X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=9a2db89dd5d1258a769afd7917c6c6b452644107;hb=55c2e38285277f647543cc936f2fc80a9c4d0359;hp=6051aa6a1ec5a595ec6f3cd0e0f5c8c75ad2a6b8;hpb=6d58edc047af16d3d632842be665ff990de74607;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 6051aa6..9a2db89 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,8 +20,6 @@ package jalview.datamodel;
 
 import jalview.analysis.*;
 
-import jalview.util.*;
-
 import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
@@ -137,7 +135,7 @@ public class Alignment implements AlignmentI
         {
           Sequence ds = new Sequence(snew.getName(),
                                      AlignSeq.extractGaps("-. ",
-              snew.getSequence()),
+              snew.getSequenceAsString()),
                                      snew.getStart(),
                                      snew.getEnd());
 
@@ -401,9 +399,9 @@ 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 +587,7 @@ 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());