X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=a836c9fc15e7bde3043ab1019a8fa5ac6ee05aef;hb=244a1460b0d7ae9a7a8c57d3a767b327788e8bd3;hp=f885bd8de19c289d1f7be17f02c0975cafc8fb71;hpb=5a6d8d69732445af2189fc4bab7a09dbd77bb829;p=jalview.git

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index f885bd8..a836c9f 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -9,113 +9,125 @@
 selected region on the alignment or on a selected sequence name. It may
 not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 <ul>
-	<li><strong>Selection</strong>
-	<ul>
-		<li><strong>Edit </strong>
-		<ul>
-			<li><strong>Copy</strong><br>
-			<em>Copys 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
-			version, the copied sequences are not available to the system
-			clipboard.</em></li>
-			<li><strong>To Upper Case</strong><em><strong><br>
-			</strong><em>Changes the case of selected region to lower case.</em> </em></li>
-			<li><strong>To Lower Case<br>
-			</strong><em>Changes the case of selected region to upper case.</em><strong>
-			</strong></li>
-			<li><strong>Toggle Case</strong><br>
-			<em>Switches the case of all residues within the selected
-			region.</em></li>
-		</ul>
-		</li>
-		<li><strong>Output to Textbox<br>
-		</strong><em>The selection area will be output to a a text window in the
-		selected alignment format. </em></li>
-		<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 will display a window
-			asking for the name of the currently selected group. Click OK to set
-			the name, cancel to use the default group name. </em></li>
-			<li><strong>Remove Group<br>
-			</strong><em>This will undefine the selected group. </em><strong> </strong></li>
-			<li><strong>Group Colour<br>
-			</strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> of
-			the group.</em><strong> </strong></li>
-			<li><strong>Boxes<br>
-			</strong><em>If selected the background of a residue within the selected
-			group will be coloured according to the assigned colour scheme.</em><strong>
-			</strong></li>
-			<li><strong>Text<br>
-			</strong><em>If selected the selected group will display text. </em></li>
-			<li><strong>Colour Text<br>
-			</strong><em>If selected the selected group will display text in a colour
-			slightly darker than the background colour of that residue.</em></li>
-			<li><strong>Border Colour <br>
-			</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>
-	</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>
-		</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><strong>Associate Structure with Sequence</strong>
-		<ul>
-			<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>
-			<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; menu item. </em></li>
-			<li><strong>Discover PDB ids<br>
-			</strong><em>This will use the service WSDBFetch, provided by the EBI, to
-			retrieve all PDB ids associated with the sequences in the alignment
-			if the sequences have valid Uniprot names or accession ids. </em></li>
-		</ul>
-		</li>
-		<li><strong>View PDB 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>
-		This entry is only present if the sequence has an <a
-			href="../features/viewingpdbs.html">associated PDB structure</a>. </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 sequence will be propagated to the hidden sequences. </em></li>
-		<li><strong>Link</strong><br>
-		<em>This menu item lists all links which have been set up in the
-		<a href="../features/preferences.html">Preferences</a> Connections
-		tab.</em><strong><br>
-		</strong></li>
-	</ul>
-	</li>
-	<li><strong>Hide Sequences</strong><br>
-	<em>This menu item lists all links which have been set up in the <a
-		href="../features/preferences.html">Preferences</a> Connections tab.
-	It is only displayed when you right click (Apple click) on a sequence
-	id. </em><strong><br>
-	<br>
-	</strong></li>
+  <li><strong>Selection</strong> 
+    <ul>
+      <li><strong>Edit </strong> 
+        <ul>
+          <li><strong>Copy</strong><br>
+            <em>Copys 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 
+            version, the copied sequences are not available to the system clipboard.</em></li>
+          <li><strong>Edit Sequence</strong><br>
+            <em>Edit the selected sequence(s) directly. Spaces will be converted 
+            to the current gap character.</em></li>
+          <li><strong>To Upper Case</strong><em><strong><br>
+            </strong><em>Changes the case of selected region to lower case.</em> 
+            </em></li>
+          <li><strong>To Lower Case<br>
+            </strong><em>Changes the case of selected region to upper case.</em><strong> 
+            </strong></li>
+          <li><strong>Toggle Case</strong><br>
+            <em>Switches the case of all residues within the selected region.</em></li>
+        </ul>
+      </li>
+      <li><strong>Output to Textbox<br>
+        </strong><em>The selection area will be output to a a text window in the 
+        selected alignment format. </em></li>
+      <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>Remove Group<br>
+            </strong><em>This will undefine the selected group. </em><strong> 
+            </strong></li>
+          <li><strong>Group Colour<br>
+            </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> 
+            of the group.</em><strong> </strong></li>
+          <li><strong>Boxes<br>
+            </strong><em>If selected the background of a residue within the selected 
+            group will be coloured according to the assigned colour scheme.</em><strong> 
+            </strong></li>
+          <li><strong>Text<br>
+            </strong><em>If selected the selected group will display text. </em></li>
+          <li><strong>Colour Text<br>
+            </strong><em>If selected the selected group will display text in a 
+            colour slightly darker than the background colour of that residue.</em></li>
+          <li><strong>Border Colour <br>
+            </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>
+    </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>
+        </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><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 
+        sequence will be propagated to the hidden sequences. </em></li>
+      <li><strong>Link</strong><br>
+        <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> 
+        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>).
+        </em><strong><br>
+        </strong></li>
+    </ul>
+  </li>
+  <li><strong>Structure</strong> 
+    </strong><em>This menu is only visible if you right-click on a sequence name. 
+    </em> 
+    <ul>
+      <li><strong>Associate Structure with Sequence</strong> 
+        <ul>
+          <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>
+          <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; 
+            menu item. </em></li>
+          <li><strong>Discover PDB ids<br>
+            </strong><em>This will use the service WSDBFetch, provided by the 
+            EBI, to retrieve all PDB ids associated with the sequences in the 
+            alignment if the sequences have valid Uniprot names or accession ids. 
+            </em></li>
+        </ul>
+      </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>
+        These entries will only be present if the sequence has <a
+			href="../features/viewingpdbs.html">associated PDB structures</a>.</em><br>
+      </li>
+    </ul>
+  </li>
+  <li><strong>Hide Sequences</strong><br>
+    <em>Hides the currently selected sequences in this alignment view.</em><strong><br>
+    <br>
+    </strong></li>
 </ul>
 </body>
 </html>