-<html>\r
-<head><title>Hidden Regions</title></head>\r
-<body>\r
-Now you see them, now you dont \r
-</body>\r
-</html>\r
+<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>
+<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>
git://source.jalview.org / jalview.git / blobdiff