X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=13fe656793c44b226851761ef5bed6d16a8ca710;hb=a6db1aeb58e79d976b1e176103a3722ae7f28240;hp=cab871c874fb5d1f064fdee0a2f225120c0d1636;hpb=4fdcc803d2e906c7f21912d8d004b57589a048be;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index cab871c..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 proteins can be retrieved via Jalview's new - Ensembl REST - client. Support for import of Ensembl data allows: -
- 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.
- Sequence variant data
  Jalview - propagates variant annotation on genomic regions onto - transcripts and protein products, complete with associated - metadata such as clinical significance.
Ensembl and ENA 'show cross-references' - support
The Calculations menu's 'Show - cross-references' now offers Ensembl as well as EMBLCDS and - Uniprot when CDS/Protein mapping data is available for download or - display. This allows variant annotation to be added directly to an - alignment of UniProt sequences.
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 with free-text search, or 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.
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