<th><em>New Features</em></th>
<th><em>Issues Resolved</em></th>
</tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
+ <em>08/02/2021</em></strong></td>
+ <td align="left" valign="top"><em>Improved control of
+ Jalview's use of network services</em>
+ <ul>
+ <li>
+ <!-- JAL-3814 -->New .jalview_properties token controlling
+ launch of the news browser (like -nonews argument)
+ </li>
+ <li>
+ <!-- JAL-3813 -->New .jalview_properties token controlling
+ download of linkout URLs from
+ www.jalview.org/services/identifiers
+ </li>
+ <li>
+ <!-- JAL-3812 -->New .jalview_properties token controlling
+ download of BIOJSHTML templates
+ </li>
+ <li>
+ <!-- JAL-3811 -->New 'Discover Web Services' option to trigger
+ a one off JABAWS discovery if autodiscovery was disabled
+ </li>
+ </ul></td>
+ <td align="left" valign="top">
+ <ul>
+ <li></li>
+ </ul>
+ </td>
+ </tr>
<tr>
<td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
- <em>27/10/2020</em></strong></td>
+ <em>29/10/2020</em></strong></td>
<td align="left" valign="top">
<ul>
+
</ul>
</td>
<td align="left" valign="top">
<ul>
<li>
<!-- JAL-3765 -->Find doesn't always highlight all matching
- positions in a sequence
+ positions in a sequence (bug introduced in 2.11.1.2)
+ </li>
+ <li>
+ <!-- JAL-3760 -->Alignments containing one or more protein
+ sequences can be classed as nucleotide
+ </li>
+ <li>
+ <!-- JAL-3748 -->CDS alignment doesn't match original CDS
+ sequences after alignment of protein products (known defect
+ first reported for 2.11.1.0)
+ </li>
+ <li>
+ <!-- JAL-3725 -->No tooltip or popup menu for genomic
+ features outwith CDS shown overlaid on protein
+ </li>
+ <li>
+ <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
+ correctly mapped by Jalview (e.g. affects viral CDS with
+ ribosomal slippage, since 2.9.0)
+ </li>
+ <li>
+ <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
+ CDS features
+ </li>
+ <li>
+ <!-- JAL-3700 -->Selections in CDS sequence panel don't
+ always select corresponding protein sequences
+ </li>
+ <li>
+ <!-- JAL-3759 --> <em>Make groups from selection</em> for a
+ column selection doesn't always ignore hidden columns
+ </li>
+ </ul> <em>Installer</em>
+ <ul>
+ <li>
+ <!-- JAL-3611 -->Space character in Jalview install path on
+ Windows prevents install4j launching getdown
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3248 -->Fixed typos and specified compatible gradle
+ version numbers in doc/building.md
</li>
</ul>
</td>
<!-- JAL-3127 -->Sequence ID colourscheme not re-applied
when alignment view restored from project (since Jalview 2.11.0)
</li>
+ <li>
+ <!-- JAL-3749 -->Duplicate CDS sequences are generated when
+ protein products for certain ENA records are repeatedly
+ shown via Calculate->Show Cross Refs
+ </li>
</ul>
</td>
</tr>
<p>
<strong>Jalview 2.11.1.3</strong>
</p>
- <p>Jalview 2.11.1.3 is the third patch release, fixing a bug
- introduced in last weeks Jalview 2.11.1.1 release affecting display
- of Jalview's example project for some users. Together, these
- releases include fixes for a number of critical bugs, and also contains a
- handful of new features suggested by the Jalview community.</p>
+ <p>Jalview 2.11.1.3 is the third patch release in the 2.11.1
+ series. Critical bugs resolved in this release include:</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>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>
+ <li>Find doesn't highlight all motif matches for a sequence.</li>
+ <li>Mouse over highlighting, CDS reconstruction and problems
+ with virtual feature popups when working with linked CDS/Protein
+ alignments.</li>
+ <li>Result of aligning protein sequences linked to CDS results
+ in incorrect CDS alignment.</li>
+ <li>Jalview installer doesn't correctly install Jalview on
+ paths containing spaces.</li>
</ul>
<p>
- For the full release notes, see <a href="releases.html#Jalview.2.11.1.1">the
- Jalview 2.11.1.1 release notes</a>.
+ For the full release notes, see <a
+ href="releases.html#Jalview.2.11.1.3">the Jalview 2.11.1.3
+ release notes</a>.
</p>
<p>
<strong>Known Issues</strong>
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>
+ quadrant of the alignment window.</li>
</ul>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff