You can associate an annotation with a sequence by preceding its
-definition with the line: SEQUENCE_REF seq_name [startIndex]
+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
SEQUENCE_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
+following commands (respectively):
+
+GRAPHLINE graph_name value label colour
+
+COLOUR graph_name colour
COMBINE graph_1_name graph_2_name
-GRAPHLINE graph_name value label colour
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.
+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 ++
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
+ hide=false
+ hidecols=false
An example Annotation file is given below:
#Comment lines follow the hash symbol JALVIEW_ANNOTATION @@ -76,6 +132,13 @@ 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