<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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.
+ href="featuresFormat.html">Sequence Features File</a>, and
+ introduced primarily for use with the Jalview applet.
</p>
<p>
alignment window.
</p>
<p>
- <strong>THE ANNOTATION FILE FORMAT</strong> <br />An annotation file
- consists of lines containing an instruction followed by tab
+ <strong>THE ANNOTATION FILE FORMAT</strong> <br />An annotation
+ file consists of lines containing an instruction followed by tab
delimited fields. Any lines starting with "#" are
considered comments, and ignored. The sections below describe the
structure of an annotation file.
</ul>
<p>
At the end of this document, you can also find notes on <a
- href="#compatibility"
- >compatibility</a> of annotation files across different versions of
- Jalview. An <a href="#exampleann">example annotation file</a> is
- also provided along with instructions on how to import it to
- Jalview.
+ href="#compatibility">compatibility</a> of annotation files
+ across different versions of Jalview. An <a href="#exampleann">example
+ annotation file</a> is also provided along with instructions on how to
+ import it to Jalview.
</p>
<hr />
<p>
followed by a <em>description</em> for the row, which is shown in a
tooltip when the user mouses over the annotation row's label. Since
Jalview 2.7, the description field may also contain HTML tags (in
- the same way as a <a href="featuresFile.html">sequence feature's</a>
- label), providing the text is enclosed in an <html/> tag.
+ the same way as a <a href="featuresFormat.html">sequence
+ feature's</a> label), providing the text is enclosed in an
+ <html/> tag.
<ul>
<em>Please note: URL links embedded in HTML descriptions are
not yet supported.</em>
<em>GRAPH_TYPE</em>. The allowed values of <em>GRAPH_TYPE</em> and
corresponding interpretation of each <em>Value</em> are shown below:
+
<ul>
<li><strong>BAR_GRAPH</strong><br> Plots a histogram with
</ul>
</p>
<p>
- <strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br /> Groups
- of sequences and column ranges can be defined using a tab delimited
- statement like:
+ <strong><a name="groupdefs">SEQUENCE_GROUP</a></strong><br />
+ Groups of sequences and column ranges can be defined using a tab
+ delimited statement like:
</p>
<pre>SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	<em>Sequences</em>
</pre>
<tr>
<td width="50%">hide</td>
<td>Boolean (default false) indicating whether the rows in
- this group should be marked as hidden.<br />
- <em>Note:</em> if the group is sequence associated (specified by
+ this group should be marked as hidden.<br /> <em>Note:</em>
+ if the group is sequence associated (specified by
SEQUENCE_REF), then all members will be hidden and marked as
represented by the reference sequence.
</td>