patch for JAL-1853 - use given gap character to reconstruct alignment

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index f73fb74..a6f4310 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -179,7 +179,9 @@ public class AlignmentView
         sgrps[g] = new ScGroup();
         sgrps[g].sg = new SequenceGroup(sg);
         addedgps[g] = false;
-        seqsets.set(g, sg.getSequences(null));
+        // can't set entry 0 in an empty list
+        // seqsets.set(g, sg.getSequences(null));
+        seqsets.add(sg.getSequences());
       }
       // seqsets now contains vectors (should be sets) for each group, so we can
       // track when we've done with the group
@@ -463,6 +465,7 @@ public class AlignmentView
    * alignment.
    * 
    * @param c
+   *          gap character to use to recreate the alignment
    * @return
    */
   private SequenceI[] getVisibleSeqs(char c)
@@ -470,10 +473,10 @@ public class AlignmentView
     SequenceI[] aln = new SequenceI[sequences.length];
     for (int i = 0, j = sequences.length; i < j; i++)
     {
-      aln[i] = sequences[i].getSeq('-');
+      aln[i] = sequences[i].getSeq(c);
     }
     // Remove hidden regions from sequence objects.
-    String seqs[] = getSequenceStrings('-');
+    String seqs[] = getSequenceStrings(c);
     for (int i = 0, j = aln.length; i < j; i++)
     {
       aln[i].setSequence(seqs[i]);