From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 6 Jun 2016 11:55:58 +0000 (+0100)
Subject: JAL-1944 bugfix for wrong alignment numbering when exporting an alignment and export... 
X-Git-Tag: Release_2_10_0~187
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ff3943fa5e1978e90b901a181916dbf790c93cb9;p=jalview.git

JAL-1944 bugfix for wrong alignment numbering when exporting an alignment and export hidden sequences is enabled
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index aa07a93..7ab8311 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1325,10 +1325,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       alignmentToExport = viewport.getAlignment();
-      alignmentStartEnd = viewport.getAlignment()
-              .getVisibleStartAndEndIndex(
-                      viewport.getColumnSelection().getHiddenColumns());
     }
+    alignmentStartEnd = alignmentToExport
+            .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+                    .getHiddenColumns());
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
             omitHidden, alignmentStartEnd, settings);
     return ed;