From 7173f016824ca1dfa0ad0c9ee0e5b2cb46143d2f Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 1 Sep 2015 17:15:21 +0100 Subject: [PATCH] patch for JAL-1853 - use given gap character to reconstruct alignment --- src/jalview/datamodel/AlignmentView.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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]); -- 1.7.10.2