Hidden Regions
Use the keyboard key "H" to hide / reveal selected columns and sequences. To hide / reveal only selected sequences, use "Shift H", to hide / reveal only selected columns, use "Control H".
Hiding Sequences
To hide selected sequences in an alignment, use the "View
-> Hide -> Selected Sequences" menu item or simply select "Hide
Sequences" from the Popup menu after a right click on the sequence
Ids.
Hidden sequences will not be used in any calculations, editing or web service alignments performed on visible sequences.
Hidden Sequences Representatives
A more advanced hide involves a right-mouse click on a sequence, then
selecting "SequenceID -> Represent Group with
SequenceId". Using this method of hiding sequences, any edits
performed on the visible group representative will be propogated to all
the sequences in that group.
The hidden representative sequences will not be used in any calculations
or web service alignments (nb. this may change in the future).
Warning:The representative sequence groups feature is
not fully implemented in the jalview 2.2 release, following the
introduction of Multiple views.
Hiding Columns
To hide selected columns in an alignment, use the "View
-> Hide -> Selected Columns" menu item, or right click within
a region of selected columns in the scale above the alignment (only
available in non wrapped mode) and select "Hide
Columns".
When an alignment view contains hidden columns, certain constraints apply:
Column Separability
Calculations where hidden columns are excluded, and a single analysis
performed on the result, are termed column-separable. The
simple Tree and PCA calculations are column separable because
essentially the same results would be obtained if the excluded hidden
columns were replaced by gaps as the input to the calculation.
Multiple Sequence alignment and secondary structure prediction are both non-column-separable, and so the exclusion of hidden regions leads to only 'locally optimal' results - sometimes different to that obtained when using the full alignment.