4 <title>The Alignment Annotations File</title>
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8 <p><strong>The Alignment Annotations File</strong></p>
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9 <p>Alignment annotations can be imported onto an alignment since
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10 version 2.08 of Jalview, via an annotations file. It is a simple ASCII
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11 text file consisting of tab delimited records similar to the <a
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12 href="featuresFormat.html">Sequence Features File</a>, and introduced
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13 primarily for use with the Jalview applet.</p>
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14 <p>Alignment annotations files are imported into Jalview in the
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17 <li>from the command line<strong><pre>
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18 -annotations <<em>Annotations filename</em>></pre></strong></li>
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19 <li>Dragging an annotations file onto an alignment window</li>
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20 <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
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21 menu of an alignment window.</li>
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24 <p><strong>Annotations File Format</strong></p>
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25 <p>The File consists of lines containing an instruction followed by
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26 tab delimited fields, and any lines starting with "#" are
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27 ignored. The first non-commented out line of a valid Annotations file
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28 must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
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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>
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30 <p>The <em>GRAPH_TYPE</em> field, which appears first, defines the
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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 "|"
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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
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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>
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35 Plots a histogram with labels below each bar.<br>
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36 <em>number</em>,<em>text character</em></li>
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38 Draws a line between values on the annotation row.<br>
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39 <em>number</em></li>
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41 For a row consisting of text labels and/or secondary structure symbols.<br>
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42 <em>{Secondary Structure Symbol}</em>,<em>text label</em><br>
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43 Currently supported secondary structure structure symbols are <em>H</em> (for helix) and <em>E</em> (for strand)</li>
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45 Any or all value fields may be left empty, as well as the BAR_GRAPH's
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46 text character field, and either or both of the text-label and secondary
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47 structure symbol fields of the NO_GRAPH type annotation rows.
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49 <p>You can associate an annotation with a sequence by preceding its
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50 definition with the line:
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51 <pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre>
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52 All Annotations defined after a SEQUENCE_REF command will then be
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53 associated with that sequence, and the first field in the Value field
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54 list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
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55 <p>Sequence associations are turned off for subsequent annotation
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57 <pre>SEQUENCE_REF	ALIGNMENT</pre>
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59 <p><em>LINE_GRAPH</em> type annotations can be given a colour
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60 (specified as 24 bit RGB triplet in hexadecimal or comma separated
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61 values), combined onto the same vertical axis, and have ordinate lines
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62 (horizontal lines at a particular vertical axis value) using the
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63 following commands (respectively):
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64 <pre>COLOUR	<em>graph_name</em>	<em>colour</em>
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65 COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>
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66 GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em><strong><em>
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67 </em></strong></pre>
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68 <h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>
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69 <p>Groups of sequences can be defined using the tab delimited line</p>
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70 <pre>SEQUENCE_GROUP Group_Name Group_Start Group_End Sequences</pre>
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71 <p>The sequences can be defined by alignment index and a range of sequences can
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72 be defined in a comma delimited field such as</p>
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73 <p>2-5,8-15,20,22</p>
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74 <p>Enter * to select all groups. </p>
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75 <p>If the alignment indices are not known, enter -1 then a tab delimited list
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76 of sequence ids. </p>
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77 <p>If the SEQUENCE_REF has been defined, the group_start and group_end will be
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78 relative to the sequence residue numbering, otherwise the group_start and group_end
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79 will be the alignment column indices. </p>
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80 <p>The group can (optionally) be assigned various visualisation properties via
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81 another tab delimited line thus:</p>
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82 <pre>PROPERTIES Group_name tab_delimited_key_value_pairs
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84 <p>The key_value_pairs allow you to define a description and to colour the group
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85 in various ways. All, none or some of the following values could be used for
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87 <p>description=Text <br>
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88 colour=Helix Propensity<br>
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91 outlineColour=red <br>
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92 displayBoxes=true<br>
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93 displayText=false<br>
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94 colourText=false<br>
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97 textColThreshold=0</p>
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99 <p>An example Annotation file is given below:
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100 <pre>#Comment lines follow the hash symbol
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102 SEQUENCE_REF	FER1_MESCR	5
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103 BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
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104 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
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105 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
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106 BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
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107 NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
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108 NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
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109 COLOUR	Bar Graph 2	blue
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110 COLOUR	Red Values	255,0,0
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111 COLOUR	Green Values	green
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112 COLOUR	Purple Letters	151,52,228
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113 COMBINE	Green Values	Red Values
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114 GRAPHLINE	Red Values	2.6	threshold	black
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116 SEQUENCE_GROUP Group_A 30 50 *
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117 SEQUENCE_GROUP Group_B 1 351 2-5
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118 SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
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119 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
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120 PROPERTIES Group_B outlineColour=red
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121 PROPERTIES Group_C colour=Clustal
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