3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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21 <title>The Alignment Annotations File</title>
25 <p><strong>The Alignment Annotations File</strong></p>
26 <p>Alignment annotations can be imported onto an alignment since
27 version 2.08 of Jalview, via an annotations file. It is a simple ASCII
28 text file consisting of tab delimited records similar to the <a
29 href="featuresFormat.html">Sequence Features File</a>, and introduced
30 primarily for use with the Jalview applet.</p>
31 <p>Alignment annotations files are imported into Jalview in the
34 <li>from the command line<strong><pre>
35 -annotations <<em>Annotations filename</em>></pre></strong></li>
36 <li>Dragging an annotations file onto an alignment window</li>
37 <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
38 menu of an alignment window.</li>
41 <p><h3><font face="Arial, Helvetica, sans-serif">Format of an Annotations File</font></h3>
42 <p>The file consists of lines containing an instruction followed by
43 tab delimited fields, and any lines starting with "#" are
44 ignored. The first non-commented out line of a valid Annotations file
45 must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
46 <p>A row of annotation is added with a line like <strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Description</em> (optional)	<em>Values</em></pre></strong></p>
48 The <em>GRAPH_TYPE</em> field, which appears first, defines the
49 appearance of the annotation row when rendered by Jalview. The next
50 field is the row <em>label</em> for the annotation. This may be
51 followed by a <em>description</em> for the row, which is shown in a
52 tooltip when the user mouses over the annotation row's label. Since
53 Jalview 2.7, the description field may also contain html in the same
54 way as a <a href="featuresFile.html">sequence feature's</a> label,
55 providing the html is enclosed in an <html/> tag.
57 <ul><em>Please note: URL links embedded in HTML descriptions will
58 be supported in a future release of Jalview</em>
61 <p>The final <em>Values</em>
62 field contains a series of "|" separated value fields. Each
63 value field is itself a comma separated list of fields of a particular
64 type defined by the annotation row's GRAPH_TYPE. The allowed values of
65 GRAPH_TYPE and the format of their respective value fields (with the
66 trailing "<strong>|</strong>" symbol) are shown below:
69 <li>BAR_GRAPH<br> Plots a histogram with labels below each
70 bar.<br> <em>number</em>,<em>text character</em>,<em>Tooltip
73 <li>LINE_GRAPH<br> Draws a line between values on the
74 annotation row.<br> <em>number</em>
76 <li>NO_GRAPH<br> For a row consisting of text labels and/or
77 secondary structure symbols.<br> <em>{Secondary Structure
78 Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br> Currently
79 supported secondary structure structure symbols are <em>H</em> (for
80 helix) and <em>E</em> (for strand)</li>
82 Any or all value fields may be left empty, as well as the BAR_GRAPH's
83 text character field, and either or both of the text-label and secondary
84 structure symbol fields of the NO_GRAPH type annotation rows.</p>
85 <p>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.
87 <p><h3><font face="Arial, Helvetica, sans-serif">SEQUENCE_REF and GROUP_REF</font></h3>
89 default, annotation is associated with the alignment as a whole.
90 However, it is also possible to have an annotation row associated with
91 a specific sequence, or a sequence group. Clicking the annotation
92 label for sequence or group associated annotation will highlight the
93 associated rows in the alignment, and double clicking will select
94 those rows, allowing further analysis. While group associated
95 annotation remains associated with a particular alignment, sequence
96 associated annotation can move with a sequence - so copying a sequence
97 to another alignment will also copy its associated annotation.
99 <p>You can associate an annotation with a sequence by preceding its
100 definition with the line:
101 <pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre>
102 All Annotations defined after a SEQUENCE_REF command will then be
103 associated with that sequence, and the first field in the Value field
104 list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
106 <p>Sequence associations are turned off for subsequent annotation
108 <pre>SEQUENCE_REF	ALIGNMENT</pre>
110 <p>Similarly, since Jalview 2.5, group associated annotation can be defined by preceding the row definitions with the line:
111 <pre>GROUP_REF	<em>group_name</em></pre>
112 Group association is turned off for subsequent annotation rows by:
113 <pre>GROUP_REF	<em>ALIGNMENT</em></pre>
115 <h3><font face="Arial, Helvetica, sans-serif">LINE_GRAPH Grouping</font></h3>
116 <p><em>LINE_GRAPH</em> type annotations can be given a colour
117 (specified as 24 bit RGB triplet in hexadecimal or comma separated
118 values), combined onto the same vertical axis, and have ordinate lines
119 (horizontal lines at a particular vertical axis value) using the
120 following commands (respectively):
121 <pre>COLOUR	<em>graph_name</em>	<em>colour</em>
122 COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>
123 GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em><strong><em>
126 <h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.5) ROWPROPERTIES</font></h3>
127 <p>The visual display properties for a set of annotation rows can be modified using the following tab-delimited line:</p>
128 <pre>ROWPROPERTIES	<em>Row label</em>	<em>centrelabs=true( or false)</em>	<em>showalllabs=true(default is false)</em>	<em>scaletofit=true (default is false)</em></pre>
129 <p>This sets the visual display properties according to the given values for all the annotation rows with labels matching <em>Row label</em>. The properties mostly affect the display of multi-character column labels, and are as follows:
130 <ul><li><em>centrelabs</em> Centre each label on its column.</li>
131 <li><em>showalllabs</em> Show every column label rather than only the first of a run of identical labels (setting this to true can have a drastic effect on secondary structure rows).</li>
132 <li><em>scaletofit</em> Shrink each label's font size so that the label fits within the column. Useful when annotating an alignment with a specific column numbering system. (<em>Not available in Jalview applet due to AWT 1.1 limitations</em>)</li>
134 <h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>
135 <p>Groups of sequences can be defined using the tab delimited line</p>
136 <pre>SEQUENCE_GROUP Group_Name Group_Start Group_End <em>Sequences</em></pre>
137 <p>The sequences can be defined by alignment index and a range of sequences can
138 be defined in a comma delimited field such as</p>
139 <p>2-5,8-15,20,22</p>
140 <p>Enter * to select all groups. </p>
141 <p><strong>Note:</strong> If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list
142 specifying the sequence ids. </p>
143 <p>If the SEQUENCE_REF has been defined, the group_start and group_end will be
144 relative to the sequence residue numbering, otherwise the group_start and group_end
145 will be the alignment column indices. </p>
146 <p>The group can (optionally) be assigned various visualisation properties via
147 another tab delimited line thus:</p>
148 <pre>PROPERTIES Group_name tab_delimited_key_value_pairs
150 <p>The key_value_pairs allow you to define a description and to colour the group
151 in various ways. All, none or some of the following values could be used for
153 <p>description=Text <br>
154 colour=Helix Propensity<br>
157 outlineColour=red <br>
158 displayBoxes=true<br>
159 displayText=false<br>
163 textColThreshold=0<br>
165 <!-- Not yet implemented in 2.5 release
167 hidecols=false<br> -->
168 showunconserved=false</p>
169 <ul><li><em>New Features in 2.4:</em><br>if the <strong>idColour</strong> property
170 is given without specifying a colour scheme with the <strong>colour</strong>
171 property, then the idColour will also be used to colour the sequence.</li>
172 <li>the <strong>colour</strong> property can take either a colour scheme name,
173 or a single colour specification (either a colour name like 'red' or an RGB
174 triplet like 'ff0066'). If a single colour is specified, then the group
175 will be coloured with that colour.</li>
176 <!-- <li><em>New Features in 2.5</em></li>
177 <li>hide and hidecols instruct jalview to hide the sequences or columns covered by the group.</li> -->
178 <li>Sequence associated Groups<br>If a group is defined after a valid
179 <em>SEQUENCE_REF</em> sequence reference statement, the sequence representative
180 for the group will be set to the referenced sequence.<!-- <br><strong>Note:</strong> if the <em>hide</em>
181 property is set then only the representative sequence for the group will be shown in the alignment.--></li>
182 <li>The interpretation of the COMBINE statement in <em>Version 2.8.1</em> was refined
183 so that only annotation line graphs with the given names ands the same
184 <strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong> scope are grouped.</li>
187 <p>An example Annotation file is given below:
188 <pre>#Comment lines follow the hash symbol
190 SEQUENCE_REF	FER1_MESCR	5
191 BAR_GRAPH	Bar Graph 1	<html>an <em>html tooltip</em> for Bar graph 1.</html>	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
192 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
193 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
194 BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
195 NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
196 NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
197 COLOUR	Bar Graph 2	blue
198 COLOUR	Red Values	255,0,0
199 COLOUR	Green Values	green
200 COLOUR	Purple Letters	151,52,228
201 COMBINE	Green Values	Red Values
202 GRAPHLINE	Red Values	2.6	threshold	black
204 SEQUENCE_GROUP	Group_A	30	50	*
205 SEQUENCE_GROUP	Group_B	1	351	2-5
206 SEQUENCE_GROUP	Group_C	12	14	-1	seq1	seq2	seq3
207 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
208 PROPERTIES	Group_B	outlineColour=red
209 PROPERTIES	Group_C	colour=Clustal
212 <p><em>Last updated for version 2.8.1</em></p>