X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=e5e1fdb2ca619bc813da39906dd907cd10d6faf7;hb=25aaaa87042b3f507ad4348120df7dd073182759;hp=5012124ff843f0b36ceb218ce3c7787336a9225e;hpb=5f9c8558cfee09b2ba2a13226f5bd4188e299135;p=jalview.git

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 5012124..e5e1fdb 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -1,6 +1,6 @@
 <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.
@@ -60,8 +60,10 @@ 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_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
@@ -166,7 +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/>
@@ -204,10 +206,33 @@ 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_DEF 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>
-
-<hr/>
+<!-- 	<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 
