Hidden Regions

From: jprocter Date: Tue, 22 Aug 2006 13:25:47 +0000 (+0000) Subject: added note on column-separability X-Git-Tag: Release_2_1~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=deee703aa93ab0a08d1a5e2aae30cfb14c72ee8d;p=jalview.git added note on column-separability --- diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html index 172ce80..c5266d7 100644 --- a/help/html/features/hiddenRegions.html +++ b/help/html/features/hiddenRegions.html @@ -1,50 +1,53 @@ - -Hidden Regions - -

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) -

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.
-

The analysis and web service calculations where hidden columns are - excluded are termed column-separable. Calculations which - are not column-separable will be performed on the whole alignmnent - or sequence set, not just the visible regions.

- - + +Hidden Regions + +

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) +

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.

+ +