<html>
-
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
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+ * Jalview is free software: you can redistribute it and/or
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+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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+ * Jalview is distributed in the hope that it will be useful, but
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+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<head>
<title>Sequence Features File</title>
</head>
contains tab separated text fields. <strong>No comments are
allowed</strong>.</p>
<p>The first set of lines contain type definitions:<strong>
-<pre><em>Feature label</em>	<em>Feature Colour</em></pre> </strong>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)).</p>
+<pre><em>Feature label</em>	<em>Feature Colour</em><!-- 	<em>Feature links</em> --></pre> </strong>A feature
+type has a text label, and a colour specification. This can be either:
+<ul>
+ <li>A single colour specified as either a red,green,blue 24 bit
+ triplet in hexadecimal (eg. 00ff00) or as comma separated numbers
+ (ranging from 0 to 255))</li>
+ <li>A <a href="featureschemes.html">graduated colourscheme</a> specified as a "|" separated list
+ of fields:<pre>
+<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
+</pre>The fields are as follows
+ <ul>
+ <li><em>mincolor</em> and <em>maxcolor</em><br>
+ Colour triplets specified as hexadecimal or comma separated values</li>
+ <li><em>absolute</em><br>
+ An optional switch indicating that the <em>minvalue</em> and <em>maxvalue</em>
+ parameters should be left as is, rather than rescaled according to the
+ range of scores for this feature type.
+ <li><em>minvalue</em> and <em>maxvalue</em><br>
+ Minimum and maximum values defining the range of scores for which the colour range will be defined over. If minvalue is greater than maxvalue then the linear mapping will have negative gradient.
+ </li>
+ <li><em>thresholdtype</em> <br>
+ Either "none", "below", or "above". <em>below</em>
+ and <em>above</em> require an additional <em>threshold value</em>
+ which is used to control the display of features with a score either
+ below or above the value.</li>
+ </ul>
+ </li>
+</ul>
+</p>
<p>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
are two alternate ways of referring to a sequence, either by its text
ID, or its index in an associated alignment.
<pre>
-<em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em></pre>
+<em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em>	<em>score (optional)</em></pre>
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
the sequenceId field will be used in preference to the sequenceIndex
field.
</p>
-<p>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).<br>
-<em>Attaching Links to Sequence Features</em>
-<br>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
-<a href="../menus/popupMenu.html#sqid.popup">links submenu</a> of the
-popup menu which is obtained by right-clicking when a link symbol is
+<p>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).<br>
+<em>Attaching Links to Sequence Features</em> <br>
+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 <a
+ href="../menus/popupMenu.html#sqid.popup">links submenu</a> of the
+popup menu which is obtained by right-clicking when a link symbol is
displayed in the tooltip.<br>
<em>Non-positional features</em><br>
-Specify the <em>start</em> and <em>end</em> for a feature to be <strong>0</strong> 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 <em>start</em> and <em>end</em> for a feature to be <strong>0</strong>
+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.
+<em>Scores</em><br>
+Scores can be associated with sequence features, and used to sort sequences or shade the alignment (this was added in jalview 2.5). The score field is optional, and malformed scores will be ignored.
</p>
-
<p>Feature annotations can be collected into named groups by
prefixing definitions with lines of the form:<strong><pre>startgroup	groupname</pre></strong>..
and subsequently post-fixing the group with:<strong><pre>endgroup	groupname</pre></strong>Feature
git://source.jalview.org / jalview.git / blobdiff