Jalview 2.11 - new installer and new capabilities
Jalview 2.11 introduces support for loading VCF files, and new
filters and shading models for sequence features. Under the hood,
we've addressed many bugs, and also made some important changes in
the way the Jalview desktop is installed and launched.
- The Jalview Launcher and Update System.
Jalview's new installation model means you'll only need to
download and install Jalview once. After installation, Jalview
will automatically keep itself up to date. The launcher also sets
Jalview's memory automatically, so you'll never again have to
manually configure Java's memory settings.
We are grateful
to ej Technologies for providing a free open source project
license for install4j,
and also to Three
Rings Design for Jalview's new over the air update system: Getdown.
- VCF Support. Proteins and genomic contigs with
chromosomal location annotation (such as protein coding genes
retrieved from Ensembl) can be annotated with variants imported from a local VCF file.
- Feature filters and attribute colourschemes. A new
Feature Display
Settings dialog allows filters and feature attribute based
colourschemes to be constructed, and a new filters column
added to the Feature
Settings dialog. Jalview's sequence feature datamodel has also
been further optimised, and is now maintained as a separate
library IntervalStoreJ (available at https://github.com/bartongroup/IntervalStoreJ)
- Alternative tables for CDS translation. The Translate as cDNA option now
offers alternative amino acid coding schemes.
- PCA plots stored in Jalview Projects. The PCA viewer user interface has
also been improved.
- Backup files. Jalview will automatically
create backups when overwriting existing files, and - unlike with
earlier versions - should Jalview crash during a save, the original
file will be unaffected. The Backups tab in
Jalview's preferences dialog allows the number and format of
backup filenames to be configured.
The full list of bugs fixed in this release can be found in the 2.11 Release Notes.
Jalview and Java 11, and onwards
The Jalview application comes bundled with its own independent
Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
runtime which will be kept up to date. A Java 11 based installation
is available from the Jalview development pages.
Saying goodbye...
Long time Jalview users will notice
that this release no longer features the
Vamsas desktop menu, or a Distributed
Annotation System (DAS) tab on the feature settings dialog.
DAS is no longer supported by major bioinformatics databases, and we
decided that it was no longer feasible to maintain either JDAS or
the VAMSAS client library which rely on out-dated Java XML binding
technologies.
Next up...
Keep an eye on the Jalview web site for
news about JalviewJS - the web based JavaScript implementation of
Jalview. Whilst Jalview 2.11 has been in development, we have also
been working with Prof. Bob Hanson (Jmol and JSmol) to enable
Jalview to run as both a Java application and a JavaScript app in a
web page. To find out more, open http://www.jalview.org/jalview-js/
in Chrome or Firefox.