Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / examples / groovy / PIDmatrix.groovy

diff --git a/examples/groovy/PIDmatrix.groovy b/examples/groovy/PIDmatrix.groovy
index 4e2ad8d..76b9de7 100644 (file)
--- a/examples/groovy/PIDmatrix.groovy
+++ b/examples/groovy/PIDmatrix.groovy
@@ -22,11 +22,12 @@
 import jalview.analysis.scoremodels.ScoreModels
 import jalview.analysis.scoremodels.SimilarityParams
 
-// call the method below
-printSimilarityMatrix(false,true,SimilarityParams.Jalview)
+// generate matrix for current selection using standard Jalview PID
+
+printSimilarityMatrix(true,true,SimilarityParams.Jalview)
 
 /** 
- * prints a sequence similarity matrix in PHYLIP format. 
+ * this function prints a sequence similarity matrix in PHYLIP format. 
  * printSimilarityMatrix(selected-only, include-ids, pidMethod)
  * 
  * Allowed values for pidMethod:
@@ -55,13 +56,13 @@ printSimilarityMatrix(false,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()