3 <head><title>Annotations File Format</title></head>
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6 <p><strong>Alignment Annotations File Format</strong><strong><br>
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8 Note: This format is primarily intended to be used for the applet, which does
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9 not have an XML parser and where file size must be kept to a minimum to reduce
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11 <p>A precalculated annotations fiile can read onto an alignment from the command
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12 line ("-annotations"), by drag and dropping the the annotations file
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13 onto an alignment or by selecting from the File menu "Load Features / Annotations".</p>
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14 <p>The File is in tab delimited format. The file must have the line JALVIEW_ANNOTATION
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15 as an identifier. Then a block of annotations are added in the form GRAPH_TYPE
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17 <p>GRAPH_TYPE can be either BAR_GRAPH, LINE_GRAPH or NO_GRAPH. The values are
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18 per alignment column, separated by "|". Multiple content per column
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19 can be separated with commas, Jalview will display the content if it interprates
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20 the content as a text label, or secondary structure character (H or E)</p>
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21 <p>You can optionally associate an annotation with a sequence by adding a line
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22 SEQUENCE_REFseq_namestartIndex All Annotations after a SEQUENCE_REF will be
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23 associated with that sequence. Use SEQUENCE_REF ALIGNMENT to cancel the associtations.</p>
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24 <p>The visual graphs can be coloured or combined with other graphs, or have an
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25 arbitrary line drawn at a certain value using the following lines.</p>
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26 <p><font size="3" face="Courier New, Courier, mono">COLOUR<tab>graph name<tab>colour<br>
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27 COMBINE<tab>graph 1 name<tab>graph 2 name<br>
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28 GRAPHLINE<tab>graph name<tab>value<tab>label<tab>colour</font></p>
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29 <p>An example Annotation file may look like this:</p>
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30 <p><font size="3" face="Courier New, Courier, mono">#Comment lines follow the hash symbol<br>
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31 JALVIEW_ANNOTATION<br>
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32 SEQUENCE_REF FER1_MESCR 5<br>
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33 BAR_GRAPH<tab>Bar Graph 1<tab>||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>
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34 LINE_GRAPH<tab>Green Values<tab>1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2<br>
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35 LINE_GRAPH<tab>Red Values<tab>2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2<br>
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36 BAR_GRAPH<tab>Bar Graph<tab>2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4<br>
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37 NO_GRAPH<tab>Icons <tab>||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||<br>
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38 NO_GRAPH<tab>Purple Letters<tab>m|y|p|r|o|t|e|i|n</font></p>
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39 <p><font size="3" face="Courier New, Courier, mono">COLOUR<tab>Bar Graph 2<tab>blue<br>
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40 COLOUR<tab>Red Values<tab>255,0,0<br>
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41 COLOUR<tab>Green Values<tab>green<br>
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42 COLOUR<tab>Purple Letters<tab>151,52,228<br>
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43 COMBINE<tab>Green Values<tab>Red Values</font></p>
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44 <p><font size="3" face="Courier New, Courier, mono">GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black
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