-<html>\r
-<head>\r
-<title>Multiple Alignment Views</title>\r
-</head>\r
-<body>\r
-<p><strong>Multiple Alignment Views<strong></p>\r
-<p>Multiple alignment views allow's the same alignment to be viewed in\r
-many different ways, either as multiple alignment tabs, or simultaneously in\r
-linked alignment windows. A view is an independent visualization of\r
-the same alignment, so each may have a different ordering, colouring,\r
-row and column hiding and seuqence feature and annotation display\r
-setting, but alignment, feature and annotation edits are common to\r
-all, since this affects the underlying data.\r
-</p>\r
-<p>\r
-A new view is created using the <strong>"View→New View"</strong> menu item, or by pressing\r
-<strong>Control+T</strong>. A newly created view will be identical to\r
-the view it was created from, but any changes to the way the alignment\r
-is coloured or displayed will only affect the new view.\r
-</p>\r
-<p>A particular view may focus on some specific aspect of an alignment -\r
-for example, hiding all but the region of an alignment containing a\r
-particular domain. <strong>Right-clicking</strong> a view's tab opens\r
-the View Name dialog box, allowing it to be renamed to something more\r
-meaningful.\r
-</p>\r
-<p><strong>Viewing Multiple Views Simultaneously</strong></p>\r
-<p>Multiple views of an alignment are, by default, gathered together as tabs\r
-within a single alignment window. They can be viewed simultanously by\r
-pressing <strong>X</strong> (or via\r
-<strong>"View→Expand"</strong>) to expand each view\r
-into its own linked alignment window. Expanded views are gathered\r
-back into into a single tabbed alignment window by pressing\r
-<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>).\r
-</p>\r
-<p><strong>Tree Viewers and Multiple Views</strong></p>\r
-<p>A tree calculated on a particular view, or loaded onto it, is by\r
-default associated with just that view. However, the <a\r
-href="../calculations/treeviewer.html">Tree Viewer's</a> \r
-<strong>"View→Associate leaves"</strong> submenu\r
-allows a tree's view association to be changed to to any or all other\r
-views.</p>\r
-<p><em>Multiple Views were introduced in Jalview 2.2</em></p></body>\r
-</html>
\ No newline at end of file
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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>Multiple Alignment Views</title>
+</head>
+<body>
+ <p>
+ <strong>Multiple Alignment Views</strong>
+ </p>
+ <p>Multiple alignment views allow 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
+ different ordering, colouring, row and column hiding and sequence
+ feature and annotation display setting, but alignment, feature and
+ annotation edits are common to all, since this affects the
+ underlying data.</p>
+ <p>
+ Create a new view using the <strong>"View→New
+ View"</strong> menu item, or by pressing <strong>Control+T</strong>. A
+ newly 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 tab
+ opens the View Name dialog box, allowing it to be renamed to
+ something more meaningful.
+ </p>
+ <p>
+ <strong>Viewing Multiple Views Simultaneously</strong>
+ </p>
+ <p>
+ Multiple views of an alignment are, by default, gathered together as
+ tabs within a single alignment window. They can be viewed
+ simultanously by pressing <strong>X</strong> (or via <strong>"View→Expand"</strong>)
+ to expand each view into its own linked alignment window. Expanded
+ views are gathered back 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
+ default associated with just that view. However, the <a
+ href="../calculations/treeviewer.html">Tree Viewer's</a> <strong>"View→Associate
+ leaves"</strong> submenu allows a tree's view association to be
+ changed to to any or all other views.
+ </p>
+ <p>
+ The results of a <a href="../calculations/pca.html">PCA
+ 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>
+ <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> -->
+ <p>
+ <em>Multiple Views were introduced in Jalview 2.2</em>
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff