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

Class SpectrumMatch

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

  • Constructor Details

    • SpectrumMatch

      public SpectrumMatch()
      Constructor for the spectrum match.

    • SpectrumMatch

      public SpectrumMatch(String spectrumFile, String spectrumTitle)
      Constructor for the spectrum match.
      Parameters:
      spectrumFile - The name of the file containing the spectrum.
      spectrumTitle - The title of the spectrum.

  • Method Details

    • setPeptideAssumptionMap

      public void setPeptideAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> peptideAssumptionsMap)
      Sets the peptide assumption map.
      Parameters:
      peptideAssumptionsMap - the peptide assumption map

    • setTagAssumptionMap

      public void setTagAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> tagAssumptionsMap)
      Sets the tag assumption map.
      Parameters:
      tagAssumptionsMap - the tag assumption map

    • getKey

      public static long getKey(String spectrumFile, String spectrumTitle)
      Returns a key to use for the spectrum match based on the file where the spectrum was found and its title.
      Parameters:
      spectrumFile - The name of the file containing the spectrum.
      spectrumTitle - The title of the spectrum.
      Returns:
      The key as long.

    • getBestPeptideAssumption

      public PeptideAssumption getBestPeptideAssumption()
      Getter for the best peptide assumption.
      Returns:
      the best peptide assumption for the spectrum

    • setBestPeptideAssumption

      public void setBestPeptideAssumption(PeptideAssumption bestPeptideAssumption)
      Setter for the best peptide assumption.
      Parameters:
      bestPeptideAssumption - the best peptide assumption for the spectrum

    • getBestTagAssumption

      public TagAssumption getBestTagAssumption()
      Getter for the best tag assumption.
      Returns:
      the best tag assumption for the spectrum

    • setBestTagAssumption

      public void setBestTagAssumption(TagAssumption bestTagAssumption)
      Setter for the best tag assumption.
      Parameters:
      bestTagAssumption - the best tag assumption for the spectrum

    • getSpectrumFile

      public String getSpectrumFile()
      Returns the name of the file where this spectrum was found.
      Returns:
      The name of the file where this spectrum was found.

    • setSpectrumFile

      public void setSpectrumFile(String spectrumFile)
      Sets the spectrum file name.
      Parameters:
      spectrumFile - The spectrum file name.

    • getSpectrumTitle

      public String getSpectrumTitle()
      Returns the title of the spectrum.
      Returns:
      The title of the spectrum.

    • setSpectrumTitle

      public void setSpectrumTitle(String spectrumTitle)
      Sets the spectrum title.
      Parameters:
      spectrumTitle - The spectrum title.

    • 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

    • getAdvocates

      public HashSet<Integer> getAdvocates()
      Returns the advocates supporting hits for this spectrum.
      Returns:
      The advocates supporting hits for this spectrum.

    • getAllPeptideAssumptions

      public TreeMap<Double,ArrayList<PeptideAssumption>> getAllPeptideAssumptions(int advocateId)
      Returns all peptide assumptions for the specified search engine indexed by their score. Null if none found.
      Parameters:
      advocateId - the desired advocate ID
      Returns:
      all assumptions

    • getAllTagAssumptions

      public TreeMap<Double,ArrayList<TagAssumption>> getAllTagAssumptions(int advocateId)
      Returns all tag assumptions for the specified search engine indexed by their score. Null if none found.
      Parameters:
      advocateId - the desired advocate ID
      Returns:
      all assumptions

    • getAllPeptideAssumptions

      public java.util.stream.Stream<PeptideAssumption> getAllPeptideAssumptions()
      Returns a stream of all peptide assumptions
      Returns:
      a stream of all peptide assumptions

    • getAllTagAssumptions

      public java.util.stream.Stream<TagAssumption> getAllTagAssumptions()
      Returns a stream of all tag assumptions
      Returns:
      a stream of all tag assumptions

    • getPeptideAssumptionsMap

      public HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> getPeptideAssumptionsMap()
      Returns the peptide assumptions map: advocate id > score > list of assumptions.
      Returns:
      the assumptions map

    • getTagAssumptionsMap

      public HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> getTagAssumptionsMap()
      Returns the tag assumptions map: advocate id > score > list of assumptions.
      Returns:
      the assumptions map

    • addPeptideAssumption

      public void addPeptideAssumption(int advocateId, PeptideAssumption peptideAssumption)
      Add a hit.
      Parameters:
      advocateId - the index of the advocate of the new hit
      peptideAssumption - the new identification assumption

    • addTagAssumption

      public void addTagAssumption(int advocateId, TagAssumption tagAssumption)
      Add a hit.
      Parameters:
      advocateId - the index of the advocate of the new hit
      tagAssumption - the new identification assumption

    • 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

    • removePeptideAssumption

      public void removePeptideAssumption(PeptideAssumption peptideAssumption)
      Removes an assumption from the mapping.
      Parameters:
      peptideAssumption - the peptide assumption to remove

    • removeTagAssumption

      public void removeTagAssumption(TagAssumption tagAssumption)
      Removes an assumption from the mapping.
      Parameters:
      tagAssumption - the tag assumption to remove

    • hasPeptideAssumption

      public boolean hasPeptideAssumption()
      Indicates whether the spectrum match contains a peptide assumption.
      Returns:
      a boolean indicating whether the spectrum match contains a peptide assumption

    • hasTagAssumption

      public boolean hasTagAssumption()
      Indicates whether the spectrum match contains a tag assumption.
      Returns:
      a boolean indicating whether the spectrum match contains a tag assumption

    • hasPeptideAssumption

      public boolean hasPeptideAssumption(int advocateId)
      Indicates whether the spectrum match contains a peptide assumption for the given advocate (see the Advocate class).
      Parameters:
      advocateId - The index of the advocate
      Returns:
      a boolean indicating whether the spectrum match contains an assumption for the given advocate

    • hasTagAssumption

      public boolean hasTagAssumption(int advocateId)
      Indicates whether the spectrum match contains a tag assumption for the given advocate (see the Advocate class).
      Parameters:
      advocateId - The index of the advocate
      Returns:
      a boolean indicating whether the spectrum match contains an assumption for the given advocate