</head>
<body>
<p>
- <strong>Jalview 2.11.1</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.
- We've moved to a <em>four</em> number scheme to help you (and us!)
- keep track of patch and bug fix releases (which we used to denote
- with a 'b').
+ 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>
<ul>
- <li><strong><a href="features/importvcf.html#attribs">Standard
- attributes for filtering variants</a></strong> (e.g. position, QUAL field etc) a new feature suggested by
- a user at the Jalview booth during ISMB 2019.</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.</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>
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 2.11 - new installer and new capabilities</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><strong>The Jalview Launcher and Update System</strong>.
- 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 ej Technologies for providing a free open source project
- license for <a
- href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a>,
- and also to <a
- href="https://en.wikipedia.org/wiki/Three_Rings_Design">Three
- Rings Design</a> for Jalview's new over the air update system: <a
- href="https://github.com/threerings/getdown">Getdown</a>.</li>
- <li><strong>VCF Support</strong>. Proteins and genomic contigs with
- chromosomal location annotation (such as protein coding genes
- retrieved from Ensembl) can be annotated with variants <a
- href="features/importvcf.html">imported from a local VCF file</a>.</li>
- <li><strong>Feature filters and attribute colourschemes</strong>. A new
- <a href="features/featureschemes.html">Feature Display
- Settings</a> dialog allows filters and feature attribute based
- colourschemes to be constructed, and a new <em>filters</em> column
- added to the <a href="features/featuresettings.html">Feature
- Settings</a> dialog. Jalview's sequence feature datamodel has also
- been further optimised, and is now maintained as a separate
- library <em>IntervalStoreJ</em> (available at https://github.com/bartongroup/IntervalStoreJ)</li>
- <li><strong>Alternative tables for CDS translation</strong>. The <a
- href="menus/alwcalculate.html">Translate as cDNA</a> option now
- offers alternative amino acid coding schemes.</li>
- <li><strong>PCA plots stored in Jalview Projects</strong>. The <a
- href="calculations/pca.html">PCA viewer</a> user interface has
- also been improved.</li>
- <li><strong>Backup files</strong>. Jalview will automatically
- create backups when overwriting existing files, and - unlike with
- earlier versions - should Jalview crash during a save, the original
- file will be unaffected. The <a
- href="features/preferences.html#backups">Backups tab</a> in
- Jalview's preferences dialog allows the number and format of
- backup filenames to be configured.</li>
- </ul>
- <p>
- The full list of bugs fixed in this release can be found in the <a
- href="releases.html#Jalview.2.11.0">2.11 Release Notes</a>.
- </p>
- <p>
- <strong>Jalview and Java 11, and onwards</strong>
- </p>
- <p>The Jalview application comes bundled with its own independent
- Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8
- runtime which will be kept up to date. A Java 11 based installation
- is available from the Jalview development pages.</p>
- <p>
- <em>Saying goodbye...</em><br>Long time Jalview users will notice
- that this release no longer features the
- <em>Vamsas</em> desktop menu, or a <em>Distributed
- Annotation System (DAS)</em> tab on the feature settings dialog.
- DAS is no longer supported by major bioinformatics databases, and we
- decided that it was no longer feasible to maintain either JDAS or
- the VAMSAS client library which rely on out-dated Java XML binding
- technologies.
- </p>
- <p>
- <em>Next up...</em><br /> Keep an eye on the Jalview web site for
- news about JalviewJS - the web based JavaScript implementation of
- Jalview. Whilst Jalview 2.11 has been in development, we have also
- been working with Prof. Bob Hanson (Jmol and JSmol) to enable
- Jalview to run as both a Java application and a JavaScript app in a
- web page. To find out more, open <em>http://www.jalview.org/jalview-js/</em>
- in Chrome or Firefox.
+ <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>
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</html>
git://source.jalview.org / jalview.git / commitdiff