2.5 hidden capabilities

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

diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html
index 3f7b599..aae73e8 100644 (file)
--- a/help/html/features/hiddenRegions.html
+++ b/help/html/features/hiddenRegions.html
@@ -7,7 +7,9 @@
 <p>Use the keyboard key &quot;H&quot; to hide / reveal selected
 columns and sequences. To hide / reveal only selected sequences, use
 &quot;Shift H&quot;, to hide / reveal only selected columns, use
-&quot;Control H&quot;.</p>
+&quot;Control H&quot;. You can also use &quot;Shift&quot; and
+&quot;Control&quot; together to hide everything but the currently
+selected region.</p>
 <p><strong><em>Hiding Sequences</em></strong><br>
 To hide selected sequences in an alignment, use the <strong>&quot;View
 -&gt; Hide -&gt; Selected Sequences&quot;</strong> menu item or simply select <strong>&quot;Hide
@@ -23,13 +25,22 @@ performed on the visible group representative will be propogated to all
 the sequences in that group. <br>
 The hidden representative sequences will not be used in any calculations
 or web service alignments (<em>nb. this may change in the future</em>).
-<br>
-<blockquote><em><strong>Warning:</strong>hidden
-representative sequence groups are only partly implemented in the
-jalview 2.2 release. When a hidden representative group is created in
-one alignment view, it will be propagated to all other views. Similarly,
-revealing the represented sequences in one view will reveal them in all
-other views. This will be resolved in a future Jalview release. </em></blockquote>
+<p><strong><em>Hidden Sequence Representatives and
+Multiple Views</em></strong><br>
+<em>A word of warning: hidden representative sequence groups are
+(still) only partly implemented in the jalview 2.5 release, and we hope
+to deal with the following issues in the future.</em><br>
+Currently, represented hidden groups are only made correctly if there is
+just one alignment view. When multiple views on an alignment exist, then
+the represented group will be displayed correctly in the view in which
+it was made, but in other views, both representative and hidden
+sequences will be visible, but will behave as if they are grouped. <br>
+Hidden representatives are propagated correctly to a new view if they
+exist in the current view. However, if the represented sequences are
+revealed in any one view, then in all other views they will simply be
+marked as hidden, and their association with the representative sequence
+will be lost.<br>
+</blockquote>
 </p>
 <p><strong><em>Hiding Columns</em></strong><br>
 To hide selected columns in an alignment, use the <strong>&quot;View
@@ -50,8 +61,8 @@ constraints apply:
        <li><a href="../webservices/msaclient.html">Multiple Sequence
        Alignments</a> are performed locally on on each visible chunk of the input,
        and concatenated with the hidden regions to form the final result.
-       </p>
-       </li>
+</p>
+</li>
 </ul>
 <p><strong>Column Separability</strong><br>
 Calculations where hidden columns are excluded, and a single analysis