From 96433cd123131e1a572be3bce03be00d61367876 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 19 Aug 2011 11:06:22 +0100 Subject: [PATCH] JAL-908 JAL-912 JAL-516 documented annotation HTML description line and general tidyup of group associated annotation documentation for 2.7 update. --- help/html/features/annotationsFormat.html | 87 +++++++++++++++++++---------- 1 file changed, 59 insertions(+), 28 deletions(-) diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index 38d17e2..682edfd 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -37,51 +37,81 @@ following ways:
menu of an alignment window.

-

Annotations File Format

-

The File consists of lines containing an instruction followed by +

Format of an Annotations File

+

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:

-Any or all value fields may be left empty, as well as the BAR_GRAPH's +

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: + +

+ Any or all value fields may be left empty, as well as the BAR_GRAPH's text character field, and either or both of the text-label and secondary structure symbol fields of the NO_GRAPH type annotation rows.

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 +

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

-

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 Grouping

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 +121,7 @@ following commands (respectively): COMBINE graph_1_name graph_2_name GRAPHLINE graph_name value label colour +

(Since Jalview 2.5) ROWPROPERTIES

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)
@@ -153,7 +184,7 @@ property, then the idColour will also be used to colour the sequence. 
#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
-- 
1.7.10.2