Package org.biojava.bio.proteomics

Class Digest

java.lang.Object
org.biojava.bio.proteomics.Digest
public class Digest extends Object
This class contains methods for calculating the results of proteolytic digestion of a protein sequence this class is not designed to be thread safe
Author:
Michael Jones, Mark Schreiber (refactoring, some documentation)

  • Field Details

  • Constructor Details

    • Digest

      public Digest()
      Creates a new Digest Bean

  • Method Details

    • setProtease

      public void setProtease(Protease protease)

    • setSequence

      public void setSequence(Sequence sequence)

    • getSequence

      public Sequence getSequence()

    • setMaxMissedCleavages

      public void setMaxMissedCleavages(int maxMissedCleavages)
      Sets the maximum number of partial digest products to be annotated.
      Parameters:
      maxMissedCleavages - the max number of partial digest products

    • addDigestFeatures

      public void addDigestFeatures() throws BioException, ChangeVetoException
      Adds peptides as features to the Sequence in this class. The feature will contain a small annotation specifying the protease with the key "protease". For Example: 
      


         Sequence sequence = ...

         Digest bioJavaDigest = new Digest();



         bioJavaDigest.setMaxMissedCleavages(2);

         bioJavaDigest.setProtease(ProteaseManager.getProteaseByName(Protease.ASP_N));

         bioJavaDigest.setSequence(sequence);

         bioJavaDigest.addDigestFeatures();
      Throws:
      BioException - if the Protease or Sequence are null.
      ChangeVetoException