X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=a448aaa174103c5bab74fefb0f557ba61f3165e5;hb=a566d9d95be9aafbd3dea5ae2fc2b99718d546aa;hp=42cb24f51f45270866e4d9a9ffb62a70e2b5f878;hpb=d55d3f563be502c1ca37228fbcdabfc57e111eb8;p=jalview.git
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- Jalview 2.11.1
-
-
- Jalview 2.11.1.0 is the first minor release for the 2.11 series.
- We've moved to a four number scheme to help you (and us!)
- keep track of patch and bug fix releases (which we used to denote
- with a 'b').
+ 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.
- - Standard
- attributes for filtering variants (e.g. position, QUAL field etc) a new feature suggested by
- a user at the Jalview booth during ISMB 2019.
+ - 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+)
-
- See the 2.11.1.0
- release notes for full details of bugs fixed and new known issues.
-
-
- Jalview 2.11 - new installer and new capabilities
-
- 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.
+ Critical bug fixes include
- - 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.
+ - 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, 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.
-
-
- 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
+