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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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- * Jalview is free software: you can redistribute it and/or
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--->
-<head>
-<meta name="generator" content="HTML Tidy, see www.w3.org">
-<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
-
-<pre>
-<strong> -features <<em>Features filename</em>></strong>
-</pre>
-</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:
-
-<pre>
-<strong><em>Feature label</em>	<em>Feature Colour</em>
-<!-- 	<em>Feature links</em> --></strong>
-</pre>
-
-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>
-[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
-</pre>
-
-The fields are as follows:
-
-<ul>
-<li><em>label</em><br>
- Indicate that the feature description should be used to create a
-colour for features of this type.<br>
-<em>Note: if no threshold value is needed then the final '|' may be
-ommitted.<br>
-This keyword was added in Jalview 2.6</em></li>
-
-<li><em>mincolor</em> and <em>maxcolor</em><br>
- Colour triplets specified as hexadecimal or comma separated values
-(may be left blank for a <em>label</em> style colourscheme, but
-remember to specify the remaining fields)</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>
-
-<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. Each feature can optionally include some descriptive text
-which is displayed in a tooltip when the mouse is near the feature on that
-sequence (and can also be used to generate a colour the feature).</p>
-
-<p>If your sequence annotation is already available in GFF Format (see <a href="http://www.sanger.ac.uk/resources/software/gff/spec.html">http://www.sanger.ac.uk/resources/software/gff/spec.html</a>),
-then you can leave it as is, after first adding a line containing
-only 'GFF' after any Jalview feature colour definitions (<em>this mixed format capability was added in Jalview 2.6</em>). Alternately, you can use Jalview's own sequence feature
-annotation format, which additionally allows HTML and URLs to be
-directly attached to each piece of annotation.</p>
-
-<p><strong>Jalview's sequence feature annotation format</strong></p>
-<p>
-Each feature is specified as a tab-separated series of columns as defined below:
-<pre>
-<em>description</em>	<em>sequenceId</em>	<em>sequenceIndex</em>	<em>start</em>	<em>end</em>	<em>featureType</em>	<em>score (optional)</em>
-</pre>
-
-This format allows two alternate ways of referring to a sequence, either by
-its text ID, or its index in an associated alignment. 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 2.5).
-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:
-
-<pre>
-<strong>startgroup groupname</strong>
-</pre>
-
-.. and subsequently post-fixing the group with:
-
-<pre>
-<strong>endgroup groupname</strong>
-</pre>
-
-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
-GFF
-FER_CAPAA	GffGroup	domain	3	93	.	.
-</pre>
-</body>
-</html>
-
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