public void endSubHit() {
   try {
     subHits.add(makeSubHit());
   } catch (BioException be) {
     be.printStackTrace();
   }
 }
 public void endSearch() {
   try {
     resultAnnotation = AnnotationFactory.makeAnnotation(resultPreAnnotation);
     target.add(makeSearchResult());
   } catch (BioException be) {
     System.err.println("Failed to build SeqSimilaritySearchResult:");
     be.printStackTrace();
   }
 }
Beispiel #3
0
  public void parseInputFile(File inputFile) throws IOException {
    geneFeatures.clear();
    otherRecords.clear();

    try {
      GFFEntrySet gffEntries = GFFTools.readGFF(inputFile);

      Iterator itr = gffEntries.lineIterator();
      int count = 0;
      int intronFeatures = 0;
      LinkedList<GFFRecord> cdsRecs = new LinkedList<GFFRecord>();

      while (itr.hasNext()) {
        Object val = itr.next();
        if (val instanceof GFFRecord) {
          GFFRecord rec = (GFFRecord) val;
          count += 1;

          if (rec.getFeature().endsWith("gene")) {
            GeneFeatures gf = new GeneFeatures(rec);
            geneFeatures.put(gf.id, gf);
          } else if (rec.getFeature().equals("CDS")) {
            cdsRecs.addLast(rec);
          } else {
            otherRecords.add(rec);
          }
        }
      }

      for (GFFRecord rec : cdsRecs) {
        Map<String, List<String>> attrs = decodeAttrMap(rec);
        if (geneFeatures.containsKey(attrs.get("Parent").get(0))) {
          geneFeatures.get(attrs.get("Parent").get(0)).addCDS(rec, attrs);
        } else {
          System.err.println("Unknown CDS Parent: " + attrs.get("Parent").get(0));
        }
      }

      for (String k : geneFeatures.keySet()) {
        GeneFeatures gf = geneFeatures.get(k);
        if (gf.cds != null && gf.cds.size() > 1) {
          intronFeatures++;
        }
      }

      System.err.println("# GFF Records: " + count);
      System.err.println("# Gene Feature Sets: " + geneFeatures.size());
      System.err.println("\t# Intron-Features: " + intronFeatures);

    } catch (ParserException e) {
      e.printStackTrace();
    } catch (BioException e) {
      e.printStackTrace();
    }
  }