From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 6 Sep 2015 16:17:49 +0000 (+0100)
Subject: JAL-1368 JAL-1628 revise documentation in line with code for VIEW_SETREF, VIEW_HIDECO... 
X-Git-Tag: Release_2_10_0~485
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=80f48b214af181a923d116e4fa5aa83c32f40bbc;p=jalview.git

JAL-1368 JAL-1628 revise documentation in line with code for VIEW_SETREF, VIEW_HIDECOLS, and VIEW_HIDE_INSERTIONS.
---

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 2f030fc..ce29e82 100755
--- 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