X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=5115c19374566cc46eaac00f5ea0dbda5ff39b09;hp=ed6f5c263624db37d6154d3345604ad82f6b3c89;hpb=a4806ceb8d534d99eb00fbf9157ff79c95da0939;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index ed6f5c2..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,57 +24,48 @@

- What's new in Jalview 2.10.4b1 ? + Jalview 2.11 - major and minor new features

This is the first patch release for Jalview 2.10.4. It includes - the following new patches:

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.

HGVS nomenclature used for variant annotation retrieved - from Uniprot
Uniprot import fails for some sequences (Cannot import - features with multiple variant elements)
Clustal files with sequence positions in right-hand column - are now parsed correctly
Wrap view - export to SVG - IDs shown but not alignment - area in exported graphic
F2/Keyboard mode edits work when Overview window has input - focus
Windows specific fixes: -
- Annotation panel set too high when annotation added to - view
- Updated search paths for Chimera default installation
- Windows File Shortcuts can be dragged onto the Jalview - Desktop
- Drag URL from Chrome, Firefox, IE to Jalview desktop on - Windows doesn't open file:
  Dragging the currently open - URL and links from a page viewed in Firefox or Chrome on - Windows is now fully supported.
  - If you are using Edge, only links in the page - can be dragged.
  - With Internet Explorer, only the currently open - URL in the browser can be dropped onto Jalview. -
-

Highlights in the 2.10.4 series include:

Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
Critical patches for running Jalview on OSX with Java 10
Easier adjustment of the Alignment ID panel and Annotation panel
Improved support for mapping between 3D Structures and Uniprot Protein Sequences
Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
New buttons on the Structure Chooser for adding structures - to an existing view, and disabling automatic superposition - according to linked alignments
Annotation transfer between Chimera and Jalview (formerly only - available in 'Experimental' mode)
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 2.10.4 - Release Notes. + 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): JalviewÂ only displays old news feed items