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<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<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>
+ <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
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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