<html>
-
-<head>
-<title>Sequence Features File</title>
-</head>
-
-<body>
-<p><strong>Sequence Features File</strong></p>
-<p>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.</p>
-<p>Features files are imported into Jalview in the following ways:<br>
-<ul>
- <li>from the command line<strong><pre>
- -features <<em>Features filename</em>></pre></strong></li>
- <li>Dragging a features file onto an alignment window</li>
- <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
- menu of an alignment window.</li>
-</ul>
-</p>
-<p><strong>Sequence Features File Format</strong></p>
-<p>A features file is a simple ASCII text file, where each line
-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><!-- 	<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
-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.
-<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
-sequenceId should be given as "ID_NOT_SPECIFIED", otherwise
-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
-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 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 2.4.X). 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
-grouping was introduced in version 2.08, and used to control whether a
-set of features are either hidden or shown together in the <a
- href="seqfeatures.html">sequence Feature settings dialog box</a>.</p>
-<p>A complete example is shown below :
-<pre>
-domain	red
-metal ion-binding site	00ff00
-transit peptide	0,105,215
-chain	225,105,0
-modified residue	105,225,35
-signal peptide	0,155,165
-helix	ff0000
-strand	00ff00
-coil	cccccc
-Your Own description here	FER_CAPAA	-1	3	93	domain
-Your Own description here	FER_CAPAN	-1	48	144	chain
-Your Own description here	FER_CAPAN	-1	50	140	domain
-Your Own description here	FER_CAPAN	-1	136	136	modified residue
-Your Own description here	FER1_LYCES	-1	1	47	transit peptide
-Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide
-Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain
-startgroup	secondarystucture
-PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
-PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
-endgroup	secondarystructure
-</pre>
-</li>
-</p>
-</body>
-</html>
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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