From 8b0ad7a1cd2800549ccc31f90e8450445eb654c1 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 31 Mar 2020 22:53:24 +0100 Subject: [PATCH] JAL-3407 updated release date to 2nd April, and first draft of release notes --- help/help/html/releases.html | 6 ++- help/help/html/whatsNew.html | 117 +++++++++++++----------------------------- 2 files changed, 40 insertions(+), 83 deletions(-) diff --git a/help/help/html/releases.html b/help/help/html/releases.html index 205a129..06ff979 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -58,7 +58,7 @@ li:before { 2.11.1 .0
- 30/03/2020 + 2/04/2020

@@ -83,6 +83,10 @@ li:before { position if reopened
+ Feature Settings dialog title includes name + of associated view +
Font anti-aliasing in alignment views enabled by default

- Jalview 2.11.1 + Jalview 2.11.1.0

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'). + 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.

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.
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.
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.

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. -

- 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. + 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.