<html>
-<head><title>What's new ?</title></head>
+<!--
+ * 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
+ * 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/>.
+-->
+<head>
+<title>What's new ?</title>
+</head>
<body>
-<p><strong>What's new ?</strong> </p>
-
-<p><strong>Jalview Version 2.2</strong></p>
-<p>Multiple views with different styles, colours, hidden regions for one alignment
-</p>
-<p>Easily add, amend and delete sequence features
-</p>
-<p>"Reload" alignment from File or URL to revert to original
-</p>
-<p>"Save" to current filename or "Save As" to new filename
-</p>
-<p>Set different text colour for dark or light background
-</p>
-<p>Right align sequence ids
-</p>
-<p>Set colour of lower case residues in a user defined colour scheme
-</p>
-<p>Menu Rearrangements: New <strong>Format</strong> for alignment layout and <strong>Select</strong> for region selection.
-</p>
-</p><p>Menu item accelerator keys added
-</p>
-<p>Control-V pastes sequences to active window, Control-Shift-V pastes to a new window.
-</p>
-<p>Raise/Minimise alignment and all associated windows from desktop window's <strong>window</strong> menu
-</p>
-<p>Select and colour whole branches of a tree</p>
-<p>'New Window' button on the 'Output to Text box' alignment output
-option to open a new alignment window after editing.</p>
-<p><strong>Issues Resolved</strong></p>
-</p>
-<p>
-Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system.
-</p>
-<p>Remove empty columns - if empty columns exist at the end of the
-alignment bug fixed.
-</p>
-<p>DAS feature fetching slowed down, doesn't overload DAS servers
-</p>
-<p>DAS feature fetching can be cancelled
-</p>
-<p>Correct display of > and < symbols for feature descriptions without explicit <html> tags.
-</p>
-<p>Zoom working in PCA viewer
-</p>
-<p>Sequence Descriptions retained after running a web service
-</p>
-<p> </p>
-<p>See the <a href="releases.html">Release History</a> page for details of all
- new features and resolved issues. </p>
+ <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