<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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>
- </p>
- <p>Jalview 2.8 includes a brand new logo, which you'll see in file
- browsers, splash screens, and also on the new look Jalview site.</p>
- <p>
- In addition to our new look, Jalview 2.8 includes a number of new
- features.. some of which have been in development since July 2010. The
- highlights are below, and - as usual, for a comprehensive list, take a
- look at the <a href="releases.html#Jalview2.8">Jalview 2.8 Release
- Notes</a>.
- </p>
- <p>
- <strong>Highlights in Jalview Version 2.8</strong>
- </p>
- <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>Support for <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</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
+ <p>
+ <strong>What's new in Jalview 2.10.3b1 ?</strong>
+ </p>
+ <p>
+ This release - Jalview 2.10.3b1 is the January 2018 patch release for Version 2.10.3 was released in November 2017. The major focus was to
+ improve Jalview's sequence features datamodel and the scalability of
+ the alignment rendering system. The bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
+ Release Notes</a>.
+ </p>
+ <p>The highlights for Jalview 2.10.3 include:
+ </p>
+ <ul>
+ <li>Faster and more responsive UI when importing and working
+ with wide alignments and handling hundreds and thousands of
+ sequence features</li>
+ <li>Improved usability with <a
+ href="features/pdbsequencefetcher.html">PDB</a> and <a
+ href="features/uniprotsequencefetcher.html">UniProt</a> Free Text
+ Search dialog, and new tab for retrieval of sequences for lists of
+ IDs.
</li>
- </ul></li>
- <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE alignment quality scores</a> (thanks to Paolo Tomassi 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 new JDAS Distributed Annotation client library)</li>
- <li>Export sequence database annotation as <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 (a select list - see the <a
- href="releases.html#Jalview2.8">release history</a> for full details)
- </strong>
- </p>
- <p>
- <strong>Issues in the Jalview Desktop</strong>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service<!--<a href='http://issues.jalview.org/browse/JAL-636'>JAL-636</a>-->
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-368'>JAL-368</a>] - -->
- <!--[<a href='http://issues.jalview.org/browse/JAL-153'>JAL-153</a>] - -->Stop
- windows being moved outside desktop on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-758'>JAL-758</a>] - -->Filetype
- associations not installed for webstart launch
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-849'>JAL-849</a>] - -->Jalview
- does not always retrieve progress of a JABAWS job execution in full
- once it is complete
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-983'>JAL-983</a>] - -->View
- all structures superposed fails with exception
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-994'>JAL-994</a>] - -->Jnet
- job queues forever if a very short sequence is submitted for
- prediction
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1022'>JAL-1022</a>] - -->Structure
- view highlighting doesn't work on windows 7
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1026'>JAL-1026</a>] - -->Jalview
- desktop fails to launch with exception when using proxy
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1031'>JAL-1031</a>] - -->Tree
- calculation reports 'you must have 2 or more sequences
- selected' when selection is empty
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1062'>JAL-1062</a>] - -->DAS
- Sequence retrieval with range qualification results in sequence xref
- which includes range qualification
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1111'>JAL-1111</a>] - -->Cannot
- close news reader when JABAWS server warning dialog is shown
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1131'>JAL-1131</a>] - -->Edited
- sequence not submitted to web service
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1134'>JAL-1134</a>] - -->Jalview
- 2.7 Webstart and InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
- <ul>
- <li>The workaround for webstart is to go into the Security
- panel (gatekeeper symbol) under System settings, and select the
- 'allow any code to run' setting.</li>
- </ul>
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1144'>JAL-1144</a>] - -->Annotation
- panel not given a scroll bar when sequences with alignment annotation
- are pasted into the alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1148'>JAL-1148</a>] - -->Sequence
- associated annotation rows not associated when loaded from jalview
- project
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1145'>JAL-1145</a>] - -->Exceptions
- when copy/paste sequences with grouped annotation rows to new window
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] - -->Browser
- launch fails with NPE on java 1.7
- </li>
-
- </ul>
-
- <strong>Issues specific to the JalviewLite Applet</strong>
- <ul>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-962'>JAL-962</a>] - -->Sequence
- features are momentarily displayed before they are hidden using
- hidefeaturegroups applet parameter
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-965'>JAL-965</a>] - -->loading
- features via javascript API automatically enables feature display
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1170'>JAL-1170</a>] - -->scrollToColumnIn
- javascript API method doesn't work
- </li>
- </ul>
- <strong>Issues affecting both applet and application</strong>
- <ul>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1007'>JAL-1007</a>] - -->Redundancy
- removal fails for rna alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1033'>JAL-1033</a>] - -->PCA
- window shows grey box when first opened on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1086'>JAL-1086</a>] - -->Letters
- coloured pink in sequence logo when alignment coloured with clustalx
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1099'>JAL-1099</a>] - -->Choosing
- fonts without letter symbols defined causes exceptions and redraw
- errors
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1123'>JAL-1123</a>] - -->Initial
- PCA plot view is not same as manually reconfigured view
- </li>
- </ul>
+ <li>Short names assigned to sequences retrieved from UniProt</li>
+ <li>Groovy console upgraded to 2.4.12 (improved support for Java 9)</li>
+ </ul>
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ Remember, please enable the <em>Experimental Features</em> option in
+ the Jalview Desktop's <em>Tools</em> menu, and then restart Jalview
+ if you want to try out features below:
+ </p>
+ <ul>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
+ </ul>
+
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff