<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<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
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>
-<strong>Warning:</strong>The representative sequence groups feature is
-not fully implemented in the jalview 2.2 release, following the
-introduction of Multiple views.</p>
+<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
-> Hide -> Selected Columns"</strong> menu item, or right click within
<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
git://source.jalview.org / jalview.git / blobdiff