()
| 4772 | } |
| 4773 | |
| 4774 | @Override |
| 4775 | public synchronized String next() throws IOException { |
| 4776 | if (forFaItr != null && forFaItr.hasNext()) { |
| 4777 | ++numReadsParsed; |
| 4778 | ArrayList<String> segments = forFaItr.nextSegments(); |
| 4779 | while (segments != null) { |
| 4780 | if (!segments.isEmpty()) { |
| 4781 | String seq = connect(segments, graph, lookahead); |
| 4782 | if (seq.length() >= k) { |
| 4783 | return seq; |
| 4784 | } |
| 4785 | } |
| 4786 | ++numReadsParsed; |
| 4787 | segments = forFaItr.nextSegments(); |
| 4788 | } |
| 4789 | forFaItr = null; |
| 4790 | } |
| 4791 | |
| 4792 | if (forFqItr != null && forFqItr.hasNext()) { |
| 4793 | ++numReadsParsed; |
| 4794 | ArrayList<String> segments = forFqItr.nextSegments(); |
| 4795 | while (segments != null) { |
| 4796 | if (!segments.isEmpty()) { |
| 4797 | String seq = connect(segments, graph, lookahead); |
| 4798 | if (seq.length() >= k) { |
| 4799 | return seq; |
| 4800 | } |
| 4801 | } |
| 4802 | ++numReadsParsed; |
| 4803 | segments = forFqItr.nextSegments(); |
| 4804 | } |
| 4805 | forFqItr = null; |
| 4806 | } |
| 4807 | |
| 4808 | if (revFaItr != null && revFaItr.hasNext()) { |
| 4809 | ++numReadsParsed; |
| 4810 | ArrayList<String> segments = revFaItr.nextSegments(); |
| 4811 | while (segments != null) { |
| 4812 | if (!segments.isEmpty()) { |
| 4813 | String seq = connect(segments, graph, lookahead); |
| 4814 | if (seq.length() >= k) { |
| 4815 | return seq; |
| 4816 | } |
| 4817 | } |
| 4818 | ++numReadsParsed; |
| 4819 | segments = revFaItr.nextSegments(); |
| 4820 | } |
| 4821 | revFaItr = null; |
| 4822 | } |
| 4823 | |
| 4824 | if (revFqItr != null && revFqItr.hasNext()) { |
| 4825 | ++numReadsParsed; |
| 4826 | ArrayList<String> segments = revFqItr.nextSegments(); |
| 4827 | while (segments != null) { |
| 4828 | if (!segments.isEmpty()) { |
| 4829 | String seq = connect(segments, graph, lookahead); |
| 4830 | if (seq.length() >= k) { |
| 4831 | return seq; |
nothing calls this directly
no test coverage detected