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<body>
<p>
- <strong>What's new in Jalview 2.10.2 ?</strong>
- </p>
- <p>This August 2018 release of Jalview introduces new user interface features, improved and more extensible tree and PCA analysis, more robust 3D structure viewing with UCSF Chimera and an updated service client for JABAWS. The full list of bug fixes and new features can be found in the <a
- href="releases.html#Jalview.2.10.2"> 2.10.2 Release Notes</a>, but the
- highlights are below.
+ <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, RNA secondary structure
+ annotation, and those running Jalview on OSX with Java 10.</p>
<ul>
- <li><strong>New dialog and faster and more
- configurable Tree and PCA calculations</strong><br> Menu entries for
- calculating PCA and different types of tree have been replaced by
- a single <a href="calculations/calculations.html"><em>Calculations</em>
- dialog box</a>. The underlying implementation for the PCA and tree
- calculations have been made faster and more memory efficient.</li>
- <li><strong>Extensible score models</strong><br />A new
- framework has also been created for the score models used to
- calculate distances between sequences and shade alignments. This
- framework allows import of substitution matrices in NCBI and
- AAIndex format.<br />
- <strong>PCA Bug Fixes</strong>. Jalview's implementation of PCA
- differed in its treatment of gaps and non-standard residues. The
- BLOSUM62 matrix also included a typo that affected results. See the
- <a href="releases.html#2102scoremodelbugs">2.10.2 release note
- about score model bugs</a> for details and how to reinstate legacy
- behaviour.</li>
- <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
- alignment, protein conservation analysis, and protein disorder and
- RNA secondary structure prediction services are now provided by <a
- href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
- Several of the programs provided as JABAWS 2.2 services have been
- updated, so their options and parameters have changed.</li>
- <li><strong>URL linkouts to other bioinformatics
- databases</strong><br />New preferences for <a
- href="webServices/urllinks.html">opening web pages for
- database cross-references</a> via the UK Elixir's EMBL-EBI's MIRIAM
- database and identifiers.org services.</li>
- <li><strong>Showing and hiding regions</strong> <br /> <a
- href="menus/popupMenu.html#hideinserts">Hide insertions</a> in the
- PopUp menu has changed its behaviour. Prior to 2.10.2, columns
- were only shown or hidden according to gaps in the sequence under
- the popup menu. Now, only columns that are gapped in all selected
- sequences as well as the sequence under the popup menu are hidden,
- and column visibility outside the selected region is left as is.
- This makes it easy to filter insertions from the alignment view
- (just select the region containing insertions to remove) without
- affecting the rest of the hidden columns.</li>
- <li><strong>Gap count - a.k.a. the Occupancy
- Annotation Row</strong><br /> Another way to filter columns according to
- the presence of gaps is to enable the <strong>Occupancy
- Annotation</strong> row via Jalview's Preferences. This annotation row
- shows a histogram of the number of aligned residues at each
- column. The <a href="features/columnFilterByAnnotation.html">Select
- By Annotation</a> dialog now also includes a percentage threshold
- mode, to make it easy to filter alignments to show only those
- columns with a particular fraction of aligned sequences.</li>
- <li><strong>Recent search history for Find, PDBe and
- Uniprot</strong><br />Easily repeat a previous search for <a
- href="features/search.html#queryhistory">Find</a> and the free
- text search system (for querying Uniprot and the PDBe).</li>
- <li><strong>Improved Overview Window</strong><br />The <a
- href="features/overview.html">alignment overview</a> is now easier
- to use when working with alignments of more than 5000 rows and
- columns, and features a new pop-up menu that allows hidden regions
- to be excluded from the overview. It also works with CDS/Protein
- alignments and MSA views in wrapped mode.</li>
- <li><strong>3D Structure</strong><br />Jalview's communication
- with UCSF Chimera has been made more robust, particularly when
- working with many structures and long sequences. Regions in
- structures that correspond to hidden regions in an alignment view
- are now left un-coloured, making it easier to highlight specific
- features in 3D. See below for <a href="#experimental">experimental
- features for exchanging annotation between Chimera and Jalview.</a></li>
+ <li>Jalview's default memory limit increased to 1G. If you have
+ problems starting Jalview 2.10.5 and you have 1G or less
+ physical memory on your machine, you will need to <a
+ href="memory.html#memsetting">reduce the memory</a> allocated to
+ Jalview.
+ </li>
+ <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>
- <strong>Scripting</strong><br />New <a
- href="http://www.jalview.org/examples/groovy">groovy examples</a>
- demonstrate Jalview 2.10.2 APIs for creation of data-driven
- colourschemes, and custom alignment file handlers. The <a
- href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
- introduced in Jalview 2.10 has also been refactored to allow
- efficient counting across multiple feature types. Please be aware
- that feature counter scripts created for earlier versions will not
- execute in Jalview 2.10.2.
- </p>
- <p>
- <strong><a name="experimental">Experimental Features</a></strong>
+ 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 bug fixes and improvements 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 help make Jalview better !
</p>
<p>
- This release of Jalview introduces an <em>Experimental Features</em>
- option in the Jalview Desktop's <em>Tools</em> menu that allows you
- to try out features that are still in development. To access the
- experimental features below - first enable the <strong>Tools→Enable
- Experimental Features</strong> option, and then restart Jalview.
+ <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.</p>
+ <em>Known Issues</em>
<ul>
- <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
- <a href="features/chimera.html#experimental">new entries in
- the Chimera viewer's Chimera menu</a> allow positional annotation to
- be exchanged between Chimera and Jalview.</li>
+ <li>OSX: The 'Open File' dialog for Jalview's Groovy Console
+ appears with the title 'Save As', and attempting to select a file to load yields a FileNotFound exception.</br>The workaround is to first clear the 'Untitled' filename before selecting the file you wish to load.
+ </li>
+ <li>OSX: Links don't open when clicked on or via the Sequence or Alignment window popup menu.</li>
+ <li>OSX (Webstart): Jalview only displays old news feed items</li>
</ul>
-
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