X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=0f0c7f1b747950a5cb60530e7ee2b8fe441182db;hb=aad3cb1e3d4250bebbf709624e3e15530a377df0;hp=3538ff4b1738f95e0516332b803c139306ed7206;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git
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- 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): Jalview only displays old news feed items
-