Package com.compomics.util.parameters.identification.advanced

Class SequenceMatchingParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
All Implemented Interfaces:
Serializable
public class SequenceMatchingParameters extends ExperimentObject
The sequence matching options.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Field Details

  • Constructor Details

    • SequenceMatchingParameters

      public SequenceMatchingParameters()
      Constructor for empty preferences.

  • Method Details

    • getStringMatching

      public static SequenceMatchingParameters getStringMatching()
      Returns preferences for simple string matching.
      Returns:
      preferences for simple string matching

    • getDefaultSequenceMatching

      public static SequenceMatchingParameters getDefaultSequenceMatching()
      Returns default preferences from amino acid matching.
      Returns:
      default preferences from amino acid matching

    • getSequenceMatchingType

      public SequenceMatchingParameters.MatchingType getSequenceMatchingType()
      Returns the sequence matching type.
      Returns:
      the sequence matching type

    • setSequenceMatchingType

      public void setSequenceMatchingType(SequenceMatchingParameters.MatchingType sequenceMatchingType)
      Sets the sequence matching type.
      Parameters:
      sequenceMatchingType - the sequence matching type

    • getLimitX

      public double getLimitX()
      Returns the maximal share of X's a match can contain, range [0.0-1.0]. Null if not set.
      Returns:
      the maximal share of X's a match can contain

    • setLimitX

      public void setLimitX(double limitX)
      Sets the maximal share of X's a match can contain, range [0.0-1.0].
      Parameters:
      limitX - the maximal share of X's a match can contain

    • isSameAs

      public boolean isSameAs(SequenceMatchingParameters sequenceMatchingPreferences)
      Indicates whether another sequence matching preferences is the same as this one.
      Parameters:
      sequenceMatchingPreferences - the other sequence matching preferences
      Returns:
      whether another sequence matching preferences is the same as this one

    • getShortDescription

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

    • isEnzymaticTagsOnly

      public boolean isEnzymaticTagsOnly()
      Returns true if tags should only be mapped to enzymatic peptides.
      Returns:
      true if tags should only be mapped to enzymatic peptides

    • setEnzymaticTagsOnly

      public void setEnzymaticTagsOnly(boolean enzymaticTagsOnly)
      Sets whether tags should only be mapped to enzymatic peptides.
      Parameters:
      enzymaticTagsOnly - the enzymaticTagsOnly to set

    • getMaxPtmsPerTagPeptide

      public int getMaxPtmsPerTagPeptide()
      Returns the maximum number of PTMs to consider when mapping tags to protein sequences.
      Returns:
      the maximum number of PTMs to consider when mapping tags to protein sequences

    • setMaxPtmsPerTagPeptide

      public void setMaxPtmsPerTagPeptide(int numberOfPtmsPerTagPeptide)
      Sets the maximum number of PTMs to consider when mapping tags to protein sequences.
      Parameters:
      numberOfPtmsPerTagPeptide - the maxPtmsPerTagPeptide to set

    • getMinAminoAcidScore

      public int getMinAminoAcidScore()
      Returns the minimum amino acid score.
      Returns:
      the minAminoAcidScore

    • setMinAminoAcidScore

      public void setMinAminoAcidScore(int minAminoAcidScore)
      Set the minimum amino acid score.
      Parameters:
      minAminoAcidScore - the minAminoAcidScore to set

    • getMinTagLength

      public int getMinTagLength()
      Returns the minimum tag length.
      Returns:
      the minTagLength

    • setMinTagLength

      public void setMinTagLength(int minTagLength)
      Set the minimum tag length.
      Parameters:
      minTagLength - the minTagLength to set