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,
- combined onto the same vertical axis, and have abscissa (lines of
- constant value - so they are horizontal) at particular
- values using the following lines (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
-
-
-
+ 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
Marks the first sequence in the
+ alignment, or alternately, the one specified by the most recent SEQUENCE_REF
+ statement, as the reference
+ sequence for the alignment.
+
+ HIDE_INSERTIONS
This command hides all gapped
+ positions in the current target sequence. Any columns already hidden
+ will be re-displayed.
The current target sequence is
+ either the one specified by the most recent SEQUENCE_REF
+ statement, the alignment's reference sequence, or the first sequence
+ in the alignment.
+
+ VIEW_HIDECOLS
Modifies the visibility of columns in
+ the view. The statement is followed by a single argument consisting
+ of a comma separated series of single integers or integer pairs
+ (like 3-4). These define columns (starting from the
+ left-hand column 0) that should be marked as hidden in the alignment
+ 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 ++ + +