Annotations File Format
-The File consists of lines containing an instruction followed by +
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
The GRAPH_TYPE field, which appears first, defines the -appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. 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 the format of their respective value fields (with the trailing "|" symbol) are shown below:
A row of annotation is added with a line like GRAPH_TYPE Label Description (optional) Values
+ The GRAPH_TYPE field, which appears first, 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 in the same + way as a sequence feature's label, + providing the html 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 the format of their respective value fields (with the + trailing "|" symbol) 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.
-You can associate an annotation with a sequence by preceding its +
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-
Since version 2.5, Jalview allows annotation rows to be associated with a group defined on the alignment, by preceding the annotation row with the line: +
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 association is turned off for subsequent annotation rows by:
GROUP_REF ALIGNMENT-Annotations may be associated with both a sequence and a group, however - group annotations are still experimental and unexpected behaviour may be observed when editing alignments containing both group and sequence associated annotation rows. + +
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 @@ -91,6 +122,7 @@ following commands (respectively): 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)@@ -101,13 +133,13 @@ GRAPHLINE graph_name value label colo
Groups of sequences can be defined using the tab delimited line
-SEQUENCE_GROUP Group_Name Group_Start Group_End Sequences+
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.
+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.
@@ -147,13 +179,16 @@ property, then the idColour will also be used to colour the sequence. SEQUENCE_REF sequence reference statement, the sequence representative for the group will be set to the referenced sequence. +
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,+ +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 @@ -166,13 +201,14 @@ 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 +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+
Last updated for version 2.8.1