[Jalview-announce] Jalview 2.3

[jalview-announce at jalview.org]

Hello Jalview users,

Jalview 2.3 is now ready and available to download from 
http://www.jalview.org


New Features in the latest release:

   * Jmol 11.0.2 integration.
     Jmol is an open source structure viewer written in Java, so fits 
naturally with Jalview. The integration allows all the features from the 
original Jalview Structure viewer, such as colouring structures from 
alignment colours and mouse over structure / alignment highlighting. 
Jmol 11.0.2 is not Java 1.1 compatible so Jmol applet will only run in 
Web Browsers with Java 1.4 plug-in or greater. If the web browser uses 
Java 1.1 only, the original Jalview Structure viewer is still available.

   * For the first time you will be able to save the structure view 
along with your alignments within the Jalview XML file format.

   * Slide sequences with cursor keys - very useful editing feature 
which has been missing from Jalview.

   * Edit sequence in place - another highly requested editing feature, 
allows residues/sequences to be altered in place.

   * EMBL CDS features - CDS regions marked on sequences retrieved using 
WsDBFetch sequence fetcher from EBI.

   * DAS Feature mapping

   * Feature ordering - layering of features on the alignment can be 
optimized by a button on the Feature Settings window.

   * Alignment Properties - View simple alignment statistics and 
predefined alignment properties.

   * Annotation Scores

   * Sort by scores - if scores exist in the alignment, Jalview will 
recognise them and allow the user to sort the sequences by the available 
scores.

   * Feature/annotation editing in applet - Previously only available in 
the application, but has proven to be very useful in web alignment 
editing tools.

   * Annotation file - extensions have been made to add alignment 
properties and scores to sequence and alignment annotations.



Issues Resolved :

    * Headless state operation in 2.2.1

    * Incorrect and unstable DNA pairwise alignment

    * Cut and paste of sequences with annotation

    * Feature group display state in XML

    * Feature ordering in XML

    * blc file iteration selection using filename # suffix

    * Stockholm alignment properties

    * Stockholm alignment secondary structure annotation

    * 2.2.1 applet had no feature transparency

    * Number pad keys can be used in cursor mode

    * Jalview Structure Viewer mirror image resolved