From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 23 Apr 2014 16:15:04 +0000 (+0100)
Subject: JAL-1486 todo for 2.8.2 release
X-Git-Tag: Jalview_2_9~196^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=57adc61c263418567e382e0969582eb2887841bb;p=jalview.git

JAL-1486 todo for 2.8.2 release
---

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();