<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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+ *
+ * Jalview is free software: you can redistribute it and/or
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+ * of the License, or (at your option) any later version.
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+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<head>
<title>Hidden Regions</title>
</head>
<p>Use the keyboard key "H" to hide / reveal selected
columns and sequences. To hide / reveal only selected sequences, use
"Shift H", to hide / reveal only selected columns, use
-"Control H".</p>
+"Control H". You can also use "Shift" and
+"Control" 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>"View
-> Hide -> Selected Sequences"</strong> menu item or simply select <strong>"Hide
A more advanced hide involves a right-mouse click on a sequence, then
selecting <strong>"SequenceID -> Represent Group with
SequenceId"</strong>. Using this method of hiding sequences, any edits
-performed on the visible group representative will be propogated to all
+performed on the visible group representative will be propagated 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>"View
alignment</a></strong> and <strong><a href="../calculations/pca.html">PCA</a></strong>
calculations will only be performed using the <em>visible</em> parts of
the alignment.</li>
- <li><a href="../webservices/msaclient.html">Multiple Sequence
+ <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