Congrats Jim and Ben and Mungo and Geoff. Thanks for the shout out. Bob
On Thu, Jul 4, 2019, 7:37 PM Jim Procter <[email protected]> wrote: > We are quite excited about the release of Jalview 2.11.0! > > This major release 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 forinstall4j > <https://www.ej-technologies.com/products/install4j/overview.html>, > and also toThree Rings Design > <https://en.wikipedia.org/wiki/Three_Rings_Design>for Jalview's new > over the air update system:Getdown > <https://github.com/threerings/getdown>. > > * > > *VCF Support*. Proteins and genomic contigs with chromosomal > location annotation (such as protein coding genes retrieved from > Ensembl) can be annotated with variantsimported from a local VCF > file <http://www.jalview.org/help/html/features/importvcf.html>. > > * > > *Feature filters and attribute colourschemes*. A newFeature Display > Settings > <http://www.jalview.org/help/html/features/featureschemes.html>dialog > allows filters and feature attribute based colourschemes to be > constructed, and a new/filters/column added to theFeature Settings > <http://www.jalview.org/help/html/features/featuresettings.html > >dialog. > Jalview's sequence feature datamodel has also been further > optimised, and is now maintained as a separate > library/IntervalStoreJ/(available > athttps://github.com/bartongroup/IntervalStoreJ) > > * > > *Alternative tables for CDS translation*. TheTranslate as cDNA > <http://www.jalview.org/help/html/menus/alwcalculate.html>option now > offers alternative amino acid coding schemes. > > * > > *PCA plots stored in Jalview Projects*. ThePCA viewer > <http://www.jalview.org/help/html/calculations/pca.html>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. TheBackups tab > <http://www.jalview.org/help/html/features/preferences.html#backups>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 the2.11 > Release Notes > <http://www.jalview.org/help/html/releases.html#Jalview.2.11.0>. > > *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. > > Best wishes for 4th of July from Jim, Ben, Suzanne, Mungo, Geoff and > also Bob! > > -- > ------------------------------------------------------------------- > Dr JB Procter, Jalview Coordinator, The Barton Group > Division of Computational Biology, School of Life Sciences > University of Dundee, Dundee DD1 5EH, UK. > +44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk > > _______________________________________________ > Jalview-dev mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev >
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