<html>
-<head><title>What's new ?</title></head>
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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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+ * This file is part of Jalview.
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+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>What's new ?</title>
+</head>
<body>
-<p><strong>What's new ?</strong> </p>
-<p>If you are reading this then you will already have seen some of the recent changes
- made to Jalview.<br>
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window. </p>
-<p>If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:</p>
-<ul>
- <li>Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.</li>
- <li>To insert or edit the gaps in one sequence in alignment, the
- "Shift" key must be held down when dragging the mouse.</li>
- <li>To insert or edit gaps for a group of sequences, the
- "Alt" key (or in X windows the "Control"
- key) must be held down.</li>
- <li>Selecting colour schemes in the colour menu either sets just the
- "background" colourscheme for the alignment, or - when
- the tickbox "Apply colour to all groups" is ticked,
- applies the scheme to the background and all groups defined on the alignment.</li>
- <li>Use the right mouse button (apple and click on the Mac) whilst
- the pointer is within the selection area to access the "define" region menu to
- define a new region, give it a name, and change its colourscheme and display
- properties.</li>
- <li>Conservation is automatically updated whenever the alignment is edited</li>
- <li>There is no "quick draw" option</li>
- <li>Edits can be undone, and redone!</li>
-</ul>
+ <p>
+ <strong>What's new in Jalview 2.10.2 ?</strong>
+ </p>
+ <p>
+ Full details about Jalview 2.10.2 are in the <a
+ href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
+ highlights are below.
+ </p>
+ <ul>
+ <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
+ Several of the programs provided as services have been updated, so
+ their options and parameters have changed.</li>
+ <li>New preferences for <a href="webServices/urllinks.html">opening
+ web pages for database cross-references</a> via the UK Elixir's
+ EMBL-EBI's MIRIAM database and identifiers.org services.
+ </li>
+ <li><em>Showing and hiding regions</em>
+ <ul>
+ <li><a href="menus/popupMenu.html#hideinserts">Hide
+ insertions</a> in the PopUp menu has changed its behaviour.
+ Prior to 2.10.2, columns were only shown or hidden according
+ to gaps in the sequence under the popup menu. Now, only
+ columns that are gapped in all selected sequences as well as
+ the sequence under the popup menu are hidden, and column
+ visibility outside the selected region is left as is. This
+ makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove)
+ without affecting the rest of the hidden columns.</li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the <strong>Tools→Enable
+ Experimental Features</strong> option, and then restart Jalview.
+ </p>
+ <ul>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff