From: jprocter Date: Mon, 1 Jun 2009 15:54:54 +0000 (+0000) Subject: graduated feature colour documentation X-Git-Tag: Release_2_5~301 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=57995b2366441dcc9d6eef7448c04d173c332fa5;p=jalview.git graduated feature colour documentation --- diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index 6b86d22..2e40a19 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -27,10 +27,35 @@ parser is available.

contains tab separated text fields. No comments are allowed.

The first set of lines contain type definitions: -

Feature label	Feature Colour
A feature -type has a text label, and a colour (specified as a red,green,blue 24 -bit triplet either in hexadecimal (eg. 00ff00) or as comma separated -numbers (ranging from 0 to 255)).

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

The remaining lines in the file are the sequence annotation definitions, where the now defined features are attached to regions on particular sequences, optionally with some descriptive text (displayed @@ -38,7 +63,7 @@ in a tooltip when the mouse is near the feature on that sequence). There are two alternate ways of referring to a sequence, either by its text ID, or its index in an associated alignment. 

-description	sequenceId	sequenceIndex	start	end	featureType
+description sequenceId sequenceIndex start end featureType score (optional) Normally, sequence features are associated with sequences rather than alignments, and the sequenceIndex field is given as "-1". In order to specify a sequence by its index in a particular alignment, the @@ -46,23 +71,26 @@ sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the sequenceId field will be used in preference to the sequenceIndex field.

-

The description may contain simple HTML -document body tags if enclosed by "<html></html>" and -these will be rendered as formatted tooltips in the Jalview Application -(the Jalview applet is not capable of rendering HTML tooltips, so all -formatting tags will be removed).
-Attaching Links to Sequence Features -
Any anchor tags in an html formatted description line will be translated -into URL links. A link symbol will be displayed adjacent to any feature which -includes links, and these are made available from the -links submenu of the -popup menu which is obtained by right-clicking when a link symbol is +

The description may contain simple HTML document body tags if +enclosed by "<html></html>" and these will be +rendered as formatted tooltips in the Jalview Application (the Jalview +applet is not capable of rendering HTML tooltips, so all formatting tags +will be removed).
+Attaching Links to Sequence Features
+Any anchor tags in an html formatted description line will be translated +into URL links. A link symbol will be displayed adjacent to any feature +which includes links, and these are made available from the links submenu of the +popup menu which is obtained by right-clicking when a link symbol is displayed in the tooltip.
Non-positional features
-Specify the start and end for a feature to be 0 in order to attach it to the whole sequence. -Non-positional features are shown in a tooltip when the mouse hovers over the seuqence ID panel, and any embedded links can be accessed from the popup menu. +Specify the start and end for a feature to be 0 +in order to attach it to the whole sequence. Non-positional features are +shown in a tooltip when the mouse hovers over the sequence ID panel, and +any embedded links can be accessed from the popup menu. +Scores
+Scores can be associated with sequence features, and used to sort sequences or shade the alignment (this was added in jalview 2.4.X). The score field is optional, and malformed scores will be ignored.

-

Feature annotations can be collected into named groups by prefixing definitions with lines of the form:

startgroup	groupname
.. and subsequently post-fixing the group with:
endgroup	groupname
Feature