X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=a448aaa174103c5bab74fefb0f557ba61f3165e5;hb=a566d9d95be9aafbd3dea5ae2fc2b99718d546aa;hp=00f94661de6105662b8c2458ffd24a3979c1d67f;hpb=8b0ad7a1cd2800549ccc31f90e8450445eb654c1;p=jalview.git
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- 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 2.11.1.3
+ Jalview 2.11.1.3 is the third 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.
+
+ - 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.
- - 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
+