Alignment Annotations File Format

A precalculated annotations fiile can read onto an alignment from the command line ("-annotations"), by drag and dropping the the annotations file onto an alignment or by selecting from the File menu "Load Features / Annotations".

The File is in tab delimited format. The file must have the line JALVIEW_ANNOTATION as an identifier. Then a block of annotations are added in the form GRAPH_TYPE Label Values

GRAPH_TYPE can be either BAR_GRAPH, LINE_GRAPH or NO_GRAPH. The values are per alignment column, separated by "|". Multiple content per column can be separated with commas, Jalview will display the content if it interprates the content as a text label, or secondary structure character (H or E)

You can optionally associate an annotation with a sequence by adding a line SEQUENCE_REFseq_namestartIndex All Annotations after a SEQUENCE_REF will be associated with that sequence. Use SEQUENCE_REF ALIGNMENT to cancel the associtations.

The visual graphs can be coloured or combined with other graphs, or have an arbitrary line drawn at a certain value using the following lines.

COLOUR<tab>graph name<tab>colour
COMBINE<tab>graph 1 name<tab>graph 2 name
GRAPHLINE<tab>graph name<tab>value<tab>label<tab>colour

An example Annotation file may look like this:

#Comment lines follow the hash symbol
JALVIEW_ANNOTATION
SEQUENCE_REF FER1_MESCR 5
BAR_GRAPH<tab>Bar Graph 1<tab>||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
LINE_GRAPH<tab>Green Values<tab>1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
LINE_GRAPH<tab>Red Values<tab>2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
BAR_GRAPH<tab>Bar Graph<tab>2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
NO_GRAPH<tab>Icons <tab>||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
NO_GRAPH<tab>Purple Letters<tab>m|y|p|r|o|t|e|i|n

COLOUR<tab>Bar Graph 2<tab>blue
COLOUR<tab>Red Values<tab>255,0,0
COLOUR<tab>Green Values<tab>green
COLOUR<tab>Purple Letters<tab>151,52,228
COMBINE<tab>Green Values<tab>Red Values

GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black