-<html>\r
-<head><title>What's new ?</title></head>\r
-<body>\r
-<p><strong>What's new ?</strong> </p>\r
-<p>Jalview Version 2.08</p>\r
-<p> <a href="editing/index.html">Editing</a> can be locked to the selection area. \r
- Any edits made within the locked area do not affect the rest of the alignment.</p>\r
-<p> Keyboard editing - press F2 to toggle <a href="features/cursorMode.html">cursor mode</a> On / Off. For a full list \r
- of keyboard controls, look <a href="keys.html">here</a>.</p>\r
-<p> <a href="features/search.html">Create sequence features from searches</a>. \r
- Previously, the regions of sequences highlighted as the result of\r
- searches were added as new regions in the alignment. Now, the sequence region\r
- selected by a search can be used to define named sequences features\r
- attached to the sequence, rather than the alignment.\r
- </p>\r
-<p>Sequence feature display and rendering has also been enhanced, with\r
- the addition of sequence feature groups (which can be used to show\r
- or hide a set of feature types <em>en masse</em>) and user defined\r
- feature colours as well as transparency controls, using the <a\r
- href="features/seqfeatures.html">Sequence Feature Settings</a>\r
- window. The <a href="features/featuresFormat.html">Features file</a>\r
- has also been extended to accomodate these enhancements.</p>\r
-<p>Alignment annotation and colouring is also considerably\r
- enhanced. Precalculated symbolic and quantitative annotations (text labels,\r
- secondary structure symbols and multiple scalar graphs) can now be\r
- loaded onto alignments via the <a\r
- href="features/annotationsFormat.html">Annotation\r
- File</a>. Additionally, the <a\r
- href="colourSchemes/annotationColouring.html">Annotation\r
- Colouring</a> dialog box allows an alignment to be coloured based on\r
- any of the graphed quantities with which it is annotated.</p>\r
-<p>Rendering speed has been improved by disabling anti-aliasing via\r
- the <strong>Smooth Fonts</strong>\r
- option in the <strong>View \r
- menu</strong> (its default set in <strong>Preferences</strong>). In addition, response\r
- times when editing alignments can be reduced by turning off the automatic\r
- calculation of amino acid property Consensus (which has been\r
- reintroduced to the <strong>Calculate</strong> menu as <strong>Autocalculate Consensus</strong>).<br>\r
-</p>\r
-<p><strong>Issues Resolved</strong></p>\r
-<ul>\r
-<li>Drag & Drop now works on common Linux desktops (at least KDE\r
-and Gnome)</li>\r
-<li>Jalview XML Archive Input/Output is now faster (using an\r
-internal Jalview schema), and sequence description strings are now\r
-preserved in the archive.</li>\r
-<li>Jalview can now correctly read and write <a\r
-href="http://salilab.org/modeller/modeller.html">MODELLER</a> style\r
-PIR description lines for proteins with a PDB reference.\r
-</li>\r
-</ul>\r
-<p>See the <a href="releases.html">Release History</a> page for details of all\r
- new features and resolved issues. </p>\r
-</body>\r
-</html>\r
+<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
+ *
+ * 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>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
+ </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>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff