-<html>\r
-<head>\r
-<title>Sequence Feature Settings Dialog Box</title>\r
-</head>\r
-<body>\r
-<p><strong>Sequence Feature Settings Dialog Box</strong></p>\r
-<p>Select <strong>View→Feature Settings...</strong> menu entry in\r
-an alignment window to open the feature settings dialog box, which\r
-allows you to precisely control the presence and appearance of\r
-sequence features for the current alignment.</p>\r
-<center>\r
- <img src="featureSettings.gif" width="432" height="327"> <br>\r
- Sequence Feature\r
- Settings for the Jalview Application</img></center>\r
-<p>The top section of the dialog box lists all the sequence feature\r
- groups, along with a tickbox for each that controls whether its\r
- features are displayed. The table in the middle lists all the\r
- features in the currently selected groups, along with their display\r
- colour and whether they are currently being displayed (only the\r
- ticked features and groups are displayed). <strong><em>You can change the\r
- colour used for a feature in the associated alignment by clicking on\r
- its colour box.</em></strong></p>\r
-<p><strong>Transparency and Feature Ordering</strong></p><p>\r
- It is important to realise that sequence features are often not\r
- distinct and often overlap (for example, a metal binding site\r
- feature may be attached to one position along a stretch of sequence\r
- marked with a secondary structure feature).</p>\r
-<p>The ordering of the sequence features in the dialog box list is the\r
- order used by jalview for rendering sequence features. A feature at\r
- the bottom of the list is rendered <em>below</em> a feature higher\r
- up in the list.<br><em><strong>You can change the order of a feature\r
- by dragging it up and down the list with the\r
- mouse</strong></em>.</p>\r
-<p>\r
- The <strong><em>transparency slider setting</em></strong> (currently only available\r
- in the application version) controls the visibility of features\r
- rendered below other features. Reducing the transparency will mean\r
- that features at the top of the list can obscure features lower\r
- down, and increasing it allows the user to 'see through' the upper\r
- layers of a set of features.</p>\r
-<p><strong><em>You can save all features, with their current colours and visibility \r
- in a Jalview format file. </em></strong>\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<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="351" height="350">
+<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 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>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>
+<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>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>
+</html>
git://source.jalview.org / jalview.git / blobdiff