X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=6bb2e3a8e27c7134b152111ba4ba95a1e5261f07;hb=f27f81a74bbe1be141d23df8aba578515e3179a2;hp=9cf53587bffe76b81ee79c7468345b43d9197d68;hpb=fd6fc6bbcf3cf91b6f218729cc014997782053b1;p=jalview.git

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 9cf5358..6bb2e3a 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,4 +1,24 @@
 <html>
+<!--
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
 <head>
 <title>Popup Menu</title>
 </head>
@@ -11,10 +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>
+          </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>&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 
@@ -38,18 +72,22 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
       <li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>
         <em>Opens the dialog box for creating sequence features over the currently 
         selected region on each selected sequence.</em></li>
-      <li><strong>Group</strong><br>
-        <em>Group Operations</em> 
-        <ul>
-          <li><strong>Group</strong><em>This is the first entry in the
-	  menu, and will display the currently selected group's
-	  name. Selecting it displays a window allowing the name and
-	  description for this group to be edited. Click OK to set the
-	  new name and decription, and cancel to leave the existing
-	  name and description unchanged.</em></li>
+      <li><strong>Create Group<br>
+            </strong><em>This will define a new group from the current selection.</em><strong> 
+            </strong></li>
           <li><strong>Remove Group<br>
             </strong><em>This will undefine the selected group. </em><strong> 
             </strong></li>
+          <li><strong>Edit (New) Group</strong><br>
+        <em>Group Editing Menu</em> <br />Options in this menu modify
+					the name and display properties of the currently selected group, or
+					a new group defined using the current selection.
+					<ul>
+          <li><strong>Name: &lt;Group&gt;</strong> or <strong>Edit name and description</strong><br><em>The first entry in the
+	  menu displays the name for the currently selected group, if it has one. Selecting this option opens a window allowing the name and
+	  description for this group to be edited. Click OK to set the
+	  new name and decription, and cancel to leave the existing
+	  name and description unchanged.</em></li>
           <li><strong>Group Colour<br>
             </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> 
             of the group.</em><strong> </strong></li>
@@ -66,20 +104,37 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
             </strong><em>Selecting this will display a &quot;Colour Chooser&quot; 
             window. Select a colour than press OK to set the border colour of 
             a group.</em></li>
-        </ul>
+	<li><strong>Show Unconserved<br>
+  	  </strong><em>When this is selected, all symbols in the group matching the consensus sequence at that column will be rendered as a '.', highlighting mutations in the group area.
+    	</em></li>
+	    	    </ul>
       </li>
+<!-- not available in 2.5 yet
+    <li><strong>Group Links<br>
+    </strong><em>This menu is only visible if there are group links available for the current selection.
+    </em> 
+    <ul>
+    <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
+    <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
+    <li><em>Sequence and ID links</em> allow you to send sets of IDs and sequences associated with the current selection to a web server.</li>
     </ul>
+    <em>Group Links were added in Jalview 2.5</em></li>
+-->    </ul>
   </li>
   <li><strong>Sequence Id<br>
     </strong><em>This menu is only visible if you right-click on a sequence name. 
     </em> 
     <ul>
-      <li><strong>Edit Name/Description<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
+						tooltip.</em></li>
+			<li><strong>Edit Name/Description<br>
         </strong><em>You may edit the name and description of each sequence. A 
         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 
@@ -89,7 +144,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
         Connections tab.<br>
         Since Jalview 2.4, links will also be made for database cross 
         references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
-        <br>Since Jalview 2.4.1, links are also shown for non-positional sequence features attached to 
+        <br>Since Jalview 2.5, links are also shown for non-positional sequence features attached to 
         the sequence, and any regular-expression based URL links that 
         matched the description line.
         </em><strong><br>
@@ -105,11 +160,11 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
           <li><strong>From File<br>
             </strong><em>Load a PDB file from local disk which will be associated 
             with this sequence. This file will be used if the user subsequently 
-            clicks on &quot;View PDB Structure&quot; menu item.</em></li>
+            clicks on &quot;View Structure&quot; menu item.</em></li>
           <li><strong>Enter PDB id<br>
             </strong><em>Enter the PDB id from an input window. This PDB id will 
             be used by the service WSDBFetch, provided by the EBI, to fetch the 
-            PDB file if the user subsequently clicks on &quot;View PDB Structure&quot; 
+            PDB file if the user subsequently clicks on its &quot;View Structure&quot; 
             menu item. </em></li>
           <li><strong>Discover PDB ids<br>
             </strong><em>This will use the service WSDBFetch, provided by the 
@@ -120,11 +175,28 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
       </li>
       <li><strong>View Structure<br>
         </strong><em> If the sequence has an associated PDB file added by one 
-        of the methods described above, Jalview will display a 3D interactive 
-        viewer of the file.<br>
+        of the methods described above, Jalview will open a 3D interactive 
+        view of the file.<br>
         These entries will only be present if the sequence has <a
-			href="../features/viewingpdbs.html">associated PDB structures</a>.</em><br>
+			href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
+			If the sequence or alignment has RNA structure, then <strong>2D RNA</strong> entries will also be present enabling you to open a linked view of the RNA structure in <a href="../features/varna.html">VARNA</a>.</em><br>
       </li>
+      <p><em>Other menu entries may also be shown if the current selection includes sequences with associated structure data:</em><br>
+  <ul>
+    <li><strong>&quot;Structure&#8594;View all <em>N</em>
+        structures<br/>
+    </strong><em>Opens a new window containing all structures associated
+      with the current selection, superposed according to the currently selected region of the alignment.<br/>(This
+      capability was added in Jalview 2.7)</em>
+    </li>
+    <li><strong>&quot;Structure&#8594;View all <em>N</em>
+        representative structures<br/>
+    </strong><em>Open a new window containing exactly one structure per
+      currently selected sequence.<br />
+    (The View representative structures option was introduced in
+        Jalview 2.8.1)</em></li>
+  </ul>
+  <br> 
     </ul>
   </li>
   <li><strong>Hide Sequences</strong><br>
