Example #1
0
  @Override
  public NucSeq generateCompositeSequence(
      ArrayList<Part> composition, Object additionalRequirements) {
    StringBuffer sb = new StringBuffer();
    for (Part p : composition) {
      sb.append(p.getSeq().getSeq());
    }
    NucSeq outnuc = new NucSeq(sb.toString());
    outnuc.setTransient();

    int offset = 0;
    for (Part p : composition) {
      String parseq = p.getSeq().getSeq();
      for (Annotation ann : p.getSeq().getAnnotations()) {
        Feature afeature = ann.getFeature();
        String name = ann.getName();
        Color forColor = ann.getForwardColor();
        Color revColor = ann.getReverseColor();
        int Start = offset + ann.getStart();
        int End = offset + ann.getEnd();
        Person user = ann.getAuthor();
        boolean plusstrandtrue = ann.isForwardStrand();
        String symbol = ann.getSymbol();

        Annotation newann;
        if (afeature == null) {
          newann =
              new Annotation(
                  name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
          newann.setTransient();
        } else {
          newann =
              new Annotation(
                  afeature, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
          newann.setTransient();
        }
        System.out.println("Generated annotation: " + newann.getName());
      }
      offset += parseq.length();
    }

    return outnuc;
  }
Example #2
0
  @Override
  public NucSeq generatePlasmidSequence(Plasmid p) {
    String out = "";
    out += p.getPart().getSeq().getSeq();
    out += p.getVector().getSeq().getSeq();
    NucSeq outnuc = new NucSeq(out);
    outnuc.setTransient();

    for (Annotation ann : p.getPart().getSeq().getAnnotations()) {
      Feature afeature = ann.getFeature();
      String name = ann.getName();
      Color forColor = ann.getForwardColor();
      Color revColor = ann.getReverseColor();
      int Start = ann.getStart();
      int End = ann.getEnd();
      Person user = ann.getAuthor();
      boolean plusstrandtrue = ann.isForwardStrand();
      String symbol = ann.getSymbol();

      Annotation newann;
      if (afeature == null) {
        newann =
            new Annotation(
                name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
        newann.setTransient();
      } else {
        newann =
            new Annotation(
                afeature, outnuc, forColor, revColor, Start, End, user, plusstrandtrue, symbol);
        newann.setTransient();
      }
      System.out.println("Generated annotation: " + newann.getName());
    }

    String parseq = p.getPart().getSeq().getSeq();
    int offset = parseq.length();

    for (Annotation ann : p.getVector().getSeq().getAnnotations()) {
      Feature afeature = ann.getFeature();
      String name = ann.getName();
      Color forColor = ann.getForwardColor();
      Color revColor = ann.getReverseColor();
      int Start = offset + ann.getStart();
      int End = offset + ann.getEnd();
      Person user = ann.getAuthor();
      boolean plusstrandtrue = ann.isForwardStrand();
      String symbol = ann.getSymbol();

      Annotation newann;
      if (afeature == null) {
        newann =
            new Annotation(
                name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
        newann.setTransient();
      } else {
        newann =
            new Annotation(
                afeature, outnuc, forColor, revColor, Start, End, user, plusstrandtrue, symbol);
        newann.setTransient();
      }
      System.out.println("Generated annotation: " + newann.getName());
    }
    return outnuc;
  }