JAL-1368 JAL-1628 revise documentation in line with code for VIEW_SETREF, VIEW_HIDECO...

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 2f030fc..ce29e82 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -207,7 +207,7 @@ Group association is turned off for subsequent annotation rows by:
 </p>
 <hr/>
 <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 reference sequences and  hidden regions for an alignment view.</p>
+Since Jalview 2.9, the Annotations file has also supported the definition of reference sequences and hidden regions for an alignment view.</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
@@ -215,23 +215,27 @@ Since Jalview 2.9, the Annotations file has also supported the definition of ref
                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
+               <em>VIEW_SETREF</em> marks the first sequence in the alignment, or
+               alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
+               statement, 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>
+               <em>HIDE_INSERTIONS</em>This command hides all gapped positions in the
+               current target sequence. Any columns already hidden will be
+               re-displayed.<br />
+               <br>The current target sequence is either the one specified by
+               the most recent <em>SEQUENCE_REF</em> statement, the alignment's
+               reference sequence, or the first sequence in 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).
+               <em>VIEW_HIDECOLS</em> modifies the visibility of columns in the view.
+               The statement is followed by a single argument consisting of a comma
+               separated series of single integers or integer pairs (like <em>3-4</em>).
+               These define columns (starting from the left-hand column 0) that
+               should be marked as hidden in the alignment view.
+       </p>
+
        <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