X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fgroovy%2FPIDmatrix.groovy;fp=examples%2Fgroovy%2FPIDmatrix.groovy;h=3ff4b3928d8555d36a143bc8cec327a9805eae25;hb=1bb5184297b3c8ed376845412511c7c8d7ebe1d7;hp=4e2ad8db1f56e8c21dd74b3fdd19ea99b6cf6c86;hpb=7a968a25437adc55c83ef3beba16684a8af90cc4;p=jalview.git

diff --git a/examples/groovy/PIDmatrix.groovy b/examples/groovy/PIDmatrix.groovy
index 4e2ad8d..3ff4b39 100644
--- 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: