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

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:

  • Constructor Details

    • PeptideVariantsParameters

      public PeptideVariantsParameters()
      Constructor.

  • 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 peptideVariantsParameters)
      Indicates whether another peptide variant parameters is the same as this one.
      Parameters:
      peptideVariantsParameters - the other parameters
      Returns:
      whether another peptide variant parameters is the same as this one

    • getShortDescription

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

    • getNoVariantParameters

      public static PeptideVariantsParameters getNoVariantParameters()
      Returns the parameters corresponding to no variants allowed.
      Returns:
      the parameters 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