- String o_seq;
- Sequence s = new Sequence("MySeq",
- o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
- String orig_gapped;
- Sequence s_gapped = new Sequence(
- "MySeq",
- orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
- 39, 80);
- String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
- s_gapped.setDatasetSequence(s);
- String sub_gapped_s;
- Sequence s_subsequence_gapped = new Sequence(
- "MySeq",
- sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
- 43, 77);
-
- s_subsequence_gapped.setDatasetSequence(s);
- SeqCigar c_null = new SeqCigar(s);
- String cs_null = c_null.getCigarstring();
- if (!cs_null.equals("42M"))
- {
- System.err
- .println("Failed to recover ungapped sequence cigar operations:"
- + ((cs_null == "") ? "empty string" : cs_null));
- }
- testCigar_string(s_gapped, ex_cs_gapped);
- SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
- if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
- {
- System.err.println("Failed parseCigar(" + ex_cs_gapped
- + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
- + "'");
- }
- testSeqRecovery(gen_sgapped, s_gapped);
- // Test dataset resolution
- SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
- if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
- {
- System.err
- .println("Failed recovery for subsequence of dataset sequence");
- }
- // width functions
- if (sub_gapped.getWidth() != sub_gapped_s.length())