+ if (source instanceof HMMFile)
+ {
+ AlignmentI alignment = viewport.getAlignment();
+ SequenceI seq = alignment
+ .getSequenceAt(alignment.getAbsoluteHeight() - 1);
+ seq.setIsHMMConsensusSequence(true);
+ AlignmentAnnotation[] annots = viewport.getAlignment()
+ .getAlignmentAnnotation();
+ for (AlignmentAnnotation annot : annots)
+ {
+ if ("RF".equals(annot.label)
+ || annot.label.contains("Reference"))
+ {
+ seq.mapToReference(annot);
+ break;
+ }
+ }
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ alignment.insertSequenceAt(0, seq);
+ viewport.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+
+ }