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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
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* This file is part of Jalview.
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* Jalview is free software: you can redistribute it and/or
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+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
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* 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.
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- * 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.
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+ -->
<head>
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong><br/>
- Jalview 2.8 includes a number of enhancements and new features that
- have been in development since July 2010. It is also the first Jalview
- release to incorporate RNA visualization features developed by Lauren
- Lui and Jan Engelhart during their Google Summer of Code projects
- (http://code.google.com/soc/). As usual you can find the highlights
- below, but to see the comprehensive list take a look at the look at
- the <a href="releases.html#Jalview2.8">Jalview 2.8 Release Notes</a>.
- </p>
- <strong>Highlights in Jalview Version 2.8</strong>
- <ul>
- <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a>
- client and new JABAWS 2.0 Services
- </strong>
- <ul>
- <li><a href="webServices/AACon.html">AACon alignment
- conservation</a></li>
- <li><a href="webServices/proteinDisorder.html">Protein
- disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
- <li>Clustal Omega for creating huge protein alignments</li>
- </ul></li>
- <li><strong><a href="na/index.html">RNA</a></strong>
- <ul>
- <li>Import sequence and alignment associated WUSS or VIENNA
- dot-bracket notation from files and the <strong>RFAM</strong>
- database
+ <p>
+ <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, 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>Interactive editing of RNA secondary structure annotation</li>
- <li>Colour scheme for purine/pyrimidine and to highlight RNA
- helices</li>
- <li>RNA canonical <a
- href="calculations/structureconsensus.html">base pair consensus
- score</a> and sequence logo
- </li>
- <li>Embedded <a href="features/varna.html">VARNA</a> RNA
- secondary structure viewer in the Desktop
- </li>
- </ul></li>
- <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE
- alignment quality scores</a> (thanks to Paolo di Tomasso of the Notredame
- Group)
- </li>
- <li><a href="colourSchemes/annotationColouring.html">Per
- sequence alignment annotation shading</a></li>
- <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more
- export options, and switch between different PCA modes and residue
- score models
- </li>
- <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database
- fetcher</a> GUI
- </li>
- <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
- JDAS Distributed Annotation client library (see
- http://code.google.com/p/jdas))</li>
- <li>Export sequence database annotation as an <a
- href="io/exportseqreport.html">HTML report</a></li>
- <li>Normalised <a href="calculations/consensus.html">Sequence
- Logo Display</a></li>
- </ul>
- <p>
- <strong>Issues resolved in the Jalview Desktop</strong>
- </p>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service</li>
- <li>Stop windows being moved outside desktop on OSX</li>
- <li>Jnet job queues forever if a very short sequence is submitted
- for prediction</li>
- <li>Structure view highlighting doesn't work on windows 7</li>
- <li>Jalview desktop fails to launch with exception when using
- proxy</li>
- <li>DAS Sequence retrieval with range qualification results in
- sequence xref which includes range qualification</li>
- <li>Cannot close news reader when JABAWS server warning dialog is
- shown</li>
- <li>Edited sequence not submitted to web service</li>
- <li>Jalview 2.7 InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
- <ul>
- <li>If you use webstart then you may need to go into the
- Security panel (<em>a.k.a</em> the gatekeeper) in your System
- Settings, and select the 'allow any code to run' option.
- </li>
- </ul>
- </li>
- </ul>
- <p>
- <strong>Issues specific to the JalviewLite Applet</strong>
- </p>
- <ul>
- <li>Sequence features are momentarily displayed before they are
- hidden using hidefeaturegroups applet parameter</li>
- <li>loading features via javascript API automatically enables
- feature display</li>
- <li>scrollToColumnIn javascript API method doesn't work</li>
- </ul>
- <p>
- <strong>Issues affecting both applet and application</strong>
- </p>
- <ul>
- <li>Redundancy removal fails for rna alignment</li>
- <li>PCA window shows grey box when first opened on OSX</li>
- <li>Letters coloured pink in sequence logo when alignment
- coloured with clustalx</li>
- </ul>
+ <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