+ Sequence Feature Settings for the Jalview Application (version 2.11) +
Sequence Feature Settings Dialog Box
++ Select View→Feature Settings... in an alignment + window to open the feature settings dialog box, which allows + precise control of the visibility and appearance of sequence features for + an alignment view. +
+ 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. When many groups are present, their names may + be truncated, but the full name is shown in a tooltip when the mouse + hovers over their checkbox.
+Feature colour schemes and filters +
+ The table in the middle lists all the feature types in the currently + selected groups, along with their display style, any configured + filters, and a tickbox indicating whether the type is enabled for + display.
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).The colour used for a feature can + be changed by clicking on its colour box. To configure the shading + style or filter for a feature, click its configuration box. +
+
+ Feature settings pop-up menu
Right-click
+ on a feature to open a pop-up menu that allows you to
+
+ Transparency and Feature Ordering +
+Sequence features represent a variety of different types of + positional annotation, 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.
+
+ Use the Optimise order button to adjust the + feature render ordering to place features that on average cover shorter regions + of sequence above features annotating longer regions. +
++ The transparency slider 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. +
- 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. + You can save all features, with their + current colours and visibility in a Jalview format file.
-
- 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
- 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
- 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.
+ 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. A dialog box
+ is shown if there are no features to use for sorting sequences. To
+ order the alignment using a specific feature type, use the
+ sort by .. entries in the pop-up menu for that type.
When
+ a selected region exists, only features lying within the columns
+ containing the selected region will be considered, but all sequences
+ (including those not selected) will be reordered.
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. -