- int phase = 0;
- try {
- phase = Integer.parseInt(sf.getPhase());
- } catch (NumberFormatException e)
- {
- // ignore
- }
- /*
- * phase > 0 on first codon means 5' incomplete - skip to the start
- * of the next codon; example ENST00000496384
- */
- int begin = sf.getBegin();
- int end = sf.getEnd();
- if (ranges.isEmpty() && phase > 0)
- {
- fivePrimeIncomplete = true;
- begin += phase;
- if (begin > end)
- {
- continue; // shouldn't happen?
- }
- }
- ranges.add(new int[] { begin, end });
- mappedDnaLength += Math.abs(end - begin) + 1;