set of theoretic proteins.
 boolean contains(java.lang.String aProtein)
          Returns a boolean indicating whether a protein was found in this protein match
static boolean contains(java.lang.String sharedKey, java.lang.String uniqueKey)
          Returns a boolean indicating whether a protein match contains another set of matches.
static java.lang.String[] getAccessions(java.lang.String key)
          Returns a list of accessions from the given key
 java.lang.String getKey()
          returns the key of a match
 java.lang.String getMainMatch()
          Returns the main match accession after protein inference
 int getNProteins()
          Returns the number of proteins for this match
static int getNProteins(java.lang.String matchKey)
          Returns the number of proteins for the match corresponding to the given key
 int getPeptideCount()
          Returns the number of peptides found
 java.util.ArrayList<java.lang.String> getPeptideMatches()
          getter for the peptide matches
static java.lang.String getProteinMatchKey(Peptide peptide)
          Convenience method which returns the protein key of a peptide
 java.util.ArrayList<java.lang.String> getTheoreticProteinsAccessions()
          Returns the accessions of the possible theoretic proteins
 boolean isDecoy()
          methods indicates if the protein match is a decoy one
static boolean isDecoy(java.lang.String key)
          Convenience method indicating whether a match is decoy based on the match key
 void setMainMatch(java.lang.String mainMatch)
          Sets the main protein accession after protein inference
 
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

ProteinMatch

public ProteinMatch()
Constructor for the protein match


ProteinMatch

public ProteinMatch(java.lang.String proteinAccession)
Constructor for the protein match

Parameters:
protein - the matching protein

ProteinMatch

public ProteinMatch(Peptide peptide)
Constructor for the protein match

Parameters:
peptideMatch - The corresponding peptide match
Method Detail

getTheoreticProteinsAccessions

public java.util.ArrayList<java.lang.String> getTheoreticProteinsAccessions()
Returns the accessions of the possible theoretic proteins

Returns:
the accessions of the possible theoretic proteins

addTheoreticProtein

public void addTheoreticProtein(java.lang.String proteinAccession)
setter for the matching protein

Parameters:
protein - the matching protein

getMainMatch

public java.lang.String getMainMatch()
Returns the main match accession after protein inference

Returns:
the main match accession after protein inference

setMainMatch

public void setMainMatch(java.lang.String mainMatch)
Sets the main protein accession after protein inference

Parameters:
mainMatch - the main match

getPeptideMatches

public java.util.ArrayList<java.lang.String> getPeptideMatches()
getter for the peptide matches

Returns:
subordinated peptide matches

addPeptideMatch

public void addPeptideMatch(java.lang.String peptideMatchKey)
add a subordinated peptide match

Parameters:
peptideMatch - a peptide 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

isDecoy

public static boolean isDecoy(java.lang.String key)
Convenience method indicating whether a match is decoy based on the match key

Parameters:
key - the match key
Returns:
a boolean indicating whether a match is decoy

getKey

public java.lang.String getKey()
Description copied from class: Match
returns the key of a match

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

getProteinMatchKey

public static java.lang.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 static int getNProteins(java.lang.String matchKey)
Returns the number of proteins for the match corresponding to the given key

Parameters:
matchKey - the given key
Returns:
the number of proteins for this match

getNProteins

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

Returns:
the number of proteins for this match

contains

public static boolean contains(java.lang.String sharedKey,
                               java.lang.String uniqueKey)
Returns a boolean indicating whether a protein match contains another set of matches.

Parameters:
sharedKey - the key of the protein of interest
uniqueKey - the key of the protein supposedly contained
Returns:
a boolean indicating whether a protein match contains another set of matches.

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(java.lang.String 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

getAccessions

public static java.lang.String[] getAccessions(java.lang.String key)
Returns a list of accessions from the given key

Parameters:
key - the given key
Returns:
the corresponding list of accessions


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