* 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>
+<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