X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=5115c19374566cc46eaac00f5ea0dbda5ff39b09;hp=2b792e0fcf98496c5a0e8b76bd305788221b3830;hpb=73ab7e843ed0a215b8794b0734b9c6ed7590756e;p=jalview.git
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- What's new in Jalview 2.10.2 ?
-
- This August 2018 release of Jalview introduces new user interface features, improved and more extensible tree and PCA analysis, more robust 3D structure viewing with UCSF Chimera and an updated service client for JABAWS. The full list of bug fixes and new features can be found in the 2.10.2 Release Notes, but the
- highlights are below.
+ Jalview 2.11 - major and minor new features
+ 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.
- - New dialog and faster and more
- configurable Tree and PCA calculations
Menu entries for
- calculating PCA and different types of tree have been replaced by
- a single Calculations
- dialog box. The underlying implementation for the PCA and tree
- calculations have been made faster and more memory efficient.
- - Extensible score models
A new
- framework has also been created for the score models used to
- calculate distances between sequences and shade alignments. This
- framework allows import of substitution matrices in NCBI and
- AAIndex format.
- PCA Bug Fixes. Jalview's implementation of PCA
- differed in its treatment of gaps and non-standard residues. The
- BLOSUM62 matrix also included a typo that affected results. See the
- 2.10.2 release note
- about score model bugs for details and how to reinstate legacy
- behaviour.
- - Update to JABAWS 2.2
Jalview's
- alignment, protein conservation analysis, and protein disorder and
- RNA secondary structure prediction services are now provided by JABAWS 2.2.
- Several of the programs provided as JABAWS 2.2 services have been
- updated, so their options and parameters have changed.
- - URL linkouts to other bioinformatics
- databases
New preferences for opening web pages for
- database cross-references via the UK Elixir's EMBL-EBI's MIRIAM
- database and identifiers.org services.
- - Showing and hiding regions
Hide insertions in the
- PopUp menu has changed its behaviour. Prior to 2.10.2, columns
- were only shown or hidden according to gaps in the sequence under
- the popup menu. Now, only columns that are gapped in all selected
- sequences as well as the sequence under the popup menu are hidden,
- and column visibility outside the selected region is left as is.
- This makes it easy to filter insertions from the alignment view
- (just select the region containing insertions to remove) without
- affecting the rest of the hidden columns.
- - Recent search history for Find, PDBe and
- Uniprot
Easily repeat a previous search for Find and the free
- text search system (for querying Uniprot and the PDBe).
- - Improved Overview Window
The alignment overview is now easier
- to use when working with alignments of more than 5000 rows and
- columns, and features a new pop-up menu that allows hidden regions
- to be excluded from the overview. It also works with CDS/Protein
- alignments and MSA views in wrapped mode.
- - 3D Structure
Jalview's communication
- with UCSF Chimera has been made more robust, particularly when
- working with many structures and long sequences. Regions in
- structures that correspond to hidden regions in an alignment view
- are now left un-coloured, making it easier to highlight specific
- features in 3D. See below for experimental
- features for exchanging annotation between Chimera and Jalview.
+ - 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.
- Scripting
New groovy examples
- demonstrate Jalview 2.10.2 APIs for creation of data-driven
- colourschemes, and custom alignment file handlers. The FeatureAnnotationWorker
- introduced in Jalview 2.10 has also been refactored to allow
- efficient counting across multiple feature types. Please be aware
- that feature counter scripts created for earlier versions will not
- execute in Jalview 2.10.2.
-
-
- Experimental Features
+ The full list of bugs fixed in this release can be found in the 2.11 Release Notes.
- This release of Jalview introduces an Experimental Features
- option in the Jalview Desktop's Tools menu that allows you
- to try out features that are still in development. To access the
- experimental features below - first enable the Tools→Enable
- Experimental Features option, and then restart Jalview.
+ 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
- - Annotation transfer between Chimera and Jalview
Two
- new entries in
- the Chimera viewer's Chimera menu allow positional annotation to
- be exchanged between Chimera and Jalview.
+ - 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
-