X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=cc91c62af551daea5874f5abcfc1b839ddfc7b54;hp=aaef948117dca8f89c44e32ec52d549612d0cd6f;hb=433635c8784cfa421da35e45aa24dd6f16a8bf6b;hpb=e6322a597de6a9d28819a643a598f5e7d60c0242 diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index aaef948..cc91c62 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,46 +24,63 @@

- Jalview 2.11 - major and minor new features + Jalview 2.11.1.2

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.

Jalview 2.11.1.2 is the second patch release, fixing a bug + introduced in last weeks Jalview 2.11.1.1 release affecting display + of Jalview's example project for some users. Together, these + releases include fixes for a number of critical bugs, and also contains a + handful of new features suggested by the Jalview community.

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 - based on Three Rings' Getdown system.
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.
PCA plots stored in Jalview Projects
The PCA - viewer has also been enhanced and the user interface revised.
+
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

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

- The full list of bugs fixed in this release can be found in the 2.11 Release Notes. + For the full release notes, see the + Jalview 2.11.1.1 release notes.

- Jalview and Java 11, 13, and onwards + Known Issues

The Jalview application comes bundled with its own independent - Java installation which will be updated automatically from - www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8 - runtime, but installations will be migrated to the latest Java - release once remaining issues have been addressed.

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