From: Jim Procter Date: Fri, 21 Sep 2018 16:52:05 +0000 (+0100) Subject: JAL-2843 slight restructuring of feature file help page for navigation and readability. X-Git-Tag: Release_2_11_0~2^2~4^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d67163ac3bcc9ff0c1890576b6e469c455b89e0e;p=jalview.git JAL-2843 slight restructuring of feature file help page for navigation and readability. --- diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index 4d13dcd..0226175 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -26,17 +26,20 @@

Sequence Features File +

-

The Sequence features file (which used to be known as the - "Groups file" prior to version 2.08) is a simple way of getting your - own sequence annotations into Jalview. It was introduced to allow - sequence features to be rendered in the Jalview applet, and so is - intentionally lightweight and minimal because the applet is often - used in situations where data file size must be kept to a minimum, - and no XML parser is available.

+ +

The Sequence features File provides a simple way of getting + your own sequence features into Jalview. It also allows feature + display styles and filters to be saved and imported to another + alignment. Users familiar with the earliest versions of Jalview will + know that features files were originally termed 'groups' files, and + that the format was was designed as a space efficient format to + allow sequence features to be rendered in the Jalview applet.

Features files are imported into Jalview in the following ways:
+

-

-

Sequence Features File Format

A features file is a simple ASCII text file, where each line contains tab separated text fields. No comments are - allowed. + allowed. Its structure consists of three blocks:

+ +

- Feature Colours + Feature Colours

The first set of lines contain feature type definitions and their colours:

-Feature label	Feature Colour
+<Feature Type>	<Feature Style>
 
 
- A feature type has a text label, and a colour specification. This can - be either: - -