Hidden Regions
-Use the keyboard key "H" to hide / reveal selected columns and sequences.
-To hide selected sequences from 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.
-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 sequences will not be used in any calculations or web service alignments.
-
-
To hide selected columns from 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".
-Hidden columns will not be used in any calculations. This allows you to eg.
- create trees from the visible alignment and ignore any poorly aligned sections
- of the alignment, without cutting and deleting them permanently from your alignment.
- It is possible to retrieve the input data to any trees, PCA analysis windows
- which were created from alignments containing hidden columns by using the "File
- -> Input Data..." menu item from the tree window.
Editing the alignment is bound by the hidden columns, ie you cannot move residues - across a hidden column boundary.
-Any web service alignments performed on sequences which contain hidden columns - send the alignment as a series of chunks delimited by the hidden columns.
--
-
- - + + + +
+ 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 propagated 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.
++
+
+ +