From 5f9c8558cfee09b2ba2a13226f5bd4188e299135 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 20 Jan 2015 14:31:36 +0000 Subject: [PATCH] JAL-1304 revamped annotation file documentation structure to make it more usable --- help/html/features/annotationsFormat.html | 222 ++++++++++++++++------------- 1 file changed, 125 insertions(+), 97 deletions(-) diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index 141379f..5012124 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -30,8 +30,10 @@ version 2.08 of Jalview, via an annotations file. It is a simple ASCII text file consisting of tab delimited records similar to the Sequence Features File, and introduced primarily for use with the Jalview applet.

-

Alignment annotations files are imported into Jalview in the -following ways:
+ +

Importing annotation files
+Alignment annotations files are imported into Jalview in the +following ways:

-

Format of an Annotations File

-

The file consists of lines containing an instruction followed by -tab delimited fields, and any lines starting with "#" are -ignored. The first non-commented out line of a valid Annotations file +

+ Exporting annotation files
An annotation file + can be created for any alignment view from the "Export + Annotations ..." entry in the File menu of an + alignment window. +

+

THE ANNOTATION FILE FORMAT +
An annotation file consists of lines containing an instruction followed by +tab delimited fields. Any lines starting with "#" are considered comments, and +ignored. The sections below describe the structure of an annotation file. +

+

+ At the end of this document, you can also find notes on compatibility of annotation files across + different versions of Jalview. An example + annotation file is also provided along with instructions on how to + import it to Jalview. +

+
+

Header line
The first non-commented out line of a valid Annotations file must begin with :

JALVIEW_ANNOTATION

-

A row of annotation is added with a line like 

GRAPH_TYPE	Label	Description (optional)	Values

+
+

LINE_GRAPH, BAR_GRAPH and NO_GRAPH
+Labels, secondary structure, histograms and line graphs are added with a line like 

GRAPH_TYPE	Label	Description (optional)	Values

- The GRAPH_TYPE field, which appears first, defines the + Here, the GRAPH_TYPE field in the first column defines the appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. This may be followed by a description for the row, which is shown in a tooltip when the user mouses over the annotation row's label. Since - Jalview 2.7, the description field may also contain html in the same - way as a sequence feature's label, - providing the html is enclosed in an <html/> tag. + Jalview 2.7, the description field may also contain HTML tags (in the same + way as a sequence feature's label), + providing the text is enclosed in an <html/> tag. -