From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 23 Apr 2014 16:15:57 +0000 (+0100)
Subject: Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch
X-Git-Tag: Release_2_8_1~4^2~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=667a8cca213c8114236d2edbf22dbbcf52784508;hp=8020522c6122821d7ccab2048ef23a471c8f4b95;p=jalview.git

Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch
---

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 0238073..6d77acc 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -197,6 +197,7 @@ public class FormatAdapter extends AppletFormatAdapter
     {
       // TODO consider using AlignmentView to prune to visible region
       // TODO prune sequence annotation and groups to visible region
+      // TODO: JAL-1486 - set start and end for output correctly. basically, AlignmentView.getVisibleContigs does this.
       Alignment alv = new Alignment(replaceStrings(
               alignment.getSequencesArray(), omitHidden));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();