3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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23 <title>The Alignment Annotations File</title>
27 <p><strong>The Alignment Annotations File</strong></p>
28 <p>Alignment annotations can be imported onto an alignment since
29 version 2.08 of Jalview, via an annotations file. It is a simple ASCII
30 text file consisting of tab delimited records similar to the <a
31 href="featuresFormat.html">Sequence Features File</a>, and introduced
32 primarily for use with the Jalview applet.</p>
33 <p>Alignment annotations files are imported into Jalview in the
36 <li>from the command line<strong><pre>
37 -annotations <<em>Annotations filename</em>></pre></strong></li>
38 <li>Dragging an annotations file onto an alignment window</li>
39 <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
40 menu of an alignment window.</li>
43 <p><h3><font face="Arial, Helvetica, sans-serif">Format of an Annotations File</font></h3>
44 <p>The file consists of lines containing an instruction followed by
45 tab delimited fields, and any lines starting with "#" are
46 ignored. The first non-commented out line of a valid Annotations file
47 must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
48 <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>
50 The <em>GRAPH_TYPE</em> field, which appears first, defines the
51 appearance of the annotation row when rendered by Jalview. The next
52 field is the row <em>label</em> for the annotation. This may be
53 followed by a <em>description</em> for the row, which is shown in a
54 tooltip when the user mouses over the annotation row's label. Since
55 Jalview 2.7, the description field may also contain html in the same
56 way as a <a href="featuresFile.html">sequence feature's</a> label,
57 providing the html is enclosed in an <html/> tag.
59 <ul><em>Please note: URL links embedded in HTML descriptions will
60 be supported in a future release of Jalview</em>
63 <p>The final <em>Values</em>
64 field contains a series of "|" separated value fields. Each
65 value field is itself a comma separated list of fields of a particular
66 type defined by the annotation row's GRAPH_TYPE. The allowed values of
67 GRAPH_TYPE and the format of their respective value fields (with the
68 trailing "<strong>|</strong>" symbol) are shown below:
71 <li>BAR_GRAPH<br> Plots a histogram with labels below each
72 bar.<br> <em>number</em>,<em>text character</em>,<em>Tooltip
75 <li>LINE_GRAPH<br> Draws a line between values on the
76 annotation row.<br> <em>number</em>
78 <li>NO_GRAPH<br> For a row consisting of text labels and/or
79 secondary structure symbols.<br> <em>{Secondary Structure
80 Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br> Currently
81 supported secondary structure structure symbols are <em>H</em> (for
82 helix) and <em>E</em> (for strand)</li>
84 Any or all value fields may be left empty, as well as the BAR_GRAPH's
85 text character field, and either or both of the text-label and secondary
86 structure symbol fields of the NO_GRAPH type annotation rows.</p>
87 <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.
89 <p><h3><font face="Arial, Helvetica, sans-serif">SEQUENCE_REF and GROUP_REF</font></h3>
91 default, annotation is associated with the alignment as a whole.
92 However, it is also possible to have an annotation row associated with
93 a specific sequence, or a sequence group. Clicking the annotation
94 label for sequence or group associated annotation will highlight the
95 associated rows in the alignment, and double clicking will select
96 those rows, allowing further analysis. While group associated
97 annotation remains associated with a particular alignment, sequence
98 associated annotation can move with a sequence - so copying a sequence
99 to another alignment will also copy its associated annotation.
101 <p>You can associate an annotation with a sequence by preceding its
102 definition with the line:
103 <pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre>
104 All Annotations defined after a SEQUENCE_REF command will then be
105 associated with that sequence, and the first field in the Value field
106 list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
108 <p>Sequence associations are turned off for subsequent annotation
110 <pre>SEQUENCE_REF	ALIGNMENT</pre>
112 <p>Similarly, since Jalview 2.5, group associated annotation can be defined by preceding the row definitions with the line:
113 <pre>GROUP_REF	<em>group_name</em></pre>
114 Group association is turned off for subsequent annotation rows by:
115 <pre>GROUP_REF	<em>ALIGNMENT</em></pre>
117 <h3><font face="Arial, Helvetica, sans-serif">LINE_GRAPH Grouping</font></h3>
118 <p><em>LINE_GRAPH</em> type annotations can be given a colour
119 (specified as 24 bit RGB triplet in hexadecimal or comma separated
120 values), combined onto the same vertical axis, and have ordinate lines
121 (horizontal lines at a particular vertical axis value) using the
122 following commands (respectively):
123 <pre>COLOUR	<em>graph_name</em>	<em>colour</em>
124 COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>
125 GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em><strong><em>
128 <h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.5) ROWPROPERTIES</font></h3>
129 <p>The visual display properties for a set of annotation rows can be modified using the following tab-delimited line:</p>
130 <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>
131 <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:
132 <ul><li><em>centrelabs</em> Centre each label on its column.</li>
133 <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>
134 <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>
136 <h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>
137 <p>Groups of sequences can be defined using the tab delimited line</p>
138 <pre>SEQUENCE_GROUP Group_Name Group_Start Group_End <em>Sequences</em></pre>
139 <p>The sequences can be defined by alignment index and a range of sequences can
140 be defined in a comma delimited field such as</p>
141 <p>2-5,8-15,20,22</p>
142 <p>Enter * to select all groups. </p>
143 <p><strong>Note:</strong> If the alignment indices are not known, enter -1, followed by a tab and then a tab delimited list
144 specifying the sequence ids. </p>
145 <p>If the SEQUENCE_REF has been defined, the group_start and group_end will be
146 relative to the sequence residue numbering, otherwise the group_start and group_end
147 will be the alignment column indices. </p>
148 <p>The group can (optionally) be assigned various visualisation properties via
149 another tab delimited line thus:</p>
150 <pre>PROPERTIES Group_name tab_delimited_key_value_pairs
152 <p>The key_value_pairs allow you to define a description and to colour the group
153 in various ways. All, none or some of the following values could be used for
155 <p>description=Text <br>
156 colour=Helix Propensity<br>
159 outlineColour=red <br>
160 displayBoxes=true<br>
161 displayText=false<br>
165 textColThreshold=0<br>
167 <!-- Not yet implemented in 2.5 release
169 hidecols=false<br> -->
170 showunconserved=false</p>
171 <ul><li><em>New Features in 2.4:</em><br>if the <strong>idColour</strong> property
172 is given without specifying a colour scheme with the <strong>colour</strong>
173 property, then the idColour will also be used to colour the sequence.</li>
174 <li>the <strong>colour</strong> property can take either a colour scheme name,
175 or a single colour specification (either a colour name like 'red' or an RGB
176 triplet like 'ff0066'). If a single colour is specified, then the group
177 will be coloured with that colour.</li>
178 <!-- <li><em>New Features in 2.5</em></li>
179 <li>hide and hidecols instruct jalview to hide the sequences or columns covered by the group.</li> -->
180 <li>Sequence associated Groups<br>If a group is defined after a valid
181 <em>SEQUENCE_REF</em> sequence reference statement, the sequence representative
182 for the group will be set to the referenced sequence.<!-- <br><strong>Note:</strong> if the <em>hide</em>
183 property is set then only the representative sequence for the group will be shown in the alignment.--></li>
184 <li>The interpretation of the COMBINE statement in <em>Version 2.8.1</em> was refined
185 so that only annotation line graphs with the given names ands the same
186 <strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong> scope are grouped.</li>
189 <p>An example Annotation file is given below:
190 <pre>#Comment lines follow the hash symbol
192 SEQUENCE_REF	FER1_MESCR	5
193 BAR_GRAPH	Bar Graph 1	<html>an <em>html tooltip</em> for Bar graph 1.</html>	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
194 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
195 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
196 BAR_GRAPH	Bar Graph 2	1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
197 NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
198 NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
199 COLOUR	Bar Graph 2	blue
200 COLOUR	Red Values	255,0,0
201 COLOUR	Green Values	green
202 COLOUR	Purple Letters	151,52,228
203 COMBINE	Green Values	Red Values
204 GRAPHLINE	Red Values	2.6	threshold	black
206 SEQUENCE_GROUP	Group_A	30	50	*
207 SEQUENCE_GROUP	Group_B	1	351	2-5
208 SEQUENCE_GROUP	Group_C	12	14	-1	seq1	seq2	seq3
209 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
210 PROPERTIES	Group_B	outlineColour=red
211 PROPERTIES	Group_C	colour=Clustal
214 <p><em>Last updated for version 2.8.1</em></p>