/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.proteomics; import java.util.LinkedList; import java.util.List; import java.util.ListIterator; import org.biojava.bio.Annotation; import org.biojava.bio.BioException; import org.biojava.bio.SmallAnnotation; import org.biojava.bio.seq.Feature; import org.biojava.bio.seq.Sequence; import org.biojava.bio.symbol.Location; import org.biojava.bio.symbol.RangeLocation; import org.biojava.bio.symbol.Symbol; import org.biojava.utils.ChangeVetoException; /** * 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 * @author Mark Schreiber (refactoring, some documentation) */ public class Digest { private Protease protease; private Sequence sequence; private int maxMissedCleavages = 0; public static String PEPTIDE_FEATURE_TYPE = "Peptide"; private LinkedList peptideQue; /** Creates a new Digest Bean*/ public Digest() { /*try{ protease = new Protease(); }catch (Exception e){ //Should never happen e.printStackTrace(); }*/ } public void setProtease(Protease protease) { this.protease = protease; } public void setSequence(Sequence sequence) { this.sequence = sequence; } public Sequence getSequence() { return sequence; } /** * Sets the maximum number of partial digest products to be annotated. * @param maxMissedCleavages the max number of partial digest products */ public void setMaxMissedCleavages(int maxMissedCleavages) { this.maxMissedCleavages = maxMissedCleavages; } /** 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. */ public void addDigestFeatures() throws BioException, ChangeVetoException { peptideQue = new LinkedList(); if(protease == null){ throw new BioException("Protease is null, use Digest.setProtease()"); } if(sequence == null){ throw new BioException("Sequence is null, use Digest.setSequence()"); } List cleaveSites = protease.getCleaveageResidues().toList(); boolean endoProtease = protease.isEndoProtease(); List notCleave = protease.getNotCleaveResidues().toList(); //Returns null if the list is empty if(notCleave == null){ notCleave = new LinkedList(); } int nTerm = 1; if(cleaveSites == null || notCleave == null){ throw new BioException("Protease contains null parameter"); } for (int j = 1; j <= sequence.length(); j++) { Symbol aa = sequence.symbolAt(j); if(cleaveSites.contains(aa)){ if (endoProtease) { boolean cleave = true; if (j < sequence.length()) { Symbol nextAA = sequence.symbolAt(j+1); if(notCleave.contains(nextAA)){ cleave = false; } } if (cleave) { Location loc = new RangeLocation(nTerm, j); peptideQue.add(loc); nTerm = j + 1; } } else { if (j > 1) { Location loc = new RangeLocation(nTerm, j-1); peptideQue.add(loc); //System.out.println(peptideQue); nTerm = j; } } } } if (nTerm <= sequence.length()) { Location loc = new RangeLocation(nTerm, sequence.length()); peptideQue.add(loc); } addMissedCleavages(); //Now add the locations as Peptide freatures to the Sequence for(ListIterator li = peptideQue.listIterator(); li.hasNext(); ){ createPeptideFeature((Location)li.next()); } } private void addMissedCleavages() throws BioException { LinkedList missedList = new LinkedList(); if(maxMissedCleavages>0){ for(ListIterator li = peptideQue.listIterator(); li.hasNext(); ){ Location loc = (Location)li.next(); Location loc2 = null; int min = loc.getMin(); int max = 0; //Get the numMissedCleavages location ahead of the current location int numAdvanced = 0; for(int i=0; i