Alignment Annotations File Format
-
- Note: This format is primarily intended to be used for the applet, which does
- not have an XML parser and where file size must be kept to a minimum to reduce
- download time.
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.
+ +Importing annotation files
+Alignment annotations files are imported into Jalview in the
+following ways:
+
+ -annotations <Annotations filename>
+ Exporting annotation files
An annotation file
+ can be created for any alignment view from the "Export
+ Annotations ..." entry in the File menu of an
+ alignment window.
+
THE ANNOTATION FILE FORMAT
+
An annotation file consists of lines containing an instruction followed by
+tab delimited fields. Any lines starting with "#" are considered comments, and
+ignored. The sections below describe the structure of an annotation file.
+
+ At the end of this document, you can also find notes on compatibility of annotation files across + different versions of Jalview. An example + annotation file is also provided along with instructions on how to + import it to Jalview. +
+Header line
The first non-commented out line of a valid Annotations file
+must begin with :JALVIEW_ANNOTATION
LINE_GRAPH, BAR_GRAPH and NO_GRAPH
+Labels, secondary structure, histograms and line graphs are added with a line like GRAPH_TYPE Label Description (optional) Values
+ Here, the GRAPH_TYPE field in the first column 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 tags (in the same + way as a sequence feature's label), + providing the text 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 corresponding interpretation of each Value 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. +
+COMBINE, COLOUR and GRAPHLINE for line graphs
+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 ++ +
ROWPROPERTIES
+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: +
SEQUENCE_GROUP
+Groups of sequences and column ranges can be defined using a tab delimited statement like:
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.
+Note: If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list +of sequence IDs.
+If a SEQUENCE_REF has been defined, then group_start and group_end will be + relative to the sequence residue numbering, otherwise the group_start and group_end + will be alignment column indices.
+PROPERTIES
This statement allows various visualisation properties to be assigned to a named group. This takes a series of tab-delimited key=value pairs:
PROPERTIES Group_name tab_delimited_key_value_pairs ++
The currently supported set of sequence group key-value pairs that can be provided here are :
+| Key | Value |
| description | Text - may include simple HTML tags |
| colour | A string resolving to a valid Jalview colourscheme (e.g. Helix Propensity) |
| pidThreshold | A number from 0-100 specifying the Percent Identity Threshold for colouring columns in the group or alignment |
| consThreshold | A number from 0-100 specifying the degree of bleaching applied for conservation colouring |
| outlineColour | Line colour used for outlining the group (default is red) |
| displayBoxes | Boolean (default true) controlling display of shaded box for each alignment position |
| displayText | Boolean (default true) controlling display of text for each alignment position |
| colourText | Boolean (default false) specifying whether text should be shaded by applied colourscheme |
| textCol1 | Colour for text when shown on a light background |
| textCol2 | Colour for text when shown on a dark background |
| textColThreshold | Number from 0-100 specifying switching threshold between light and dark background |
| idColour | Colour for highlighting the Sequence ID labels for this group If idColour is given but colour is not, then idColor will also be used for the group background colour. |
| showunconserved | Boolean (default false) indicating whether residues should only be shown that are different from current reference or consensus sequence |
| hide | Boolean (default false) indicating whether the rows in this group should be marked as hidden. Note: if the group is sequence associated (specified by SEQUENCE_REF), then all members will be hidden and marked as represented by the reference sequence. |
Specifying colours in PROPERTIES key-value pairs
+The colour property can take either a colour scheme name,
+ or a single colour specification (either a colour name like 'red' or an RGB
+ triplet like 'ff0066'). If a single colour is specified, then the group
+ will be coloured with that colour.
SEQUENCE_REF and GROUP_REF
+ By
+ default, annotation is associated with the alignment as a whole.
+ However, it is also possible to have an annotation row associated with
+ a specific sequence, or a sequence group. Clicking the annotation
+ label for sequence or group associated annotation will highlight the
+ associated rows in the alignment, and double clicking will select
+ those rows, allowing further analysis. While group associated
+ annotation remains associated with a particular alignment, sequence
+ associated annotation can move with a sequence - so copying a sequence
+ to another alignment will also copy its associated annotation.
+
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+ +
VIEW_SETREF, VIEW_HIDECOL and HIDE_INSERTIONS
+Since Jalview 2.9, the Annotations file has also supported the definition of reference sequences and hidden regions for an alignment view.
+ VIEW_SETREF takes either a single sequence ID string, or a + numeric index (second argument), and attempts to assign a + corresponding sequence as the reference + sequence for the alignment. +
+ VIEW_HIDECOLS takes either a single argument consisting of a + comma separated series of integer pairs like + 3-4. These integer pairs define columns (starting from the + left-hand column 0) that should be marked as hidden in the alignment + view. + ++ HIDE_INSERTIONS takes a either a single sequence ID or a + numeric index, or no arguments. This command marks all gapped + positions in a specified sequence (either the one located by the + arguments, the current SEQUENCE_REF, or the reference sequence for the + view). +
COMPATIBILITY NOTES
+ The interpretation of the COMBINE statement in Version 2.8.1 was refined
+ so that only annotation line graphs with the given names ands the same
+ SEQUENCE_REF and GROUP_REF scope are grouped.
EXAMPLES
+An example Annotation file is given below. Copy and paste the contents into a text file and load it onto the Jalview example protein alignment.
#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 ++ + +