<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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/>.
+ * 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>).
<p><strong><em>Hidden Sequence Representatives and
Multiple Views</em></strong><br>
<em>A word of warning: hidden representative sequence groups are
-only partly implemented in the jalview 2.2 release, and the following
-issues will be resolved in the future.</em><br>
+(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
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
git://source.jalview.org / jalview.git / blobdiff