Sequence Feature Settings Dialog Box

From: jprocter Date: Tue, 8 May 2007 17:18:23 +0000 (+0000) Subject: optimise order X-Git-Tag: Release_2_3~19 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4071cebc54ec047178d127d432597c2324dac35f optimise order --- diff --git a/help/html/features/featureSettings.gif b/help/html/features/featureSettings.gif index 6ecccde..92e5e7f 100755 Binary files a/help/html/features/featureSettings.gif and b/help/html/features/featureSettings.gif differ diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 81af8d0..fe592c3 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -1,45 +1,46 @@ - - -Sequence Feature Settings Dialog Box - - -

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.

- -

- 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 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 + + +

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.

+ +

+ 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 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. +

+ +