<strong>View→Overview window</strong>
</p>
<p>Select the overview window menu item to get a navigable image
- of the whole alignment.</p>
+ 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>
- <img src="overview.gif" width="407" height="137">
+ <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>
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