<html>
-<head>
-<title>Hidden Regions</title>
-</head>
-<body>
-<p><strong>Hidden Regions</strong></p>
-<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". 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
-Sequences"</strong> from the Popup menu after a right click on the sequence
-Ids.</p>
-<p>Hidden sequences will not be used in any calculations, editing or
-web service alignments performed on visible sequences.</p>
-<p><strong><em>Hidden Sequences Representatives</em></strong><br>
-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
-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
-(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
-a region of selected columns in the scale above the alignment (only
-available in non wrapped mode) and select <strong>"Hide
-Columns"</strong>.</p>
-<p>When an alignment view contains hidden columns, certain
-constraints apply:
-<ul>
- <li>Editing the alignment is bound by the hidden columns, <em>i.e.</em>
- you cannot move residues across a hidden column boundary.</li>
- <li><strong><a href="../calculations/tree.html">Tree</a></strong>,
- <strong><a href="../calculations/pairwise.html">pairwise
- 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
- 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>
-</ul>
-<p><strong>Column Separability</strong><br>
-Calculations where hidden columns are excluded, and a single analysis
-performed on the result, are termed <em>column-separable</em>. The
-simple Tree and PCA calculations are column separable because
-essentially the same results would be obtained if the excluded hidden
-columns were replaced by gaps as the input to the calculation.</p>
-<p>Multiple Sequence alignment and secondary structure prediction
-are both non-column-separable, and so the exclusion of hidden regions
-leads to only 'locally optimal' results - sometimes different to that
-obtained when using the full alignment.</p>
-<p> </p>
-<p> </p>
-<p> </p>
-</body>
-</html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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/>.
+-->
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