void printSimilarityMatrix(boolean selview=false, boolean includeids=true, SimilarityParams pidMethod) {
- def currentAlignFrame = jalview.bin.Jalview.getCurrentAlignFrame()
+ def currentAlignFrame = Jalview.getCurrentAlignFrame()
jalview.gui.AlignViewport av = currentAlignFrame.getCurrentView()
jalview.datamodel.AlignmentView seqStrings = av.getAlignmentView(selview)
- if (!selview) {
+ if (!selview || av.getSelectionGroup()==null) {
start = 0
end = av.getAlignment().getWidth()
seqs = av.getAlignment().getSequencesArray()