X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=13fe656793c44b226851761ef5bed6d16a8ca710;hb=54cbe6eeaf683e042246c657716514d80e561a9c;hp=e1b00c4d8cc42b2cac8f7202446613fce070e204;hpb=7ee8954fcde2074b3418a4c58d4e091bc6064315;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index e1b00c4..13fe656 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,51 +24,50 @@
- What's new ?
+ What's new in Jalview 2.10.5 ?
+ Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, RNA secondary structure
+ annotation, and those running Jalview on OSX with Java 10.
+
+ - Jalview's default memory limit increased to 1G.
If you have
+ problems starting Jalview 2.10.5 and you have 1G or less
+ physical memory on your machine, you will need to reduce the memory allocated to
+ 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 made more reliable.
+
- Jalview 2.10 is the next major release in the Jalview 2 series. Full
- details are in the Jalview
- 2.10 Release Notes, but the highlights are below.
+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The
+ majority of bug fixes and improvements 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 help make Jalview better !
- Highlights in Jalview 2.10
+ 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.
+ Known Issues
- - Ensembl sequence fetcher. Annotated Genes,
- transcripts and proteins can be retrieved via Jalview's new Ensembl REST
- client. Support for import of Ensembl data also allows:
-
- - Sequence variant data. Jalview
- propagates variant annotation imported via Ensembl onto
- protein products, complete with associated metadata such as
- clinical significance.
- - Aligned locus view. Transcripts
- retrieved for a gene identifier via the Ensembl or
- EnsemblGenomes sequence databases are automatically aligned to
- their reference genome.
-
- - Working with structures.
-
- - More accurate structure mappings.
- Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
- to match structures
- to UniProt sequences, even for structures containing
- multiple copies of a sequence.
- - Import structures as mmCIF. Jalview
- now downloads data from the EMBL-EBI's PDBe site as mmCIF.
- This allows very large structures to be imported, such as the HIV virus capsid assembly.
-
- - UniProt Free Text Search. The new search
- dialog for UniProt allows you to browse and retrieve sequences
- from UniProt with free-text search and more structured queries
- - Reference sequence based alignment
- visualisation.. When a reference sequence is defined for the
- alignment, the alignment column ruler is now numbered according to
- the reference sequence. The reference sequence for alignment views
- can also be saved and restored from Jalview projects.
-
+ - 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
-