</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.4 ?</strong>
- </p>
- <p>
- This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
+ <strong>What's new in Jalview 2.10.5 ?</strong>
</p>
+ <p>Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, RNA secondary structure
+ annotation, and those running Jalview on OSX with Java 10.</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>
+ <li>Jalview's default memory limit increased to 1G. <br/>If you have
+ problems starting Jalview 2.10.5 and you have 1G or less
+ physical memory on your machine, you will need to <a
+ href="memory.html#memsetting">reduce the memory</a> allocated to
+ Jalview.
+ </li>
+ <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 made more reliable.</li>
</ul>
<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>. The
+ majority of bug fixes and improvements 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 help make Jalview better !
+ </p>
+ <p>
+ <strong>Jalview and Java 10</strong>
</p>
+ <p>This release addresses a critical bug for OSX users who are
+ running Jalview with Java 10 which can prevent files being saved
+ correctly through the 'Save As' dialog box.</p>
+ <em>Known Issues</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>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff