- Hidden sequence markers and representative - sequence bolding included when exporting alignment as EPS, - SVG, PNG or HTML. Display of these can be - configured via the Format menu or in batch mode with a - jalview properties file. -
Corrupted display when switching to wrapped mode when sequence panel's vertical scrollbar is visible. @@ -118,11 +130,8 @@ li:before {
'.' inserted into RNA secondary structure - annotation when columns are inserted into an alignment -
- '.' written into RNA secondary structure - annotation when writing out Stockholm format + annotation when columns are inserted into an alignment, + and when exporting as Stockolm flatfile.
Jalview annotation rows containing upper diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index ed6f5c2..ac086c8 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,57 +24,30 @@
- 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.
- 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
-
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)
+
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 !

- 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.