X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=a5144125e5eafb5df51a07d7dc5ce5cb9beb161f;hb=713db61b4724485414159cfc145f9ffa4a24bb6d;hp=44ba59a3fdb1bdd53b17d51a600dd62ae1272baa;hpb=ac5cc638b08386985f91503c81b27263230046e3;p=jalview.git

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 44ba59a3..a514412 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -6,6 +6,11 @@
 <ul>
   <li><strong>File</strong> 
     <ul>
+      <li><strong>Fetch Sequence</strong><br>
+        <em>Shows a dialog window in which you can select known ids from Uniprot, 
+        EMBL, EMBLCDS or PDB database using Web Services provided by the European 
+        Bioinformatics Institute. See <a href="features/seqfetch.html">Sequence 
+        Fetcher</a></em>.</li>
       <li><strong>Save As<br>
         </strong><em>Save the alignment to local file. A file selection window 
         will open, use the &quot;Files of type:&quot; selection box to determine 
@@ -79,8 +84,7 @@
         can 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>
+        see the format of the copied residues FASTA.</em></li>
       <li><strong>Paste </strong> 
         <ul>
           <li><strong>To New Alignment<br>
@@ -202,6 +206,11 @@
         <br>
         Note: The retrieved information will update the sequence start and end 
         labels if they are incorrect. </em></li>
+      <li><strong>Seqence Settings </strong><br>
+        <em>If features have been added to the alignment then the priority of 
+        rendering the features can be altered so that overlapping features can 
+        be displayed or hidden. See <a href="features/seqfeatures.html">Sequence 
+        Features</a>.</em></li>
       <li><strong><a href="../features/overview.html">Overview Window</a><br>
         </strong><em>A scaled version of the alignment will be displayed in a 
         small window. A red box will indicate the currently visible area of the 
@@ -271,7 +280,11 @@
       <li><strong>Principal Component Analysis</strong><br>
         <em>Shows a spatial clustering of the sequences based on the BLOSUM62 
         scores in the alignment. See <a href="../calculations/pca.html">Principal 
-        Component Analysis</a>.</em> <br>
+        Component Analysis</a>.</em> </li>
+      <li><strong>Translate cDNA</strong><br>
+        <em>If you are viewing a cDNA alignment a very simple translation service 
+        is available. The translation ignores all gaps in the cDNA sequences. 
+        </em> <br>
       </li>
     </ul>
   </li>
@@ -295,7 +308,7 @@
             sequences.</em></li>
         </ul>
       </li>
-      <li><strong>Secondary Structure Prediction</strong>
+      <li><strong>Secondary Structure Prediction</strong> 
         <ul>
           <li><strong>JPred Secondary Structure Prediction</strong><br>
             <em>Secondary structure prediction by network consensus. The behaviour