The Alignment Annotations File

From 811f68c1dc1e4c409751b785203ed0a7289529b3 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 11 Dec 2006 16:20:19 +0000 Subject: [PATCH] clarified help documentation for annotation file format and tweaked reader code to ensure input commutes with output. --- help/html/features/annotationsFormat.html | 164 ++++++++++++++--------------- src/jalview/io/AnnotationFile.java | 12 +-- 2 files changed, 88 insertions(+), 88 deletions(-) diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index ba9bc99..b5a52f5 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -1,82 +1,82 @@ - - -The Alignment Annotations File - - -

The Alignment Annotations File

Alignment annotations can be imported onto an alignment since - version 2.08 of Jalview, via an annotations file. It is a simple - ASCII text file consisting of tab - delimited records similar to the Sequence Features File, and - introduced primarily for use with the Jalview applet.

Alignment annotations files are imported into Jalview in the -following ways:
-

from the command line
- -annotations <Annotations filename>
Dragging an annotations file onto an alignment window
Via the "Load Features / Annotations" entry in the -File menu of an alignment window.

Annotations File Format

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

GRAPH_TYPE
This is can be either of "BAR_GRAPH", - "LINE_GRAPH" or "NO_GRAPH", defining the type of - annotation row that is being described. -
Values
This field is a series - of symbols and/or quantities separated by the pipe symbol "|", - mapped onto the columns of the alignment.
Some types of annotation - can display both text, symbols and quantities at each column, and these are - separated with commas within the pipe-delimited Value field. Jalview - will display the content if it's values are appropriate for the type - of the annotation being defined:
- BAR_GRAPH
  text - character,number
- LINE_GRAPH
  number
- NO_GRAPH
  text label,H or E for helix or strand - symbol
-

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

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

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,+
-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
-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
-COLOUR	Red Values	255,0,0
-COLOUR	Green Values	green
-COLOUR	Purple Letters	151,52,228
-COMBINE	Green Values	Red Values
-GRAPHLINE	Red Values	2.6	threshold	black
-

- - + + + +The Alignment Annotations File + + + +

The Alignment Annotations File

Alignment annotations can be imported onto an alignment since +version 2.08 of Jalview, via an annotations file. It is a simple ASCII +text file consisting of tab delimited records similar to the Sequence Features File, and introduced +primarily for use with the Jalview applet.

Alignment annotations files are imported into Jalview in the +following ways:
+

from the command line
+ -annotations <Annotations filename>
Dragging an annotations file onto an alignment window
Via the "Load Features / Annotations" entry in the File + menu of an alignment window.

Annotations File Format

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:

BAR_GRAPH
+ Plots a histogram with labels below each bar.
+ number,text character
LINE_GRAPH
+ Draws a line between values on the annotation row.
+ number
NO_GRAPH
+ For a row consisting of text labels and/or secondary structure symbols.
+ {Secondary Structure Symbol},text label
+ Currently supported secondary structure structure symbols are H (for helix) and E (for strand)

+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. +

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

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

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,+
+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
+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
+COLOUR	Red Values	255,0,0
+COLOUR	Green Values	green
+COLOUR	Purple Letters	151,52,228
+COMBINE	Green Values	Red Values
+GRAPHLINE	Red Values	2.6	threshold	black
+

+ + diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 04861a2..9f9ca20 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -101,17 +101,17 @@ public class AnnotationFile if(row.annotations[j]!=null) { comma = ""; - if (row.annotations[j].displayCharacter.length() > 0 - && !row.annotations[j].displayCharacter.equals(" ")) - { - text.append(row.annotations[j].displayCharacter); - comma = ","; - } if (row.annotations[j].secondaryStructure!=' ') { text.append(comma + row.annotations[j].secondaryStructure); comma = ","; } + if (row.annotations[j].displayCharacter.length() > 0 + && !row.annotations[j].displayCharacter.equals(" ")) + { + text.append(row.annotations[j].displayCharacter); + comma = ","; + } if (row.annotations[j].value!=0f) { color = row.annotations[j].colour; -- 1.7.10.2