</div>
</td>
</tr>
+
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+ <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>
+ <!-- JAL-3035 -->DAS sequence retrieval and annotation
+ capabilities removed from the Jalview Desktop
+ </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>
+ <!-- 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+ unmarshalling has been replaced by JAXB for Jalview projects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>
+ <li>
+ <!-- JAL-2865 -->Tree and PCA calculation fails for selected
+ region if columns were selected by dragging right-to-left
+ and the mouse moved to the left of the first column.
+ </li>
+ <li>
+ <!-- JAL-2846 -->Error message for trying to load in invalid
+ URLs doesn't tell users the invalid URL
+ </li>
+ </ul>
+ <em>Editing</em>
+ <ul>
+ <li>
+ <!-- JAL-2822 -->Start and End should be updated when
+ sequence data at beginning or end of alignment added/removed
+ via 'Edit' sequence
+ </li>
+ <li>
+ <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
+ sequence features correctly when start of sequence is
+ removed (Known defect since 2.10)
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ </ul>
+ <em>New Known Defects</em>
+ <ul>
+ <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>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-3101 -->Default memory for Jalview webstart and
+ InstallAnywhere increased to 1G.
+ </li>
+ <li>
+ <!-- JAL-247 -->Hidden sequence markers and representative
+ sequence bolding included when exporting alignment as EPS,
+ SVG, PNG or HTML. <em>Display is configured via the
+ Format menu, or for command-line use via a jalview
+ properties file.</em>
+ </li>
+ <li>
+ <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON.
+ </li>
+ <li>
+ <!-- JAL-3065 -->Change in recommended way of starting
+ Jalview via a Java command line: add jars in lib directory
+ to CLASSPATH, rather than via the deprecated java.ext.dirs
+ property.
+ </li>
+ </ul>
+ <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3047 -->Support added to execute test suite
+ instrumented with <a href="http://openclover.org/">Open
+ Clover</a>
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-3104 -->Poorly scaled bar in quality annotation
+ row shown in Feredoxin Structure alignment view of example
+ alignment.
+ </li>
+ <li>
+ <!-- JAL-2854 -->Annotation obscures sequences if lots of
+ annotation displayed.
+ </li>
+ <li>
+ <!-- JAL-3107 -->Group conservation/consensus not shown
+ for newly created group when 'Apply to all groups'
+ selected
+ </li>
+ <li>
+ <!-- JAL-3087 -->Corrupted display when switching to
+ wrapped mode when sequence panel's vertical scrollbar is
+ visible.
+ </li>
+ <li>
+ <!-- JAL-3003 -->Alignment is black in exported EPS file
+ when sequences are selected in exported view.</em>
+ </li>
+ <li>
+ <!-- JAL-3059 -->Groups with different coloured borders
+ aren't rendered with correct colour.
+ </li>
+ <li>
+ <!-- JAL-3092 -->Jalview could hang when importing certain
+ types of knotted RNA secondary structure.
+ </li>
+ <li>
+ <!-- JAL-3095 -->Sequence highlight and selection in
+ trimmed VARNA 2D structure is incorrect for sequences that
+ do not start at 1.
+ </li>
+ <li>
+ <!-- JAL-3061 -->'.' inserted into RNA secondary structure
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockholm flatfile.
+ </li>
+ <li>
+ <!-- JAL-3053 -->Jalview annotation rows containing upper
+ and lower-case 'E' and 'H' do not automatically get
+ treated as RNA secondary structure.
+ </li>
+ <li>
+ <!-- JAL-3106 -->.jvp should be used as default extension
+ (not .jar) when saving a jalview project file.
+ </li>
+ <li>
+ <!-- JAL-3105 -->Mac Users: closing a window correctly
+ transfers focus to previous window on OSX
+ </li>
+ </ul>
+ <em>Java 10 Issues Resolved</em>
+ <ul>
+ <li>
+ <!-- JAL-2988 -->OSX - Can't save new files via the File
+ or export menus by typing in a name into the Save dialog
+ box.
+ </li>
+ <li>
+ <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
+ of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
+ 'look and feel' which has improved compatibility with the
+ latest version of OSX.
+ </li>
+ </ul>
+ </div>
+ </td>
+ </tr>
<tr>
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
- <em>5/06/2018</em></strong>
+ <em>7/06/2018</em></strong>
</div>
</td>
<td><div align="left">
<em></em>
<ul>
<li>
- <!-- JAL-1460 -->Windows File Shortcuts can be dragged
- onto the Jalview Desktop
- </li>
- <li>
<!-- JAL-2920 -->Use HGVS nomenclature for variant
annotation retrieved from Uniprot
</li>
+ <li>
+ <!-- JAL-1460 -->Windows File Shortcuts can be dragged
+ onto the Jalview Desktop
+ </li>
</ul>
</div></td>
<td><div align="left">
<ul>
<li>
<!-- JAL-3017 -->Cannot import features with multiple
- variant elements
+ variant elements (blocks import of some Uniprot records)
</li>
<li>
<!-- JAL-2997 -->Clustal files with sequence positions in
not alignment area in exported graphic
</li>
<li>
+ <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
+ window has input focus
+ </li>
+ <li>
<!-- JAL-2992 -->Annotation panel set too high when
- annotation added to view
+ annotation added to view (Windows)
</li>
<li>
- <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
- window has input focus
+ <!-- JAL-3009 -->Jalview Desktop is slow to start up when
+ network connectivity is poor
</li>
<li>
<!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
git://source.jalview.org / jalview.git / blobdiff