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[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 070b927..76d9f72 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -160,7 +160,6 @@ public class Alignment implements AlignmentI
 \r
                 if (current.getLength() > i)\r
                 {\r
-                    /* MC Should move this to a method somewhere */\r
                     if (!jalview.util.Comparison.isGap(current.getCharAt(i)))\r
                     {\r
                         delete = false;\r
@@ -475,9 +474,9 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < sequences.size(); i++)\r
         {\r
             Sequence seq = (Sequence) sequences.elementAt(i);\r
-            seq.sequence = seq.sequence.replace('.', gc);\r
-            seq.sequence = seq.sequence.replace('-', gc);\r
-            seq.sequence = seq.sequence.replace(' ', gc);\r
+            seq.setSequence( seq.getSequence().replace('.', gc) );\r
+            seq.setSequence( seq.getSequence().replace('-', gc) );\r
+            seq.setSequence( seq.getSequence().replace(' ', gc) );\r
         }\r
     }\r
 \r