- sub_gapped.getFullWidth();
- if (sub_gapped.hasDeletedRegions())
- {
- System.err.println("hasDeletedRegions is incorrect.");
- }
- // Test start-end region SeqCigar
- SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
- if (sub_se_gp.getWidth() != 41)
- {
- System.err.println(
- "SeqCigar(seq, start, end) not properly clipped alignsequence.");
- }
- System.out.println("Original sequence align:\n" + sub_gapped_s +
- "\nReconstructed window from 8 to 48\n"
- + "XXXXXXXX" + sub_se_gp.getSequenceString('-') + "..."
- + "\nCigar String:" + sub_se_gp.getCigarstring() + "\n"
- );
- SequenceI ssgp = sub_se_gp.getSeq('-');
- System.out.println("\t " + ssgp.getSequence());
- for (int r = 0; r < 10; r++)
- {
- sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
- int sl = sub_se_gp.getWidth();
- int st = sl - 1 - r;
- for (int rs = 0; rs < 10; rs++)
- {
- int e = st + rs;
- sub_se_gp.deleteRange(st, e);
- String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
- System.out.println(st + "," + e + "\t:" + ssgapedseq);
- st -=3;
- }
- }