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<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>
+<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>
+<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
+<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 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, 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.
+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></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
+<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:<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>
+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
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>
-</li>
-</p>
</body>
</html>
+
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