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. +
+ 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_INSERTIONSThis 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. -
+
+ 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.
+ 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 ++ 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,+ @@ -268,6 +423,6 @@ PROPERTIES Group_A description=This is the description colour=Helix Pro PROPERTIES Group_B outlineColour=red PROPERTIES Group_C colour=Clustal- +