3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
20 <title>What's new ?</title>
24 <strong>What's new ?</strong><br/>
25 Jalview 2.8 includes a number of enhancements and new features that
26 have been in development since July 2010. It is also the first Jalview
27 release to incorporate RNA visualization features developed by Lauren
28 Lui and Jan Engelhart during their Google Summer of Code projects
29 (http://code.google.com/soc/). As usual you can find the highlights
30 below, but to see the comprehensive list take a look at the look at
31 the <a href="releases.html#Jalview2.8">Jalview 2.8 Release Notes</a>.
33 <strong>Highlights in Jalview Version 2.8</strong>
35 <li><strong>Improved <a href="webServices/JABAWS.html">JABAWS</a>
36 client and new JABAWS 2.0 Services
39 <li><a href="webServices/AACon.html">AACon alignment
41 <li><a href="webServices/proteinDisorder.html">Protein
42 disorder</a> - DisEMBL, RONN, GlobPlot and IUPred</li>
43 <li>Clustal Omega for creating huge protein alignments</li>
45 <li><strong><a href="na/index.html">RNA</a></strong>
47 <li>Import sequence and alignment associated WUSS or VIENNA
48 dot-bracket notation from files and the <strong>RFAM</strong>
51 <li>Interactive editing of RNA secondary structure annotation</li>
52 <li>Colour scheme for purine/pyrimidine and to highlight RNA
55 href="calculations/structureconsensus.html">base pair consensus
56 score</a> and sequence logo
58 <li>Embedded <a href="features/varna.html">VARNA</a> RNA
59 secondary structure viewer in the Desktop
62 <li>Parse and display <a href="io/tcoffeescores.html">T-COFFEE
63 alignment quality scores</a> (thanks to Paolo di Tomasso of the Notredame
66 <li><a href="colourSchemes/annotationColouring.html">Per
67 sequence alignment annotation shading</a></li>
68 <li>Enhanced <a href="calculations/pca.html">PCA viewer</a>: more
69 export options, and switch between different PCA modes and residue
72 <li>New Jalview Desktop <a href="webServices/dbreffetcher.html">database
75 <li>Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
76 JDAS Distributed Annotation client library (see
77 http://code.google.com/p/jdas))</li>
78 <li>Export sequence database annotation as an <a
79 href="io/exportseqreport.html">HTML report</a></li>
80 <li>Normalised <a href="calculations/consensus.html">Sequence
84 <strong>Issues resolved in the Jalview Desktop</strong>
87 <li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
89 <li>Stop windows being moved outside desktop on OSX</li>
90 <li>Jnet job queues forever if a very short sequence is submitted
92 <li>Structure view highlighting doesn't work on windows 7</li>
93 <li>Jalview desktop fails to launch with exception when using
95 <li>DAS Sequence retrieval with range qualification results in
96 sequence xref which includes range qualification</li>
97 <li>Cannot close news reader when JABAWS server warning dialog is
99 <li>Edited sequence not submitted to web service</li>
100 <li>Jalview 2.7 InstallAnywhere installer doesn't unpack and run
103 <li>If you use webstart then you may need to go into the
104 Security panel (<em>a.k.a</em> the gatekeeper) in your System
105 Settings, and select the 'allow any code to run' option.
111 <strong>Issues specific to the JalviewLite Applet</strong>
114 <li>Sequence features are momentarily displayed before they are
115 hidden using hidefeaturegroups applet parameter</li>
116 <li>loading features via javascript API automatically enables
118 <li>scrollToColumnIn javascript API method doesn't work</li>
121 <strong>Issues affecting both applet and application</strong>
124 <li>Redundancy removal fails for rna alignment</li>
125 <li>PCA window shows grey box when first opened on OSX</li>
126 <li>Letters coloured pink in sequence logo when alignment
127 coloured with clustalx</li>