The Alignment Annotations File
Alignment annotations can be imported onto an alignment since version 2.08 of Jalview, via an annotations file. It is a simple ASCII text file consisting of tab delimited records similar to the Sequence Features File, and introduced primarily for use with the Jalview applet.
Alignment annotations files are imported into Jalview in the
following ways:
-annotations <Annotations filename>
Annotations File Format
The File consists of lines containing an instruction followed by
tab delimited fields, and any lines starting with "#" are
ignored. The first non-commented out line of a valid Annotations file
must begin with :JALVIEW_ANNOTATION
A row of annotation is added with a line like GRAPH_TYPE Label Values
The GRAPH_TYPE field, which appears first, defines the appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. The final Values field contains a series of "|" separated value fields. Each value field is itself a comma separated list of fields of a particular type defined by the annotation row's GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "|" symbol) are shown below:
You can associate an annotation with a sequence by preceding its
definition with the line: SEQUENCE_REF seq_name [startIndex]
All Annotations defined after a SEQUENCE_REF command will then be
associated with that sequence, and the first field in the Value field
list will (optionally) be placed at the startIndex'th column.
Sequence associations are turned off for subsequent annotation
definitions by: SEQUENCE_REF ALIGNMENT
LINE_GRAPH type annotations can be given a colour
(specified as 24 bit RGB triplet in hexadecimal or comma separated
values), combined onto the same vertical axis, and have ordinate lines
(horizontal lines at a particular vertical axis value) using the
following commands (respectively): COLOUR graph_name colour
COMBINE graph_1_name graph_2_name
GRAPHLINE graph_name value label colour
An example Annotation file is given below:
#Comment lines follow the hash symbol JALVIEW_ANNOTATION SEQUENCE_REF FER1_MESCR 5 BAR_GRAPH Bar Graph 1 ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+ LINE_GRAPH Green Values 1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2 LINE_GRAPH Red Values 2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2 BAR_GRAPH Bar Graph 2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4 NO_GRAPH Icons ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H|||||| NO_GRAPH Purple Letters m|y|p|r|o|t|e|i|n COLOUR Bar Graph 2 blue COLOUR Red Values 255,0,0 COLOUR Green Values green COLOUR Purple Letters 151,52,228 COMBINE Green Values Red Values GRAPHLINE Red Values 2.6 threshold black