<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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><strong>Jalview Version 2.4</strong></p>
+<p><strong>Highlights in Jalview Version 2.5</strong></p>
<ul>
- VAMSAS Interoperation Client<br>
- DAS Sequence Fetching<br>
- PFAM full alignment retrieval<br>
- DNA/Protein Product traversal (Experimental)</br>
- .. (more to come)<br>
- URL links can be generated using regular
- expressions and created for sequence database cross references<br>
+ 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>
-<p><strong>Issues Resolved</strong></p>
+<em>Jalview Desktop:</em>
<ul>
- .. (more to come)
+ 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>
-
-<--<p><strong>Jalview Version 2.3</strong></p>
+<em>JalviewLite:</em>
<ul>
- Jmol 11.0.2 integration<br>
- PDB views stored in Jalview XML files<br>
- Slide sequences<br>
- Edit sequence in place<br>
- EMBL CDS features<br>
- DAS Feature mapping<br>
- Feature ordering<br>
- Alignment Properties<br>
- Annotation Scores<br>
- Sort by scores<br>
- Feature/annotation editing in applet<br>
+ 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</strong></p>
+<p><strong>Issues Resolved (a select list)</strong></p>
<ul>
- Headless state operation in 2.2.1 <br>
- Incorrect and unstable DNA pairwise alignment <br>
- Cut and paste of sequences with annotation <br>
- Feature group display state in XML<br>
- Feature ordering in XML<br>
- 2.2.1 applet had no feature transparency<br>
- Number pad keys can be used in cursor mode<br>
- Structure Viewer mirror image resolved</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>
git://source.jalview.org / jalview.git / blobdiff