X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=8b86a8252cc135b922726e4a9c945c30e8efa6ec;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=58b379b6e362260f6c2f207c20a7a69b840971c7;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 58b379b..8b86a82 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -245,7 +245,7 @@ public class AlignmentView
                 else
                 {
                   alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                           mseq[s].getSequence());
+                                           mseq[s].getSequenceAsString());
                   if (mseq[s].getStart() <= mseq[s].getEnd())
                   {
                     alignment[s].setEnd(mseq[s].getEnd());
@@ -277,7 +277,7 @@ public class AlignmentView
                   else
                   {
                     alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                             oseq.getSequence());
+                                             oseq.getSequenceAsString());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
                       alignment[s].setEnd(oseq.getEnd());
@@ -304,7 +304,7 @@ public class AlignmentView
             else
             {
               alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                       hseq.getSequence());
+                                       hseq.getSequenceAsString());
               if (hseq.getEnd() >= hseq.getStart())
               {
                 alignment[s].setEnd(hseq.getEnd());
@@ -333,7 +333,7 @@ public class AlignmentView
               else
               {
                 alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                         mseq[s].getSequence());
+                                         mseq[s].getSequenceAsString());
                 if (mseq[s].getEnd() >= mseq[s].getStart())
                 {
                   alignment[s].setEnd(mseq[s].getEnd());
@@ -367,7 +367,7 @@ public class AlignmentView
                   else
                   {
                     alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                             oseq.getSequence());
+                                             oseq.getSequenceAsString());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
                       alignment[s].setEnd(oseq.getEnd());