-<html>\r
-<head>\r
-<title>Multiple Alignment Views</title>\r
-</head>\r
-<body>\r
-<p><strong>Multiple Alignment Views</strong></p>\r
-<p>Multiple alignment views allows the same alignment to be viewed\r
-independently in many different ways simultaneously. Each view is an\r
-independent visualization of the same alignment, so each may have a\r
-different ordering, colouring, row and column hiding and seuqence\r
-feature and annotation display setting, but alignment, feature and\r
-annotation edits are common to all, since this affects the underlying\r
-data.</p>\r
-<p>Create a new view using the <strong>"View→New\r
-View"</strong> menu item, or by pressing <strong>Control+T</strong>. A newly\r
-created view will be identical to the view it was created from, but any\r
-changes to the way the alignment is coloured or displayed will only\r
-affect the new view.</p>\r
-<p>A particular view may focus on some specific aspect of an\r
-alignment - for example, hiding all but the region of an alignment\r
-containing a particular domain. <strong>Right-clicking</strong> a view's\r
-tab opens the View Name dialog box, allowing it to be renamed to\r
-something more meaningful.</p>\r
-<p><strong>Viewing Multiple Views Simultaneously</strong></p>\r
-<p>Multiple views of an alignment are, by default, gathered together\r
-as tabs within a single alignment window. They can be viewed\r
-simultanously by pressing <strong>X</strong> (or via <strong>"View→Expand"</strong>)\r
-to expand each view into its own linked alignment window. Expanded views\r
-are gathered back into into a single tabbed alignment window by pressing\r
-<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>).\r
-</p>\r
-<p><strong>Hidden Sequence Representatives and Multiple\r
-Views</strong></p>\r
-<p>There are some unexpected interactions between hidden sequence\r
-representatives and their display in multiple views. See the\r
-corresponding entry in the <a href="hiddenRegions.html">documentation\r
-for hidden regions</a>.</p>\r
-<p><strong>Structure and Analysis Viewers and Multiple\r
-Views</strong></p>\r
-<p>A tree calculated on a particular view, or loaded onto it, is by\r
-default associated with just that view. However, the <a\r
- href="../calculations/treeviewer.html">Tree Viewer's</a> <strong>"View→Associate\r
-leaves"</strong> submenu allows a tree's view association to be changed to\r
-to any or all other views.</p>\r
-<p>The results of a <a href="../calculations/pca.html">PCA\r
-calculation</a> on a particular view may also be associated with other\r
-views, using the PCA Viewer's <strong>"View→Associate\r
-Nodes"</strong> submenu.</p>\r
-<p>Currently, a <a href="pdbviewer.html">PDB Structure Viewer</a>\r
-opened on a structure associated with a sequence in a particular view\r
-will only be associated with the seuqence as displayed in that view. <br>\r
-<em>This will be resolved in a future release</em><!-- also, by default, only be associated\r
-with the sequence as it is displayed in that view. The\r
-"View→Associate View" submenu allows the association of\r
-alternative views.</p> -->\r
-<p><em>Multiple Views were introduced in Jalview 2.2</em></p>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>Multiple Alignment Views</title>
+</head>
+<body>
+<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>
+<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 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 / commitdiff