-
- /*
- if (newFrame)
- {
- FileLoader loader = new FileLoader();
- AlignFrame aFrame = new AlignFrame(new Alignment(new SequenceI[1]),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- Desktop.addInternalFrame(aFrame, aFrame.getTitle(),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- aFrame.setTitle(
- af.getName() + "Aligned to " + hmm.getName() + "'s HMM");
- af.getViewport().setAlignment(null);
-
- aFrame.loadJalviewDataFile(inputTemp.getAbsolutePath(),
- DataSourceType.FILE, FileFormat.Stockholm, null);
-
-
-
- Map<Integer, SequenceI> copy = new HashMap<>(
- hmmSeqs);
- addSeqs(aFrame, copy);
- SequenceI seq = aFrame.getViewport().getAlignment()
- .getSequenceAt(0);
- seq.getHMM().mapToReferenceAnnotation(aFrame, seq);
- addSeqs(af, hmmSeqs);
- }
- else
- {
- af.getViewport().getAlignment().getSequences().clear();
- af.setIsRecurring(true);
- af.loadJalviewDataFile(inputTemp.getAbsolutePath(),
- DataSourceType.FILE, FileFormat.Stockholm, null);
- af.setIsRecurring(false);
- addSeqs(af, hmmSeqs);
- }
- */