<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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>Jalview 2.5.1 is a bug fix release for the 2.5 version of
-Jalview. See the <a href="releases.html#Jalview2.5.1">release
-history</a> for the bugs that this release resolves.</p>
-<p><strong>Highlights in Jalview Version 2.5</strong></p>
-<ul>
- Linked viewing of nucleic acid sequences and structures<br/>
- Automatic Scrolling option in View menu to display the
- currently highlighted region of an alignment.<br/>
- Order an alignment by sequence length, or using the average score or total feature count for each sequence.<br/>
- Shading features by score or associated description<br/>
- Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).<br/>
- New hide/show options including Shift+Control+H to hide everything but the currently selected region.<br/>
-</ul>
-<em>Jalview Desktop:</em>
-<ul>
- Fetch DB References capabilities and UI expanded to support
- retrieval from DAS sequence sources<br/>
- Enable or disable non-positional feature and database
- references in sequence ID tooltip from View menu in application.<br/>
- Group-associated consensus, sequence logos and conservation
- plots<br/>
- Symbol distributions for each column can be exported and
- visualized as sequence logos<br/>
- Jalview Java Console<br/>
- New webservice for submitting sequences and IDs to <a
- href="webServices/index.html#envision2">Envision2</a> Workflows<br/>
- Improved VAMSAS synchronization and sharing of selections.<br/>
-</ul>
-<em>JalviewLite:</em>
-<ul>
- Middle button resizes annotation row height<br/>
- New Parameters - including default tree display settings.<br/>
- Non-positional features displayed in ID tooltip<br/>
-</ul>
-<p><strong>Issues Resolved (a select list)</strong></p>
-<ul>
- <ul>
- Source field in GFF files parsed as feature source rather
- than description<br/>
- Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).<br/>
- URL links generated for all feature links (bugfix)<br/>
- Codons containing ambiguous nucleotides translated as 'X' in
- peptide product<br/>
- Match case switch in find dialog box works for both sequence
- ID and sequence string and query strings do not have to be in upper
- case to match case-insensitively.<br/>
- Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)<br/>
- Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.<br/>
- </ul>
- <em>Desktop Issues</em>
- <ul>
- Better handling of exceptions during sequence retrieval<br/>
- PDB files retrieved from URLs are cached properly<br/>
- Sequence description lines properly shared via VAMSAS<br/>
- Sequence fetcher fetches multiple records for all data
- sources<br/>
- Ensured that command line das feature retrieval completes
- before alignment figures are generated.<br/>
- Reduced time taken when opening file browser for first time.<br/>
- User defined group colours properly recovered from Jalview projects.<br/>
- </ul>
-</ul>
+ <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>Improved JABA client and new JABAWS 2.0 Services
+ <ul>
+ <li>AACon alignment conservation</li>
+ <li>Protein disorder - DisEMBL, RONN, GlobPlot and IUPred</li>
+ <li>Clustal Omega - huge protein alignments</li>
+ </ul>
+ </li>
+ <li><strong>Support for RNA</strong>
+ <ul>
+ <li>Import sequence and alignment associated WUSS or VIENNA
+ secondary structure notation from stockholm and clustalW files or
+ as jalview annotation.</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 base pair consensus score and sequence logo</li>
+ <li>Embedded <a href="http://varna.lri.fr/">VARNA</a> RNA
+ secondary structure viewer in the Desktop
+ </li>
+ </ul> See <a href="na/index.html">Nucleic Acid Support</a> for full
+ details.</li>
+ <li>Parse and display T-COFFEE alignment quality scores</li>
+ <li>Shade individual sequence positions according to alignment
+ annotation scores</li>
+ <li>Enhanced PCA viewer: more export options, and switch between
+ different PCA modes and residue score models</li>
+ <li>New Jalview Desktop database fetcher GUI</li>
+ <li>Support for DAS 1.6 and DAS 2.0 sources</li>
+ <li>Export sequence database annotation as HTML report</li>
+ <li>Normalised Sequence Logo Display</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>
-<p> </p>
-<p>See the <a href="releases.html">Release History</a> page for
-details of all new features and resolved issues.</p>
+ <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>
+ <em>General</em>
+ <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