From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 20 Oct 2017 14:25:49 +0000 (+0100)
Subject: JAL-547 only generate matrix for current selection if available. better comments.
X-Git-Tag: Release_2_10_3b1~102^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1bb5184297b3c8ed376845412511c7c8d7ebe1d7;p=jalview.git

JAL-547 only generate matrix for current selection if available. better comments.
---

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: