X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=b86f3d0b746aed5fbf9ff2aeaaaf4e7f765dd27d;hp=60769a4cde71ced02fdb6679c244febcb213b7bc;hpb=e0a45c41828a768c21554df80e95b56daae4906d;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 60769a4..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,76 +24,48 @@

- What's new in Jalview 2.10.2 ? -

- Full details about Jalview 2.10.2 are in the 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 UI, and faster and more configurable - implementation for PCA, Neighbour-Joining and UPGMA Trees
- Menu entries for calculating PCA and different types of tree have - been replaced by a single Calculations dialog box.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. A new framework has - also been created for the score models used to calculate distances - between sequences. This framework allows import of substitution - matrices in NCBI and AAIndex format, and custom score models to be - created via a groovy script.
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 services have been updated, so - their options and parameters have changed.
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 histories for Find and the free - text search system (for querying Uniprot and the PDBe).
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.

- Experimental Features + The full list of bugs fixed in this release can be found in the 2.11 Release Notes.

- This release of Jalview includes a new option in the Jalview Desktop - that allows you to try out features that are still in development. - To access the features described below, please 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): JalviewÂ only displays old news feed items

- 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. -