Package org.moltools.design.data

Examples of org.moltools.design.data.SequenceElementContainer.addToEnd()

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            nucs[i] = SNPNucleotides.pop();
          }
          SNP snp = new SNP(nucs, "SNP " + (++SNPno)); //$NON-NLS-1$
          //and add it to the element on the stack
          SequenceElementContainer e = (SequenceElementContainer) elementStack.peek();
          e.addToEnd(snp);
          inSNP = false;
        }
      }
      else if (current == inDelBeginSymbol) {
        elementStack.push(new InDel("InDel " + (++InDelno), "", "InDel " + (++InDelno), acidType)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
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          throw new SequenceFormatException("Too many InDel end symbols"); //$NON-NLS-1$
        }
        InDel indel = (InDel) elementStack.pop();
        SequenceElementContainer e = (SequenceElementContainer) elementStack.peek();

        e.addToEnd(indel);
      }
      else {
        //No special symbol, so is either nucleotide, degenerate nucleotide or invalid symbol
        Nucleotide n = NucleotideSequenceHandler.getNucleotide(current, acidType);
        if (n == null) { //invalid
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        }
        if (NucleotideSequenceHandler.isPoly(n)) { //degenerate nucleotide (SNP)
          SNP snp = new SNP( ( (DegenerateNucleotide) n).getPossible(),
                            "SNP" + (++SNPno)); //$NON-NLS-1$
          SequenceElementContainer e = (SequenceElementContainer) elementStack.peek();
          e.addToEnd(snp);
        }
        else { //normal nucleotide
          SequenceElementContainer e = (SequenceElementContainer) elementStack.peek();
          e.addToEnd(n);
        }
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          SequenceElementContainer e = (SequenceElementContainer) elementStack.peek();
          e.addToEnd(snp);
        }
        else { //normal nucleotide
          SequenceElementContainer e = (SequenceElementContainer) elementStack.peek();
          e.addToEnd(n);
        }
      }
    }
    elements.addAll(root.getElements());
    String seqString = sequenceOf(elements);
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            nucs[i] = SNPNucleotides.pop();
          }
          SNP snp = new SNP(nucs, "SNP " + (++SNPno)); //$NON-NLS-1$
          //and add it to the element on the stack
          SequenceElementContainer e = elementStack.peek();
          e.addToEnd(snp);
          inSNP = false;
        }
      }
      else if (current == inDelBeginSymbol) {
        elementStack.push(new InDel("InDel " + (++InDelno),"", "InDel " + (++InDelno), acidType)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
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          throw new IllegalArgumentException("Too many InDel end symbols"); //$NON-NLS-1$
        }
        InDel indel = (InDel) elementStack.pop();
        SequenceElementContainer e = elementStack.peek();

        e.addToEnd(indel);
      }
      else {
        //No special symbol, so is either nucleotide, degenerate nucleotide or invalid symbol
        Nucleotide n = NucleotideSequenceHandler.getNucleotide(current, acidType);
        if (n == null) { //invalid
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        }
        if (NucleotideSequenceHandler.isPoly(n)) { //degenerate nucleotide (SNP)
          SNP snp = new SNP( ( (DegenerateNucleotide) n).getPossible(),
                            "SNP" + (++SNPno)); //$NON-NLS-1$
          SequenceElementContainer e = elementStack.peek();
          e.addToEnd(snp);
        }
        else { //normal nucleotide
          SequenceElementContainer e = elementStack.peek();
          e.addToEnd(n);
        }
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          SequenceElementContainer e = elementStack.peek();
          e.addToEnd(snp);
        }
        else { //normal nucleotide
          SequenceElementContainer e = elementStack.peek();
          e.addToEnd(n);
        }
      }
    }
    elements.addAll(root.getElements());
    return sequenceOf(elements);
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