<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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>Overview Window</title></head>
+ * 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.
-</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><img src="overview.gif" width="407" height="137"></p>
-<p> </p>
+ <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