From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 1 Sep 2015 16:15:21 +0000 (+0100)
Subject: patch for JAL-1853 - use given gap character to reconstruct alignment
X-Git-Tag: Release_2_10_0~514^2~3^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7173f016824ca1dfa0ad0c9ee0e5b2cb46143d2f;p=jalview.git

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
--- 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]);