Multiple Alignment Views
-Multiple alignment views allows the same alignment to be viewed +
Multiple Alignment Views
+Multiple alignment views allow the same alignment to be viewed independently in many different ways simultaneously. Each view is an independent visualization of the same alignment, so each may have a -different ordering, colouring, row and column hiding and seuqence +different ordering, colouring, row and column hiding and sequence feature and annotation display setting, but alignment, feature and annotation edits are common to all, since this affects the underlying data.
@@ -16,6 +36,7 @@ View" menu item, or by pressing Control+T. A newl created view will be identical to the view it was created from, but any changes to the way the alignment is coloured or displayed will only affect the new view. +A particular view may focus on some specific aspect of an alignment - for example, hiding all but the region of an alignment containing a particular domain. Right-clicking a view's @@ -26,9 +47,15 @@ something more meaningful.
as tabs within a single alignment window. They can be viewed simultanously by pressing X (or via "View→Expand") to expand each view into its own linked alignment window. Expanded views -are gathered back into into a single tabbed alignment window by pressing -G, or by selecting "View→Gather"). +are gathered back into a single tabbed alignment window by pressing +G, or by selecting "View→Gather". +Hidden Sequence Representatives and Multiple +Views
+There are some unexpected interactions between hidden sequence +representatives and their display in multiple views. See the +corresponding entry in the documentation +for hidden regions.
Structure and Analysis Viewers and Multiple Views
A tree calculated on a particular view, or loaded onto it, is by @@ -40,11 +67,13 @@ to any or all other views.
calculation on a particular view may also be associated with other views, using the PCA Viewer's "View→Associate Nodes" submenu. -A PDB Structure Viewer opened on a -structure associated with a sequence in a particular view will also, by -default, only be associated with the sequence as it is displayed in that -view. The "View→Associate View" submenu allows the -association of alternative views.
+PDB Structure Viewers +opened on a structure associated with a sequence in a particular view are now (as of Jalview 2.3) associated with the same sequence in all views. This means that when 'Colour by Sequence' is selected in the structure view, the colour will be updated to the colours given in the view with the current input focus. +
Multiple Views were introduced in Jalview 2.2