Alignment annotations files are imported into Jalview in the
-following ways:
+
+
Importing annotation files
+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 +
+ 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
A row of annotation is added with a line like GRAPH_TYPE Label 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. 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:
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.
-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- -
Since version 2.5, Jalview allows annotation rows to be associated with a group defined on the alignment, by preceding the annotation row with the line: -
GROUP_REF group_name-Group association is turned off for subsequent annotation rows by -
GROUP_REF ALIGNMENT-Annotations may be associated with both a sequence and a group, however - group annotations are still experimental and unexpected behaviour may be observed when editing alignments containing both group and sequence associated annotation rows. -
LINE_GRAPH type annotations can be given a colour +
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
@@ -75,72 +125,129 @@ following commands (respectively):
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
+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+
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.
-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 +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 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
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.
-
An example Annotation file is given below: + 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 views on the alignment, and definition of hidden regions.
+ 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 ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+ +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 +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 @@ -150,12 +257,12 @@ 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 +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