X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=cc91c62af551daea5874f5abcfc1b839ddfc7b54;hb=433635c8784cfa421da35e45aa24dd6f16a8bf6b;hp=8150b800abec8b0e2ba031efcd9c446d57860ed9;hpb=4a7dd845b8ad35105ca24b531d36989ae764cdd5;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index 8150b80..cc91c62 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,81 +24,63 @@

- Jalview 2.11 - new installer and new capabilities + 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.

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.
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. -

- Jalview and Java 11, 13, 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. + For the full release notes, see the + Jalview 2.11.1.1 release notes.

- 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. + 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