</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10.2 ?</strong>
</p>
<p>
- Jalview 2.9.1 is the next major release in the Jalview 2.9 series. Full details are in the
- <a href="releases.html#Jalview.2.9.1">Jalview 2.9.1 Release Notes</a>.
+ 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>New UI, and faster and more configurable
+ implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
+ Menu entries for calculating PCA and different types of tree have
+ been replaced by a single <em>Calculations</em> dialog box. The
+ underlying implementation for the PCA and tree calculations have
+ been made faster and more memory efficient. A new framework has
+ also been created for the score models used to calculate distances
+ between sequences. This framework allows import of substitution
+ matrices in NCBI and AAIndex format, and custom score models to be
+ created via a groovy script.</li>
+ <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>
+ <li>Recent search histories for <a
+ href="features/search.html#queryhistory">Find</a> and the free
+ text search system (for querying Uniprot and the PDBe).</li>
+ </ul>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
</p>
<p>
- <strong>Highlights in Jalview 2.9.1</strong>
+ 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>
-
+ <p>
+ <strong>Scripting</strong><br />New <a
+ href="http://www.jalview.org/examples/groovy">groovy examples</a>
+ demonstrate Jalview 2.10.2 APIs for creation of data-driven
+ colourschemes, and custom alignment file handlers. The <a
+ href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
+ introduced in Jalview 2.10 has also been refactored to allow
+ efficient counting across multiple feature types. Please be aware
+ that feature counter scripts created for earlier versions will not
+ execute in Jalview 2.10.2.
+ </p>
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