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
-
-
+
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
+
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 +