Multiple Alignment Views
-Multiple alignment views allow's the same alignment to be viewed in -many different ways, either as multiple alignment tabs, or simultaneously in -linked alignment windows. A view is an independent visualization of -the same alignment, so each may have a different ordering, colouring, -row and column hiding and seuqence feature and annotation display -setting, but alignment, feature and annotation edits are common to -all, since this affects the underlying data. -
--A new view is created 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 into a single tabbed alignment window by pressing -G, or by selecting "View→Gather"). -
-Tree 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.
-Multiple Views were introduced in Jalview 2.2
- \ No newline at end of file + + +Multiple Alignment Views
+Multiple alignment views allows 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 +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 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.
+Currently, a PDB Structure Viewer
+opened on a structure associated with a sequence in a particular view
+will only be associated with the seuqence as displayed in that view.
+This will be resolved in a future release
+
Multiple Views were introduced in Jalview 2.2
+ +