</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.2 ?</strong>
+ <strong>What's new in Jalview 2.10.3b1 ?</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.
+ This is the January 2018 patch release, which addresses critical bugs including trackpad function in OSX, and display of multiple 3D structures.
+ The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
+ Release Notes</a>. In addition, Jalview 2.10.3 provides:
</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- been replaced by a single 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>Faster and more responsive UI when importing and working
+ with wide alignments and handling hundreds and thousands of
+ sequence features</li>
+ <li>Improved usability with <a
+ href="features/pdbsequencefetcher.html">PDB</a> and <a
+ href="features/uniprotsequencefetcher.html">UniProt</a> Free Text
+ Search dialog, and new tab for retrieval of sequences for lists of
+ IDs.
</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>Short names assigned to sequences retrieved from UniProt</li>
+ <li>Groovy console upgraded to 2.4.12 (improved support for Java 9)</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.
+ Remember, please enable the <em>Experimental Features</em> option in
+ the Jalview Desktop's <em>Tools</em> menu, and then restart Jalview
+ if you want to try out features below:
</p>
<ul>
<li><em>Annotation transfer between Chimera and Jalview</em><br />Two
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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