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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
--->
+ -->
<head>
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong><br /> Jalview 2.8.0b1 is a bugfix
- release for Jalview version 2.8. <br /> As usual you can find the
- highlights below, and the comprehensive list is given in the <a
- href="releases.html#Jalview2.8.0b1">Jalview 2.8.0b1 Release Notes</a>.
- </p>
<p>
- This bug fix release includes numerous minor enhancements made over
- the last 12 months. Importantly, it is also the first release that
- provides Jalview as a trusted application, signed with a certificate
- donated to us by <a href="certum.eu">Certum</a>.
+ <strong>What's new in Jalview 2.10.5 ?</strong>
</p>
- <strong>Enhancements and new features</strong>
- <ul>
- <li>Allow disorder predictions to be made on the current
- selection (or visible selection) in the same way that JPred works</li>
- <li>allow import of data from gzipped files</li>
- <li>Improved per-sequence 'colour-by-annotation' performance</li>
- <li>Support '' style escaping of quotes in Newick files</li>
- <li>group options for JABAWS service by command line name</li>
- <li>Select primary source when selecting authority in database
- fetcher GUI</li>
- <li>COMBINE statement uses current SEQUENCE_REF and GROUP_REF
- scope to group annotation rows</li>
- <li>add .mfa to FASTA file extensions recognised by Jalview</li>
- <li>groovy scripting for headless jalview operation</li>
- <li>Output in Stockholm format</li>
- </ul>
- <strong>Bug fixes</strong>
- <ul>
- <li>Uniprot and PDB database cross-reference fetching works
- properly</li>
- <li>'View all structures' in the desktop is more reliable</li>
- <li>Web services parameter dialog box shows the options enabled
- for different presets</li>
- <li>Interactive creation of RNA secondary structure works more
- smoothly</li>
- <li>Keyboard mode 'P' command jumps to the right place</li>
- <li>Improved support for parsing database cross-references via
- Stockholm and Rfam database</li>
- <li>Improved semantics in annotation files for grouping
- annotation rows associated with particular sequences and groups</li>
- <li>More robust DNA->Amino acid translation</li>
- <li>Improved Headless-mode operation for DAS annotation
- retrieval, groovy script execution and alignment figure generation</li>
- <li>annotation label tooltip text needs to be wrapped</li>
- </ul>
+ <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>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>
+ 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 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><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. The 'Save As' dialog for
+ Jalview's Groovy Console remains affected - we hope to address this
+ in the next major release.</p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff