From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 22 Jan 2015 17:28:43 +0000 (+0000)
Subject: JAL-1372 JAL-1169 documentation for new commands HIDE_INSERTIONS AND VIEW_SETREF
X-Git-Tag: Jalview_2_9~108^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=24c13cae7ab462fb159be2daa62ef7e7c812e0e9;p=jalview.git

JAL-1372 JAL-1169 documentation for new commands HIDE_INSERTIONS AND VIEW_SETREF
---

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 5012124..90dfd9b 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -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 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
@@ -204,10 +206,27 @@ 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, 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>
+	<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