+ if (source instanceof HMMFile)
+ {
+ // TODO: absorb into viewport.addAlignment above ?
+ AlignmentI alignment = viewport.getAlignment();
+ SequenceI seq = alignment
+ .getSequenceAt(alignment.getHeight() - 1);
+ if (seq.hasHMMProfile())
+ {
+ /*
+ * fudge: move HMM consensus sequence from last to first
+ */
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ alignment.insertSequenceAt(0, seq);
+ }
+ viewport.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ // update HMM colour optionsĀ
+ if (alignFrame != null)
+ {
+ alignFrame.buildColourMenu();
+ }
+ }