Package com.compomics.util.experiment.identification.filtering

Class PeptideAssumptionFilter

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
All Implemented Interfaces:
Serializable
public class PeptideAssumptionFilter extends ExperimentObject
This class filters peptide assumptions based on various properties.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • PeptideAssumptionFilter

      public PeptideAssumptionFilter()
      Constructor with default settings.

    • PeptideAssumptionFilter

      public PeptideAssumptionFilter(int minPepLength, int maxPepLength, double maxMzDeviation, boolean isPpm, boolean unknownModification, Integer minMissedCleavages, Integer maxMissedCleavages, Integer minIsotopes, Integer maxIsotopes)
      Constructor for an Identification filter.
      Parameters:
      minPepLength - the minimal peptide length allowed (0 or less for disabled)
      maxPepLength - the maximal peptide length allowed (0 or less for disabled)
      maxMzDeviation - the maximal m/z deviation allowed (0 or less for disabled)
      isPpm - boolean indicating the unit of the allowed m/z deviation (true: ppm, false: Da)
      unknownModification - shall peptides presenting unknown modifications be removed
      minMissedCleavages - the minimum number of missed cleavages allowed (null for disabled)
      maxMissedCleavages - the maximum number of missed cleavages allowed (null for disabled)
      minIsotopes - the minimum number of isotopes allowed (null for disabled)
      maxIsotopes - the maximum number of isotopes allowed (null for disabled)

  • Method Details

    • setFilterFromSearchParameters

      public void setFilterFromSearchParameters(SearchParameters searchParameters)
      Updates the filter based on the search parameters.
      Parameters:
      searchParameters - the search parameters where to take the information from

    • validatePeptide

      public boolean validatePeptide(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, DigestionParameters digestionPreferences)
      Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.
      Parameters:
      peptide - the peptide to validate
      sequenceMatchingPreferences - the sequence matching preferences containing the maximal share of X's allowed
      digestionPreferences - the digestion preferences
      Returns:
      a boolean indicating whether the peptide passed the test

    • validateProteins

      public boolean validateProteins(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider)
      Validates a peptide depending on its protein inference status.
      Parameters:
      peptide - the peptide
      sequenceMatchingPreferences - the sequence matching preferences
      sequenceProvider - a sequence provider
      Returns:
      a boolean indicating whether the peptide passed the test

    • validateModifications

      public boolean validateModifications(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceMatchingParameters modificationSequenceMatchingPreferences, ModificationParameters modificationProfile)
      Verifies that the definition of every modification name is available.
      Parameters:
      peptide - the peptide of interest
      sequenceMatchingPreferences - the sequence matching preferences for peptide to protein mapping
      modificationSequenceMatchingPreferences - the sequence matching preferences for modification to peptide mapping
      modificationProfile - the modification profile of the identification
      Returns:
      a boolean indicating whether the peptide passed the test

    • validatePrecursor

      public boolean validatePrecursor(PeptideAssumption assumption, String spectrumFile, String spectrumTitle, SpectrumProvider spectrumProvider, SearchParameters searchParameters)
      Validates the mass deviation of a peptide assumption.
      Parameters:
      assumption - the considered peptide assumption
      spectrumFile - the file of the spectrum used to get the precursor
      spectrumTitle - the file of the spectrum used to get the precursor
      spectrumProvider - the spectrum provider
      searchParameters - the search parameters
      Returns:
      a boolean indicating whether the given assumption passes the filter

    • removeUnknownModifications

      public boolean removeUnknownModifications()
      Returns a boolean indicating whether unknown modifications shall be removed.
      Returns:
      a boolean indicating whether unknown modifications shall be removed

    • setRemoveUnknownModifications

      public void setRemoveUnknownModifications(boolean unknownModification)
      Set whether unknown modifications shall be removed.
      Parameters:
      unknownModification - whether unknown modifications shall be removed

    • isIsPpm

      public boolean isIsPpm()
      Indicates whether the mass tolerance is in ppm (true) or Dalton (false).
      Returns:
      a boolean indicating whether the mass tolerance is in ppm (true) or Dalton (false)

    • setIsPpm

      public void setIsPpm(boolean isPpm)
      Sets whether the mass tolerance is in ppm (true) or Dalton (false).
      Parameters:
      isPpm - a boolean indicating whether the mass tolerance is in ppm (true) or Dalton (false)

    • getMaxMzDeviation

      public double getMaxMzDeviation()
      Returns the maximal m/z deviation allowed.
      Returns:
      the maximal mass deviation allowed

    • setMaxMzDeviation

      public void setMaxMzDeviation(double maxMzDeviation)
      Sets the maximal m/z deviation allowed.
      Parameters:
      maxMzDeviation - the maximal mass deviation allowed

    • getMaxPepLength

      public int getMaxPepLength()
      Returns the maximal peptide length allowed.
      Returns:
      the maximal peptide length allowed

    • setMaxPepLength

      public void setMaxPepLength(int maxPepLength)
      Sets the maximal peptide length allowed.
      Parameters:
      maxPepLength - the maximal peptide length allowed

    • getMinPepLength

      public int getMinPepLength()
      Returns the maximal peptide length allowed.
      Returns:
      the maximal peptide length allowed

    • setMinPepLength

      public void setMinPepLength(int minPepLength)
      Sets the maximal peptide length allowed.
      Parameters:
      minPepLength - the maximal peptide length allowed

    • getMinIsotopes

      public Integer getMinIsotopes()
      Returns the minimal number of isotopes allowed (inclusive).
      Returns:
      the minimal number of isotopes allowed

    • setMinIsotopes

      public void setMinIsotopes(Integer minIsotopes)
      Sets the minimal number of isotopes allowed (inclusive).
      Parameters:
      minIsotopes - the minimal number of isotopes allowed

    • getMaxIsotopes

      public Integer getMaxIsotopes()
      Returns the maximal number of isotopes allowed (inclusive).
      Returns:
      the maximal number of isotopes allowed

    • setMaxIsotopes

      public void setMaxIsotopes(Integer maxIsotopes)
      Sets the maximal number of isotopes allowed (inclusive).
      Parameters:
      maxIsotopes - the maximal number of isotopes allowed

    • isSameAs

      public boolean isSameAs(PeptideAssumptionFilter anotherFilter)
      Indicates whether this filter is the same as another one.
      Parameters:
      anotherFilter - another filter
      Returns:
      a boolean indicating that the filters have the same parameters

    • getShortDescription

      public String getShortDescription()
      Returns a short description of the parameters.
      Returns:
      a short description of the parameters

    • getMinMissedCleavages

      public Integer getMinMissedCleavages()
      Returns the minimum number of missed cleavages. Null means no limit.
      Returns:
      the minMissedCleavages

    • setMinMissedCleavages

      public void setMinMissedCleavages(Integer minMissedCleavages)
      Set the minimum number of missed cleavages. Null means no limit.
      Parameters:
      minMissedCleavages - the minMissedCleavages to set

    • getMaxMissedCleavages

      public Integer getMaxMissedCleavages()
      Returns the maximum number of missed cleavages. Null means no limit.
      Returns:
      the maxMissedCleavages

    • setMaxMissedCleavages

      public void setMaxMissedCleavages(Integer maxMissedCleavages)
      Set the maximum number of missed cleavages. Null means no limit.
      Parameters:
      maxMissedCleavages - the maxMissedCleavages to set