From: jprocter <Jim Procter>
Date: Wed, 12 Nov 2008 10:55:12 +0000 (+0000)
Subject: rewording and clarification
X-Git-Tag: Jalview_2_4_0b2~42
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f6125c8d22fa28c5b38506e7c9926dcaa10a9629;p=jalview.git

rewording and clarification
---

diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index b11e96b..6b86d22 100755
--- 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/features/preferences.html b/help/html/features/preferences.html
index c173212..36646d6 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -86,9 +86,12 @@ vbersion of the font to sequence labels.</p>
   <li>Each top level parenthesis will yield a URL containing the text matched within that parenthesis.
   </li>
   <li>Regions matching sub-parentheseses within a top-level parenthesis will be concatenated to form the text inserted into the URL for the top-level parenthesis.</li>
-  <em>Please Note: the regular expressions supported by Jalview are those provided by the <a href="www.javaregex.com">Stevesoft javaregex package</a>. 
+  <em>Please Note:
+  <ul><li>The regular expressions supported by Jalview are those provided by the <a href="www.javaregex.com">Stevesoft javaregex package</a>.
+  </li><li>Some characters must be escaped when specifying them as a match within a regular expression.</li></ul>  
   <br>Many Thanks to Bernd Brand of the Free University of Amsterdam for testing this new regular-expression expansion feature!
   </em>
+  <em>
   </ul>
   </p>
 <p><em>Default Browser (Unix)</em><br>