<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* 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.
- *
+ *
* 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
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong>
- </p>
- <p>
- The Jalview 2.7 release features new web services, and important
- improvements to the way in which Jalview handles alignments and
- associated PDB structures, as well as numerous minor improvements and
- bug fixes. Version 2.7 of the JalviewLite applet also features a
- significantly enhanced Javascript API enabling it to be more easily
- integrated with javascript based web applications. <br /> For full
- details see the <a href="releases.html#Jalview2.7">Jalview 2.7
- release history</a>.
- </p>
- <p>
- <strong>Highlights in Jalview Desktop Version 2.7</strong>
- </p>
- <ul>
- <li>New <a href="features/viewingpdbs.html">structure viewer
- options</a>:
- <ul>
- <li>Colour and superimpose 3D structures of complexes and
- multi-domain chains using several different alignments</li>
- <li>Drag and drop to associate PDB files with sequences that
- have the same name</li>
- <li>Open and superimpose all associated structures for the
- current selection</li>
- </ul>
- <li>New web services for <a href="webServices/shmr.html">alignment
- analysis</a></li>
- <li>Improved graphical user interface for <a
- href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>services.
- </li>
- <li>Sort associated alignment views option in tree viewer</li>
- <li>Default colours for <a
- href="colourSchemes/annotationColouring.html">shading alignment
- by quantitative annotation</a>.
- </li>
- <li><a href="webServices/newsreader.html">Jalview Desktop RSS
- reader</a> - following important updates at <a
- href="http://www.jalview.org/feeds/desktop/rss">http://www.jalview.org/feeds/desktop/rss</a>
- </ul>
-
- <p>
- <strong>Issues Resolved (a select list - see the <a
- href="releases.html#Jalview2.7">release history</a> for full details)
- </strong>
- </p>
- <p>
- <strong>Issues in the Jalview Desktop</strong>
- <ul>
- <li>Problems viewing associated structures for sequences
- retrieved from UNIPROT</li>
- <li>Problems viewing Jalview projects from older versions in
- version 2.6</li>
- <li>Preservation of hidden annotation rows and tree bootstrap
- values in projects</li>
- <li>Newly added JABAWS servers not always visible in web services
- menu</li>
- </ul>
- <strong>Issues specific to the JalviewLite Applet</strong>
- <ul>
- <li>Layout problems when lots of annotation rows are displayed</li>
- <li><= shown as = in annotation row tooltip</li>
- <li>export features raises exception when no features exist</li>
- <li>relative URLs not handled properly when used in parameters
- and annotation files</li>
- </ul>
- <strong>Issues affecting both applet and application</strong>
- <ul>
- <li>sequence numbering not preserved in MSF alignment output</li>
- <li>sequence associated secondary structure not correctly parsed
- in interleaved stockholm</li>
- <li>sequences containing lowercase letters are not properly
- associated with their pdb files</li>
- <li>Jalview PDB file reader does not extract sequence from deoxy
- nucleotide chains correctly</li>
- <li>Sequence length given in alignment properties window is off
- by 1</li>
- </ul>
+ <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
+ </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>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff