-A more advanced hide involves a right-mouse click on a sequence, then selecting
- <strong>"SequenceID -> Represent Group with SequenceId"</strong>. Using this method
- of hiding sequences, any edits performed on the visible group representative
- will be propogated to all 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>)
+A more advanced hide involves a right-mouse click on a sequence, then
+selecting <strong>"SequenceID -> Represent Group with
+SequenceId"</strong>. Using this method of hiding sequences, any edits
+performed on the visible group representative will be propagated to all
+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>).
+<p><strong><em>Hidden Sequence Representatives and
+Multiple Views</em></strong><br>
+<em>A word of warning: hidden representative sequence groups are
+(still) only partly implemented in the jalview 2.5 release, and we hope
+to deal with the following issues 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>