X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;fp=help%2Fhtml%2Ffeatures%2FannotationsFormat.html;h=4c8ad39f1bc5dc385c804dd537577ecc41f9da0c;hb=de255c8c87707a2cd2a2a15f5ad04ed10fe5846d;hp=60c9e23c032134734686d8fe852b7b358487086b;hpb=d924d4634167f98c9fd94df6714a6589c1368da3;p=jalview.git

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 60c9e23..4c8ad39 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -211,38 +211,43 @@ 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_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>
-<!-- 	<p>
+  <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>
+  <!-- 	<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> 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>
-	<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>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>
+  <p>
+    <em>VIEW_SETREF</em><br />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="../calculations/referenceseq.html">reference
+      sequence</a> for the alignment.
+  </p>
+  <p>
+    <em>HIDE_INSERTIONS</em><br />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>VIEW_HIDECOLS</em><br />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/>
+  <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 
  <strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong> scope are grouped.</p>