fixed use of PID rather than 'Comparison' Alignment percentage id

calculation.

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d953598..9deb7e2 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -223,8 +223,8 @@ public class Alignment implements AlignmentI
         if (!del.contains( (SequenceI) sel.elementAt(i)) ||\r
             !del.contains( (SequenceI) sel.elementAt(j)))\r
         {\r
-\r
-          float pid = Comparison.compare( (SequenceI) sel.elementAt(j),\r
+          // use PID instead of Comparison (which is really not pleasant)\r
+          float pid = Comparison.PID( (SequenceI) sel.elementAt(j),\r
                                          (SequenceI) sel.elementAt(i));\r
 \r
           if (pid >= threshold)\r