X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=d83d1050ae19f3e079e89395f506108a0de1a6f2;hb=ee1b736c169686999ac41f09911a08a9eb517954;hp=66f4284eba7a7584c49e04bb5b8a04e1d27cf224;hpb=f902741a45fba3856958b893e37c74344d397a60;p=jalview.git

diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 66f4284..d83d105 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -6,65 +6,76 @@
 <ul>
   <li><strong>View</strong></li>
 </ul>
-<blockquote>
+<blockquote> 
   <ul>
     <li><strong>Font<br>
-      </strong><em>Change the font of the display from the
-      &quot;Choose Font&quot; dialog box, which is shown when this
-      item is selected. <br>
+      </strong><em>Change the font of the display from the &quot;Choose Font&quot; 
+      dialog box, which is shown when this item is selected. Select a &quot;Monospaced&quot; 
+      font for fast rendering of your alignment. The checkbox labelled &quot;Monospaced&quot; 
+      indicates whether the chosen font uses characters all of the same width.<br>
+      </em></li>
+    <li><strong>Smooth Fonts</strong><em><br>
+      If selected, the alignment will be drawn with anti-aliasing on which looks 
+      better, but performace is reduced.<br>
       </em></li>
     <li><strong>Wrap<br>
-      </strong><em>When ticked, the alignment display is
-      &quot;<a href="../features/wrap.html">wrapped</a>&quot; to the
-      width of the alignment window. This is useful if your alignment
-      has only a few sequences to view its full width at once.<br>
-      Options are available to show the residue numbering at the start and/or
-      end of an alignment as well as showing the alignment position above each
+      </strong><em>When ticked, the alignment display is &quot;<a href="../features/wrap.html">wrapped</a>&quot; 
+      to the width of the alignment window. This is useful if your alignment has 
+      only a few sequences to view its full width at once.<br>
+      Options are available to show the residue numbering at the start and/or 
+      end of an alignment as well as showing the alignment position above each 
       sequence row. <br>
-      <strong>NOTE</strong>: When in wrapped alignment view, the
-      alignment cannot be edited or have regions selected on it. <br>
+      <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot 
+      be edited or have regions selected on it. <br>
       </em><strong> </strong></li>
     <li><strong>Show Full Sequence ID<br>
-      </strong><em>If this box is selected the sequence name will have the start
+      </strong><em>If this box is selected the sequence name will have the start 
       and end position of the sequence appended to the name, in the format NAME/START-END<br>
       </em></li>
     <li><strong>Boxes</strong><em><br>
-      If this is selected the background of a residue will be coloured using the
-      selected background colour. Useful if used in conjunction with &quot;Colour
+      If this is selected the background of a residue will be coloured using the 
+      selected background colour. Useful if used in conjunction with &quot;Colour 
       Text.&quot; <br>
       </em></li>
     <li><strong>Text<br>
-      </strong><em>If this is selected the residues will be displayed using the
+      </strong><em>If this is selected the residues will be displayed using the 
       standard 1 character amino acid alphabet.<br>
       </em></li>
     <li><strong>Colour Text<br>
-      </strong><em>If this is selected the residues will be coloured according
-      to the background colour associated with that residue. The colour is slightly
+      </strong><em>If this is selected the residues will be coloured according 
+      to the background colour associated with that residue. The colour is slightly 
       darker than background so the amino acid symbol remains visible. <br>
       </em></li>
     <li><strong>Show Gaps<br>
-      </strong><em>When this is selected, gap characters will be displayed as &quot;.&quot;
-      or &quot;-&quot;. If unselected, then gap characters will appear as blank spaces.
-      <br>
+      </strong><em>When this is selected, gap characters will be displayed as 
+      &quot;.&quot; or &quot;-&quot;. If unselected, then gap characters will 
+      appear as blank spaces. <br>
       You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>
       </em></li>
     <li><strong>Show Annotations<br>
-      </strong><em>If this is selected the &quot;Annotation Panel&quot; will be
-      displayed below the alignment. The default setting is to display the conservation
+      </strong><em>If this is selected the &quot;Annotation Panel&quot; will be 
+      displayed below the alignment. The default setting is to display the conservation 
       calculation, quality calculation and consensus values as bar charts. </em><br>
     </li>
-    <li><strong>Sequence Features<br>
-      </strong><em>If the sequence names are Swissprot entries Jalview will use
-      the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> from the EBI. Features which are
-      1 residue in length are coloured red, sequences longer than 1 residue are
-      coloured blue. Move the mouse over a coloured feature to display the details
-      of the feature. <br>
-      Note: The retrieved information will update the sequence start and end labels
-      if they are incorrect. <br>
+    <li><strong>Fetch Sequence Features<br>
+      </strong><em>If the sequence names are Swissprot entries Jalview will use 
+      the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> 
+      from the EBI. Features which are 1 residue in length are coloured red, sequences 
+      longer than 1 residue are coloured blue. Move the mouse over a coloured 
+      feature to display the details of the feature. <br>
+      Note: The retrieved information will update the sequence start and end labels 
+      if they are incorrect. </em><br>
+    </li>
+    <li><strong>Show Sequence Features</strong><br><em>Show or
+        hide sequence features on this alignment.</em></li>
+    <li><strong>Seqence Feature Settings...</strong><em><br>
+      <em>Control the colour and display of sequence features on the
+      alignment. See <a
+      href="../features/featuresettings.html">Sequence Feature Settings</a>.</em><br>
       </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 alignment.
+      </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 alignment. 
       Move the visible region using the mouse. </em><strong> </strong></li>
   </ul>
 </blockquote>