From: jprocter <Jim Procter>
Date: Thu, 11 Mar 2010 17:12:45 +0000 (+0000)
Subject: feature settings type popup menu
X-Git-Tag: Release_2_5~131
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8e068512cd4573dc4388dfca63072c95f294ef84;p=jalview.git

feature settings type popup menu
---

diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index 05d1a51..7c4840d 100755
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -18,12 +18,19 @@ currently selected groups, along with their display colour and whether
 they are currently being displayed (only the ticked features and groups
 are displayed). <strong><em>You can change the colour used
 for a feature in the associated alignment by clicking on its colour box.</em></strong></p>
+<p><strong><em>Feature settings pop-up menu</em></strong><br>
+<strong>Right-click</strong> on a feature to open a pop-up menu that
+allows you to sort the alignment or current selection using that feature
+type (see below), or create a feature colourscheme based on either the
+scores associated with that feature or from the feature's description
+(e.g. to distinguish different names associated with a DOMAIN feature).</p>
 <p><strong>Ordering alignment by features</strong><br>
-Right click on a feature type to order the alignment by either the
-feature's score, or the number of features of that type. The 'Order by
-Score' and 'Order by Density' buttons will order the alignnment based on
-the average score or total number of currently active features and
-groups on each sequence. (Experimental - added in jalview 2.4.1)</p>
+The 'Order by Score' and 'Order by Density' buttons will order the
+alignment based on the average score or total number of currently active
+features and groups on each sequence.<br>
+<em>Feature sorting and colour feature by score and description was
+introduced in jalview 2.4.1</em></p>
+
 <p><strong>Transparency and Feature Ordering</strong></p>
 <p>It is important to realise that sequence features are often not
 distinct and often overlap (for example, a metal binding site feature
@@ -44,10 +51,6 @@ visibility of features rendered below other features. Reducing the
 transparency will mean that features at the top of the list can obscure
 features lower down, and increasing it allows the user to 'see through'
 the upper layers of a set of features.</p>
-<p><strong>Right-click</strong> on a feature to open a pop-up menu
-that allows you to sort the alignment or current selection using that
-feature type, or create a graduated feature colourscheme based on the
-scores associated with that feature.</p>
 <p><strong><em>You can save all features, with their
 current colours and visibility in a Jalview format file. </em></strong></p>
 </body>