</head>
<body>
<p>
+ <strong>Jalview 2.10.2b1 bugfix release</strong>
+ </p>
+ <p>
+ This is patch release for 2.10.2. See the <a
+ href="releases.html#Jalview.2.10.2b1">release notes</a>.
+ </p>
+ <p>
<strong>What's new in Jalview 2.10.2 ?</strong>
</p>
<p>
- Full details about Jalview 2.10.2 are in the <a
- href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
- highlights are below.
+ Version 2.10.2 was released in August 2017, and introduced 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.
</p>
<ul>
- <li><strong>New UI, and faster and more configurable
- implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
- Menu entries for calculating PCA and different types of tree have
- been replaced by a single <em>Calculations</em> dialog box. The
- underlying implementation for the PCA and tree calculations have
- been made faster and more memory efficient. A new framework has
- also been created for the score models used to calculate distances
- between sequences. This framework allows import of substitution
- matrices in NCBI and AAIndex format, and custom score models to be
- created via a groovy script.</li>
+ <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+ calculating PCA and different types of tree have been replaced by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 services have been updated, so
- their options and parameters have changed.</li>
- <li>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><em>Showing and hiding regions</em>
- <ul>
- <li><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>
- </ul></li>
- <li>Recent search histories for <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>
</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>
</p>
<p>
- This release of Jalview includes a new option in the Jalview Desktop
- that allows you to try out features that are still in development.
- To access the features described below, please first enable the <strong>Tools→Enable
+ 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.
</p>
<ul>
the Chimera viewer's Chimera menu</a> allow positional annotation to
be exchanged between Chimera and Jalview.</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>
+
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</html>
git://source.jalview.org / jalview.git / blobdiff