++Sequence Feature Settings for the Jalview Application
Sequence Feature Settings Dialog Box
+Select View→Feature Settings... 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.
+
+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). You can change the colour or +shading style used for a feature in the associated alignment by clicking +on its colour box.
+
+ Selecting alignment columns by feature
+ Double-click a feature to add all the columns where
+ that feature is found to the current column selection. Shift+Double-click
+ will add all the columns where that feature is not
+ found. You can also find these options in the feature's pop-up menu
+ (see below).
+ Select columns by feature was added in Jalview 2.8.1
+
Feature settings pop-up menu
+Right-click 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 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).
Ordering alignment by features
+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 sort by .. entries in the pop-up
+menu for that type.
+Feature sorting and graduated feature colouring was introduced
+in jalview 2.5
Transparency and Feature Ordering
+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).
+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 below a feature higher up in
+the list.
+You can change the order of a feature by
+dragging it up and down the list with the mouse.
The Optimise order button (currently +only available in the application) will re-order the feature render +ordering based on the average length of each feature type.
+The transparency slider setting +(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.
+You can save all features, with their +current colours and visibility in a Jalview format file.
+ +