<p>
<strong>The Java Console, Logging and Reporting Bugs<br /></strong>
</p>
- <p>Like most programs, Jalview produces a series of messages
- during its operation, often referred to as 'logs'. These logs can be
- extremely useful for diagnosing and helping the Jalview developers
- find a workaround for specific problems that you might encounter.</p>
+ <p>
+ Like most programs, Jalview contains bugs, despite our best efforts.
+ However, Jalview also produces a series of messages during its
+ operation, often referred to as 'logs'. These logs provide a record
+ of Jalview's operation. They can also be extremely useful when <a
+ href="#reportingbugs">reporting bugs</a>, since they help the
+ Jalview developers diagnose and find a workaround for specific
+ problems that you might encounter.
+ </p>
<p>
The primary place to look for logs is in the <a href="#java_console">Java
Console</a> which you can open from within Jalview by going to the <em>Tools</em>
are not shown in the Jalview Console. The location of these depends
on how you launched Jalview:</p>
<p>
- <strong>Jalview Desktop Installations</strong><br />If you are using
+ <strong>Jalview Desktop Installation Launch Logs</strong><br />If you are using
a standard desktop version of Jalview installed from one of our
install4j installers, then messages about Jalview's initial launch
can be found in
by default
</li>
</ul>
- <p><strong>Jalview Executable Jar</strong><br/>If you are using the Jalview executable jar file (also
+ <p><strong>Jalview Executable Jar Launch Logs</strong><br/>If you are using the Jalview executable jar file (also
used by bioconda and OSX homebrew installations) then the default run class (
<em>jalview.bin.Launcher</em> -- a minimised launcher that will set
memory and linux dpi settings before re-launching
composer or issue tracker).
</p>
- <h3>Reporting Bugs</h3>
+ <p><strong><a name="reportingbugs">Reporting Bugs</a></strong></p>
<p>
If you come across a problem in Jalview where something is not
</head>
<body>
<p>
- <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.
+ <strong>Jalview 2.11.1.1</strong>
</p>
+ <p>Jalview 2.11.1.1 is the first patch release for Jalview version
+ 2.11.1. In addition to fixes for some critical it also contains a
+ handful of new features suggested by the Jalview community.</p>
+ <ul>
+ <li>Shift+arrow keys navigate to next gap or residue in cursor
+ mode (enable with F2)</li>
+ <li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to
+ 2.23</li>
+ <li>Improved recognition of GZipped files from local disk or
+ retrieved via the web</li>
+ <li>EMBL and EMBL CDS database records retrieved from the
+ European Nucleotide Archive's Data API as 'EMBL Flatfile' records</li>
+ <li>Improved <a href="logging.html">Java Console and
+ logging</a> to help track down problems
+ </li>
+ <li>Improved support for Hi-DPI (4K) screens when running on
+ Linux (Requires Java 11+)</li>
+ </ul>
+ <p>Critical bug fixes include</p>
<ul>
- <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>
+ <li>Jalview runs correctly when launched with Turkish language
+ settings</li>
+ <li>Peptide-to-CDS tracking broken when multiple EMBL gene
+ products shown for a single contig (such as viral genomes)</li>
+ <li>Errors encountered when processing variants from VCF files
+ yield "Error processing VCF: Format specifier '%s'" on the console</li>
+ <li>Count of features not shown can be wrong when there are
+ both DNA and Protein features mapped to the position under
+ the cursor</li>
+ <li>Sequence ID for reference sequence is clipped when Right
+ align Sequence IDs enabled</li>
+ <li>Find doesn't report matches that span hidden gapped columns</li>
+ <li>Jalview ignores file format parameter specifying output
+ format when exporting an alignment via the command line</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.
+ For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
+ Jalview 2.11.1.1 release notes</a>.
</p>
<p>
- <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>.
+ <strong>Known Issues</strong>
</p>
+ <ul>
+ <li>We've had reports from a small number of windows 10 users
+ who see a warning dialog pop up when Jalview tries to save a new
+ version of an existing file. If you are affected by this bug and
+ this latest version of Jalview doesn't fix it, please let us know!</li>
+ <li>Co-located features exported and re-imported are ordered
+ differently when shown on alignment and in tooltips. (Also affects
+ v2.11.1.0)</li>
+ <li>Drag and drop of alignment file onto alignment window when
+ in a HiDPI scaled mode in Linux only works for the top left
+ quadrant of the alignment window</li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff