X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=eeee788cf296fb3697dbc6acc23ef8b4a4f6dba7;hb=f27f81a74bbe1be141d23df8aba578515e3179a2;hp=90dfd9bc22a8a59ec78892033503387b6f3366c2;hpb=24c13cae7ab462fb159be2daa62ef7e7c812e0e9;p=jalview.git

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 90dfd9b..eeee788 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -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/>
@@ -206,8 +206,8 @@ 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/>
-Since Jalview 2.9, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
+<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
@@ -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
