<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 2.8.0b1)
+ * 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.
- *
+ *
* 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/>.
+ * 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 2.5.1 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>
+ <p>
+ <strong>What's new ?</strong><br /> Jalview 2.8.0b1 is a bugfix
+ release for Jalview version 2.8. <br /> As usual you can find the
+ highlights below, and the comprehensive list is given in the <a
+ href="releases.html#Jalview2.8.0b1">Jalview 2.8.0b1 Release Notes</a>.
+ </p>
+ <p>
+ This bug fix release includes numerous minor enhancements made over
+ the last 12 months. Importantly, it is also the first release that
+ provides Jalview as a trusted application, signed with a certificate
+ donated to us by <a href="certum.eu">Certum</a>.
+ </p>
+ <strong>Enhancements and new features</strong>
<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/>
+ <li>Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred works</li>
+ <li>allow import of data from gzipped files</li>
+ <li>Improved per-sequence 'colour-by-annotation' performance</li>
+ <li>Support '' style escaping of quotes in Newick files</li>
+ <li>group options for JABAWS service by command line name</li>
+ <li>Select primary source when selecting authority in database
+ fetcher GUI</li>
+ <li>COMBINE statement uses current SEQUENCE_REF and GROUP_REF
+ scope to group annotation rows</li>
+ <li>add .mfa to FASTA file extensions recognised by Jalview</li>
+ <li>groovy scripting for headless jalview operation</li>
+ <li>Output in Stockholm format</li>
</ul>
- <em>Desktop Issues</em>
+ <strong>Bug fixes</strong>
<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>
+ <li>Uniprot and PDB database cross-reference fetching works
+ properly</li>
+ <li>'View all structures' in the desktop is more reliable</li>
+ <li>Web services parameter dialog box shows the options enabled
+ for different presets</li>
+ <li>Interactive creation of RNA secondary structure works more
+ smoothly</li>
+ <li>Keyboard mode 'P' command jumps to the right place</li>
+ <li>Improved support for parsing database cross-references via
+ Stockholm and Rfam database</li>
+ <li>Improved semantics in annotation files for grouping
+ annotation rows associated with particular sequences and groups</li>
+ <li>More robust DNA->Amino acid translation</li>
+ <li>Improved Headless-mode operation for DAS annotation
+ retrieval, groovy script execution and alignment figure generation</li>
+ <li>annotation label tooltip text needs to be wrapped</li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff