<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
+<head>
+<title>Sequence Feature Settings Dialog Box</title>
+</head>
+<body>
+<p><strong>Sequence Feature Settings Dialog Box</strong></p>
+<p>Select <strong>View→Feature Settings...</strong> menu entry
+in an alignment window to open the feature settings dialog box, which
+allows you to precisely control the presence and appearance of sequence
+features for the current alignment.</p>
+<center><img src="featureSettings.gif" width="400" height="452">
+<br>
+Sequence Feature Settings for the Jalview Application</img></center>
+<p>The top section of the dialog box lists all the sequence feature
+groups, along with a tickbox for each that controls whether its features
+are displayed. The table in the middle lists all the features in the
+currently selected groups, along with their display style and whether
+they are currently being displayed (only the ticked features and groups
+are displayed). <strong><em>You can change the colour or
+shading style 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 toggle the type of colouring used for the feature.
+Features may be highlighted with either a single colour or a <a
+ href="featureschemes.html">feature colourscheme</a> 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>
+The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort the
+alignment based on the average score or total number of currently active
+features and groups on each sequence. To order the alignment using a
+specific feature type, use the <em>sort by ..</em> entries in the pop-up
+menu for that type.<br>
+<em>Feature sorting and graduated feature colouring was introduced
+in jalview 2.5</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
+may be attached to one position along a stretch of sequence marked with
+a secondary structure feature).</p>
+<p>The ordering of the sequence features in the dialog box list is
+the order used by jalview for rendering sequence features. A feature at
+the bottom of the list is rendered <em>below</em> a feature higher up in
+the list.<br>
+<em><strong>You can change the order of a feature by
+dragging it up and down the list with the mouse</strong></em>.</p>
+<p>The <strong><em>Optimise order</em></strong> button (currently
+only available in the application) will re-order the feature render
+ordering based on the average length of each feature type.</p>
+<p>The <strong><em>transparency slider setting</em></strong>
+(currently only available in the application version) controls the
+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><em>You can save all features, with their
+current colours and visibility in a Jalview format file. </em></strong></p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff