-<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>
+
+<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></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)). The text label may contain simple HTML
+document body tags if enclosed by "<html></html>"
+and 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.</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></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>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>