X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;fp=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=2e18baead82803c0cd8425b372300b8842e87c10;hp=0f0c7f1b747950a5cb60530e7ee2b8fe441182db;hb=a9f2db2f1688164dd54da7521509c135d7fdf042;hpb=0c1ab6aa5767dc2ff0f40f694af9b0181148b1f5 diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index 0f0c7f1..2e18bae 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,58 +24,62 @@

- 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 2.11.1.1

Jalview 2.11.1.1 is the first patch release for Jalview version + 2.11.1. In addition to fixes for some critical bugs, it also + contains a handful of new features suggested by the Jalview + community.

Shift+arrow keys navigate to next gap or residue in cursor + mode (enable with F2)
Support import of VCF 4.3 by updating HTSJDK from 2.12 to + 2.23
Improved recognition of GZipped files from local disk or + retrieved via the web
EMBL and EMBL CDS database records retrieved from the + European Nucleotide Archive's Data API as 'EMBL Flatfile' records
Improved Java Console and + logging to help track down problems +
Improved support for Hi-DPI (4K) screens when running on + Linux (Requires Java 11+)

Critical bug fixes include

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.
Jalview runs correctly when launched with Turkish language + settings
Peptide-to-CDS tracking broken when multiple EMBL gene + products shown for a single contig (such as viral genomes)
Errors encountered when processing variants from VCF files + yield "Error processing VCF: Format specifier '%s'" on the console
Count of features not shown can be wrong when there are + both DNA and Protein features mapped to the position under + the cursor
Sequence ID for reference sequence is clipped when Right + align Sequence IDs enabled
Find doesn't report matches that span hidden gapped columns
Jalview ignores file format parameter specifying output + format when exporting an alignment via the command line

- See the 2.11.1.0 - release notes for full details of bugs fixed and new known issues. + For the full release notes, see the + Jalview 2.11.1.1 release notes.

- 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. + Known Issues

We've had reports from a small number of windows 10 users + who see a warning dialog pop up when Jalview tries to save a new + version of an existing file. If you are affected by this bug and + this latest version of Jalview doesn't fix it, please let us know!
Co-located features exported and re-imported are ordered + differently when shown on alignment and in tooltips. (Also affects + v2.11.1.0)
Drag and drop of alignment file onto alignment window when + in a HiDPI scaled mode in Linux only works for the top left + quadrant of the alignment window