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:

• from the command line

   -annotations <Annotations filename>

• Dragging an annotations file onto an alignment window
• Via the "Load Features / Annotations" entry in the File menu of an alignment window.

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

• GRAPH_TYPE
  This is can be either of "BAR_GRAPH", "LINE_GRAPH" or "NO_GRAPH", defining the type of annotation row that is being described.
• Values
  This field is a series of symbols and/or quantities separated by the pipe symbol "|", mapped onto the columns of the alignment.
  Some types of annotation can display both text, symbols and quantities at each column, and these are separated with commas within the pipe-delimited Value field. Jalview will display the content if it's values are appropriate for the type of the annotation being defined:
  • BAR_GRAPH
    text character,number
  • LINE_GRAPH
    number
  • NO_GRAPH
    text label,H or E for helix or strand symbol

You can associate an annotation with a sequence by preceding its definition with the line:

SEQUENCE_REF	seq_name	[startIndex]

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