From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 11 Aug 2006 14:20:24 +0000 (+0000)
Subject: 2.1 updates
X-Git-Tag: Release_2_1~100
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cd17a7112faa46e4e9fbfbcfc785a549f3baa107;p=jalview.git

2.1 updates
---

diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html
index 8e28a33..432cfcb 100755
--- a/help/html/menus/alwedit.html
+++ b/help/html/menus/alwedit.html
@@ -23,8 +23,7 @@
     also do this by pressing &lt;CTRL&gt; and C (&lt;APPLE&gt; and C on MacOSX). 
     <br>
     If you try to paste the clipboard contents to a text editor, you will see 
-    the format of the copied residues is a tab separated list</em><br>
-    NAME START_RES END_RES SEQUENCE </li>
+    the format of the copied residues FASTA.</em></li>
   <li><strong>Paste </strong> 
     <ul>
       <li><strong>To New Alignment<br>
@@ -48,9 +47,12 @@
     window. All selected sequences, residues and marked columns will be deselected. 
     </em><em> <br>
     Use &lt;ESCAPE&gt; to deselect all.</em></li>
-  <li><strong>Invert Selection<br>
+  <li><strong>Invert Sequence Selection<br>
     </strong><em>Any sequence ids currently not selected will replace the current 
     selection. </em></li>
+  <li><strong>Invert Column Selection<br>
+    </strong><em>Any columns currently not selected will replace the current column 
+    selection. </em></li>
   <li><strong>Undefine Groups<br>
     </strong><em>The alignment will be reset with no defined groups.<br>
     <strong>WARNING</strong>: This cannot be undone.</em></li>
@@ -82,16 +84,15 @@
     is discarded. Press the &quot;Apply&quot; button to remove redundant 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 (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>
+    </strong><em>When selected, the alignment will be kept at minimal 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 for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>. 
     </em></li>
 </ul>
-  <blockquote>&nbsp;</blockquote>
-</body>
+  </body>
 </html>