+
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 +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 used -for a feature in the associated alignment by clicking on its colour box.
+are displayed). You can change the colour or +shading style used for a feature in the associated alignment by clicking +on its colour box. +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
-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)
+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