<em></em>
<ul>
<li>
+ <!-- JAL-247 -->Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. <em>Display is configured via the
+ Format menu, or for command-line use via a jalview
+ properties file.</em>
+ </li>
+ <li>
+ <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON
+ </li>
+ <li>
<!-- JAL-3065 -->Change in recommended way of starting
Jalview via a Java command line: add jars in lib directory
to CLASSPATH, rather than via the deprecated java.ext.dirs
property.
</li>
</ul>
- </div></td>
+ <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3047 -->Support added to execute test suite
+ instrumented with <a href="http://openclover.org/">Open
+ Clover</a>
+ </li>
+ </ul>
+ </div></td>
<td><div align="left">
<em></em>
<ul>
<li>
- <!-- JAL-247 -->Hidden sequence markers and representative
- sequence bolding included when exporting alignment as EPS,
- SVG, PNG or HTML. <em>Display of these can be
- configured via the Format menu or in batch mode with a
- jalview properties file.</em>
- </li>
- <li>
<!-- JAL-3087 -->Corrupted display when switching to
wrapped mode when sequence panel's vertical scrollbar is
visible.
</li>
<li>
<!-- JAL-3061 -->'.' inserted into RNA secondary structure
- annotation when columns are inserted into an alignment
- </li>
- <li>
- <!-- JAL-3061 -->'.' written into RNA secondary structure
- annotation when writing out Stockholm format
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockolm flatfile.
</li>
<li>
<!-- JAL-3053 -->Jalview annotation rows containing upper
</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.4b1 ?</strong>
+ <strong>What's new in Jalview 2.10.5 ?</strong>
</p>
- <p>This is the first patch release for Jalview 2.10.4. It includes
- the following new patches:</p>
+ <p>Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, and RNA secondary structure
+ annotation.</p>
<ul>
- <li>HGVS nomenclature used for variant annotation retrieved
- from Uniprot</li>
- <li>Uniprot import fails for some sequences (Cannot import
- features with multiple variant elements)</li>
- <li>Clustal files with sequence positions in right-hand column
- are now parsed correctly</li>
- <li>Wrap view - export to SVG - IDs shown but not alignment
- area in exported graphic</li>
- <li>F2/Keyboard mode edits work when Overview window has input
- focus</li>
- <li>Windows specific fixes:
- <ul>
- <li>Annotation panel set too high when annotation added to
- view</li>
- <li>Updated search paths for Chimera default installation</li>
- <li>Windows File Shortcuts can be dragged onto the Jalview
- Desktop</li>
- <li>Drag URL from Chrome, Firefox, IE to Jalview desktop on
- Windows doesn't open file:<br /> Dragging the currently open
- URL and links from a page viewed in Firefox or Chrome on
- Windows is now fully supported.<br />
- <strong>If you are using Edge</strong>, only links in the page
- can be dragged.<br />
- <strong>With Internet Explorer</strong>, only the currently open
- URL in the browser can be dropped onto Jalview.
- </li>
- </ul>
+ <li>EPS, PNG and SVG export now includes hidden sequence
+ markers, and representative sequences are marked in bold.</li>
+ <li>Ensembl Client updated for Ensembl Rest API v7.<br />The
+ latest Ensembl API is not backwards compatible with earlier
+ versions of Jalview, so if you require Ensembl functionality you
+ will need to install this release.
</li>
+ <li>Improved support for VIENNA extended dot-bracket notation
+ for RNA secondary structure</li>
+ <li>Positional and selected region highlighting in VARNA
+ 'trimmed sequence' view now more reliable</li>
</ul>
- <p>Highlights in the 2.10.4 series include:</p>
- <ul>
- <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
- <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
- <li>Critical patches for running Jalview on OSX with Java 10</li>
- <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
- <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
- <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
- <li>New buttons on the Structure Chooser for adding structures
- to an existing view, and disabling automatic superposition
- according to linked alignments</li>
- <li>Annotation transfer between Chimera and Jalview <em>(formerly only
- available in 'Experimental' mode)</em></li>
- </ul>
+ <p>The majority of improvement in 2.10.5 are due to Jalview users
+ contacting us via the jalview-discuss email list. Thanks to everyone
+ who took the time to do this !</p>
<p>
- The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
- Release Notes</a>.
+ The full list of bugs fixed in this release can be found in the <a
+ href="releases.html#Jalview.2.10.5">2.10.5 Release Notes</a>.
</p>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff