- 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 - 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. -
++ 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
+
+ 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 (not applet).
+
+ 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 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. +