From 175bfe14bb3ba5d6312e677d9f86f0ff7b2dcac7 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 8 Dec 2008 12:44:07 +0000 Subject: [PATCH] order by feature documentation --- help/html/features/featuresettings.html | 78 ++++++++++++++++--------------- help/html/releases.html | 1 + 2 files changed, 42 insertions(+), 37 deletions(-) diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 7b0132b..6eb895e 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -4,43 +4,47 @@

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 +

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. -

+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.

Ordering alignment by features
+Right click on a feature type to order the alignment by either the +feature's score, or the number of features of that type. The 'Order by +Score' and 'Order by Density' buttons will order the alignnment based on +the average score or total number of currently active features and +groups on each sequence. (Experimental - added in jalview 2.4.1)

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.

diff --git a/help/html/releases.html b/help/html/releases.html index 3286434..afe8ba3 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -41,6 +41,7 @@

Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)

New hidden columns and rows and representatives capabilities in annotations file (in progress - not yet fully implemented)

Order an alignment in order of average feature score or total feature count

-- 1.7.10.2