the sequences in that group. <br>
The hidden representative sequences will not be used in any calculations
or web service alignments (<em>nb. this may change in the future</em>).
-<br>
-<strong>Warning:</strong>The representative sequence groups feature is
-not fully implemented in the jalview 2.2 release, following the
-introduction of Multiple views.</p>
+<p><strong><em>Hidden Sequence Representatives and
+Multiple Views</em></strong><br>
+<em>A word of warning: hidden representative sequence groups are
+only partly implemented in the jalview 2.2 release, and the following
+issues will be resolved in the future.</em><br>
+Currently, represented hidden groups are only made correctly if there is
+just one alignment view. When multiple views on an alignment exist, then
+the represented group will be displayed correctly in the view in which
+it was made, but in other views, both representative and hidden
+sequences will be visible, but will behave as if they are grouped. <br>
+Hidden representatives are propagated correctly to a new view if they
+exist in the current view. However, if the represented sequences are
+revealed in any one view, then in all other views they will simply be
+marked as hidden, and their association with the representative sequence
+will be lost.<br>
+</blockquote>
+</p>
<p><strong><em>Hiding Columns</em></strong><br>
To hide selected columns in an alignment, use the <strong>"View
-> Hide -> Selected Columns"</strong> menu item, or right click within
git://source.jalview.org / jalview.git / blobdiff