+ 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 sequence + feature and annotation display setting, but alignment, feature and + annotation edits are common to all, since this affects the + underlying data.
++ Create a new view using the "View→New + View" menu item, or by pressing Control+T. A + newly 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 tab + opens the View Name dialog box, allowing it to be renamed to + something more meaningful. +
++ Viewing Multiple Views Simultaneously +
++ Multiple views of an alignment are, by default, gathered together 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 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 + default associated with just that view. However, the Tree Viewer's "View→Associate + leaves" submenu allows a tree's view association to be + changed to to any or all other views. +
++ The results of a PCA + calculation on a particular view may also be associated with other + views, using the PCA Viewer's "View→Associate + Nodes" submenu. +
++ 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 +
+ +