X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=0cf5661b1143ce17b00aba690d18e3b6a8288807;hb=dd5cb7fd04f5a82757bee9666bdb13aadb35f7d9;hp=42cb24f51f45270866e4d9a9ffb62a70e2b5f878;hpb=d55d3f563be502c1ca37228fbcdabfc57e111eb8;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index 42cb24f..0cf5661 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,99 +24,33 @@

- Jalview 2.11.1 + Welcome to Jalview Version $$Version-Rel$$ !! +
Please take a + look at the release + notes for this build. Read on for the highlights.

- Jalview 2.11.1.0 is the first minor release for the 2.11 series. - We've moved to a four number scheme to help you (and us!) - keep track of patch and bug fix releases (which we used to denote - with a 'b'). + Highlights in 2.11.2

Standard - attributes for filtering variants (e.g. position, QUAL field etc) a new feature suggested by - a user at the Jalview booth during ISMB 2019.

- See the 2.11.1.0 - release notes for full details of bugs fixed and new known issues. -

- 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. +

New features for working with 3D Structure
+ Jalview 2.11.2 features a number of new capabilities:

Linked viewing with ChimeraX and PyMol
Simply configure your prefered viewer for 3D molecular data in Jalview's structure preferences, make sure that Jalview can locate the viewer's installation, and open a new view via the 3D Structure Chooser!
View predicted protein structures via 3D-Beacons
+ Jalview 2.11.2's Structure Chooser includes a client for the 3D-Beacons Network, a new service that allows predicted and observed 3D models for proteins in Uniprot from a range of resources, including AlphaFold DB, SWISS-MODEL and a growing number of other resources. +

Retrieval

- Jalview and Java 11, and onwards + For the full release notes, see the Jalview 2.11.1.4 + release notes.
-
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. + Known Issues
+
New known issues in this release affect recovery of CDS/Protein + relationships from project files, and interactive selection of + protein sequences from a tree built on linked nucleotide sequences. + We will provide patches for these issues as soon as possible.
+