Package com.compomics.util.parameters.identification.search

Class DigestionParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.search.DigestionParameters
All Implemented Interfaces:
Serializable
public class DigestionParameters extends ExperimentObject
This class groups the parameters for the digestion of proteins.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • DigestionParameters

      public DigestionParameters()
      Constructor for empty parameters.

  • Method Details

    • clone

      public static DigestionParameters clone(DigestionParameters digestionParameters)
      Clones the given parameters.
      Parameters:
      digestionParameters - the parameters to clone
      Returns:
      a new object containing the same parameters

    • getDefaultParameters

      public static DigestionParameters getDefaultParameters()
      Returns default digestion parameters. Trypsin specific with two missed cleavages.
      Returns:
      default digestion parameters

    • hasEnzymes

      public boolean hasEnzymes()
      Returns a boolean indicating whether enzyme settings were set.
      Returns:
      a boolean indicating whether enzyme settings were set

    • getEnzymes

      public ArrayList<Enzyme> getEnzymes()
      Returns the enzymes used for digestion in a list.
      Returns:
      the enzymes used for digestion in a list

    • setEnzymes

      public void setEnzymes(ArrayList<Enzyme> enzymes)
      Sets the enzymes used for digestion.
      Parameters:
      enzymes - the enzymes used for digestion in a list

    • addEnzyme

      public void addEnzyme(Enzyme enzyme)
      Adds an enzyme. The specificity of the enzyme is set by default to specific and the number of allowed missed cleavages to 0.
      Parameters:
      enzyme - an enzyme used for digestion.

    • clear

      public void clear()
      Clears the parameters.

    • clearEnzymes

      public void clearEnzymes()
      Clears the enzymes set including specificity and missed cleavages.

    • getnMissedCleavages

      public Integer getnMissedCleavages(String enzymeName)
      Returns the number of allowed missed cleavages for the given enzyme. Null if not set.
      Parameters:
      enzymeName - the name of the enzyme
      Returns:
      the number of allowed missed cleavages

    • setnMissedCleavages

      public void setnMissedCleavages(String enzymeName, int enzymeMissedCleavages)
      Sets the number of allowed missed cleavages.
      Parameters:
      enzymeName - the name of the enzyme
      enzymeMissedCleavages - the number of allowed missed cleavages

    • getSpecificity

      public DigestionParameters.Specificity getSpecificity(String enzymeName)
      Returns the expected specificity of the given enzyme. Null if not set.
      Parameters:
      enzymeName - the name of the enzyme
      Returns:
      the specificity

    • setSpecificity

      public void setSpecificity(String enzymeName, DigestionParameters.Specificity enzymeSpecificity)
      Sets the expected specificity of the enzyme.
      Parameters:
      enzymeName - the name of the enzyme
      enzymeSpecificity - the expected specificity of the enzyme

    • getCleavageParameter

      public DigestionParameters.CleavageParameter getCleavageParameter()
      Returns the cleavage parameters.
      Returns:
      the cleavage parameters

    • setCleavageParameter

      public void setCleavageParameter(DigestionParameters.CleavageParameter cleavageParameter)
      Sets the cleavage parameters.
      Parameters:
      cleavageParameter - the cleavage parameters

    • getShortDescription

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

    • isSameAs

      public boolean isSameAs(DigestionParameters otherDigestionParameters)
      Returns a boolean indicating whether these digestion parameters are the same as the given other parameters.
      Parameters:
      otherDigestionParameters - the other digestion parameters
      Returns:
      a boolean indicating whether these digestion parameters are the same as the given other parameters

    • getXTandemFormat

      public String getXTandemFormat()
      Get the X! Tandem enzyme format.
      Returns:
      the enzyme X! Tandem format as String

    • getMyriMatchFormat

      public String getMyriMatchFormat()
      Get the MyriMatch enzyme format. In case multiple enzymes are present all possible cleavage sites will be included.
      Returns:
      the enzyme MyriMatch format as String