JAL-1628 tweak signature of core annotation printer for outputting hidden columns...

[jalview.git] / help / html / features / annotationsFormat.html

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 90dfd9b..72691ce 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -60,7 +60,7 @@ ignored. The sections below describe the structure of an annotation file.
 <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>
@@ -168,7 +168,7 @@ of sequence IDs. </p>
 <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/>
@@ -206,7 +206,7 @@ Group association is turned off for subsequent annotation rows by:
 <pre>GROUP_REF&#9;<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
@@ -220,6 +220,12 @@ Since Jalview 2.9, the Annotations file has also supported the definition of vie
                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