</head>
<body>
<p>
- <strong>Jalview 2.11 - major and minor new features</strong>
+ <strong>Jalview 2.11.1.0</strong>
+ </p>
+ <p>
+ Jalview 2.11.1.0 is the first minor release for the 2.11 series.
+ Along with a number of critical bug fixes and improvements it brings
+ new functionality for mapping sequence features between CDS and
+ Protein alignments. It is also the first release made under a new <em>four</em>
+ number versioning scheme, which will allow us to keep track of
+ patches and bug fixes.
</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><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>
+ <li><strong>Virtual Features</strong><br />In previous
+ versions of Jalview, specific nucleotide sequence features such as
+ genomic variants and exons were transferred to protein products on
+ import. Jalview 2.11.1 instead provides 'virtual features' that
+ can be enabled and overlaid on linked CDS/Protein views via their
+ <a href="features/splitView.html#virtualfeats">Sequence
+ Features dialog</a>. This allows more analyses of nucleotide and
+ peptide sequence features on alignments in a more flexible and
+ memory efficient way than in earlier versions.<br />
+ <em>Note: Virtual features work best when variants are
+ annotated with CSQ fields. Please <a
+ href="features/importvcf.html#computepepvariants">see this
+ Groovy script workaround</a> if you are working with VCF files
+ without CSQ fields.
+ </em></li>
+ <li><strong>Improved VCF data import</strong><br /> <a
+ href="features/importvcf.html#attribs">Standard attributes for
+ filtering variants</a> (e.g. position, QUAL field etc) are now
+ extracted from VCF files. This new feature was suggested by a user
+ at the Jalview booth during ISMB 2019.</li>
+ <li><strong>Extended feature attributes are exported
+ in GFF3</strong><br />Complex attributes from VCF files can be exported
+ and imported via GFF3</li>
+ <li><strong>Updated Jalview Installer and Launcher</strong><br />Jalview's
+ installation packages are now built with Install4j 8, which brings
+ better support for Linux and improved control of file
+ associations. New <a href="memory.html#jvm">parameters on the
+ Jalview launcher</a> allow an upper memory limit to be specified <em>via</em>
+ a Jalview launch file, to prevent it from hogging your system.</li>
</ul>
<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>.
+ See the <a href="releases.html#Jalview.2.11.1.0">2.11.1.0
+ release notes</a> for full details of bugs fixed and new known issues.
</p>
<p>
- <strong>Jalview and Java 11, 13, and onwards</strong>
+ <em>JalviewJS News</em><br />With the release of Jalview 2.11.1.0,
+ the team are now focused on bringing JalviewJS to full production.
+ To follow our progress take a look at <em>http://www.jalview.org/jalview-js/</em>
+ and follow updates on our new <a
+ href="https://github.com/jalview/jalview-js/">JalviewJS
+ Releases github repository</a>.
</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>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