- { name });
- setTitle(fullName);
-
- /*
- * if (!aa.isValidStruc()) { throw new
- * IllegalArgumentException("Invalid RNA structure annotation"); } final
- * String struc = aa.getRNAStruc();
- *
- * String strucseq = seq.getSequenceAsString();
- *
- * String gappedTitle = sname + " (with gaps)"; String rnaTitle =
- * gappedTitle; RNA gapped = new RNA(rnaTitle); try {
- * gapped.setRNA(strucseq, replaceOddGaps(struc)); } catch
- * (ExceptionUnmatchedClosingParentheses e2) { e2.printStackTrace(); } catch
- * (ExceptionFileFormatOrSyntax e3) { e3.printStackTrace(); }
- * models.put(gapped, new RnaModel(rnaTitle, aa, seq, gapped, true, null));
- *
- * String trimmedTitle = "trimmed " + sname; rnaTitle = trimmedTitle; RNA
- * trimmed = trimRNA(gapped, rnaTitle); models.put(trimmed, new
- * RnaModel(rnaTitle, aa, seq, trimmed, false, null));
- */
- // vab = new AppVarnaBinding(Arrays.asList(new RNA[]
- // { trimmed, gapped }));
- // vab = new AppVarnaBinding();
- // // String seqName = seq.getName();
- // // String name = sname + " trimmed to " + seqName;
- // initVarna(name);