</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10.4b1 ?</strong>
</p>
- <p>
- Jalview 2.9.0b2 is a bug fix release for Jalview 2.9.
- The release of Jalview 2.9 in September 2015 included
- a multitude of bug fixes and minor improvements (both small, and
- rather big!), it also brings major new capabilities for codon-level
- analysis of protein alignments and the retrieval and manipulation of
- structural data.</p><p>For the patches since version 2.9 was released, see the
- <a href="releases.html#Jalview.2.9.0b2">Jalview 2.9.0b2 Release Notes</a>.
- </p>
- <p>
- <strong>Highlights in Jalview 2.9</strong>
+ <p>This is the first patch release for Jalview 2.10.4. It includes
+ the following new patches:</p>
<ul>
- <li><strong>Visualisation, editing and analysis of
- cDNA and Protein alignments</strong><br />A new <a
- href="features/splitView.html">Split View</a> window allows linked
- protein and nucleotide sequence alignments to be viewed, edited,
- and analysed as one. <br />cDNA alignments can also be
- reconstructed from protein alignments calculated by Jalview's web
- services, and update in response to edits in the amino acid view.<br />To
- start experimenting with cDNA/Protein analysis, jut drop a file
- containing cDNA sequences which code for proteins in an existing
- alignment, and Jalview will do the rest.</li>
- <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
- 2.9 provides full support for the use of Chimera to view 3D
- structures linked to alignment views in the Jalview Desktop. We've
- also included support for saving Chimera sessions in Jalview
- project files.<br />Jalview and Chimera communicate using local
- web server connections, which may cause firewall alerts on some
- systems, but has the advantage of allowing bidirectional
- communication. Communication between Jalview and Chimera is now
- much more responsive, and selected regions in Chimera are now
- shown as highlighted regions in the Jalview desktop.</li>
- <li><strong>Interactive querying of the PDBe</strong><br />Jalview
- users can now <a href="features/pdbsequencefetcher.html">browse</a> and <a href="features/viewingpdbs.html">retrieve 3D structure</a> data from the PDB
- via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
- Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
- et al 2014</a>). Developed in collaboration with the PDBe group at
- EMBL-EBI, the interface allows both structured and free-text
- queries to be performed, and allows automatic selection of the
- most relevant structures for an alignment acording to a variety of
- criteria.</li>
- <li><strong>Improved support for RNA visualisation</strong><br />Jalview
- 2.9 integrates the latest version of the <a
- href="features/varna.html">VARNA RNA Viewer</a>, and VARNA views
- can also now be stored in Jalview projects. We've also dealt with
- a number of lingering bugs in the VARNA/Jalview interface,
- including the loss of pseudoknots when RNA secondary structure is
- shown VARNA.</li>
- <li><strong>Protein Secondary Structure predictions
- with JPred4</strong><br />Jalview includes a number of new features for
- working with secondary structure predictions from the JPred4
- server. These include new <a href="menus/popupMenu.html#hideinserts">popup menu actions</a> to automatically hide insertions and highlight
- mutations in an alignment with respect to a <a href="calculations/referenceseq.html">Reference
- Sequence</a>. Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable
- SVG HTML export</a> was also developed specifically for the JPred4
- server.</li>
+ <li>HGVS nomenclature used for variant annotation retrieved
+ from Uniprot</li>
+ <li>Uniprot import fails for some sequences (Cannot import
+ features with multiple variant elements)</li>
+ <li>Clustal files with sequence positions in right-hand column
+ are now parsed correctly</li>
+ <li>Wrap view - export to SVG - IDs shown but not alignment
+ area in exported graphic</li>
+ <li>F2/Keyboard mode edits work when Overview window has input
+ focus</li>
+ <li>Windows specific fixes:
+ <ul>
+ <li>Annotation panel set too high when annotation added to
+ view</li>
+ <li>Updated search paths for Chimera default installation</li>
+ <li>Windows File Shortcuts can be dragged onto the Jalview
+ Desktop</li>
+ <li>Drag URL from Chrome, Firefox, IE to Jalview desktop on
+ Windows doesn't open file:<br /> Dragging the currently open
+ URL and links from a page viewed in Firefox or Chrome on
+ Windows is now fully supported.<br />
+ <strong>If you are using Edge</strong>, only links in the page
+ can be dragged.<br />
+ <strong>With Internet Explorer</strong>, only the currently open
+ URL in the browser can be dropped onto Jalview.
+ </li>
+ </ul>
+ </li>
</ul>
-
+ <p>Highlights in the 2.10.4 series include:</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