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>
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_name+Group 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 ++ + +