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<p>
- <strong>What's new in Jalview 2.10.1 ?</strong>
- </p>
- <p>
- Jalview 2.10.1 was released on 29th November 2016. Full details are
- in the <a href="releases.html#Jalview.2.10.1">Jalview 2.10.1
- Release Notes</a>, but the highlights are below. This is also the
- first release to include contributions from Kira Mourão, who
- joined Jalview's core development team in October 2016.
+ <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><strong>More memory efficient</strong><br />We've slimmed
- down the consensus analysis data structures used by Jalview so
- even wider alignments can be worked with.</li>
- <li><strong>Select highlighted region</strong><br />Press 'B'
- or use the new menu option in the alignment window's Select menu
- to mark columns containing highlighted regions generated from
- structure selections, mouse-overs, or resulting from a Find
- operation.</li>
- <li><strong>New custom link mechanism for opening URLs
- for database cross references.</strong><br /> If you have customised URL
- links in your Jalview preferences, then you may already have seen
- the <a href="#warning"> warning dialog (see below).</a></li>
- <li><strong>New command line export option for BioJS
- MSAviewer</strong><br />A number of small bugs with the HTML export
- functions from the Jalview desktop were also fixed.</li>
- <li><strong>Small but significant changes to the
- physicochemical properties and consensus calculations</strong><br />Threonine
- is no longer considered a non-hydrophobic residue in the protein
- conservation calculation, and minor bugs addressed in PID and
- consensus colouring.</li>
- <li><strong>Correct display of disulphide bond
- features</strong><br /> In linked structure views, Jalview would
- highlight all residues between in addition to the two linked
- cysteines. The 'select columns by feature' function in the feature
- settings would also select all intermediate columns.
+ <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>
- <strong><a name="warning">Warning dialog about updating
- your configured URL links</a></strong><br /> In the desktop prior to Jalview
- 2.10.1, the only way to configure custom links for a particular
- database cross-reference for a sequence was to give it a name that <em>exactly</em>
- matched the database source, and a regular expression for filtering
- out any spurious matches generated when the custom linked was tested
- against the Sequence's ID string. Since the introduction of the
- $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for
- database cross-reference accession strings, and if you have custom
- links configured, Jalview will raise a warning message so let you
- know that you may need to update your links to use $DB_ACCESSION$.
+ 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>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