-<html>\r
-<body>\r
-\r
-<p>Select the overview window to get a navigable image of the whole alignment.\r
-</p>\r
-<p>The window indicates the current viewable region of the alignment, this area\r
- may be adjusted by clicking and dragging with the mouse.</p>\r
-<p>Note: It may not be possible to view very large alignments with the overview\r
- window due to lack of application memory. </p>\r
-<p><img src="../images/overview.gif" width="407" height="137"></p>\r
-</body>\r
-</html>\r
+<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>Overview Window</title>
+</head>
+<body>
+ <p>
+ <strong>View→Overview window</strong>
+ </p>
+ <p>Select the overview window menu item to get a navigable image
+ of the whole alignment. By default, gaps are shown as dark grey, in
+ the overview (since 2.10.2b1).</p>
+ <p>The red box indicates the currently viewed region of the
+ alignment, this may be moved by clicking and dragging with the
+ mouse.</p>
+ <p>Click anywhere else in the overview to centre the view on that
+ position</p>
+ <p></p>
+ <p>
+ <strong>Hiding hidden regions in the overview</strong>
+ </p>
+ <p>
+ Hidden sequences and columns are by default shown as dark-grey rows
+ and columns in the overview. Hidden regions can also be omitted
+ entirely (to make the Overview 'WYSIWIG') by <strong>Right-clicking</strong>
+ (or CMD-Clicking) to open the overview's popup menu.<br /> <br />
+ <em>The option to include/exclude hidden regions in the
+ overview was introduced in Jalview 2.10.2</em>.
+
+ <p>
+ <img src="overview.png" width="800" height="196" alt="1hdc.pfam example alignment">
+ </p>
+ <p> </p>
+ <em>Previous to 2.10.2b1, gaps were white, and sequences shown as
+ dark grey unless coloured.</em>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff