Sequence Features File
-
-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.
- -Features files are imported into Jalview in the following
-ways:
-
-
++ Sequence Features File +
+
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.
+ ++ Features files are imported into Jalview in the following ways:
+
-features <Features filename>-
Sequence Features File Format
--A features file is a simple ASCII text file, where each line -contains tab separated text fields. No comments are -allowed.
--The first set of lines contain type definitions: - -
+
+ Sequence Features File Format +
++ A features file is a simple ASCII text file, where each line + contains tab separated text fields. No comments are + allowed. +
+The first set of lines contain type definitions: +
Feature label Feature Colour-A feature type has a text label, and a colour specification. This -can be either: - -
+
[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]] -- -The fields are as follows: - -
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).
- -If your sequence annotation is already available in GFF Format (see http://www.sanger.ac.uk/resources/software/gff/spec.html), -then you can leave it as is, after first adding a line containing -only 'GFF' after any Jalview feature colour definitions (this mixed format capability was added in Jalview 2.6). 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.
- -Jalview's sequence feature annotation format
--Each feature is specified as a tab-separated series of columns as defined below: -
+The fields are as follows: + +
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).
+ ++ If your sequence annotation is already available in GFF Format (see + http://www.sanger.ac.uk/resources/software/gff/spec.html), + then you can leave it as is, after first adding a line containing + only 'GFF' after any Jalview feature colour definitions (this + mixed format capability was added in Jalview 2.6). 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. +
+ ++ Jalview's sequence feature annotation format +
+Each feature is specified as a tab-separated series of columns + as defined below: +
description sequenceId sequenceIndex start end featureType score (optional)-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. - - - -
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).
-Attaching Links to Sequence Features
-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 links
-submenu of the popup menu which is obtained by right-clicking
-when a link symbol is displayed in the tooltip.
-Non-positional features
-Specify the start and end for a feature to be
-0 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. Scores
-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.
Feature annotations can be collected into named groups by -prefixing definitions with lines of the form: - -
+ 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. + + + ++ 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).
+ +
Attaching Links + to Sequence Features
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 links submenu of the popup menu which is obtained by + right-clicking when a link symbol is displayed in the tooltip.
+ Non-positional features
Specify the start + and end for a feature to be 0 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.
Scores
+ 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. +Feature annotations can be collected into named groups by + prefixing definitions with lines of the form: +
startgroup groupname-.. and subsequently post-fixing the group with: + .. and subsequently post-fixing the group with: -+endgroup groupname-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 sequence Feature -settings dialog box. - + 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 + sequence Feature settings dialog box. + + -A complete example is shown below : -
+A complete example is shown below : +
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