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What's new ?
-
- What's new ?
Jalview 2.8.0b1 is a bugfix
- release for Jalview version 2.8.
As usual you can find the
- highlights below, and the comprehensive list is given in the Jalview 2.8.0b1 Release Notes.
-
- This bug fix release includes numerous minor enhancements made over
- the last 12 months. Importantly, it is also the first release that
- provides Jalview as a trusted application, signed with a certificate
- donated to us by Certum.
+ Jalview 2.11 - major and minor new features
- Enhancements and new features
-
- - Allow disorder predictions to be made on the current
- selection (or visible selection) in the same way that JPred works
- - allow import of data from gzipped files
- - Improved per-sequence 'colour-by-annotation' performance
- - Support '' style escaping of quotes in Newick files
- - group options for JABAWS service by command line name
- - Select primary source when selecting authority in database
- fetcher GUI
- - COMBINE statement uses current SEQUENCE_REF and GROUP_REF
- scope to group annotation rows
- - add .mfa to FASTA file extensions recognised by Jalview
- - groovy scripting for headless jalview operation
- - Output in Stockholm format
-
- Bug fixes
-
- - Uniprot and PDB database cross-reference fetching works
- properly
- - 'View all structures' in the desktop is more reliable
- - Web services parameter dialog box shows the options enabled
- for different presets
- - Interactive creation of RNA secondary structure works more
- smoothly
- - Keyboard mode 'P' command jumps to the right place
- - Improved support for parsing database cross-references via
- Stockholm and Rfam database
- - Improved semantics in annotation files for grouping
- annotation rows associated with particular sequences and groups
- - More robust DNA->Amino acid translation
- - Improved Headless-mode operation for DAS annotation
- retrieval, groovy script execution and alignment figure generation
- - annotation label tooltip text needs to be wrapped
-
+ 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.
+
+ - 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
+ via Getdown.
+
+
+ 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
+
+ Java 11 provides improved performance and better OS
+ integration, so we now recommend users select our Java 11 Jalview
+ distribution rather than the legacy Java 8 build.
+ Known Issues - update for 211
+
+ - OSX: The 'Open File' dialog for Jalview's Groovy Console
+ appears with the title 'Save As', and attempting to select a file
+ to load yields a FileNotFound exception.The workaround is to first
+ clear the 'Untitled' filename before selecting the file you wish
+ to load.
+
+ - OSX: Links don't open when clicked on or via the Sequence
+ or Alignment window popup menu.
+ - OSX (Webstart): Jalview only displays old news feed items
+