3 <title>Sequence Feature Settings Dialog Box</title>
6 <p><strong>Sequence Feature Settings Dialog Box</strong></p>
7 <p>Select <strong>View→Feature Settings...</strong> menu entry in
8 an alignment window to open the feature settings dialog box, which
9 allows you to precisely control the presence and appearance of
10 sequence features for the current alignment.</p>
12 <img src="featureSettings.gif" width="351" height="350"> <br>
14 Settings for the Jalview Application</img></center>
15 <p>The top section of the dialog box lists all the sequence feature
16 groups, along with a tickbox for each that controls whether its
17 features are displayed. The table in the middle lists all the
18 features in the currently selected groups, along with their display
19 colour and whether they are currently being displayed (only the
20 ticked features and groups are displayed). <strong><em>You can change the
21 colour used for a feature in the associated alignment by clicking on
22 its colour box.</em></strong></p>
23 <p><strong>Transparency and Feature Ordering</strong></p><p>
24 It is important to realise that sequence features are often not
25 distinct and often overlap (for example, a metal binding site
26 feature may be attached to one position along a stretch of sequence
27 marked with a secondary structure feature).</p>
28 <p>The ordering of the sequence features in the dialog box list is the
29 order used by jalview for rendering sequence features. A feature at
30 the bottom of the list is rendered <em>below</em> a feature higher
31 up in the list.<br><em><strong>You can change the order of a feature
32 by dragging it up and down the list with the
33 mouse</strong></em>.</p>
34 <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>
36 The <strong><em>transparency slider setting</em></strong> (currently only available
37 in the application version) controls the visibility of features
38 rendered below other features. Reducing the transparency will mean
39 that features at the top of the list can obscure features lower
40 down, and increasing it allows the user to 'see through' the upper
41 layers of a set of features.</p>
42 <p><strong><em>You can save all features, with their current colours and visibility
43 in a Jalview format file. </em></strong>