From: jprocter <Jim Procter>
Date: Mon, 10 Apr 2006 14:28:53 +0000 (+0000)
Subject: reworded pad gaps.
X-Git-Tag: Release_2_08~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1b81a47f3b7e3e68256dfc4367ec27adb2302e4c;p=jalview.git

reworded pad gaps.
---

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index ee8661f..9fb408d 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -148,11 +148,13 @@
         sequences. The &quot;Undo&quot; button will undo the last redundancy deletion.</em></li>
   <li><strong>Pad Gaps<br>
     </strong><em>When selected, the alignment will be kept at minimal
-    width (no empty columns before or after the first or last aligned
-    residue). This is useful when making a tree using unaligned
+    width (so there no empty columns before or after the first or last aligned
+    residue) and all sequences will be padded with gap characters to
+    the before and after their terminating residues.<br>
+    This switch is useful when making a tree using unaligned
     sequences and when working with alignment analysis programs which
     require 'properly aligned sequences' to be all the same length.<br>
-    You may set the default gap character in <a href="../features/preferences.html">preferences</a>. 
+    You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>. 
     </em></li>
         </em><br>
       </li>