<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>Multiple Alignment Views</title>
</head>
<body>
-<p><strong>Multiple Alignment Views<strong></p>
+<p><strong>Multiple Alignment Views</strong></p>
<p>Multiple alignment views allows the same alignment to be viewed
independently in many different ways simultaneously. Each view is an
independent visualization of the same alignment, so each may have a
created view will be identical to the view it was created from, but any
changes to the way the alignment is coloured or displayed will only
affect the new view.</p>
+<!-- TODO sharing selections between views -->
<p>A particular view may focus on some specific aspect of an
alignment - for example, hiding all but the region of an alignment
containing a particular domain. <strong>Right-clicking</strong> a view's
are gathered back into into a single tabbed alignment window by pressing
<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>).
</p>
+<p><strong>Hidden Sequence Representatives and Multiple
+Views</strong></p>
+<p>There are some unexpected interactions between hidden sequence
+representatives and their display in multiple views. See the
+corresponding entry in the <a href="hiddenRegions.html">documentation
+for hidden regions</a>.</p>
<p><strong>Structure and Analysis Viewers and Multiple
Views</strong></p>
<p>A tree calculated on a particular view, or loaded onto it, is by
calculation</a> on a particular view may also be associated with other
views, using the PCA Viewer's <strong>"View→Associate
Nodes"</strong> submenu.</p>
-<p>Currently, a <a href="pdbviewer.html">PDB Structure Viewer</a>
-opened on a structure associated with a sequence in a particular view
-will only be associated with the seuqence as displayed in that view. <br><em>This
-will be resolved in a future release</em><!-- also, by default, only be associated
+<p><a href="jmol.html">PDB Structure Viewers</a>
+opened on a structure associated with a sequence in a particular view are now (as of Jalview 2.3) associated with the same sequence in all views. This means that when 'Colour by Sequence' is selected in the structure view, the colour will be updated to the colours given in the view with the current input focus.
+<!--
+ also, by default, only be associated
with the sequence as it is displayed in that view. The
"View→Associate View" submenu allows the association of
alternative views.</p> -->
git://source.jalview.org / jalview.git / blobdiff