Details
Description
TIny wrinkle due to jalview.datamodel.Alignment not implementing the getSequences(hidden reps) method correctly: the conservation and consensus rows computed for a view do not include variation due to hidden representatives, whereas the group-wise rows do (but only if the group actually contained the sequences that have been represented by another).
>a
AAAAAAAAAAA
>c1
CCCCCCCCCC
>c2
CCCCCCCCCC
>c3
CCCCCCCCCC
>v
VVVVVVVVVVV
Import, show sequence logo for whole view, and enable show group consensus. Create a group containing all sequences. Note C abundance is same as in global consensus. Now press escape to clear selection. Then select c1-c3 and mark as represented by c1. The C abundance is present in the group consensus, but not the alignment consensus.
>a
AAAAAAAAAAA
>c1
CCCCCCCCCC
>c2
CCCCCCCCCC
>c3
CCCCCCCCCC
>v
VVVVVVVVVVV
Import, show sequence logo for whole view, and enable show group consensus. Create a group containing all sequences. Note C abundance is same as in global consensus. Now press escape to clear selection. Then select c1-c3 and mark as represented by c1. The C abundance is present in the group consensus, but not the alignment consensus.