- AlignmentI alignment = new Alignment(hmmAndSeqs);
- AlignFrame frame = new AlignFrame(alignment, 1, 1);
- frame.setSelectedHMMSequence(hmmSeq);
- frame.getViewport().initInformation();
- List<ArgumentI> alignArgs = new ArrayList<>();
- if (trim)
+ AlignmentI alignment = new Alignment(hmmAndSeqs);
+ AlignFrame frame = new AlignFrame(alignment, 1, 1);
+ frame.setSelectedHMMSequence(hmmSeq);
+ List<ArgumentI> alignArgs = new ArrayList<>();
+ if (trim)
+ {
+ alignArgs.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"), true,
+ true, true, null));
+ }
+ HMMAlignThread hmmalign = new HMMAlignThread(frame, true, alignArgs);
+ hmmalign.hmmalignWaitTillComplete();
+ frame = null;
+ hmmTemp.delete();
+ inputAlignmentTemp.delete();
+ inputTableTemp.delete();
+ } finally