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
@@ -114,86 +205,49 @@ definitions by:
Group association is turned off for subsequent annotation rows by:
GROUP_REF ALIGNMENT-
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 -- -
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-
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 -specifying the 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 --
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
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.
-
An example Annotation file is given below: + 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 +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 @@ -211,6 +265,5 @@ PROPERTIES Group_B outlineColour=red PROPERTIES Group_C colour=Clustal-
Last updated for version 2.8.1