- <li>Interactive editing of RNA secondary structure annotation</li>
- <li>Colour scheme for purine/pyrimidine and to highlight RNA
- helices</li>
- <li>RNA canonical <a
- href="calculations/structureconsensus.html">base pair consensus
- score</a> and sequence logo
- </li>
- <li>Embedded <a href="features/varna.html">VARNA</a> RNA
- secondary structure viewer in the Desktop
- </li>
- </ul></li>
- <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE
- alignment quality scores</a> (thanks to Paolo di Tomasso of the Notredame
- Group)
- </li>
- <li><a href="colourSchemes/annotationColouring.html">Per
- sequence alignment annotation shading</a></li>
- <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more
- export options, and switch between different PCA modes and residue
- score models
- </li>
- <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database
- fetcher</a> GUI
- </li>
- <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
- JDAS Distributed Annotation client library (see
- http://code.google.com/p/jdas))</li>
- <li>Export sequence database annotation as an <a
- href="io/exportseqreport.html">HTML report</a></li>
- <li>Normalised <a href="calculations/consensus.html">Sequence
- Logo Display</a></li>
- </ul>
- <p>
- <strong>Issues resolved in the Jalview Desktop</strong>
- </p>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service</li>
- <li>Stop windows being moved outside desktop on OSX</li>
- <li>Jnet job queues forever if a very short sequence is submitted
- for prediction</li>
- <li>Structure view highlighting doesn't work on windows 7</li>
- <li>Jalview desktop fails to launch with exception when using
- proxy</li>
- <li>DAS Sequence retrieval with range qualification results in
- sequence xref which includes range qualification</li>
- <li>Cannot close news reader when JABAWS server warning dialog is
- shown</li>
- <li>Edited sequence not submitted to web service</li>
- <li>Jalview 2.7 InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
- <ul>
- <li>If you use webstart then you may need to go into the
- Security panel (<em>a.k.a</em> the gatekeeper) in your System
- Settings, and select the 'allow any code to run' option.
- </li>
- </ul>
- </li>
- </ul>
- <p>
- <strong>Issues specific to the JalviewLite Applet</strong>
- </p>
- <ul>
- <li>Sequence features are momentarily displayed before they are
- hidden using hidefeaturegroups applet parameter</li>
- <li>loading features via javascript API automatically enables
- feature display</li>
- <li>scrollToColumnIn javascript API method doesn't work</li>
- </ul>
- <p>
- <strong>Issues affecting both applet and application</strong>
- </p>
- <ul>
- <li>Redundancy removal fails for rna alignment</li>
- <li>PCA window shows grey box when first opened on OSX</li>
- <li>Letters coloured pink in sequence logo when alignment
- coloured with clustalx</li>
- </ul>
+ <li>Short names assigned to sequences retrieved from UniProt</li>
+ </ul>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ 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
+ <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>
+