<head><title>Annotations File Format</title></head>\r
\r
<body>\r
-<p><strong>Alignment Annotations File Format<br>\r
+<p><strong>Alignment Annotations File Format</strong><strong><br>\r
</strong><br>\r
- A precalculated annotations fiile can read onto an alignment from the command \r
+ Note: This format is primarily intended to be used for the applet, which does \r
+ not have an XML parser and where file size must be kept to a minimum to reduce \r
+ download time.</p>\r
+<p>A precalculated annotations fiile can read onto an alignment from the command \r
line ("-annotations"), by drag and dropping the the annotations file \r
onto an alignment or by selecting from the File menu "Load Features / Annotations".</p>\r
<p>The File is in tab delimited format. The file must have the line JALVIEW_ANNOTATION \r
associated with that sequence. Use SEQUENCE_REF ALIGNMENT to cancel the associtations.</p>\r
<p>The visual graphs can be coloured or combined with other graphs, or have an \r
arbitrary line drawn at a certain value using the following lines.</p>\r
-<p><font size="2" face="Courier New, Courier, mono">COLOUR<tab>graph name<tab>colour<br>\r
+<p><font size="3" face="Courier New, Courier, mono">COLOUR<tab>graph name<tab>colour<br>\r
COMBINE<tab>graph 1 name<tab>graph 2 name<br>\r
GRAPHLINE<tab>graph name<tab>value<tab>label<tab>colour</font></p>\r
<p>An example Annotation file may look like this:</p>\r
-<p><font size="2" face="Courier New, Courier, mono">#Comment lines follow the hash symbol<br>\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<tab>Bar Graph 1<tab>||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>\r
BAR_GRAPH<tab>Bar Graph<tab>2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4<br>\r
NO_GRAPH<tab>Icons <tab>||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||<br>\r
NO_GRAPH<tab>Purple Letters<tab>m|y|p|r|o|t|e|i|n</font></p>\r
-<p><font size="2" face="Courier New, Courier, mono">COLOUR<tab>Bar Graph 2<tab>blue<br>\r
+<p><font size="3" face="Courier New, Courier, mono">COLOUR<tab>Bar Graph 2<tab>blue<br>\r
COLOUR<tab>Red Values<tab>255,0,0<br>\r
COLOUR<tab>Green Values<tab>green<br>\r
COLOUR<tab>Purple Letters<tab>151,52,228<br>\r
COMBINE<tab>Green Values<tab>Red Values</font></p>\r
-<p><font size="2" face="Courier New, Courier, mono">GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black \r
+<p><font size="3" face="Courier New, Courier, mono">GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black \r
</font><br>\r
</p>\r
<p><br>\r