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".
+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.
+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)
+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:
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.
+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.