X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4dfc54e201bb54ba3074ac62ae61e29135f9e099;hb=0e575263043797b2e9bbd74386cd5851c09433af;hp=ed6f5c263624db37d6154d3345604ad82f6b3c89;hpb=a4806ceb8d534d99eb00fbf9157ff79c95da0939;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index ed6f5c2..4dfc54e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,57 +24,34 @@

- What's new in Jalview 2.10.4b1 ? + What's new in Jalview 2.10.5 ?

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

Jalview 2.10.5 is a minor release that includes critical + patches for users working with Ensembl, and RNA secondary structure + annotation.

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. -
+
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.

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)
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

- 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 2.10.5 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 !

Jalview and Java 10

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. The 'Save As' dialog for + Jalview's Groovy Console remains affected - we hope to address this + in the next major release.