-<html>\r
-\r
-<head><title>Features File Format</title></head>\r
-\r
-<body>\r
-<p><strong>Sequence Features File Format</strong></p>\r
-<p>(Prior to version 2.08 known as the "Groups file")<br>\r
- A precalculated Features file can read onto an alignment from the command line \r
- ("-features"), by drag and dropping the features file onto an alignment \r
- or by selecting from the File menu "Load Features / Annotations".</p>\r
-<p>Specify the feature types first, then refer to the feature type for each sequence.</p>\r
-<p>featureType<tab>colour<br>\r
- description<tab>sequenceId<tab>sequenceIndex<tab>start<tab>end<tab>featureType</p>\r
-<p>eg<br>\r
- <font size="2" face="Courier New, Courier, mono">domain red<br>\r
- metal ion-binding site 00ff00<br>\r
- transit peptide 0,105,215<br>\r
- chain 225,105,0<br>\r
- modified residue 105,225,35<br>\r
- signal peptide 0,155,165<br>\r
- Your Own description here FER_CAPAA -1 3 93 domain<br>\r
- Your Own description here FER_CAPAN -1 48 144 chain<br>\r
- Your Own description here FER_CAPAN -1 50 140 domain<br>\r
- Your Own description here FER_CAPAN -1 136 136 modified residue<br>\r
- Your Own description here FER1_LYCES -1 1 47 transit peptide<br>\r
- Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide<br>\r
- Your Own description here Q93XJ9_SOLTU -1 49 144 chain</font></p>\r
-<p>An additional option in Jalview 2.08 is to group features in the following \r
- way: </p>\r
-<p><font size="2" face="Georgia, Times New Roman, Times, serif">STARTGROUP<tab>My feature groupA<br>\r
- ....Many Feature descriptions here<br>\r
- ENDGROUP<tab>My feature groupA</font><br>\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)).</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>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.
+</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>
git://source.jalview.org / jalview.git / blobdiff