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". You can also use "Shift" and "Control" together to hide everything but the currently selected region.

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).

Hidden Sequence Representatives and Multiple Views
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.
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.
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.

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:

- Editing the alignment is bound by the hidden columns, i.e. you cannot move residues across a hidden column boundary.
- Tree, pairwise alignment and PCA calculations will only be performed using the visible parts of the alignment.
- Multiple Sequence Alignments are performed locally on on each visible chunk of the input, and concatenated with the hidden regions to form the final result.

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.