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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index b36a0a5..a6f4310 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -465,6 +465,7 @@ public class AlignmentView
    * alignment.
    * 
    * @param c
+   *          gap character to use to recreate the alignment
    * @return
    */
   private SequenceI[] getVisibleSeqs(char c)
@@ -472,10 +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]);