-<html>\r
-\r
-<head><title>The Alignment Annotations File</title></head>\r
-\r
-<body>\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
- (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
+<html>
+
+<head>
+<title>The Alignment Annotations File</title>
+</head>
+
+<body>
+<p><strong>The Alignment Annotations File</strong></p>
+<p>Alignment annotations can be imported onto an alignment since
+version 2.08 of Jalview, via an annotations file. It is a simple ASCII
+text file consisting of tab delimited records similar to the <a
+ href="featuresFormat.html">Sequence Features File</a>, and introduced
+primarily for use with the Jalview applet.</p>
+<p>Alignment annotations files are imported into Jalview in the
+following ways:<br>
+<ul>
+ <li>from the command line<strong><pre>
+ -annotations <<em>Annotations filename</em>></pre></strong></li>
+ <li>Dragging an annotations file onto an alignment window</li>
+ <li>Via the "Load Features / Annotations" entry in the <strong>File</strong>
+ menu of an alignment window.</li>
+</ul>
+</p>
+<p><strong>Annotations File Format</strong></p>
+<p>The File consists of lines containing an instruction followed by
+tab delimited fields, and any lines starting with "#" are
+ignored. The first non-commented out line of a valid Annotations file
+must begin with :<strong><pre>JALVIEW_ANNOTATION</pre></strong></p>
+<p>A row of annotation is added with a line like <strong><pre><em>GRAPH_TYPE</em>	<em>Label</em>	<em>Values</em></pre></strong></p>
+<p>The <em>GRAPH_TYPE</em> field, which appears first, defines the
+appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. The final <em>Values</em> field contains a series of "|"
+separated value fields. Each value field is itself a comma separated list of fields of a particular type defined by the annotation row's
+GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "<strong>|</strong>" symbol) are shown below:<ul>
+ <li>BAR_GRAPH<br>
+ Plots a histogram with labels below each bar.<br>
+ <em>number</em>,<em>text character</em></li>
+ <li>LINE_GRAPH<br>
+ Draws a line between values on the annotation row.<br>
+ <em>number</em></li>
+ <li>NO_GRAPH<br>
+ For a row consisting of text labels and/or secondary structure symbols.<br>
+ <em>{Secondary Structure Symbol}</em>,<em>text label</em><br>
+ Currently supported secondary structure structure symbols are <em>H</em> (for helix) and <em>E</em> (for strand)</li>
+</ul>
+Any or all value fields may be left empty, as well as the BAR_GRAPH's
+text character field, and either or both of the text-label and secondary
+structure symbol fields of the NO_GRAPH type annotation rows.
+</p>
+<p>You can associate an annotation with a sequence by preceding its
+definition with the line: <strong><pre>SEQUENCE_REF	<em>seq_name</em>	<em>[startIndex]</em></pre></strong>
+All Annotations defined after a SEQUENCE_REF command will then be
+associated with that sequence, and the first field in the Value field
+list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
+<p>Sequence associations are turned off for subsequent annotation
+definitions by: <strong><pre>SEQUENCE_REF	ALIGNMENT</pre></strong></p>
+<p><em>LINE_GRAPH</em> type annotations can be given a colour
+(specified as 24 bit RGB triplet in hexadecimal or comma separated
+values), combined onto the same vertical axis, and have ordinate lines
+(horizontal lines at a particular vertical axis value) using the
+following commands (respectively): <strong><pre>COLOUR	<em>graph_name</em>	<em>colour</em>
+COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>
+GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em></pre></strong>
+<p>An example Annotation file is given below:
+<pre>#Comment lines follow the hash symbol
+JALVIEW_ANNOTATION
+SEQUENCE_REF	FER1_MESCR	5
+BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+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
+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
+BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
+COLOUR	Bar Graph 2	blue
+COLOUR	Red Values	255,0,0
+COLOUR	Green Values	green
+COLOUR	Purple Letters	151,52,228
+COMBINE	Green Values	Red Values
+GRAPHLINE	Red Values	2.6	threshold	black
+</pre>
+</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff