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

    • 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

      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