JAL-1645 yet more documentation tweaks

[jalview.git] / help / html / features / annotationsFormat.html

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 60c9e23..4c8ad39 100755 (executable)
--- 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>