X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=427ab2d592a782f6e34c11f9ad1ec7b32b14fc9c;hb=16019224bf7ab31b3b19e6e27aa55b4d75de6f8b;hp=a5144125e5eafb5df51a07d7dc5ce5cb9beb161f;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index a514412..427ab2d 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -6,10 +6,13 @@
 <ul>
   <li><strong>File</strong> 
     <ul>
+      <li><strong>Add Sequences</strong><em><br>
+        Add sequences to the visible alignment from file, URL, or cut &amp; paste 
+        window </em></li>
       <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 
+        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 
@@ -22,13 +25,13 @@
         and will have the same visible residue width as the open alignment. </em> 
         <ul>
           <li><strong>HTML<br>
-            </strong><em>Create a <a href="../io/index.html#export">web page</a> 
-            from your alignment.</em></li>
+            </strong><em>Create a <a href="../io/export.html">web page</a> from 
+            your alignment.</em></li>
           <li><strong>EPS<br>
-            </strong><em>Create an <a href="../io/index.html#export">Encapsulated 
-            Postscript</a> file from your alignment.</em></li>
+            </strong><em>Create an <a href="../io/export.html">Encapsulated Postscript</a> 
+            file from your alignment.</em></li>
           <li><strong>PNG<br>
-            </strong><em>Create a <a href="../io/index.html#export">Portable Network 
+            </strong><em>Create a <a href="../io/export.html">Portable Network 
             Graphics</a> file from your alignment.</em></li>
         </ul>
       </li>
@@ -52,15 +55,25 @@
         these will be printed below the alignment. If the alignment is wrapped 
         the number of residues per line of your alignment will depend on the paper 
         width or your alignment window width, whichever is the smaller. </em></li>
+      <li><strong>Export Features</strong><em><br>
+        All features visible on the alignment can be saved to file or displayed 
+        in a textbox in either Jalview or GFF format</em></li>
+      <li><strong>Export Annotations</strong><em><br>
+        All annotations visible on the alignment can be saved to file or displayed 
+        in a textbox in Jalview annotations format. </em></li>
       <li><strong>Load Associated Tree<br>
         </strong><em>Jalview can <a
       href="../calculations/treeviewer.html">view trees</a> stored in the Newick 
         file format, and associate them with the alignment. Note: the ids of the 
         tree file and your alignment MUST be the same.</em></li>
-      <li><strong>Close<br>
-        </strong><em>Close the alignment window. Make sure you have saved your 
-        alignment before you close - either as a Jalview project or by using the 
-        <strong>Save As</strong> menu.<br>
+      <li><strong>Load Features / Annotations<br>
+        </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence 
+        features</a> or <a href="../features/annotationsFormat.html">alignment 
+        annotations</a>.</em></li>
+      <li><strong>Close</strong><br>
+        <em>Close the alignment window. Make sure you have saved your alignment 
+        before you close - either as a Jalview project or by using the <strong>Save 
+        As</strong> menu.<br>
         </em></li>
     </ul>
   </li>
@@ -109,9 +122,12 @@
         alignment 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>
@@ -143,9 +159,14 @@
         shorter) 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>Adds gaps to the end of all the sequences so they are all 
-        the same length. This is useful for making a tree using unaligned sequences.<br>
-        You may set the default gap character in <a href="../features/preferences.html">preferences</a>. 
+        </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><br>
       </li>
     </ul>
@@ -154,8 +175,8 @@
     <ul>
       <li><strong>Find<br>
         </strong><em>Select this to <a href="../features/search.html">search</a> 
-        for residues, sequence name or residue position within the alignment. 
-        <br>
+        for residues, sequence name or residue position within the alignment and 
+        create new sequence features from the queries. <br>
         </em></li>
     </ul>
   </li>
@@ -164,6 +185,13 @@
       <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. </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. </em></li>
+      <li><strong>Show (all Columns / Sequences)</strong><em><br>
+        All hidden Columns / Sequences will be revealed. </em></li>
+      <li><strong>Hide (all Columns / Sequences)</strong><em><br>
+        Hides the all the currently selected Columns / Sequences</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 
@@ -197,7 +225,7 @@
         be displayed below the alignment. The default setting is to display the 
         conservation calculation, quality calculation and consensus values as 
         bar charts. </em></li>
-      <li><strong>Sequence Features<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 
@@ -206,11 +234,12 @@
         <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>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></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 
@@ -239,8 +268,11 @@
         Identity</a></em><strong>.</strong></li>
       <li><strong>Modify Identity Threshold<br>
         </strong><em>Use this to set the threshold value for colouring above Identity. 
-        Useful if the window has been closed. <br>
-        </em></li>
+        Useful if the window has been closed. </em></li>
+      <li><strong>By Annotation</strong><br>
+        <em>Colours the alignment on a per-column value from a specified annotation. 
+        See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
+      </li>
     </ul>
   </li>
   <li><strong>Calculate</strong>