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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 <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
-chain	225,105,0
-modified residue	105,225,35
-signal peptide	0,155,165
-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	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
-
-STARTGROUP	kd
-Hydrophobicity score by kD Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8
-ENDGROUP	kd
-
-GFF
-FER_CAPAA	GffGroup	domain	3	93	.	.
-</pre>
-</body>
-</html>
-
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