<html>\r
\r
-<head><title>Features File Format</title></head>\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>Note: This format is primarily intended to be used for the applet, which does \r
- not have an XML parser and where file size must be kept to a minimum to reduce \r
- download time.</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="3" 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="3" 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>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
git://source.jalview.org / jalview.git / blobdiff