doco changes.

[jalview.git] / help / html / features / annotationsFormat.html

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 18d773c..ba9bc99 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -53,33 +53,30 @@ All Annotations defined after a SEQUENCE_REF command will then be
   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&#9;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&#9;graph name&#9;colour\r
-COMBINE&#9;graph 1 name&#9;graph 2 name\r
-GRAPHLINE&#9;graph name&#9;value&#9;label&#9;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&#9;Bar Graph 1&#9;||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>\r
-  LINE_GRAPH&#9;Green Values&#9;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&#9;Red Values&#9;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&#9;Bar Graph&#9;2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4<br>\r
-  NO_GRAPH&#9;Icons &#9;||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||<br>\r
-  NO_GRAPH&#9;Purple Letters&#9;m|y|p|r|o|t|e|i|n</font></p>\r
-<p><font size="3" face="Courier New, Courier, mono">COLOUR&#9;Bar Graph 2&#9;blue<br>\r
-  COLOUR&#9;Red Values&#9;255,0,0<br>\r
-  COLOUR&#9;Green Values&#9;green<br>\r
-  COLOUR&#9;Purple Letters&#9;151,52,228<br>\r
-  COMBINE&#9;Green Values&#9;Red Values</font></p>\r
-<p><font size="3" face="Courier New, Courier, mono">GRAPHLINE&#9;Red Values&#9;2.6&#9;threshold&#9;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&#9;<em>graph_name</em>&#9;<em>colour</em>\r
+COMBINE&#9;<em>graph_1_name</em>&#9;<em>graph_2_name</em>\r
+GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<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&#9;FER1_MESCR&#9;5\r
+BAR_GRAPH&#9;Bar Graph 1&#9;||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+\r
+LINE_GRAPH&#9;Green Values&#9;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&#9;Red Values&#9;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&#9;Bar Graph&#9;2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4\r
+NO_GRAPH&#9;Icons &#9;||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||\r
+NO_GRAPH&#9;Purple Letters&#9;m|y|p|r|o|t|e|i|n\r
+COLOUR&#9;Bar Graph 2&#9;blue\r
+COLOUR&#9;Red Values&#9;255,0,0\r
+COLOUR&#9;Green Values&#9;green\r
+COLOUR&#9;Purple Letters&#9;151,52,228\r
+COMBINE&#9;Green Values&#9;Red Values\r
+GRAPHLINE&#9;Red Values&#9;2.6&#9;threshold&#9;black\r
+</pre></p>\r
 </body>\r
 </html>\r