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>
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 Description (optional) 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. This may be followed by a description for the row, which is shown in a tooltip when the user mouses over the annotation row's label. Since Jalview 2.7, the description field may also contain html in the same way as a sequence feature's label, providing the html is enclosed in an <html/> tag.
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:
Color strings can be embedded in a value field by enclosing an RGB triplet in square brackets to colour that position in an annotation row.
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
Similarly, since Jalview 2.5, group associated annotation can be defined by preceding the row definitions with the line:
GROUP_REF group_nameGroup association is turned off for subsequent annotation rows by:
GROUP_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
The visual display properties for a set of annotation rows can be modified using the following tab-delimited line:
ROWPROPERTIES Row label centrelabs=true( or false) showalllabs=true(default is false) scaletofit=true (default is false)
This sets the visual display properties according to the given values for all the annotation rows with labels matching Row label. The properties mostly affect the display of multi-character column labels, and are as follows:
Groups of sequences can be defined using the tab delimited line
SEQUENCE_GROUP Group_Name Group_Start Group_End Sequences
The sequences can be defined by alignment index and a range of sequences can be defined in a comma delimited field such as
2-5,8-15,20,22
Enter * to select all groups.
If the alignment indices are not known, enter -1 then a tab delimited list of sequence ids.
If the SEQUENCE_REF has been defined, the group_start and group_end will be relative to the sequence residue numbering, otherwise the group_start and group_end will be the alignment column indices.
The group can (optionally) be assigned various visualisation properties via another tab delimited line thus:
PROPERTIES Group_name tab_delimited_key_value_pairs
The key_value_pairs allow you to define a description and to colour the group in various ways. All, none or some of the following values could be used for a group:
description=Text
colour=Helix Propensity
pidThreshold=0
consThreshold=0
outlineColour=red
displayBoxes=true
displayText=false
colourText=false
textCol1=black
textCol2=black
textColThreshold=0
idColour=ff3322
showunconserved=false
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 <html>an <em>html tooltip</em> for Bar graph 1.</html> ||-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 SEQUENCE_GROUP Group_A 30 50 * SEQUENCE_GROUP Group_B 1 351 2-5 SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3 PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0 PROPERTIES Group_B outlineColour=red PROPERTIES Group_C colour=Clustal