<title>Multiple Alignment Views</title>
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-<p><strong>Multiple Alignment Views<strong></p>
-<p>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.</p>
-<p>A new view is created using the <strong>"View→New
+<p><strong>Multiple Alignment Views</strong></p>
+<p>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.</p>
+<p>Create a new view using the <strong>"View→New
View"</strong> menu item, or by pressing <strong>Control+T</strong>. 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.</p>
+<!-- TODO sharing selections between views -->
<p>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. <strong>Right-clicking</strong> a view's
are gathered back into into a single tabbed alignment window by pressing
<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>).
</p>
-<p><strong>Tree Viewers, PCA Viewers, and Multiple Views</strong></p>
+<p><strong>Hidden Sequence Representatives and Multiple
+Views</strong></p>
+<p>There are some unexpected interactions between hidden sequence
+representatives and their display in multiple views. See the
+corresponding entry in the <a href="hiddenRegions.html">documentation
+for hidden regions</a>.</p>
+<p><strong>Structure and Analysis Viewers and Multiple
+Views</strong></p>
<p>A tree calculated on a particular view, or loaded onto it, is by
default associated with just that view. However, the <a
href="../calculations/treeviewer.html">Tree Viewer's</a> <strong>"View→Associate
leaves"</strong> submenu allows a tree's view association to be changed to
to any or all other views.</p>
-<p>The results of a <a href="../calculations/pca.html">PCA calculation</a> on a particular view
-may also be associated with other views, using the <strong>"Associate
+<p>The results of a <a href="../calculations/pca.html">PCA
+calculation</a> on a particular view may also be associated with other
+views, using the PCA Viewer's <strong>"View→Associate
Nodes"</strong> submenu.</p>
+<p><a href="jmol.html">PDB Structure Viewers</a>
+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.
+<!--
+ 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.</p> -->
<p><em>Multiple Views were introduced in Jalview 2.2</em></p>
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git://source.jalview.org / jalview.git / blobdiff