X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FhiddenRegions.html;h=63920f51d2dbbfe754cfe948398c57262d1e40e3;hb=6f6f5dd035df25f971ab1191c76bb3bae337e950;hp=3f7b59970a12b98ac1cde5201504ac55c90e7813;hpb=bb5c8d98be1c4965b1a43b97f05b07e9ceb10343;p=jalview.git diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html index 3f7b599..63920f5 100644 --- a/help/html/features/hiddenRegions.html +++ b/help/html/features/hiddenRegions.html @@ -1,4 +1,24 @@ +
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
@@ -19,17 +41,26 @@ web service alignments performed on visible sequences.
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
@@ -47,11 +78,11 @@ constraints apply:
alignment and PCA
calculations will only be performed using the visible parts of
the alignment.
-
Column Separability
Calculations where hidden columns are excluded, and a single analysis