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: -
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.
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