<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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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><strong>Highlights in Jalview Version 2.4</strong></p>
-<ul>
- DNA and protein product highlighting<br>
- URL links generated with regular expressions<br>
- URL links for sequence database cross references<br>
- New sequence fetcher dialog and DAS Sequence Fetching<br>
- JPred Service upgraded to Jpred3<br>
- Memory monitor<br>
- PFAM full alignment retrieval<br>
- Generalised sequence database reference validation<br>
- DNA Protein Product sequence db traversal (Experimental)<br>
- VAMSAS Interoperation Client (Experimental)<br>
- export annotation rows as CSV for spreadsheet import<br>
- New application command line args and optional Groovy suport<br>
- New Applet API methods and parameters<br>
-</ul>
-<p><strong>Issues Resolved (a select list)</strong></p>
-<ul>
- Aligned cDNA translation to aligned peptide works correctly<br>
- selected region output includes visible annotations (for
- certain formats)<br>
- edit label/displaychar contains existing label/char for
- editing<br>
- Newick tree support improved for clustalW trees and preserving NHX style comments<br>
- Pathological filechooser bug avoided by not allowing
- filenames containing a ':'<br>
- Fixed exception when parsing GFF files containing global
- sequence features<br>
- Reference counting for alignment datasets<br>
- better reporting of non-fatal warnings and error messages to user when file
- parsing fails.<br>
- Save works when Jalview project is default format<br>
- Histidine should be midblue (not pink!) in Zappo<br>
- Undo recovers dataset sequence metadata when sequence
- regions are cut<br>
- PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) are read in properly<br>
- Stockholm annotation parsing fixed and improved (PFAM records)<br>
- Re-instated Full AMSA support and .amsa file association (MyHits)<br>
- annotation consisting of sequence associated scores can be
- read and written correctly to annotation file<br>
- Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet<br>
- Applet Menus are always embedded in applet window on Macs.</br>
- Newly shown features appear at top of stack (in Applet)</br>
- Secondary structure lines are drawn starting from first
- column of alignment<br>
- Uniprot XML import updated for new schema release in July 2008<br>
- Sequence feature to sequence ID match for Features file is case-insensitive<br>
- Sequence features read from Features file appended to all sequences with matching IDs<br>
- PDB structure coloured correctly for associated views containing a sub-sequence<br>
- Display name and local features preserved in results retrieved from web service<br>
- Visual delay indication for sequence retrieval and sequence fetcher initialisation<br>
- Updated Application to use DAS 1.53e version of dasobert DAS client
-</ul>
-
-<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 in Jalview 2.10.5 ?</strong>
+ </p>
+ <p>Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, and RNA secondary structure
+ annotation.</p>
+ <ul>
+ <li>EPS, PNG and SVG export now includes hidden sequence
+ markers, and representative sequences are marked in bold.</li>
+ <li>Ensembl Client updated for Ensembl Rest API v7.<br />The
+ latest Ensembl API is not backwards compatible with earlier
+ versions of Jalview, so if you require Ensembl functionality you
+ will need to install this release.
+ </li>
+ <li>Improved support for VIENNA extended dot-bracket notation
+ for RNA secondary structure</li>
+ <li>Positional and selected region highlighting in VARNA
+ 'trimmed sequence' view now more reliable</li>
+ </ul>
+ <p>
+ The full list of bugs fixed in this release can be found in the <a
+ href="releases.html#Jalview.2.10.5">2.10.5 Release Notes</a>. The majority of improvement in 2.10.5 are due to Jalview users
+ contacting us via the jalview-discuss email list. Thanks to everyone
+ who took the time to do this !</p>
+ <p><strong>Jalview and Java 10</strong></p>
+ <p>This release addresses a critical bug for OSX users who are
+ running Jalview with Java 10 which can prevent files being saved
+ correctly through the 'Save As' dialog box. The 'Save As' dialog for
+ Jalview's Groovy Console remains affected - we hope to address this
+ in the next major release.</p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff