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 (executable)
--- 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