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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Multiple Alignment Views</title>
-</head>
-<body>
- <p>
- <strong>Multiple Alignment Views</strong>
- </p>
- <p>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.</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 tab
- opens the View Name dialog box, allowing it to be renamed to
- something more meaningful.
- </p>
- <p>
- <strong>Viewing Multiple Views Simultaneously</strong>
- </p>
- <p>
- Multiple views of an alignment are, by default, gathered together as
- tabs within a single alignment window. They can be viewed
- simultanously by pressing <strong>X</strong> (or via <strong>"View→Expand"</strong>)
- to expand each view into its own linked alignment window. Expanded
- views are gathered back into a single tabbed alignment window by
- pressing <strong>G</strong>, or by selecting <strong>"View→Gather"</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 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>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff