+<p><strong>Annotations File Format</strong></p>\r
+<p>The File consists of lines containing an instruction followed by\r
+ tab delimited fields, and any lines starting with "#" are\r
+ ignored. The first non-commented out line of a valid Annotations file must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>\r
+<p>A row of annotation is added with a line like\r
+<strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Values</em></pre></strong>\r
+<ul>\r
+<li><em>GRAPH_TYPE</em><br>This is can be either of "BAR_GRAPH",\r
+ "LINE_GRAPH" or "NO_GRAPH", defining the type of\r
+ annotation row that is being described.\r
+ </li>\r
+ <li><em>Values</em><br>This field is a series\r
+ of symbols and/or quantities separated by the pipe symbol "|",\r
+ mapped onto the columns of the alignment.<br>Some types of annotation\r
+ can display both text, symbols and quantities at each column, and these are\r
+ separated with commas within the pipe-delimited Value field. Jalview\r
+ will display the content if it's values are appropriate for the type\r
+ of the annotation being defined:<ul>\r
+<li>BAR_GRAPH<br><em>text\r
+ character</em>,<em>number</em></li>\r
+<li>LINE_GRAPH<br><em>number</em></li>\r
+<li>NO_GRAPH<br><em>text label</em>,<em>H or E for helix or strand\r
+ symbol</em></li></ul>\r
+</li></ul></p>\r
+<p>You can associate an annotation with a sequence by preceding its\r
+ definition with the line:\r
+<strong><pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre></strong>\r
+All Annotations defined after a SEQUENCE_REF command will then be \r
+ associated with that sequence, and the first field in the Value\r
+ field list will (optionally) be\r
+ placed at the <em>startIndex</em>'th column.</p><p>Sequence associations\r
+ are turned off for subsequent annotation definitions by:\r
+<strong><pre>SEQUENCE_REF	ALIGNMENT</pre></strong></p>\r
+<p><em>LINE_GRAPH</em> type annotations can be given a colour\r
+ (specified as 24 bit RGB triplet in hexadecimal or comma separated values),\r
+ combined onto the same vertical axis, and have ordinate lines (horizontal\r
+ lines at a particular vertical axis value) using the following\r
+ commands (respectively):\r
+<strong><pre>COLOUR	<em>graph_name</em>	<em>colour</em>\r
+COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>\r
+GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em></pre></strong>\r
+<p>An example Annotation file is given below:\r
+<pre>#Comment lines follow the hash symbol\r
+JALVIEW_ANNOTATION\r
+SEQUENCE_REF	FER1_MESCR	5\r
+BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+\r
+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\r
+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\r
+BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4\r
+NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||\r
+NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n\r
+COLOUR	Bar Graph 2	blue\r
+COLOUR	Red Values	255,0,0\r
+COLOUR	Green Values	green\r
+COLOUR	Purple Letters	151,52,228\r
+COMBINE	Green Values	Red Values\r
+GRAPHLINE	Red Values	2.6	threshold	black\r
+</pre></p>\r