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.

Sequence Feature Settings for the Jalview Application

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). You can change the colour used for a feature in the associated alignment by clicking on its colour box.

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.