import jalview.api.FeaturesSourceI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
AlignmentI alignment = viewport.getAlignment();
SequenceI seq = alignment
.getSequenceAt(alignment.getAbsoluteHeight() - 1);
- seq.setIsHMMConsensusSequence(true);
- AlignmentAnnotation[] annots = viewport.getAlignment()
- .getAlignmentAnnotation();
- for (AlignmentAnnotation annot : annots)
+ if (seq.isHMMConsensusSequence())
{
- if ("RF".equals(annot.label)
- || annot.label.contains("Reference"))
- {
- seq.mapToReference(annot);
- break;
- }
+ /*
+ * fudge: move HMM consensus sequence from last to first
+ */
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ alignment.insertSequenceAt(0, seq);
+ alignment.setHmmConsensus(seq);
}
- alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
- alignment.insertSequenceAt(0, seq);
viewport.getAlignPanel().adjustAnnotationHeight();
viewport.updateSequenceIdColours();
-
}
}
else