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<p>
- <strong>What's new in Jalview 2.10.0b1 ?</strong>
- </p>
- <p>
- Jalview 2.10.0b1 is a patch release for 2.10, the next major release
- in the Jalview 2 series. Full details are in the <a
- href="releases.html#Jalview.2.10.0b1">Jalview 2.10b1 Release
- Notes</a>, but the highlights are below.
+ <strong>Jalview 2.11 - major and minor new features</strong>
</p>
+ <p>Jalview 2.11 introduces support for loading VCF files, and new
+ filters and shading models for sequence features. Under the hood,
+ we've addressed many bugs, and also made some important changes in
+ the way the Jalview desktop is installed and launched.</p>
<ul>
- <li>Drag and drop reinstated for the Jalview desktop on
- Windows, Linux and older OSX systems.</li>
- <li>Problems loading local PDB files have been fixed</li>
- <li>Conservation shading can be disabled for PID and consensus
- based colour scheme</li>
+ <li><em>VCF Support</em>. Proteins and genomic contigs with
+ chromosomal location annotation (such as protein coding genes
+ retrieved from Ensembl) can be annotated with variants imported
+ from a local VCF file.</li>
+ <li><em>The Jalview Launcher and Update System</em><br />
+ Jalview's new installation model means you'll only need to
+ download and install Jalview once. After installation, Jalview
+ will automatically keep itself up to date. The launcher also sets
+ Jalview's memory automatically, so you'll never again have to
+ manually configure Java's memory settings.<br />We are grateful to
+ Install4J who provided us with a free license for their
+ installation system, and Jalview's over the air update system is
+ via Getdown.</li>
</ul>
- <p><em>Major highlights of the 2.10.0 Release</em></p>
+ <p>
+ The full list of bugs fixed in this release can be found in the <a
+ href="releases.html#Jalview.2.11">2.11 Release Notes</a>.
+ </p>
+ <p>
+ <strong>Jalview and Java 11, 13, and onwards</strong>
+ </p>
+ <p>Java 11 provides improved performance and better OS
+ integration, so we now recommend users select our Java 11 Jalview
+ distribution rather than the legacy Java 8 build.</p>
+ <em>Known Issues - update for 211 </em>
<ul>
- <li><strong>Ensembl sequence fetcher</strong><br />Annotated
- Genes, transcripts and proteins can be retrieved via Jalview's new
- <a href="features/ensemblsequencefetcher.html">Ensembl REST
- client</a>. Support for import of Ensembl data allows:
- <ul>
- <li><strong>Aligned locus view</strong><br />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.</li>
- <li><strong>Sequence variant data</strong><br />Jalview
- propagates variant annotation on genomic regions onto
- transcripts and protein products, complete with associated
- metadata such as clinical significance.</li>
- </ul></li>
- <li><strong>Ensembl and ENA 'show cross-references'
- support</strong><br />The Calculations menu's <strong>'Show
- cross-references'</strong> 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.</li>
- <li><strong>Working with structures</strong>
- <ul>
- <li><strong>More accurate structure mappings</strong><br />
- Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
- to <a href="features/siftsmapping.html">match structures
- to UniProt sequences</a>, even for structures containing
- multiple copies of a sequence.</li>
- <li><strong>Import structures as mmCIF</strong><br />Jalview
- now downloads data from the EMBL-EBI's PDBe site as <a
- href="features/mmcif.html">mmCIF</a>. This allows very large
- structures to be imported, such as the HIV virus capsid
- assembly.</li>
- <li><strong>Chimera users will need to upgrade to
- 1.11.1</strong><br />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 <a href="features/chimera.html">Chimera</a>.</li>
- </ul></li>
- <li><strong>UniProt Free Text Search</strong><br />The new
- search dialog for UniProt allows you to browse and retrieve
- sequences with free-text search, or structured queries.</li>
- <li><strong>Reference sequence alignment view</strong><br />
- 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.</li>
+ <li>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.</br>The workaround is to first
+ clear the 'Untitled' filename before selecting the file you wish
+ to load.
+ </li>
+ <li>OSX: Links don't open when clicked on or via the Sequence
+ or Alignment window popup menu.</li>
+ <li>OSX (Webstart): Jalview only displays old news feed items</li>
</ul>
-
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git://source.jalview.org / jalview.git / blobdiff