X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=0f0c7f1b747950a5cb60530e7ee2b8fe441182db;hb=aad3cb1e3d4250bebbf709624e3e15530a377df0;hp=8150b800abec8b0e2ba031efcd9c446d57860ed9;hpb=4a7dd845b8ad35105ca24b531d36989ae764cdd5;p=jalview.git
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- 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 2.11.1.0
- Jalview and Java 11, 13, and onwards
+ Jalview 2.11.1.0 is the first minor release for the 2.11 series.
+ Along with a number of critical bug fixes and improvements it brings
+ new functionality for mapping sequence features between CDS and
+ Protein alignments. It is also the first release made under a new four
+ number versioning scheme, which will allow us to keep track of
+ patches and bug fixes.
- 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.
+
+ - Virtual Features
In previous
+ versions of Jalview, specific nucleotide sequence features such as
+ genomic variants and exons were transferred to protein products on
+ import. Jalview 2.11.1 instead provides 'virtual features' that
+ can be enabled and overlaid on linked CDS/Protein views via their
+ Sequence
+ Features dialog. This allows more analyses of nucleotide and
+ peptide sequence features on alignments in a more flexible and
+ memory efficient way than in earlier versions.
+ Note: Virtual features work best when variants are
+ annotated with CSQ fields. Please see this
+ Groovy script workaround if you are working with VCF files
+ without CSQ fields.
+
+ - Improved VCF data import
Standard attributes for
+ filtering variants (e.g. position, QUAL field etc) are now
+ extracted from VCF files. This new feature was suggested by a user
+ at the Jalview booth during ISMB 2019.
+ - Extended feature attributes are exported
+ in GFF3
Complex attributes from VCF files can be exported
+ and imported via GFF3
+ - Updated Jalview Installer and Launcher
Jalview's
+ installation packages are now built with Install4j 8, which brings
+ better support for Linux and improved control of file
+ associations. New parameters on the
+ Jalview launcher allow an upper memory limit to be specified via
+ a Jalview launch file, to prevent it from hogging your system.
+
- 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.
+ See the 2.11.1.0
+ release notes for full details of bugs fixed and new known issues.
- 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.
+ JalviewJS News
With the release of Jalview 2.11.1.0,
+ the team are now focused on bringing JalviewJS to full production.
+ To follow our progress take a look at http://www.jalview.org/jalview-js/
+ and follow updates on our new JalviewJS
+ Releases github repository.