Package com.compomics.util.experiment.identification.matches

Class ProteinMatch

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.IdentificationMatch
com.compomics.util.experiment.identification.matches.ProteinMatch
All Implemented Interfaces:
Serializable
public class ProteinMatch extends IdentificationMatch
This class models a protein match.
Author:
Marc Vaudel, Dominik Kopczynski
See Also:

  • Constructor Details

    • ProteinMatch

      public ProteinMatch()
      Constructor for the protein match.

    • ProteinMatch

      public ProteinMatch(String proteinAccession)
      Constructor for the protein match.
      Parameters:
      proteinAccession - the matching protein

    • ProteinMatch

      public ProteinMatch(Peptide peptide, long peptideMatchKey)
      Constructor for the protein match. Note: proteins must be set for the peptide.
      Parameters:
      peptide - the corresponding peptide match
      peptideMatchKey - the key of the peptide match

  • Method Details

    • setAccessions

      public void setAccessions(String[] newAccessions)
      Sets the accessions of the proteins in this group. Note, accessions must be sorted.
      Parameters:
      newAccessions - the accessions of the proteins in this group

    • getAccessions

      public String[] getAccessions()
      Returns the accessions of the proteins in this match.
      Returns:
      the accessions of the proteins in this match

    • getLeadingAccession

      public String getLeadingAccession()
      Returns the leading accession for this match.
      Returns:
      the leading accession for this match

    • setLeadingAccession

      public void setLeadingAccession(String leadingAccession)
      Sets the leading accession for this match.
      Parameters:
      leadingAccession - the leading accession for this match

    • isDecoy

      public boolean isDecoy()
      Returns a boolean indicating whether the given match is decoy.
      Returns:
      a boolean indicating whether the given match is decoy

    • setDecoy

      public void setDecoy(boolean decoy)
      Sets whether the given match is decoy
      Parameters:
      decoy - a boolean indicating whether the given match is decoy

    • getPeptideMatchesKeys

      public long[] getPeptideMatchesKeys()
      Getter for the peptide keys.
      Returns:
      subordinated peptide keys

    • addPeptideMatchKey

      public void addPeptideMatchKey(long peptideMatchKey)
      Add a subordinated peptide key.
      Parameters:
      peptideMatchKey - a peptide key

    • addPeptideMatchKeys

      public void addPeptideMatchKeys(long[] newKeys)
      Add a subordinated peptide key.
      Parameters:
      newKeys - peptide keys

    • setPeptideMatchesKeys

      public void setPeptideMatchesKeys(long[] peptideMatchKeys)
      Sets the peptide keys for this protein match.
      Parameters:
      peptideMatchKeys - the peptide match keys

    • getPeptideCount

      public int getPeptideCount()
      Returns the number of peptides found.
      Returns:
      the number of peptides found

    • getKey

      public long getKey()
      Description copied from class: IdentificationMatch
      Returns the key of a match.
      Specified by:
      getKey in class IdentificationMatch
      Returns:
      the key of a match

    • getProteinMatchKey

      public static long getProteinMatchKey(Peptide peptide)
      Convenience method which returns the protein key from a peptide. Note: proteins must be set for the 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(String aProtein)
      Returns a boolean indicating whether a protein was found in this protein match.
      Parameters:
      aProtein - the protein accession
      Returns:
      a boolean indicating whether a protein was found in this protein match

    • containsPeptide

      public boolean containsPeptide(long peptideKey)
      Returns a boolean indicating whether a peptide was found in this protein match.
      Parameters:
      peptideKey - the peptide key
      Returns:
      a boolean indicating whether a peptide was found in this protein match

    • getVariableModifications

      public ModificationMatch[] getVariableModifications()
      Returns the variable modifications.
      Returns:
      the variable modifications

    • setVariableModifications

      public void setVariableModifications(ModificationMatch[] variableModifications)
      Sets the variable modifications.
      Parameters:
      variableModifications - the variable modifications.

    • 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