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>
+ -features <Features filename> ++
Sequence Features File Format
-A features file is a simple ASCII text file, where each line +
+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 (specified as a red,green,blue 24
-bit triplet either in hexadecimal (eg. 00ff00) or as comma separated
-numbers (ranging from 0 to 255)). The text label may contain simple HTML
-document body tags if enclosed by "<html></html>"
-and 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.
+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, 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. +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-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 +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:startgroup groupname
..
-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.
+startgroup groupname ++ +.. 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. + +
A complete example is shown below :
domain red @@ -78,8 +208,9 @@ startgroup secondarystucture 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 . .- - +