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 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 + 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 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. +
+ +