<html>\r
\r
-<head><title>Annotations File Format</title></head>\r
+<head><title>The Alignment Annotations File</title></head>\r
\r
<body>\r
-<p><strong>Alignment Annotations File Format</strong><strong><br>\r
- </strong><br>\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
- as an identifier. Then a block of annotations are added in the form GRAPH_TYPE \r
- Label Values</p>\r
-<p>GRAPH_TYPE can be either BAR_GRAPH, LINE_GRAPH or NO_GRAPH. The values are \r
- per alignment column, separated by "|". Multiple content per column \r
- can be separated with commas, Jalview will display the content if it interprates \r
- the content as a text label, or secondary structure character (H or E)</p>\r
-<p>You can optionally associate an annotation with a sequence by adding a line \r
- SEQUENCE_REFseq_namestartIndex All Annotations after a SEQUENCE_REF will be \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="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><strong>The Alignment Annotations File</strong></p>\r
+<p>Alignment annotations can be imported onto an alignment since\r
+ version 2.08 of Jalview, via an annotations file. It is a simple\r
+ ASCII text file consisting of tab\r
+ delimited records similar to the <a\r
+ href="featuresFormat.html">Sequence Features File</a>, and\r
+ introduced primarily for use with the Jalview applet.</p>\r
+<p>Alignment annotations files are imported into Jalview in the\r
+following ways:<br>\r
+<ul>\r
+<li>from the command line<strong><pre>\r
+ -annotations <<em>Annotations filename</em>></pre></strong></li>\r
+<li>Dragging an annotations file onto an alignment window</li>\r
+<li>Via the "Load Features / Annotations" entry in the\r
+<strong>File</strong> menu of an alignment window.</li>\r
+</ul>\r
+</p>\r
+<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
+ 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<tab>Bar Graph 1<tab>||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+<br>\r
- 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>\r
- 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>\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="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="3" face="Courier New, Courier, mono">GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black \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
git://source.jalview.org / jalview.git / blobdiff