X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=0f0c7f1b747950a5cb60530e7ee2b8fe441182db;hb=03c3f8e7a5593159371fd91fdf30d9f246961da5;hp=3538ff4b1738f95e0516332b803c139306ed7206;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index 3538ff4..0f0c7f1 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,48 +24,58 @@

- Jalview 2.11 - major and minor new features + Jalview 2.11.1.0 +

+ 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.

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.

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.
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 - Install4J who provided us with a free license for their - installation system, and Jalview's over the air update system is - via Getdown.
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.

- The full list of bugs fixed in this release can be found in the 2.11 Release Notes. + See the 2.11.1.0 + release notes for full details of bugs fixed and new known issues.

- Jalview and Java 11, 13, and onwards + 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.

Java 11 provides improved performance and better OS - integration, so we now recommend users select our Java 11 Jalview - distribution rather than the legacy Java 8 build.

- Known Issues - update for 211 -

OSX: The 'Open File' dialog for Jalview's Groovy Console - appears with the title 'Save As', and attempting to select a file - to load yields a FileNotFound exception.
The workaround is to first - clear the 'Untitled' filename before selecting the file you wish - to load. -
OSX: Links don't open when clicked on or via the Sequence - or Alignment window popup menu.
OSX (Webstart): JalviewÂ only displays old news feed items