-<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>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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.<br /> <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>
+
git://source.jalview.org / jalview.git / blobdiff