X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FhiddenRegions.html;h=3bfa29312a73fe46041bb177608e4feda71456df;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=3f7b59970a12b98ac1cde5201504ac55c90e7813;hpb=bb5c8d98be1c4965b1a43b97f05b07e9ceb10343;p=jalview.git diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html index 3f7b599..3bfa293 100644 --- a/help/html/features/hiddenRegions.html +++ b/help/html/features/hiddenRegions.html @@ -1,4 +1,21 @@ + Hidden Regions @@ -7,7 +24,9 @@

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".

+"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 @@ -23,13 +42,22 @@ 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). -
-

Warning:hidden -representative sequence groups are only partly implemented in the -jalview 2.2 release. When a hidden representative group is created in -one alignment view, it will be propagated to all other views. Similarly, -revealing the represented sequences in one view will reveal them in all -other views. This will be resolved in a future Jalview release.
+

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 @@ -50,8 +78,8 @@ constraints apply:

  • 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