Updated help

[jalview.git] / help / html / menus / alignmentMenu.html

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index d6b69a3..a514412 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -6,6 +6,11 @@
 <ul>\r
   <li><strong>File</strong> \r
     <ul>\r
+      <li><strong>Fetch Sequence</strong><br>\r
+        <em>Shows a dialog window in which you can select known ids from Uniprot, \r
+        EMBL, EMBLCDS or PDB database using Web Services provided by the European \r
+        Bioinformatics Institute. See <a href="features/seqfetch.html">Sequence \r
+        Fetcher</a></em>.</li>\r
       <li><strong>Save As<br>\r
         </strong><em>Save the alignment to local file. A file selection window \r
         will open, use the &quot;Files of type:&quot; selection box to determine \r
@@ -201,6 +206,11 @@
         <br>\r
         Note: The retrieved information will update the sequence start and end \r
         labels if they are incorrect. </em></li>\r
+      <li><strong>Seqence Settings </strong><br>\r
+        <em>If features have been added to the alignment then the priority of \r
+        rendering the features can be altered so that overlapping features can \r
+        be displayed or hidden. See <a href="features/seqfeatures.html">Sequence \r
+        Features</a>.</em></li>\r
       <li><strong><a href="../features/overview.html">Overview Window</a><br>\r
         </strong><em>A scaled version of the alignment will be displayed in a \r
         small window. A red box will indicate the currently visible area of the \r
@@ -270,7 +280,11 @@
       <li><strong>Principal Component Analysis</strong><br>\r
         <em>Shows a spatial clustering of the sequences based on the BLOSUM62 \r
         scores in the alignment. See <a href="../calculations/pca.html">Principal \r
-        Component Analysis</a>.</em> <br>\r
+        Component Analysis</a>.</em> </li>\r
+      <li><strong>Translate cDNA</strong><br>\r
+        <em>If you are viewing a cDNA alignment a very simple translation service \r
+        is available. The translation ignores all gaps in the cDNA sequences. \r
+        </em> <br>\r
       </li>\r
     </ul>\r
   </li>\r
@@ -294,7 +308,7 @@
             sequences.</em></li>\r
         </ul>\r
       </li>\r
-      <li><strong>Secondary Structure Prediction</strong>\r
+      <li><strong>Secondary Structure Prediction</strong> \r
         <ul>\r
           <li><strong>JPred Secondary Structure Prediction</strong><br>\r
             <em>Secondary structure prediction by network consensus. The behaviour \r