3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
4 * Copyright (C) 2014 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <title>What's new ?</title>
25 <strong>What's new ?</strong><br/>
26 Jalview 2.8 includes a number of enhancements and new features that
27 have been in development since July 2010. It is also the first Jalview
28 release to incorporate RNA visualization features developed by Lauren
29 Lui and Jan Engelhart during their Google Summer of Code projects
30 (http://code.google.com/soc/). As usual you can find the highlights
31 below, but to see the comprehensive list take a look at the look at
32 the <a href="releases.html#Jalview2.8">Jalview 2.8 Release Notes</a>.
34 <strong>Highlights in Jalview Version 2.8</strong>
36 <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a>
37 client and new JABAWS 2.0 Services
40 <li><a href="webServices/AACon.html">AACon alignment
42 <li><a href="webServices/proteinDisorder.html">Protein
43 disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
44 <li>Clustal Omega for creating huge protein alignments</li>
46 <li><strong><a href="na/index.html">RNA</a></strong>
48 <li>Import sequence and alignment associated WUSS or VIENNA
49 dot-bracket notation from files and the <strong>RFAM</strong>
52 <li>Interactive editing of RNA secondary structure annotation</li>
53 <li>Colour scheme for purine/pyrimidine and to highlight RNA
56 href="calculations/structureconsensus.html">base pair consensus
57 score</a> and sequence logo
59 <li>Embedded <a href="features/varna.html">VARNA</a> RNA
60 secondary structure viewer in the Desktop
63 <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE
64 alignment quality scores</a> (thanks to Paolo di Tomasso of the Notredame
67 <li><a href="colourSchemes/annotationColouring.html">Per
68 sequence alignment annotation shading</a></li>
69 <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more
70 export options, and switch between different PCA modes and residue
73 <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database
76 <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
77 JDAS Distributed Annotation client library (see
78 http://code.google.com/p/jdas))</li>
79 <li>Export sequence database annotation as an <a
80 href="io/exportseqreport.html">HTML report</a></li>
81 <li>Normalised <a href="calculations/consensus.html">Sequence
85 <strong>Issues resolved in the Jalview Desktop</strong>
88 <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
90 <li>Stop windows being moved outside desktop on OSX</li>
91 <li>Jnet job queues forever if a very short sequence is submitted
93 <li>Structure view highlighting doesn't work on windows 7</li>
94 <li>Jalview desktop fails to launch with exception when using
96 <li>DAS Sequence retrieval with range qualification results in
97 sequence xref which includes range qualification</li>
98 <li>Cannot close news reader when JABAWS server warning dialog is
100 <li>Edited sequence not submitted to web service</li>
101 <li>Jalview 2.7 InstallAnywhere installer doesn't unpack and run
104 <li>If you use webstart then you may need to go into the
105 Security panel (<em>a.k.a</em> the gatekeeper) in your System
106 Settings, and select the 'allow any code to run' option.
112 <strong>Issues specific to the JalviewLite Applet</strong>
115 <li>Sequence features are momentarily displayed before they are
116 hidden using hidefeaturegroups applet parameter</li>
117 <li>loading features via javascript API automatically enables
119 <li>scrollToColumnIn javascript API method doesn't work</li>
122 <strong>Issues affecting both applet and application</strong>
125 <li>Redundancy removal fails for rna alignment</li>
126 <li>PCA window shows grey box when first opened on OSX</li>
127 <li>Letters coloured pink in sequence logo when alignment
128 coloured with clustalx</li>