X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=3a1b44a6ef095fba286bf110f71a41acc3f4b0dd;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=d945ec6e338b95a79ae2d28480d6ecadb83bb24f;hpb=398c4b5cdf953a9a3f62fa74fbc94d935bce94d7;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d945ec6..3a1b44a 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -458,11 +458,9 @@ public class Alignment implements AlignmentI
 
         while (i < sequences.size())
         {
-            SequenceI s = getSequenceAt(i);
-
-            if (s.getName().equals(name))
+            if (getSequenceAt(i).getName().equals(name))
             {
-                return s;
+                return getSequenceAt(i);
             }
 
             i++;
@@ -705,7 +703,7 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < getHeight(); i++)
         {
 
-          seqs[i] = new Sequence(getSequenceAt(i).getName(),
+          seqs[i] = new Sequence(getSequenceAt(i).getDisplayId(true),
                                  AlignSeq.extractGaps(
                                      jalview.util.Comparison.GapChars,
                                      getSequenceAt(i).getSequence()