+ 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-clicking
+ a feature type in the Feature Settings dialog
+ allows you to select columns in the alignment that contain (or do
+ not contain) features of that type. If a region of the alignment is
+ currently selected, then only features in the current selection will
+ be searched. The following keys affect the way in which selections
+ are made:
+
+ 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 were 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. +
+ +