links for non-positional features

diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index b11e96b..6b86d22 100755 (executable)
--- a/help/html/features/featuresFormat.html
+++ b/help/html/features/featuresFormat.html
@@ -30,11 +30,7 @@ allowed</strong>.</p>
 <pre><em>Feature label</em>&#9;<em>Feature Colour</em></pre> </strong>A feature
 type has a text label, and a colour (specified as a red,green,blue 24
 bit triplet either in hexadecimal (eg. 00ff00) or as comma separated
-numbers (ranging from 0 to 255)). The text label may contain simple HTML
-document body tags if enclosed by &quot;&lt;html&gt;&lt;/html&gt;&quot;
-and will be rendered as formatted tooltips in the Jalview Application
-(the Jalview applet is not capable of rendering HTML tooltips, so all
-formatting tags will be removed.</p>
+numbers (ranging from 0 to 255)).</p>
 <p>The remaining lines in the file are the sequence annotation
 definitions, where the now defined features are attached to regions on
 particular sequences, optionally with some descriptive text (displayed
@@ -50,6 +46,23 @@ sequenceId should be given as &quot;ID_NOT_SPECIFIED&quot;, otherwise
 the sequenceId field will be used in preference to the sequenceIndex
 field.
 </p>
+<p>The description may contain simple HTML
+document body tags if enclosed by &quot;&lt;html&gt;&lt;/html&gt;&quot; and
+these will be rendered as formatted tooltips in the Jalview Application
+(the Jalview applet is not capable of rendering HTML tooltips, so all
+formatting tags will be removed).<br>
+<em>Attaching Links to Sequence Features</em>
+<br>Any anchor tags in an html formatted description line will be translated 
+into URL links. A link symbol will be displayed adjacent to any feature which
+includes links, and these are made available from the 
+<a href="../menus/popupMenu.html#sqid.popup">links submenu</a> of the 
+popup menu which is obtained by right-clicking when a link symbol is 
+displayed in the tooltip.<br>
+<em>Non-positional features</em><br>
+Specify the <em>start</em> and <em>end</em> for a feature to be <strong>0</strong> in order to attach it to the whole sequence.
+Non-positional features are shown in a tooltip when the mouse hovers over the seuqence ID panel, and any embedded links can be accessed from the popup menu. 
+</p>
+
 <p>Feature annotations can be collected into named groups by
 prefixing definitions with lines of the form:<strong><pre>startgroup&#9;groupname</pre></strong>..
 and subsequently post-fixing the group with:<strong><pre>endgroup&#9;groupname</pre></strong>Feature

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index a836c9f..9cf5358 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -84,11 +84,14 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
         <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>
+      <li><a name="sqid.popup"><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>).
+        <br>Since Jalview 2.4.1, 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>
         </strong></li>
     </ul>