<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_SETREF and HIDE_INSERTIONS</a>
+ <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>
<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_SETREF, and HIDE_INSERTIONS</a></strong><br/>
+<p><strong><a name="refsandviews">VIEW_SETREF, VIEW_HIDECOL 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>
<!-- <p>
<em>VIEW_DEF</em> allows the current view to be named according to the
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