X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=6bb2e3a8e27c7134b152111ba4ba95a1e5261f07;hb=f27f81a74bbe1be141d23df8aba578515e3179a2;hp=2be60003fd17797e529ba98668f97898768c1d29;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 2be6000..6bb2e3a 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,22 +1,24 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
 <head>
 <title>Popup Menu</title>
 </head>
@@ -29,14 +31,24 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 <ul>
   <li><strong>Selection</strong> 
     <ul>
-      <li><a name="sqreport"><strong>Sequence Details ...<br>
+      <li><a name="sqreport"><strong>Sequence Details...<br>
           </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
-            and database cross references</a> normally shown in the sequence's
+            and database cross references</a>&nbsp;normally shown in the sequence's
             tooltip.</em></li>
+      <li><strong>Show Annotations...<br>
+          </strong><em>Choose to show (unhide) either All or 
+          a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+      <li><strong>Hide Annotations...<br>
+          </strong><em>Choose to hide either All or 
+          a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+      <li><a name="addrefannot"><strong>Add Reference Annotations<br>
+          </strong><em>Add to the alignment window any annotations on the selected sequences
+          which have been read from reference sources or calculated (for example, 
+          secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
       <li><strong>Edit </strong> 
         <ul>
           <li><strong>Copy</strong><br>
-            <em>Copys the selected region. In the applet version, the copied sequences 
+            <em>Copies the selected region. In the applet version, the copied sequences 
             are not available to the system clipboard.</em></li>
           <li><strong>Cut<br>
             </strong><em>Cuts the selected region from the alignment. In the applet 
@@ -122,7 +134,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
         window will be displayed asking for a new sequence name and sequence description 
         to be entered. Press OK to accept your edit. To save sequence descriptions, 
         you must save in Fasta, PIR or Jalview File format.</em></li>
-      <li><em> </em></li>
+      <li><a href="sqaddrefannot"><strong>Add Reference Annotations<br></strong><em>When enabled, copies any available alignment annotation for this sequence to the current view.</em></li>
       <li><strong>Represent Group With (Sequence Id)</strong><br>
         <em>All sequences in the current selection group will be hidden, apart 
         from (Sequence Id). Any edits performed on the visible representative 
@@ -184,9 +196,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
     (The View representative structures option was introduced in
         Jalview 2.8.1)</em></li>
   </ul>
-  <br> <li>
-      
-      </li>
+  <br> 
     </ul>
   </li>
   <li><strong>Hide Sequences</strong><br>
