Class PeptideVariantsParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
All Implemented Interfaces:
Serializable

public class PeptideVariantsParameters
extends ExperimentObject
Preferences for the allowed variants in peptide sequences.
Author:
Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

  • Method Details

    • getnAaDeletions

      public int getnAaDeletions()
      Returns the number of amino acid deletions allowed.
      Returns:
      the number of amino acid deletions allowed
    • setnAaDeletions

      public void setnAaDeletions​(int nAaDeletions)
      Sets the number of amino acid deletions allowed.
      Parameters:
      nAaDeletions - the number of amino acid deletions allowed
    • getnAaInsertions

      public int getnAaInsertions()
      Returns the number of amino acid insertions allowed.
      Returns:
      the number of amino acid insertions allowed
    • setnAaInsertions

      public void setnAaInsertions​(int nAaInsertions)
      Sets the number of amino acid insertions allowed.
      Parameters:
      nAaInsertions - the number of amino acid insertions allowed
    • getnAaSubstitutions

      public int getnAaSubstitutions()
      Returns the number of amino acid substitutions allowed.
      Returns:
      the number of amino acid substitutions allowed
    • setnAaSubstitutions

      public void setnAaSubstitutions​(int nAaSubstitutions)
      Sets the number of amino acid substitutions allowed.
      Parameters:
      nAaSubstitutions - the number of amino acid substitutions allowed
    • getnAaSwap

      public int getnAaSwap()
      Returns the number of amino acid swaps allowed.
      Returns:
      the number of amino acid swaps allowed
    • setnAaSwap

      public void setnAaSwap​(int nAaSwap)
      Sets the number of amino acid swaps allowed.
      Parameters:
      nAaSwap - the number of amino acid swaps allowed
    • getAaSubstitutionMatrix

      public AaSubstitutionMatrix getAaSubstitutionMatrix()
      Returns the amino acid substitution matrix to use.
      Returns:
      the amino acid substitution matrix to use
    • setAaSubstitutionMatrix

      public void setAaSubstitutionMatrix​(AaSubstitutionMatrix aaSubstitutionMatrix)
      Sets the amino acid substitution matrix to use.
      Parameters:
      aaSubstitutionMatrix - the amino acid substitution matrix to use
    • getVariantType

      public PeptideVariantsParameters.VariantType getVariantType()
      Returns whether the specific variant count limitations should be used.
      Returns:
      a boolean indicating whether the specific variant count limitations should be used
    • setVatiantType

      public void setVatiantType​(PeptideVariantsParameters.VariantType variantType)
      Sets whether the specific variant count limitations should be used.
      Parameters:
      variantType - a boolean indicating whether the specific variant count limitations should be used
    • getnVariants

      public int getnVariants()
      Returns the total number of variants allowed.
      Returns:
      the total number of variants allowed
    • setnVariants

      public void setnVariants​(int nVariants)
      Sets the total number of variants allowed.
      Parameters:
      nVariants - the total number of variants allowed
    • isSameAs

      public boolean isSameAs​(PeptideVariantsParameters peptideVariantsPreferences)
      Indicates whether another peptide variant preferences is the same as this one.
      Parameters:
      peptideVariantsPreferences - the other preferences
      Returns:
      whether another peptide variant 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
    • getNoVariantPreferences

      public static PeptideVariantsParameters getNoVariantPreferences()
      Returns the preferences corresponding to no variants allowed.
      Returns:
      the preferences corresponding to no variants allowed
    • getFixedVariants

      public HashMap<String,​ArrayList<SNPElement>> getFixedVariants()
      returns the fixed variants
      Returns:
      fixed variants dictionary
    • setFixedVariants

      public void setFixedVariants​(HashMap<String,​ArrayList<SNPElement>> fixedVariants)
      sets the fixed variants
      Parameters:
      fixedVariants - fixed variants dictionary