X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=13fe656793c44b226851761ef5bed6d16a8ca710;hb=refs%2Fheads%2Fbug%2FJAL-3215hydroColours;hp=f8de1f0b610ee1076612e8109a404c5c3ee97c15;hpb=21c2deb35c435e6097b0f05c83d21cfdf4929ba2;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index f8de1f0..13fe656 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,61 +24,50 @@

- What's new in Jalview 2.10 ? + 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.

+ 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 !

- 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. + 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 proteinsÂ can be retrieved via Jalview's new Ensembl REST - client. Support for import of Ensembl data allows: -
- Sequence variant data. Jalview - propagates variant annotation on genomic regions onto - transcripts and 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, and introns hidden from the view.
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.
- Chimera users will need to upgrade to - 1.11.1.If you use Chimera to view structures downloaded by - Jalview 2.10, you will need to make sure you are running the - latest version of Chimera.
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 alignment view.. - Jalview 2.9 introduced support for reference sequences. In 2.10, - 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.
Ensembl and ENA 'show cross-references' - support.The Calculations menu's 'Show - cross-references' will now offer Ensembl as well as EMBLCDS and - Uniprot when CDS/Protein mapping data is available for download or - display.
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