X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=5115c19374566cc46eaac00f5ea0dbda5ff39b09;hp=49eb03cf62cdc3819685999b84ea50c2f9f85287;hpb=50a5e8030e7a5c20d39fe46e97092e4c6711b0cb;p=jalview.git
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- What's new in Jalview 2.10.5 ?
+ Jalview 2.11 - major and minor new features
- Jalview 2.10.5 is a minor release that includes critical
- patches for users working with Ensembl, and RNA secondary structure
- annotation.
+ 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's default memory limit increased to 1G. If you have
- problems starting Jalview 2.10.5 and you have 1G or less
- physical memory on your machine, you will need to reduce the memory allocated to
- Jalview.
-
- - EPS, PNG and SVG export now includes hidden sequence
- markers, and representative sequences are marked in bold.
- - Ensembl Client updated for Ensembl Rest API v7.
The
- latest Ensembl API is not backwards compatible with earlier
- versions of Jalview, so if you require Ensembl functionality you
- will need to install this release.
-
- - Improved support for VIENNA extended dot-bracket notation
- for RNA secondary structure
- - Positional and selected region highlighting in VARNA
- 'trimmed sequence' view now more reliable
+ - 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 2.10.5 Release Notes. The
- majority of improvement in 2.10.5 are due to Jalview users
- contacting us via the jalview-discuss email list. Thanks to everyone
- who took the time to do this !
+ href="releases.html#Jalview.2.11">2.11 Release Notes.
- Jalview and Java 10
+ Jalview and Java 11, 13, and onwards
- This release addresses a critical bug for OSX users who are
- running Jalview with Java 10 which can prevent files being saved
- correctly through the 'Save As' dialog box.
- Known Issues
+ 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.
+ 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