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<!--
- * 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 2.5</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> </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 2.10.4 ?</strong>
+ </p>
+ <p>
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
+ </p>
+ <ul>
+ <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
+ <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
+ <li>Critical patches for running Jalview on OSX with Java 10</li>
+ <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
+ <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
+ <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
+ <li>New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments</li>
+ <li>Annotation transfer between Chimera and Jalview <em>(formerly only
+ available in 'Experimental' mode)</em></li>
+ </ul>
+ <p>
+ The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
+ Release Notes</a>.
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff