<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
<li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of sequences for further annotation</li>
<li><a href="#groupprops">PROPERTIES</a> to set visualisation properties for sequence groups</li>
<li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for attaching annotation to sequences and groups</li>
-<li><a href="#refsandviews">VIEW_DEF and HIDE_INSERTIONS</a> for creating new views and hiding regions based on gaps in a reference sequence</li>
-</ul>
+ <li><a href="#refsandviews">VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS</a>
+ for defining a reference sequence on the alignment and hiding regions
+ based on gaps in a reference sequence</li>
+ </ul>
<p>
At the end of this document, you can also find notes on <a
href="#compatibility">compatibility</a> of annotation files across
<tr><td width="50%">idColour</td><td>Colour for highlighting the Sequence ID labels for this group<br/>If <em>idColour</em> is given but <em>colour</em> is not, then idColor will also be used for the group background colour.</td></tr>
<tr><td width="50%">showunconserved</td><td>Boolean (default false) indicating whether residues should only be shown that are different from current reference or consensus sequence</td></tr>
<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 SEQUENCE_REF), then all members will be hidden and marked as represented by the reference sequence.</td></tr>
-<tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr></tbody>
+<!-- <tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr> --></tbody>
</table>
<p><strong>Specifying colours in PROPERTIES key-value pairs</strong><br/>
<pre>GROUP_REF	<em>ALIGNMENT</em></pre>
</p>
<hr/>
-<p><strong><a name="refsandviews">VIEW_DEF and HIDE_INSERTIONS</a></strong><br/>
-Since Jalview 2.9, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
-
-<hr/>
+<p><strong><a name="refsandviews">VIEW_SETREF, VIEW_HIDECOL and HIDE_INSERTIONS</a></strong><br/>
+Since Jalview 2.8.3, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
+<!-- <p>
+ <em>VIEW_DEF</em> allows the current view to be named according to the
+ first argument after the tab character. If a second argument is
+ provided, then a new view is created with the given name, and
+ properties.
+ </p> -->
+ <p>
+ <em>VIEW_SETREF</em> takes either a single sequence ID string, or a
+ numeric index (second argument), and attempts to assign a
+ corresponding sequence as the <a href="../features/refsequence.html">reference
+ sequence</a> for the alignment.
+ </p>
+ <em>VIEW_HIDECOLS</em> takes either a single argument consisting of a
+ comma separated series of integer pairs like
+ <em>3-4</em>. These integer pairs define columns (starting from the
+ left-hand column 0) that should be marked as hidden in the alignment
+ view.
+ </p>
+ <p>
+ <em>HIDE_INSERTIONS</em> takes a either a single sequence ID or a
+ numeric index, or no arguments. This command marks all gapped
+ positions in a specified sequence (either the one located by the
+ arguments, the current SEQUENCE_REF, or the reference sequence for the
+ view).
+ <hr/>
<p><strong><a name="compatibility">COMPATIBILITY NOTES</a></strong><br/>
The interpretation of the COMBINE statement in <em>Version 2.8.1</em> was refined
so that only annotation line graphs with the given names ands the same
git://source.jalview.org / jalview.git / blobdiff