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<p>
- <strong>Jalview 2.11 - major and minor new features</strong>
+ <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><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>
+ 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><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 <a
+ href="features/importvcf.html">imported from a local VCF file</a>.</li>
+ <li><em>Feature filters and attribute colourschemes</em>. 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><a
+ href="https://github.com/bartongroup/IntervalStoreJ">IntervalStoreJ</a></em></li>
+ <li><em>Alternative tables for CDS translation</em>. The <a
+ href="menus/alwcalculate.html">Translate as CDNA</a> option now
+ offers alternative amino acid coding schemes.</li>
+ <li><em>PCA plots stored in Jalview Projects</em><br />The <a
+ href="calculations/pca.html">PCA viewer</a> user interface has
+ also been improved.</li>
+ <li><em>Backup files</em><br />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
<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>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>
+ <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, see the <a
+ href="http://www.jalview.org/jalview-js/">JalviewJS web page</a>.
+ </p>
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git://source.jalview.org / jalview.git / blobdiff