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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>
+ <strong>Feature Colours</strong>
+ </p>
+ <p>The first set of lines contain feature type definitions and their colours:
+ <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))<br>
+ (For help with colour values, see <a href="https://www.w3schools.com/colors/colors_converter.asp">https://www.w3schools.com/colors/colors_converter.asp</a>.)</li>
+
+ <li>A <a href="featureschemes.html">graduated colourscheme</a>
+ specified as a "|" separated list of fields: <pre>
+[label <em>or</em> score<em> or</em> attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]
+</pre> The fields are as follows:
+
+ <ul>
+ <li><em>label</em><br> Indicates 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 only 'label' is required.<br> This
+ keyword was added in Jalview 2.6
+ </em></li>
+
+ <li><em>score</em><br> Indicates that the feature
+ score should be used to create a graduated colour for features of
+ this type, in conjunction with mincolor, maxcolor.<br><em>This keyword was added in Jalview 2.11.
+ It may be omitted (score is the default) if mincolor and maxcolor are specified.
+ </em></li>
+
+ <li><em>attribute|attName</em><br> Indicates that the value of feature
+ attribute 'attName' should be used to create a colour for features of
+ this type.
+ <br>For example, <em>attribute|clinical_significance</em> to colour by clinical_significance.
+ <br>To colour by range of a numeric attribute, include <em>mincolor</em> and <em>maxcolor</em>, or omit to colour by text (category).
+ <br>(Note: the value of the attribute used for colouring will also be shown in the tooltip as you mouse over features.)
+ <br>A sub-attribute should be written as, for example, CSQ:IMPACT.
+ <br><em>This keyword was added in Jalview 2.11</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.<br>If minvalue is
+ greater than maxvalue then the linear mapping will have
+ negative gradient.</li>
+
+ <li><em>novalue</em> <br>
+ Specifies the colour to use if colouring by attribute, when the attribute is absent.
+ Valid options are <em>novaluemin, novaluemax, novaluenone</em>, to use mincolor, maxcolor, or no colour.
+ <br>If not specified this will default to novaluemin.</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>
+ <strong>Feature Filters</strong>
+ </p>
+ <p>This section is optional, and allows one or more filters to be defined for each feature type.
+ <br>Only features that satisfy the filter conditions will be displayed.
+ <br>Begin with a line which is just STARTFILTERS, and end with a line which is just ENDFILTERS.
+ <br>Each line has the format:
+ <pre>featureType <em><tab></em> (filtercondition1) [and|or] (filtercondition2) [and|or]...<br></pre>
+ The parentheses are not needed if there is only one condition.
+ Combine multiple conditions with either <em>and</em> or <em>or</em> (but not a mixture).
+ <br>Each condition is written as:
+ <pre>Label <em>or</em> Score <em>or</em> AttributeName condition [value]</pre>
+ where either the label (description), (numeric) score, or (text or numeric) attribute is tested against the condition.
+ <br><em>condition</em> is not case sensitive, and should be one of
+ <ul>
+ <li><em>Contains</em> - description (or attribute) should contain the given value (not case sensitive); example <em>clinical_significance contains Pathogenic</em></li>
+ <li><em>NotContains</em> - description (or attribute) should not contain the given value</li>
+ <li><em>Matches</em> - description (or attribute) should match the given value (not case sensitive)</li>
+ <li><em>NotMatches</em> - description (or attribute) should not match the given value (not case sensitive)</li>
+ <li><em>Present</em> - attribute is present on the feature (no value required); example <em>CSQ:SIFT present</em></li>
+ <li><em>NotPresent</em> - attribute is not present on the feature (no value required)</li>
+ <li><em>EQ</em> - feature score, or specified attribute, is equal to the (numeric) value</li>
+ <li><em>NE, LT, LE, GT, GE</em> - tests for not equal to / less than / less than or equal to / greater than / greater than or equal to the value</li>
+ </ul>
+ A non-numeric value always fails a numeric test.<br>If either attribute name, or value to compare, contains spaces, then enclose in single quotes:
+ <em>'mutagenesis site' contains 'decreased affinity'</em>
+ <br>Tip: some examples of filter syntax are given below; or to see more, first configure colours and filters in Jalview, then <em>File | Export Features</em> to Textbox in Jalview Format.
+ <br><em>Feature filters were added in Jalview 2.11</em>
+ </p>
+
+ <p>
+ <strong>Feature Instances</strong>
+ </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 may also be used to generate
+ a colour for the feature).</p>
+
+ <p>
+ If your sequence annotation is already available in <a href="http://gmod.org/wiki/GFF2">GFF2</a> (http://gmod.org/wiki/GFF2) or
+ <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md">GFF3</a>
+ (http://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) format,
+ 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 (base 0) 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
helix	ff0000
strand	00ff00
coil	cccccc
+kdHydrophobicity	ccffcc|333300|-3.9|4.5|above|-2.0
+
+STARTFILTERS
+metal ion-binding site	Label Contains sulfur
+kdHydrophobicity	(Score LT 1.5) OR (Score GE 2.8)
+ENDFILTERS
+
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	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
+
+STARTGROUP	secondarystucture
PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
-endgroup	secondarystructure
+ENDGROUP	secondarystructure
+
+STARTGROUP	kd
+Hydrophobicity score by kD Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8
+ENDGROUP	kd
+
+GFF
+FER_CAPAA	GffGroup	domain	3	93	.	.
</pre>
-</li>
-</p>
</body>
</html>
+