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
- combined onto the same vertical axis, and have abscissa (lines of\r
- constant value - <em>so they are horizontal</em>) at particular\r
- values using the following lines (respectively):<!--</p>\r
-<p><font size="3" face="Courier New, Courier, mono">-->\r
-<strong><pre>COLOUR	graph name	colour\r
-COMBINE	graph 1 name	graph 2 name\r
-GRAPHLINE	graph name	value	label	colour</pre></strong></p>\r
-<p>An example Annotation file is given below:</p>\r
-<p><font size="3" face="Courier New, Courier, mono">#Comment lines follow the hash symbol<br>\r
- JALVIEW_ANNOTATION<br>\r
- SEQUENCE_REF FER1_MESCR 5<br>\r
- BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>\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<br>\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<br>\r
- BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4<br>\r
- NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||<br>\r
- NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n</font></p>\r
-<p><font size="3" face="Courier New, Courier, mono">COLOUR	Bar Graph 2	blue<br>\r
- COLOUR	Red Values	255,0,0<br>\r
- COLOUR	Green Values	green<br>\r
- COLOUR	Purple Letters	151,52,228<br>\r
- COMBINE	Green Values	Red Values</font></p>\r
-<p><font size="3" face="Courier New, Courier, mono">GRAPHLINE	Red Values	2.6	threshold	black \r
- </font><br>\r
-</p>\r
-<p><br>\r
-</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
</body>\r
</html>\r