X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fgroovy%2FPIDmatrix.groovy;h=76b9de72c25c2e1ce6c5e331ad37442f63e37c89;hb=ef7125ccaa49531e0f0930955af7a1710f6c4372;hp=3ff4b3928d8555d36a143bc8cec327a9805eae25;hpb=1bb5184297b3c8ed376845412511c7c8d7ebe1d7;p=jalview.git

diff --git a/examples/groovy/PIDmatrix.groovy b/examples/groovy/PIDmatrix.groovy
index 3ff4b39..76b9de7 100644
--- a/examples/groovy/PIDmatrix.groovy
+++ b/examples/groovy/PIDmatrix.groovy
@@ -56,13 +56,13 @@ printSimilarityMatrix(true,true,SimilarityParams.Jalview)
 
 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()