<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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
+ * 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/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<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>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>
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>
+ Jalview 2.8.2 is the first release produced by our new core
+ development team.<br /> It incorporates many minor improvements and
+ bug-fixes, and new features for working with 3D structure data,
+ shading alignments by secondary structure and generation of alignment
+ figures as Scalable Vector Graphics. <br />The majority of
+ improvements in this version of Jalview concern the desktop
+ application. As ever, the highlights are detailed below,
+ and the full list is given in the <a
+ href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
+ </p>
+ <p>
+ <strong>Annotation visualisation</strong> <br /> The alignment window
+ includes a new <em>Annotations</em> menu which provides controls for
+ the layout and display of sequence, group and alignment associated
+ annotation rows. It also now includes the <em>Autocalculated
+ Annotation</em> submenu (formerly located in the View menu), which
+ includes settings for the calculation and display of sequence
+ consensus, logos, and amino acid conservation for the alignment and
+ subgroups.
+ </p>
+ <p>
+ <strong>Sequence associated annotation</strong><br /> New controls
+ have also been added to the Sequence ID popup menu for the propagation
+ and display of sequence associated annotation such as secondary
+ structure assignments and disorder predictions. Annotation associated
+ with one or a group of sequence already shown on the alignment may be
+ shown or hidden, and any available annotation from 3D structure or
+ calculations performed in other Jalview windows can be copied to the
+ alignment
+ <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
+ The <strong>Colour by annotation</strong> function has also been
+ improved, allowing secondary structure annotation to be used to shade
+ sequences and alignment columns. Protein sequences can be coloured
+ according to the presence of a helix or sheet at each position, and
+ RNA sequences can be shaded according to each structure's stem/helix
+ pattern - which enables different RNA folding topologies to be quickly
+ identified.
+ </p>
+ <p>
+ <strong>3D Structural data analysis and display</strong><br />
+ Jalview now employs Jmol's PDB data API to retrieve secondary
+ structure assignments made by the DSSP algorithm. It can also employ
+ web services to obtain secondary structure assignments from RNA
+ structures. These assignments are shown as sequence associated
+ annotation for sequences which have cross-references to the PDB, or
+ have had PDB files associated with them via the <em>Structures</em>
+ submenu of the sequence ID popup menu. The extraction and display of
+ secondary structure and B-factor column annotation is controlled <em>via</em>
+ a new <strong>Structure</strong> tab in the Jalview Desktop's
+ Preferences dialog box.
+ </p>
+ <p>
+ <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
+ application can now be configured to employ UCSF Chimera for the
+ display of 3D structure data. UCSF Chimera is a python-based
+ high-performance molecular graphics and animation system developed by
+ the Resource for Biocomputing, Visualisation, and Informatics at the
+ University of California.<br />Jalview employs the 'StructureViz'
+ communication mechanism developed for Cytoscape by Morris et al.
+ (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
+ allows Jalview to send commands to Chimera, enabling structures to be
+ superimposed and shaded according to associated multiple aligmment
+ views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
+ would appreciate feedback ! Please send your comments to
+ jalview-discuss@jalview.org, and keep up to date with this feature's
+ development via http://issues.jalview.org/browse/JAL-1333.
+ </p>
+ <p>
+ <strong>Export of alignment figures as Scalable Vector
+ Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
+ supported by web browsers and graphics design programs, and allow
+ high-quality graphics for interactive exploration and publication.
+ Jalview now supports the generation of SVGs interactively (via the
+ Export) menu, and from the command line for server-side figure
+ generation.
+ </p>
- </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>
- <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