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Works on strings, not seqs
[jalview.git] / src / jalview / analysis / AlignmentSorter.java
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index c2814b8..27d1e7b 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -52,7 +52,8 @@ public class AlignmentSorter
 \r
         for (int i = 0; i < nSeq; i++)\r
         {\r
-            scores[i] = Comparison.PID(align.getSequenceAt(i), s);\r
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),\r
+                                       s.getSequence());\r
             seqs[i] = align.getSequenceAt(i);\r
         }\r
 \r