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<div align="center">
<strong><a name="Jalview.2.11.0">2.11.0</a><br />
- <em>29/01/2019</em></strong>
+ <em>14/05/2019 (final due date !)</em></strong>
</div>
</td>
<td><div align="left">
+ <ul>
+ <li>
+ <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
+ Viewer state is saved in Jalview Project<br />The 'Change
+ parameters' option has also been removed from the PCA
+ viewer.
+ </li>
+ <li>
+ <!-- JAL-3198 -->More efficient creation of selections and
+ multiple groups when working with large alignments
+ </li>
+ <li>
+ <!-- JAL-3200 -->Speedier import of annotation rows when
+ parsing stockholm files
+ </li>
+ <li>
+ <!-- JAL-3018 -->Update of Ensembl Rest Client to API v9.0
+ </li>
+ <li>
+ <!-- JAL-3... -->Sequence features can be filtered and
+ shaded according to any associated attributes (e.g. variant
+ attributes from VCF file, or key-value pairs imported from
+ column 9 of GFF file)
+ </li>
+ <li>
+ <!-- JAL-3139, -->More efficient sequence feature render
+ algorithm (Z-sort/transparency and filter aware)
+ </li>
+ <li>
+ <!-- JAL-2527 -->Alignment Overview now by default shows
+ only visible region of alignment (this can be changed in
+ user preferences)
+ </li>
+ <li><!-- -->
+ </li>
+ </ul>
<em>Deprecations</em>
<ul>
<li>
</ul>
<em>Release Processes</em>
<ul>
- <li>Atlassian Bamboo continuous integration server for unattended Test Suite execution</li>
- <li><!-- JAL-2864 -->Memory test suite to detect leaks in common operations</li>
+ <li>Atlassian Bamboo continuous integration server for
+ unattended Test Suite execution</li>
+ <li>
+ <!-- JAL-2864 -->Memory test suite to detect leaks in common
+ operations
+ </li>
+ <li>
+ <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
+ implementation) used for Sequence Feature collections
+ </li>
+ <li>
+ <!-- JAL-3063 -->Castor library for XML marshalling and
+ unmarshalling has been replaced by JAXB for Jalview projects
+ and XML based data retrieval clients
+ </li>
+ <li>
+ <!-- JAL -->
+
</ul>
</div></td>
<td><div align="left">
<em></em>
<ul>
<li>
+ <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
+ Jalview project involving multiple views
+ </li>
+ <li>
+ <!-- JAL-3164 -->Overview for complementary view in a linked
+ CDS/Protein alignment is not updated when Hide Columns by
+ Annotation dialog hides columns
+ </li>
+ <li>
+ <!-- JAL-3158 -->Selection highlighting in the complement of
+ a CDS/Protein alignment stops working after making a
+ selection in one view, then making another selection in the
+ other view.
+ </li>
+ <li><!-- JAL-3161 -->Annotations tooltip changes beyond visible columns</li>
+ <li>
+ <!-- JAL-3154 -->Table Columns could be re-ordered in
+ Feature Settings and Jalview Preferences panels
+ </li>
+ <li>
<!-- JAL-2865 -->Jalview hangs when closing windows
or the overview updates with large alignments.
</li>
<!-- JAL-3178 -->Nonpositional features lose feature group
on export as jalview features file
</li>
+ <li><!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
</ul>
</div></td>
</tr>
</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.5 ?</strong>
+ <strong>Jalview 2.11 - major and minor new features</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>
+ <p>Jalview 2.11 introduces support for loading VCF files, and new
+ filters and shading models for sequence features. Under the hood,
+ we've addressed many bugs, and also made some important changes in
+ the way the Jalview desktop is installed and launched.</p>
<ul>
- <li>Jalview's default memory limit increased to 1G. <br/>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 made more reliable.</li>
+ <li><em>VCF Support</em>. Proteins and genomic contigs with
+ chromosomal location annotation (such as protein coding genes
+ retrieved from Ensembl) can be annotated with variants imported
+ from a local VCF file.</li>
+ <li><em>The Jalview Launcher and Update System</em><br />
+ Jalview's new installation model means you'll only need to
+ download and install Jalview once. After installation, Jalview
+ will automatically keep itself up to date. The launcher also sets
+ Jalview's memory automatically, so you'll never again have to
+ manually configure Java's memory settings.<br />We are grateful to
+ Install4J who provided us with a free license for their
+ installation system, and Jalview's over the air update system is
+ via Getdown.</li>
</ul>
<p>
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 !
+ href="releases.html#Jalview.2.11">2.11 Release Notes</a>.
</p>
<p>
- <strong>Jalview and Java 10</strong>
+ <strong>Jalview and Java 11, 13, and onwards</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>
+ <p>Java 11 provides improved performance and better OS
+ integration, so we now recommend users select our Java 11 Jalview
+ distribution rather than the legacy Java 8 build.</p>
+ <em>Known Issues - update for 211 </em>
<ul>
<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>
+ 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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