4 <title>The Alignment Annotations File</title>
8 <p><strong>The Alignment Annotations File</strong></p>
9 <p>Alignment annotations can be imported onto an alignment since
10 version 2.08 of Jalview, via an annotations file. It is a simple ASCII
11 text file consisting of tab delimited records similar to the <a
12 href="featuresFormat.html">Sequence Features File</a>, and introduced
13 primarily for use with the Jalview applet.</p>
14 <p>Alignment annotations files are imported into Jalview in the
17 <li>from the command line<strong><pre>
18 -annotations <<em>Annotations filename</em>></pre></strong></li>
19 <li>Dragging an annotations file onto an alignment window</li>
20 <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
21 menu of an alignment window.</li>
24 <p><strong>Annotations File Format</strong></p>
25 <p>The File consists of lines containing an instruction followed by
26 tab delimited fields, and any lines starting with "#" are
27 ignored. The first non-commented out line of a valid Annotations file
28 must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
29 <p>A row of annotation is added with a line like <strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Values</em></pre></strong></p>
30 <p>The <em>GRAPH_TYPE</em> field, which appears first, defines the
31 appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. The final <em>Values</em> field contains a series of "|"
32 separated value fields. Each value field is itself a comma separated list of fields of a particular type defined by the annotation row's
33 GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "<strong>|</strong>" symbol) are shown below:<ul>
35 Plots a histogram with labels below each bar.<br>
36 <em>number</em>,<em>text character</em></li>
38 Draws a line between values on the annotation row.<br>
41 For a row consisting of text labels and/or secondary structure symbols.<br>
42 <em>{Secondary Structure Symbol}</em>,<em>text label</em><br>
43 Currently supported secondary structure structure symbols are <em>H</em> (for helix) and <em>E</em> (for strand)</li>
45 Any or all value fields may be left empty, as well as the BAR_GRAPH's
46 text character field, and either or both of the text-label and secondary
47 structure symbol fields of the NO_GRAPH type annotation rows.
49 <p>You can associate an annotation with a sequence by preceding its
50 definition with the line: <strong><pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre></strong>
51 All Annotations defined after a SEQUENCE_REF command will then be
52 associated with that sequence, and the first field in the Value field
53 list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
54 <p>Sequence associations are turned off for subsequent annotation
55 definitions by: <strong><pre>SEQUENCE_REF	ALIGNMENT</pre></strong></p>
56 <p><em>LINE_GRAPH</em> type annotations can be given a colour
57 (specified as 24 bit RGB triplet in hexadecimal or comma separated
58 values), combined onto the same vertical axis, and have ordinate lines
59 (horizontal lines at a particular vertical axis value) using the
60 following commands (respectively): <strong><pre>COLOUR	<em>graph_name</em>	<em>colour</em>
61 COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>
62 GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em></pre></strong>
63 <p>An example Annotation file is given below:
64 <pre>#Comment lines follow the hash symbol
66 SEQUENCE_REF	FER1_MESCR	5
67 BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
68 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
69 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
70 BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
71 NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
72 NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
73 COLOUR	Bar Graph 2	blue
74 COLOUR	Red Values	255,0,0
75 COLOUR	Green Values	green
76 COLOUR	Purple Letters	151,52,228
77 COMBINE	Green Values	Red Values
78 GRAPHLINE	Red Values	2.6	threshold	black