-<html>\r
-\r
-<head><title>Sequence Features File</title></head>\r
-\r
-<body>\r
-<p><strong>Sequence Features File</strong></p>\r
-<p>The Sequence features file (which used to be known as the "Groups\r
-file" prior to version 2.08) is a simple way of getting\r
-your own sequence annotations into Jalview. It was introduced to allow\r
-sequence features to be rendered in the Jalview applet, and so is\r
-intentionally lightweight and minimal because the applet is often used\r
-in situations where data file size must be kept to a minimum, and no\r
-XML parser is available.</p>\r
-<p>Features files are imported into Jalview in the following ways:<br>\r
-<ul>\r
-<li>from the command line<strong><pre>\r
- -features <<em>Features filename</em>></pre></strong></li>\r
-<li>Dragging a features file onto an alignment window</li>\r
-<li>Via the "Load Features / Annotations" entry in the\r
-<strong>File</strong> menu of an alignment window.</li>\r
-</ul>\r
-</p>\r
-<p><strong>Sequence Features File Format</strong></p>\r
-<p>A features file is a simple ASCII text file, where each line\r
-contains tab separated text fields. <strong>No comments are\r
-allowed</strong>.</p>\r
-<p>The first set of lines contain type definitions:<strong>\r
-<pre><em>Feature label</em>	<em>Feature Colour</em></pre>\r
-</strong>A feature type has a text label, and a colour (specified as a\r
-red,green,blue 24 bit triplet either in hexadecimal (eg. 00ff00) or as comma\r
-separated numbers (ranging from 0 to 255)).\r
-<p>The remaining lines in the file are the sequence annotation\r
-definitions, where the now defined features are attached to regions on\r
-particular sequences, optionally with some descriptive text (displayed\r
-in a tooltip when the mouse is near the feature on that sequence). There are two alternate ways of referring to a\r
-sequence, either by its text ID, or its index in an associated\r
-alignment.<pre>\r
-<em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em></pre>Normally,\r
-sequence features are associated with sequences rather than\r
-alignments, and the sequenceIndex field is given as "-1". In\r
-order to specify a sequence by its index in a particular alignment, the\r
-sequenceId should be given as "ID_NOT_SPECIFIED", otherwise the\r
-sequenceId field will be used in preference to the sequenceIndex field.</p><p>\r
-Feature annotations can be collected into named groups by prefixing\r
-definitions with lines of the\r
-form:<strong><pre>startgroup	groupname</pre></strong>.. and\r
-subsequently post-fixing the group\r
-with:<strong><pre>endgroup	groupname</pre></strong>Feature grouping\r
-was introduced in version 2.08, and used to control whether a set of features\r
-are either hidden or shown together in the <a href="seqfeatures.html">sequence Feature settings\r
-dialog box</a>.</p>\r
-<p>A complete example is shown below :<pre>\r
-domain	red\r
-metal ion-binding site	00ff00\r
-transit peptide	0,105,215\r
-chain	225,105,0\r
-modified residue	105,225,35\r
-signal peptide	0,155,165\r
-helix	ff0000\r
-strand	00ff00\r
-coil	cccccc\r
-Your Own description here	FER_CAPAA	-1	3	93	domain\r
-Your Own description here	FER_CAPAN	-1	48	144	chain\r
-Your Own description here	FER_CAPAN	-1	50	140	domain\r
-Your Own description here	FER_CAPAN	-1	136	136	modified residue\r
-Your Own description here	FER1_LYCES	-1	1	47	transit peptide\r
-Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide\r
-Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain\r
-startgroup	secondarystucture\r
-PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand\r
-PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix\r
-endgroup	secondarystructure\r
-</pre>\r
-</li>\r
-</p>\r
-</body>\r
-</html>\r
+<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.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
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