X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=b5f31bccc0ee0e5d3904f568d8b75c986d4eef47;hb=4d2e0d36506302cc00677527725bcccbdf27d766;hp=6051aa6a1ec5a595ec6f3cd0e0f5c8c75ad2a6b8;hpb=dc5507ccf4bf0c8b20f86aee7175c16b68ef52ea;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 6051aa6..b5f31bc 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -137,7 +137,7 @@ public class Alignment implements AlignmentI
         {
           Sequence ds = new Sequence(snew.getName(),
                                      AlignSeq.extractGaps("-. ",
-              snew.getSequence()),
+              snew.getSequenceAsString()),
                                      snew.getStart(),
                                      snew.getEnd());
 
@@ -401,9 +401,9 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < sequences.size(); i++)
         {
             Sequence seq = (Sequence) sequences.elementAt(i);
-            seq.setSequence( seq.getSequence().replace('.', gc) );
-            seq.setSequence( seq.getSequence().replace('-', gc) );
-            seq.setSequence( seq.getSequence().replace(' ', gc) );
+            seq.setSequence( seq.getSequenceAsString().replace('.', gc) );
+            seq.setSequence( seq.getSequenceAsString().replace('-', gc) );
+            seq.setSequence( seq.getSequenceAsString().replace(' ', gc) );
         }
     }
 
@@ -589,7 +589,7 @@ public class Alignment implements AlignmentI
             seqs[i] = new Sequence(currentSeq.getName(),
                                    AlignSeq.extractGaps(
                                        jalview.util.Comparison.GapChars,
-                                       currentSeq.getSequence()
+                                       currentSeq.getSequenceAsString()
                                    ),
                                    currentSeq.getStart(),
                                    currentSeq.getEnd());