-<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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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>
+ <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>
+
git://source.jalview.org / jalview.git / blobdiff