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, 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. -
-- 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.
+ 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 ++ 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,+ @@ -258,6 +423,6 @@ PROPERTIES Group_A description=This is the description colour=Helix Pro PROPERTIES Group_B outlineColour=red PROPERTIES Group_C colour=Clustal- +