BioJava:Cookbook:Sequence:ExtractGeneRegions

From BioJava

   public Sequence sequenceJustFeatues(Sequence seq, String featureName)
         throws Exception {
 
      Location loccollection = this.genLocationsOfSequence(seq, featureName);
 
      SymbolList extract = loccollection.symbols(seq);
 
      Sequence seqmodif = DNATools
            .createDNASequence(extract.seqString(), "New Sequence");
      return seqmodif;
   }
 
 
 
 
   public Sequence sequenceWithoutFeature(Sequence seq, String featureName)
         throws Exception {
      // featureName: the name of the feature which describes genes: gene or CDS
 
      Location loccollection = this.genLocationsOfFeature(seq, featureName); // see below
 
      SimpleSymbolList modif = new SimpleSymbolList(seq);
 
      Edit e = null;
 
      for (int i = seq.length(); i > 0; i--){ // this is slow. For a better implementation drop me an email
         if (loccollection.contains(i)) {
            e = new Edit(i, 1, SymbolList.EMPTY_LIST);
            modif.edit(e);
         }
      }
 
      Sequence seqmodif = DNATools.createDNASequence(modif.seqString(), "New Sequence");
      return seqmodif;
   }
 
  public Location genLocationsOfFeature(Sequence seq, String featureName)
         throws Exception {
      Location loccollection = null;
 
      for (Iterator i = seq.features(); i.hasNext();) {
         Feature f = (Feature) i.next();
 
         if (f.getType().equals(featureName)) {
 
            if (loccollection == null) {
               loccollection = f.getLocation();
            } else {
               loccollection = loccollection.union(f.getLocation());
            }
         }
      }
      return loccollection;
   }