Changed sortByPID to use the gapped PID function.

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 40ad372..8274768 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -57,7 +57,7 @@ public class AlignmentSorter {
     SequenceI seqs[]   = new SequenceI[nSeq];\r
 \r
     for (int i = 0; i < nSeq; i++) {\r
-      scores[i] = Comparison.compare(align.getSequenceAt(i),s);\r
+      scores[i] = Comparison.PID(align.getSequenceAt(i),s);\r
       seqs[i]   = align.getSequenceAt(i);\r
     }\r
 \r