<title>Release History</title>
<style>
table, th, td {
- border: solid #ccc 1px;
+ border: solid #cccccc 1px;
border-collapse: collapse;
}
-h3 {
- font-size: 110%;
- margin: 0.1rem 0 0.1rem 0;
- font-style: italic;
-}
-
-ul {
- padding-left: 1rem;
- padding-bottom: 0.25rem;
-}
ul {
+ padding: 2;
+ margin-left: 18;
list-style-type: square;
}
ul ul {
list-style-type: disc;
}
li::marker {
- color: hsla(193,100%,33%,.95);
+ color: #0084A8;
}
li {
- padding-top: 0.25rem;
+ padding-bottom: 5;
}
th {
- font-size: 125%;
- margin: 0.1rem 0 0.3rem 0;
+ font-size: 110%;
text-style: none;
font-weight: bold;
- padding: 0.5rem 1rem;
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.release {
text-align: center;
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td {
vertical-align: top;
- padding: 0.5rem;
+ padding: 10;
}
td.release {
width: 8%;
</p>
<table border="1">
<tr>
- <th class="release" align="center" valign="top" nowrap><a id="Jalview.$$Version-Rel$$">Release</th>
- <th class="new_features" align="left" valign="top">New Features</th>
- <th class="issues_resolved" align="left" valign="top">Issues Resolved</th>
+ <th class="release" width="8%" align="center" valign="top" nowrap><a id="Jalview.$$Version-Rel$$">Release</th>
+ <th class="new_features" width="46%" align="left" valign="top">New Features</th>
+ <th class="issues_resolved" width="46%" align="left" valign="top">Issues Resolved</th>
</tr>
<tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong><a id="Jalview.2">2</a><a id="Jalview.2.11">.11</a><a id="Jalview.2.11.2">.2</a><a id="Jalview.2.11.2.2">.2</a></strong>
<br />
<em>19 April 2022</em>
</td>
<td class="new_features" align="left" valign="top">
<ul>
-<li><!-- JAL-3992 --> Minor documentation fixes</li>
+<li>Minor documentation fixes <!-- JAL-3992 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3365 --> Secondary structure annotation from Pfam not displayed correctly</li>
-<li><!-- JAL-3997 --> Null pointer exceptions when displaying annotation tooltips whilst in wrapped mode</li>
+<li>Secondary structure annotation from Pfam not displayed correctly <!-- JAL-3365 --></li>
+<li>Null pointer exceptions when displaying annotation tooltips whilst in wrapped mode <!-- JAL-3997 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.2<a id="Jalview.2.11.2.1">.1</a></strong>
<br />
<em>5 April 2022</em>
</td>
<td class="new_features" align="left" valign="top">
<ul>
-<li><!-- JAL-3973 --> Distribution Tarball includes git commit and branch details</li>
+<li>Distribution Tarball includes git commit and branch details <!-- JAL-3973 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3975 --> Keyboard mode (F2) stops working after using the "Create sequence feature" dialog</li>
-<li><!-- JAL-3976 --> 3D Structure chooser fails to select structures from 3D-beacons and pops up a 'null' dialog</li>
-<li><!-- JAL-3985 --> PDB FTS query results in error dialog containing '414' [URL too long]</li>
-<li><!-- JAL-3980 JAL-3981 --> Sequence ID tooltip not shown during long running retrieval/crossref operations (affects at least 2.11.1 onwards)</li>
-<li><!-- JAL-3973 --> Cannot build Jalview 2.11.2.0 via gradle from its source tarball</li>
+<li>Keyboard mode (F2) stops working after using the "Create sequence feature" dialog <!-- JAL-3975 --></li>
+<li>3D Structure chooser fails to select structures from 3D-beacons and pops up a 'null' dialog <!-- JAL-3976 --></li>
+<li>PDB FTS query results in error dialog containing '414' [URL too long] <!-- JAL-3985 --></li>
+<li>Sequence ID tooltip not shown during long running retrieval/crossref operations (affects at least 2.11.1 onwards) <!-- JAL-3980 JAL-3981 --></li>
+<li>Cannot build Jalview 2.11.2.0 via gradle from its source tarball <!-- JAL-3973 --></li>
</ul>
-<h3>New Known Issues</h3>
+<p><em>New Known Issues</em></p>
<ul>
-<li><!-- JAL-3984 --> Keyboard mode (F2) stops working after using the "Text Colour" dialog</li>
-<li><!-- JAL-3873 --> Colour by->all views doesn't allow colouring same structure from different views (since 2.11.2.0)</li>
-<li><!-- JAL-3886 --> Pfam and Rfam alignment retrieval as gzipped stockholm doesn't work on JalviewJS build of 2.11.2</li>
-<li><!-- JAL-3972 --> Java 11 Only: Jalview 2.11.2.0 OSX install not working due to VAqua requiring sun.awt.image.MultiResolutionImage</li>
-<li><!-- JAL-3981 --> Sequence Details can take a long time to be displayed for heavily annotated sequences (all versions)</li>
+<li>Keyboard mode (F2) stops working after using the "Text Colour" dialog <!-- JAL-3984 --></li>
+<li>Colour by->all views doesn't allow colouring same structure from different views (since 2.11.2.0) <!-- JAL-3873 --></li>
+<li>Pfam and Rfam alignment retrieval as gzipped stockholm doesn't work on JalviewJS build of 2.11.2 <!-- JAL-3886 --></li>
+<li>Java 11 Only: Jalview 2.11.2.0 OSX install not working due to VAqua requiring sun.awt.image.MultiResolutionImage <!-- JAL-3972 --></li>
+<li>Sequence Details can take a long time to be displayed for heavily annotated sequences (all versions) <!-- JAL-3981 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.2<a id="Jalview.2.11.2.0">.0</a></strong>
<br />
<em>10 March 2022</em>
</td>
<td class="new_features" align="left" valign="top">
<ul>
-<li><!-- JAL-3616 JAL-3551 JAL-2322 --> Support for viewing 3D structures with ChimeraX and Pymol in addition to Jmol and Chimera.</li>
-<li><!-- JAL-3829 --> Discover 3D structure data for sequences with Uniprot references via 3D-Beacons</li>
-<li><!-- JAL-3391 --> Rank and select available structures for Uniprot sequences according to number of residues in structure mapped to positions involved in the alignment</li>
-<li><!-- JAL-2226 --> Structure annotation rows for all mapped chains in 3D structures are included in the 'Reference Annotation' for a sequence</li>
-<li><!-- JAL-1260 --> Import Genbank and EMBL format flatfiles</li>
-<li><!-- JAL-3821 --> ENA record's mol_type honoured so RNA molecules imported from ENA records are shown as RNA</li>
-<li><!-- JAL-3863 --> Support for Canonical Uniprot IDs</li>
-<li><!-- JAL-3503 --> New Preferences tab for adjusting Jalview's memory settings at launch</li>
-<li><!-- JAL-3881 --> Sequence IDs split on '_' as well as other non-alphanumerics when discovering database references with 'Fetch DB Refs'</li>
-<li><!-- JAL-3884 --> Suppressed harmless exceptions output to Console whilst discovering database references for a sequence</li>
-<li><!-- JAL-3204 --> Updated Jalview bindings for Uniprot XML schema</li>
-<li><!-- JAL-3926 --> Uniprot and PDBe autosearch option is disabled by default</li>
-<li><!-- JAL-3144 --> Reverted to Jalview 'classic' drop-down menu for selecting which database to fetch from in sequence fetcher dialog.</li>
-<li><!-- JAL-3018 --> Updated Ensembl REST Client compatibility to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster)</li>
-<li><!-- JAL-3530 --> -nowebservicediscovery command line argument to prevent automatic discovery of analysis webservices on launch</li>
-<li><!-- JAL-3618 --> Allow 'App' directories to be opened when locating Chimera, ChimeraX or Pymol binaries via filechooser opened by double clicking the Structure Preferences' path textbox</li>
-<li><!-- JAL-3632 JAL-3633 --> support for HTTP/S access via proxies that require authentication</li>
-<li><!-- JAL-3103 --> New mechanism for opening URLs with system default browser (works on OSX and Linux as well as Windows)</li>
-<li><!-- JAL-3871 JAL-3874 --> Upgraded bundled version of Jmol to 14.31.53</li>
-<li><!-- JAL-3837 --> GPL license info on splash screen and About text</li>
-</ul>
-<h3>Jalview Native App</h3>
-<ul>
-<li><!-- JAL-3830 --> New command line launcher scripts (.sh, .ps1, .bat) usable on macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option to add this to PATH, or link to it in your PATH.<br/>
+<li>Support for viewing 3D structures with ChimeraX and Pymol in addition to Jmol and Chimera. <!-- JAL-3616 JAL-3551 JAL-2322 --></li>
+<li>Discover 3D structure data for sequences with Uniprot references via 3D-Beacons <!-- JAL-3829 --></li>
+<li>Rank and select available structures for Uniprot sequences according to number of residues in structure mapped to positions involved in the alignment <!-- JAL-3391 --></li>
+<li>Structure annotation rows for all mapped chains in 3D structures are included in the 'Reference Annotation' for a sequence <!-- JAL-2226 --></li>
+<li>Import Genbank and EMBL format flatfiles <!-- JAL-1260 --></li>
+<li>ENA record's mol_type honoured so RNA molecules imported from ENA records are shown as RNA <!-- JAL-3821 --></li>
+<li>Support for Canonical Uniprot IDs <!-- JAL-3863 --></li>
+<li>New Preferences tab for adjusting Jalview's memory settings at launch <!-- JAL-3503 --></li>
+<li>Sequence IDs split on '_' as well as other non-alphanumerics when discovering database references with 'Fetch DB Refs' <!-- JAL-3881 --></li>
+<li>Suppressed harmless exceptions output to Console whilst discovering database references for a sequence <!-- JAL-3884 --></li>
+<li>Updated Jalview bindings for Uniprot XML schema <!-- JAL-3204 --></li>
+<li>Uniprot and PDBe autosearch option is disabled by default <!-- JAL-3926 --></li>
+<li>Reverted to Jalview 'classic' drop-down menu for selecting which database to fetch from in sequence fetcher dialog. <!-- JAL-3144 --></li>
+<li>Updated Ensembl REST Client compatibility to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster) <!-- JAL-3018 --></li>
+<li>-nowebservicediscovery command line argument to prevent automatic discovery of analysis webservices on launch <!-- JAL-3530 --></li>
+<li>Allow 'App' directories to be opened when locating Chimera, ChimeraX or Pymol binaries via filechooser opened by double clicking the Structure Preferences' path textbox <!-- JAL-3618 --></li>
+<li>support for HTTP/S access via proxies that require authentication <!-- JAL-3632 JAL-3633 --></li>
+<li>New mechanism for opening URLs with system default browser (works on OSX and Linux as well as Windows) <!-- JAL-3103 --></li>
+<li>Upgraded bundled version of Jmol to 14.31.53 <!-- JAL-3871 JAL-3874 --></li>
+<li>GPL license info on splash screen and About text <!-- JAL-3837 --></li>
+</ul>
+<p><em>Jalview Native App</em></p>
+<ul>
+<li>New command line launcher scripts (.sh, .ps1, .bat) usable on macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option to add this to PATH, or link to it in your PATH.<br/> <!-- JAL-3830 -->
<em>This is the recommended workaround for known issue about working directory preservation when running native application from command line.</em></li>
<li>Notarized MacOS installer for compliance with latest OSX releases (Monterey)</li>
-<li><!-- JAL-3805 --> Uninstaller application for old (InstallAnywhere based) Jalview installations removed from the OSX disk image</li>
-<li><!-- JAL-3608 --> Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview</li>
-<li><!-- JAL-3552, JAL-3609 --> Metal LaF used to improved operation on Linux Ubuntu with HiDPI display in Java 11 (still known issues with HiDPI screens in java 8 and 11. see <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)</li>
-<li><!-- JAL-3633 --> Getdown launcher inherits HTTP/S proxy configuration from jalview_properties</li>
-<li><!-- JAL- --> New Jalview Develop app - making it even easier to get at Jalview's development builds</li>
-<li><!-- JAL-3594 --> New splashscreens for Jalview, Jalview Test and Jalview Develop applications.</li>
-<li><!-- JAL-3728 --> Jalview logos shown for Jalview Java Console and other window widgets in taskbar and dock rather than anonymous 'Java' icons</li>
-</ul>
-<h3>JalviewJS</h3>
-<ul>
-<li><!-- JAL-3624 --> PDB structures mapped to Uniprot Sequences with SIFTS</li>
-<li><!-- JAL-3208 --> setprop commandline argument reinstated for JalviewJS only</li>
-<li><!-- JAL-3163 --> Missing message bundle keys are only reported once per key (avoids excessive log output in js console)</li>
-<li><!-- JAL-3168 --> Feature type is included in the title of the Feature Settings' Colour Chooser dialog</li>
-<li><!-- JAL-3279 --> Build details reported in About window</li>
-<li><!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 --> Numerous minor GUI additions and improvements in sync with Java application.</li>
-</ul>
-<h3>Development</h3>
-<ul>
-<li><!-- --> First integrated JalviewJS and Jalview release</li>
-<li><!-- JAL-3841,JAL-3248 --> Updated README and doc/building.md</li>
-<li><!-- JAL-3789, JAL-3679 --> Improved JalviewJS/Jalview build process, added support for system package provided eclipse installs on linux</li>
+<li>Uninstaller application for old (InstallAnywhere based) Jalview installations removed from the OSX disk image <!-- JAL-3805 --></li>
+<li>Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview <!-- JAL-3608 --></li>
+<li>Metal LaF used to improved operation on Linux Ubuntu with HiDPI display in Java 11 (still known issues with HiDPI screens in java 8 and 11. see <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>) <!-- JAL-3552, JAL-3609 --></li>
+<li>Getdown launcher inherits HTTP/S proxy configuration from jalview_properties <!-- JAL-3633 --></li>
+<li>New Jalview Develop app - making it even easier to get at Jalview's development builds <!-- JAL- --></li>
+<li>New splashscreens for Jalview, Jalview Test and Jalview Develop applications. <!-- JAL-3594 --></li>
+<li>Jalview logos shown for Jalview Java Console and other window widgets in taskbar and dock rather than anonymous 'Java' icons <!-- JAL-3728 --></li>
+</ul>
+<p><em>JalviewJS</em></p>
+<ul>
+<li>PDB structures mapped to Uniprot Sequences with SIFTS <!-- JAL-3624 --></li>
+<li>setprop commandline argument reinstated for JalviewJS only <!-- JAL-3208 --></li>
+<li>Missing message bundle keys are only reported once per key (avoids excessive log output in js console) <!-- JAL-3163 --></li>
+<li>Feature type is included in the title of the Feature Settings' Colour Chooser dialog <!-- JAL-3168 --></li>
+<li>Build details reported in About window <!-- JAL-3279 --></li>
+<li>Numerous minor GUI additions and improvements in sync with Java application. <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 --></li>
+</ul>
+<p><em>Development</em></p>
+<ul>
+<li>First integrated JalviewJS and Jalview release <!-- --></li>
+<li>Updated README and doc/building.md <!-- JAL-3841,JAL-3248 --></li>
+<li>Improved JalviewJS/Jalview build process, added support for system package provided eclipse installs on linux <!-- JAL-3789, JAL-3679 --></li>
<li>Install4j 9.0.x used for installer packaging</li>
-<li><!-- JAL-3930 --> Improved use of installers for unattended installation with a customizedId of "JALVIEW" in install4j's Jalview Launcher</li>
-<li><!-- JAL-3907 --> Improved compatibility of Jalview build with Java 17 (next LTS target)</li>
+<li>Improved use of installers for unattended installation with a customizedId of "JALVIEW" in install4j's Jalview Launcher <!-- JAL-3930 --></li>
+<li>Improved compatibility of Jalview build with Java 17 (next LTS target) <!-- JAL-3907 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3674 --> Slow structure commands can block Jalview execution</li>
-<li><!-- JAL-3904 --> Structure window's viewer-specific menu disappears when only one structure is shown (and many sequences:one chain mappings are present)</li>
-<li><!-- JAL-3779 --> Annotation file: PROPERTIES apply only to the first SEQUENCE_GROUP defined</li>
-<li><!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 --> Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3)</li>
-<li><!-- JAL-3761 --> Not all codon positions highlighted for overlapping exon splice sites (e.g due to RNA slippage)</li>
-<li><!-- JAL-3794 --> X was not being recognised as the unknown base in DNA sequences</li>
-<li><!-- JAL-3915 --> Removed RNAview checkbox and logic from Structure Preferences</li>
-<li><!-- JAL-3583 --> Tooltip behaviour improved (slightly)</li>
-<li><!-- JAL-3162 --> Can edit a feature so that start > end</li>
-<li><!-- JAL-2848 --> Cancel from Amend Features doesn't reset a modified graduated colour</li>
-<li><!-- JAL-3788 --> New View with automatic 'Show Overview' preference enabled results in Null Pointer Exceptions when clustal colouring is enabled</li>
-<li><!-- JAL-3275 --> Can open multiple Preferences panels</li>
-<li><!-- JAL-3633 --> Properly configure HTTPS proxy settings from Preferences</li>
-<li><!-- JAL-3949 --> Standard out logging broken: messages only routing to stderr and appear as a raw template</li>
-<li><!-- JAL-3739 --> Entering web service parameter values in numerical field doesn't update the value of the parameter until return is pressed.</li>
-<li><!-- JAL-3749 --> Resolved known issue (from 2.11.1.1) concerning duplicate CDS sequences generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs</li>
-</ul>
-<h3>JalviewJS</h3>
-<ul>
-<li><!-- JAL-3202 --> Consensus profile may include zero (rounded down) percentage values causing a divide by zero</li>
-<li><!-- JAL-3762 --> JalviewJS doesn't honour arguments passed via Info.args when there are arguments on the URL</li>
-<li><!-- JAL-3602 --> gradle closure-compiler not using UTF-8</li>
-<li><!-- JAL-3603 --> Annotation file fails to load from URL in JalviewJS</li>
-</ul>
-<h3>Development</h3>
+<li>Slow structure commands can block Jalview execution <!-- JAL-3674 --></li>
+<li>Structure window's viewer-specific menu disappears when only one structure is shown (and many sequences:one chain mappings are present) <!-- JAL-3904 --></li>
+<li>Annotation file: PROPERTIES apply only to the first SEQUENCE_GROUP defined <!-- JAL-3779 --></li>
+<li>Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3) <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 --></li>
+<li>Not all codon positions highlighted for overlapping exon splice sites (e.g due to RNA slippage) <!-- JAL-3761 --></li>
+<li>X was not being recognised as the unknown base in DNA sequences <!-- JAL-3794 --></li>
+<li>Removed RNAview checkbox and logic from Structure Preferences <!-- JAL-3915 --></li>
+<li>Tooltip behaviour improved (slightly) <!-- JAL-3583 --></li>
+<li>Can edit a feature so that start > end <!-- JAL-3162 --></li>
+<li>Cancel from Amend Features doesn't reset a modified graduated colour <!-- JAL-2848 --></li>
+<li>New View with automatic 'Show Overview' preference enabled results in Null Pointer Exceptions when clustal colouring is enabled <!-- JAL-3788 --></li>
+<li>Can open multiple Preferences panels <!-- JAL-3275 --></li>
+<li>Properly configure HTTPS proxy settings from Preferences <!-- JAL-3633 --></li>
+<li>Standard out logging broken: messages only routing to stderr and appear as a raw template <!-- JAL-3949 --></li>
+<li>Entering web service parameter values in numerical field doesn't update the value of the parameter until return is pressed. <!-- JAL-3739 --></li>
+<li>Resolved known issue (from 2.11.1.1) concerning duplicate CDS sequences generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs <!-- JAL-3749 --></li>
+</ul>
+<p><em>JalviewJS</em></p>
+<ul>
+<li>Consensus profile may include zero (rounded down) percentage values causing a divide by zero <!-- JAL-3202 --></li>
+<li>JalviewJS doesn't honour arguments passed via Info.args when there are arguments on the URL <!-- JAL-3762 --></li>
+<li>gradle closure-compiler not using UTF-8 <!-- JAL-3602 --></li>
+<li>Annotation file fails to load from URL in JalviewJS <!-- JAL-3603 --></li>
+</ul>
+<p><em>Development</em></p>
<ul>
<li>Gradle
<ul>
<li>Fixed non-fatal gradle errors during build</li>
-<li><!-- JAL-3745 --> Updated build.gradle for use with Gradle v.6.6+</li>
+<li>Updated build.gradle for use with Gradle v.6.6+ <!-- JAL-3745 --></li>
</ul>
</li>
</ul>
-<h3>Known Issues</h3>
+<p><em>Known Issues</em></p>
<ul>
-<li><!-- JAL-3764 --> Display of RESNUM sequence features are not suppressed when structures associated with a sequence are viewed with an external viewer (Regression from 2.11.1 series)</li>
+<li>Display of RESNUM sequence features are not suppressed when structures associated with a sequence are viewed with an external viewer (Regression from 2.11.1 series) <!-- JAL-3764 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11<a id="Jalview.2.11.1">.1</a><a id="Jalview.2.11.1.7">.7</a></strong>
<br />
<em>18 January 2022</em>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3703, JAL-3935 --> Files open in Jalview cannot be updated by Jalview or other applications (Windows, other non Unix/BSD OSs)</li>
+<li>Files open in Jalview cannot be updated by Jalview or other applications (Windows, other non Unix/BSD OSs) <!-- JAL-3703, JAL-3935 --></li>
</ul>
-<h3>Security</h3>
+<p><em>Security</em></p>
<ul>
-<li><!-- JAL-3937 --> Enable AIA download of HTTPS intermediate certificates.</li>
+<li>Enable AIA download of HTTPS intermediate certificates. <!-- JAL-3937 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.1<a id="Jalview.2.11.1.6">.6</a></strong>
<br />
<em>6 January 2022</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Security</h3>
+<p><em>Security</em></p>
<ul>
-<li><!-- JAL-3934 --> Version bump library dependency: Log4j 2.16.0 to 2.17.0.</li>
+<li>Version bump library dependency: Log4j 2.16.0 to 2.17.0. <!-- JAL-3934 --></li>
</ul>
</td>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.1<a id="Jalview.2.11.1.5">.5</a></strong>
<br />
<em>20 December 2021</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Security</h3>
+<p><em>Security</em></p>
<ul>
-<li><!-- JAL-3933 --> Update library dependency: Log4j 2.16.0 (was log4j 1.2.x).</li>
+<li>Update library dependency: Log4j 2.16.0 (was log4j 1.2.x). <!-- JAL-3933 --></li>
</ul>
-<h3>Development</h3>
+<p><em>Development</em></p>
<ul>
<li>Updated building instructions</li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3840 --> Occupancy calculation is incorrect for alignment columns with over -1+2^32 gaps (breaking filtering and display)</li>
-<li><!-- JAL-3833 --> Caps on Hi-DPI scaling to prevent crazy scale factors being set with buggy window-managers (linux only)</li>
+<li>Occupancy calculation is incorrect for alignment columns with over -1+2^32 gaps (breaking filtering and display) <!-- JAL-3840 --></li>
+<li>Caps on Hi-DPI scaling to prevent crazy scale factors being set with buggy window-managers (linux only) <!-- JAL-3833 --></li>
</ul>
-<h3>Development</h3>
+<p><em>Development</em></p>
<ul>
<li>Fixed non-fatal gradle errors during build</li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.1<a id="Jalview.2.11.1.4">.4</a></strong>
<br />
<em>9 March 2021</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Improved control of Jalview's use of network services via jalview_properties</h3>
+<p><em>Improved control of Jalview's use of network services via jalview_properties</em></p>
<ul>
-<li><!-- JAL-3814 --> New .jalview_properties token controlling launch of the news browser (like -nonews argument)</li>
-<li><!-- JAL-3813 --> New .jalview_properties token controlling download of linkout URLs from www.jalview.org/services/identifiers</li>
-<li><!-- JAL-3812 --> New .jalview_properties token controlling download of BIOJSHTML templates</li>
-<li><!-- JAL-3811 --> New 'Discover Web Services' option to trigger a one off JABAWS discovery if autodiscovery was disabled</li>
+<li>New .jalview_properties token controlling launch of the news browser (like -nonews argument) <!-- JAL-3814 --></li>
+<li>New .jalview_properties token controlling download of linkout URLs from www.jalview.org/services/identifiers <!-- JAL-3813 --></li>
+<li>New .jalview_properties token controlling download of BIOJSHTML templates <!-- JAL-3812 --></li>
+<li>New 'Discover Web Services' option to trigger a one off JABAWS discovery if autodiscovery was disabled <!-- JAL-3811 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3818 --> Intermittent deadlock opening structure in Jmol</li>
+<li>Intermittent deadlock opening structure in Jmol <!-- JAL-3818 --></li>
</ul>
-<h3>New Known defects</h3>
+<p><em>New Known defects</em></p>
<ul>
-<li><!-- JAL-3705 --> Protein Cross-Refs for Gene Sequence not always restored from project (since 2.10.3)</li>
-<li><!-- JAL-3806 --> Selections from tree built from CDS aren't propagated to Protein alignment (since 2.11.1.3)</li>
+<li>Protein Cross-Refs for Gene Sequence not always restored from project (since 2.10.3) <!-- JAL-3705 --></li>
+<li>Selections from tree built from CDS aren't propagated to Protein alignment (since 2.11.1.3) <!-- JAL-3806 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.1<a id="Jalview.2.11.1.3">.3</a></strong>
<br />
<em>29 October 2020</em>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3765 --> Find doesn't always highlight all matching positions in a sequence (bug introduced in 2.11.1.2)</li>
-<li><!-- JAL-3760 --> Alignments containing one or more protein sequences can be classed as nucleotide</li>
-<li><!-- JAL-3748 --> CDS alignment doesn't match original CDS sequences after alignment of protein products (known defect first reported for 2.11.1.0)</li>
-<li><!-- JAL-3725 --> No tooltip or popup menu for genomic features outwith CDS shown overlaid on protein</li>
-<li><!-- JAL-3751 --> Overlapping CDS in ENA accessions are not correctly mapped by Jalview (e.g. affects viral CDS with ribosomal slippage, since 2.9.0)</li>
-<li><!-- JAL-3763 --> Spliced transcript CDS sequences don't show CDS features</li>
-<li><!-- JAL-3700 --> Selections in CDS sequence panel don't always select corresponding protein sequences</li>
-<li><!-- JAL-3759 --> <em>Make groups from selection</em> for a column selection doesn't always ignore hidden columns</li>
+<li>Find doesn't always highlight all matching positions in a sequence (bug introduced in 2.11.1.2) <!-- JAL-3765 --></li>
+<li>Alignments containing one or more protein sequences can be classed as nucleotide <!-- JAL-3760 --></li>
+<li>CDS alignment doesn't match original CDS sequences after alignment of protein products (known defect first reported for 2.11.1.0) <!-- JAL-3748 --></li>
+<li>No tooltip or popup menu for genomic features outwith CDS shown overlaid on protein <!-- JAL-3725 --></li>
+<li>Overlapping CDS in ENA accessions are not correctly mapped by Jalview (e.g. affects viral CDS with ribosomal slippage, since 2.9.0) <!-- JAL-3751 --></li>
+<li>Spliced transcript CDS sequences don't show CDS features <!-- JAL-3763 --></li>
+<li>Selections in CDS sequence panel don't always select corresponding protein sequences <!-- JAL-3700 --></li>
+<li><em>Make groups from selection</em> for a column selection doesn't always ignore hidden columns <!-- JAL-3759 --></li>
</ul>
-<h3>Installer</h3>
+<p><em>Installer</em></p>
<ul>
-<li><!-- JAL-3611 --> Space character in Jalview install path on Windows prevents install4j launching getdown</li>
+<li>Space character in Jalview install path on Windows prevents install4j launching getdown <!-- JAL-3611 --></li>
</ul>
-<h3>Development</h3>
+<p><em>Development</em></p>
<ul>
-<li><!-- JAL-3248 --> Fixed typos and specified compatible gradle version numbers in doc/building.md</li>
+<li>Fixed typos and specified compatible gradle version numbers in doc/building.md <!-- JAL-3248 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.1<a id="Jalview.2.11.1.2">.2</a></strong>
<br />
<em>25 September 2020</em>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3757 --> Fresh install of Jalview 2.11.1.1 reports "Encountered problems opening https://www.jalview.org/examples/exampleFile_2_7.jvp"</li>
+<li>Fresh install of Jalview 2.11.1.1 reports "Encountered problems opening https://www.jalview.org/examples/exampleFile_2_7.jvp" <!-- JAL-3757 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.1<a id="Jalview.2.11.1.1">.1</a></strong>
<br />
<em>17 September 2020</em>
</td>
<td class="new_features" align="left" valign="top">
<ul>
-<li><!-- JAL-3638 --> Shift+arrow keys navigate to next gap or residue in cursor mode</li>
-<li><!-- JAL-3695 --> Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23</li>
-<li><!-- JAL-3621 --> IntervalStore library updated to v.1.1: optimisations and improvements suggested by Bob Hanson and improved compatibility with JalviewJS</li>
-<li><!-- JAL-3615 --> Retrieve GZipped stockholm formatted alignments from Pfam and Rfam</li>
-<li><!-- JAL-2656 --> Recognise GZipped content for URLs and File import (no longer based on .gz extension)</li>
-<li><!-- JAL-3570 --> Updated Spanish Translation for 2.11.1</li>
-<li><!-- JAL-3692 --> Migrate EMBL record retrieval to use latest ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and EMBL flat file</li>
-<li><!-- JAL-3667 --> Improved warning messages, debug logging and fixed Retry action when Jalview encounters errors when saving or making backup files.</li>
-<li><!-- JAL-3676 --> Enhanced Jalview Java Console:
-<ul>
+<li>Shift+arrow keys navigate to next gap or residue in cursor mode <!-- JAL-3638 --></li>
+<li>Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23 <!-- JAL-3695 --></li>
+<li>IntervalStore library updated to v.1.1: optimisations and improvements suggested by Bob Hanson and improved compatibility with JalviewJS <!-- JAL-3621 --></li>
+<li>Retrieve GZipped stockholm formatted alignments from Pfam and Rfam <!-- JAL-3615 --></li>
+<li>Recognise GZipped content for URLs and File import (no longer based on .gz extension) <!-- JAL-2656 --></li>
+<li>Updated Spanish Translation for 2.11.1 <!-- JAL-3570 --></li>
+<li>Migrate EMBL record retrieval to use latest ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and EMBL flat file <!-- JAL-3692 --></li>
+<li>Improved warning messages, debug logging and fixed Retry action when Jalview encounters errors when saving or making backup files. <!-- JAL-3667 --></li>
+<li>Enhanced Jalview Java Console: <!-- JAL-3676 --></li>
<li>Jalview's logging level can be configured</li>
<li>Copy to Clipboard Buttion</li>
+<li>Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+) <!-- JAL-3541 --></li>
+<li>RESNUM sequence features (the green ones) are not automatically displayed when associated structures are displayed or for sequences retrieved from the PDB. <!-- JAL-1842 JAL-3509 --></li>
</ul>
-</li>
-<li><!-- JAL-3541 --> Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+)</li>
-<li><!-- JAL-1842 JAL-3509 --> RESNUM sequence features (the green ones) are not automatically displayed when associated structures are displayed or for sequences retrieved from the PDB.</li>
-</ul>
-<h3>Launching Jalview</h3>
+<p><em>Launching Jalview</em></p>
<ul>
-<li><!-- JAL-3608 --> Configure Jalview Desktop's look and feel through a system property</li>
-<li><!-- JAL-3477 --> Improved built-in documentation and command line help for configuring Jalview's memory</li>
+<li>Configure Jalview Desktop's look and feel through a system property <!-- JAL-3608 --></li>
+<li>Improved built-in documentation and command line help for configuring Jalview's memory <!-- JAL-3477 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3691 --> Conservation and Quality tracks are shown but not calculated and no protein or DNA score models are available for tree/PCA calculation when launched with Turkish language locale</li>
-<li><!-- JAL-3493 --> Escape does not clear highlights on the alignment (Since Jalview 2.10.3)</li>
-<li><!-- JAL-3680 --> Alt+Left or Right arrow in cursor mode doesn't slide selected sequences, just sequence under cursor</li>
-<li><!-- JAL-3732 --> Alt+Up/Down in cursor mode doesn't move sequence under the cursor</li>
-<li><!-- JAL-3613 --> Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig</li>
-<li><!-- JAL-3696 --> Errors encountered when processing variants from VCF files yield "Error processing VCF: Format specifier '%s'" on the console</li>
-<li><!-- JAL-3697 --> Count of features not shown can be wrong when there are both local and complementary features mapped to the position under the cursor</li>
-<li><!-- JAL-3673 --> Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled</li>
-<li><!-- JAL-2983 --> Slider with negative range values not rendered correctly in VAqua4 (Since 2.10.4)</li>
-<li><!-- JAL-3685 --> Single quotes not displayed correctly in internationalised text for some messages and log output</li>
-<li><!-- JAL-3490 --> Find doesn't report matches that span hidden gapped columns</li>
-<li><!-- JAL-3597 --> Resolved memory leaks in Tree and PCA panels, Alignment viewport and annotation renderer.</li>
-<li><!-- JAL-3561 --> Jalview ignores file format parameter specifying output format when exporting an alignment via the command line</li>
-<li><!-- JAL-3667 --> Windows 10: For a minority of users, if backups are not enabled, Jalview sometimes fails to overwrite an existing file and raises a warning dialog. (in 2.11.0, and 2.11.1.0, the workaround is to try to save the file again, and if that fails, delete the original file and save in place.)</li>
-<li><!-- JAL-3509 --> Dragging a PDB file onto an alignment with sequence features displayed causes displayed features to be hidden.</li>
-<li><!-- JAL-3750 --> Cannot process alignments from HTTPS urls via command line</li>
-<li><!-- JAL-3741 --> References to http://www.jalview.org in program and documentation</li>
+<li>Conservation and Quality tracks are shown but not calculated and no protein or DNA score models are available for tree/PCA calculation when launched with Turkish language locale <!-- JAL-3691 --></li>
+<li>Escape does not clear highlights on the alignment (Since Jalview 2.10.3) <!-- JAL-3493 --></li>
+<li>Alt+Left or Right arrow in cursor mode doesn't slide selected sequences, just sequence under cursor <!-- JAL-3680 --></li>
+<li>Alt+Up/Down in cursor mode doesn't move sequence under the cursor <!-- JAL-3732 --></li>
+<li>Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig <!-- JAL-3613 --></li>
+<li>Errors encountered when processing variants from VCF files yield "Error processing VCF: Format specifier '%s'" on the console <!-- JAL-3696 --></li>
+<li>Count of features not shown can be wrong when there are both local and complementary features mapped to the position under the cursor <!-- JAL-3697 --></li>
+<li>Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled <!-- JAL-3673 --></li>
+<li>Slider with negative range values not rendered correctly in VAqua4 (Since 2.10.4) <!-- JAL-2983 --></li>
+<li>Single quotes not displayed correctly in internationalised text for some messages and log output <!-- JAL-3685 --></li>
+<li>Find doesn't report matches that span hidden gapped columns <!-- JAL-3490 --></li>
+<li>Resolved memory leaks in Tree and PCA panels, Alignment viewport and annotation renderer. <!-- JAL-3597 --></li>
+<li>Jalview ignores file format parameter specifying output format when exporting an alignment via the command line <!-- JAL-3561 --></li>
+<li>Windows 10: For a minority of users, if backups are not enabled, Jalview sometimes fails to overwrite an existing file and raises a warning dialog. (in 2.11.0, and 2.11.1.0, the workaround is to try to save the file again, and if that fails, delete the original file and save in place.) <!-- JAL-3667 --></li>
+<li>Dragging a PDB file onto an alignment with sequence features displayed causes displayed features to be hidden. <!-- JAL-3509 --></li>
+<li>Cannot process alignments from HTTPS urls via command line <!-- JAL-3750 --></li>
+<li>References to http://www.jalview.org in program and documentation <!-- JAL-3741 --></li>
</ul>
-<h3>Launching Jalview</h3>
+<p><em>Launching Jalview</em></p>
<ul>
-<li><!-- JAL-3718 --> Jalview application fails when launched the first time for a version that has different jars to the previous launched version.</li>
+<li>Jalview application fails when launched the first time for a version that has different jars to the previous launched version. <!-- JAL-3718 --></li>
</ul>
-<h3>Developing Jalview</h3>
+<p><em>Developing Jalview</em></p>
<ul>
-<li><!-- JAL-3541 --> Fixed issue with cleaning up old coverage data, causing cloverReport gradle task to fail with an OutOfMemory error.</li>
-<li><!-- JAL-3280 --> Migrated the Jalview Version Checker to monitor the release channel</li>
+<li>Fixed issue with cleaning up old coverage data, causing cloverReport gradle task to fail with an OutOfMemory error. <!-- JAL-3541 --></li>
+<li>Migrated the Jalview Version Checker to monitor the release channel <!-- JAL-3280 --></li>
</ul>
-<h3>New Known defects</h3>
+<p><em>New Known defects</em></p>
<ul>
-<li><!-- JAL-3748 --> CDS shown in result of submitting proteins in a CDS/Protein alignment to a web service is wrong when proteins share a common transcript sequence (e.g. genome of RNA viruses)</li>
-<li><!-- JAL-3576 --> Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0)</li>
-<li><!-- JAL-3702 --> Drag and drop of alignment file onto alignment window when in a HiDPI scaled mode in Linux only works for the top left quadrant of the alignment window</li>
-<li><!-- JAL-3701 --> Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)</li>
-<li><!-- JAL-3127 --> Sequence ID colourscheme not re-applied when alignment view restored from project (since Jalview 2.11.0)</li>
-<li><!-- JAL-3749 --> Duplicate CDS sequences are generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs</li>
+<li>CDS shown in result of submitting proteins in a CDS/Protein alignment to a web service is wrong when proteins share a common transcript sequence (e.g. genome of RNA viruses) <!-- JAL-3748 --></li>
+<li>Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0) <!-- JAL-3576 --></li>
+<li>Drag and drop of alignment file onto alignment window when in a HiDPI scaled mode in Linux only works for the top left quadrant of the alignment window <!-- JAL-3702 --></li>
+<li>Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch) <!-- JAL-3701 --></li>
+<li>Sequence ID colourscheme not re-applied when alignment view restored from project (since Jalview 2.11.0) <!-- JAL-3127 --></li>
+<li>Duplicate CDS sequences are generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs <!-- JAL-3749 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11.1<a id="Jalview.2.11.1.0">.0</a></strong>
<br />
<em>22 April 2020</em>
</td>
<td class="new_features" align="left" valign="top">
<ul>
-<li><!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 --> Map 'virtual' codon features shown on protein (or vice versa) for display in alignments, on structure views (including transfer to UCSF chimera), in feature reports and for export.</li>
-<li><!-- JAL-3121 --> Feature attributes from VCF files can be exported and re-imported as GFF3 files</li>
-<li><!-- JAL-3376 --> Capture VCF "fixed column" values POS, ID, QUAL, FILTER as Feature Attributes</li>
-<li><!-- JAL-3375 --> More robust VCF numeric data field validation while parsing</li>
-<li><!-- JAL-3533 --> Feature Settings dialog keeps same screen position if reopened</li>
-<li><!-- JAL-3535 --> Feature Settings dialog title includes name of associated view</li>
-<li><!-- JAL-3538 --> Font anti-aliasing in alignment views enabled by default</li>
-<li><!-- JAL-3468 --> Very long feature descriptions truncated in tooltips and menus</li>
-<li><!-- JAL-3549 --> Warn if Sort by Score or Density attempted with no feature types visible</li>
-<li><!-- JAL-3574 --> Improved support for filtering feature attributes with large integer values</li>
+<li>Map 'virtual' codon features shown on protein (or vice versa) for display in alignments, on structure views (including transfer to UCSF chimera), in feature reports and for export. <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 --></li>
+<li>Feature attributes from VCF files can be exported and re-imported as GFF3 files <!-- JAL-3121 --></li>
+<li>Capture VCF "fixed column" values POS, ID, QUAL, FILTER as Feature Attributes <!-- JAL-3376 --></li>
+<li>More robust VCF numeric data field validation while parsing <!-- JAL-3375 --></li>
+<li>Feature Settings dialog keeps same screen position if reopened <!-- JAL-3533 --></li>
+<li>Feature Settings dialog title includes name of associated view <!-- JAL-3535 --></li>
+<li>Font anti-aliasing in alignment views enabled by default <!-- JAL-3538 --></li>
+<li>Very long feature descriptions truncated in tooltips and menus <!-- JAL-3468 --></li>
+<li>Warn if Sort by Score or Density attempted with no feature types visible <!-- JAL-3549 --></li>
+<li>Improved support for filtering feature attributes with large integer values <!-- JAL-3574 --></li>
</ul>
-<h3>Jalview Installer</h3>
+<p><em>Jalview Installer</em></p>
<ul>
-<li><!-- JAL-3449 --> Versions for install4j and getdown and installer template version reported in console (may be null when Jalview launched as executable jar or via conda)</li>
-<li><!-- JAL-3393 --> Layout improvements for OSX .dmg Finder and higher quality background images</li>
-<li><!-- JAL-3394 --> New installer/application launcher generated with install4j 8.0.4</li>
-<li><!-- JAL-3420 --> Jalview File Associations shown for Unix Platforms</li>
-<li><!-- JAL-3477 --> Improved defaults for maximum memory setting when running on large memory machines</li>
+<li>Versions for install4j and getdown and installer template version reported in console (may be null when Jalview launched as executable jar or via conda) <!-- JAL-3449 --></li>
+<li>Layout improvements for OSX .dmg Finder and higher quality background images <!-- JAL-3393 --></li>
+<li>New installer/application launcher generated with install4j 8.0.4 <!-- JAL-3394 --></li>
+<li>Jalview File Associations shown for Unix Platforms <!-- JAL-3420 --></li>
+<li>Improved defaults for maximum memory setting when running on large memory machines <!-- JAL-3477 --></li>
</ul>
-<h3>Release processes</h3>
+<p><em>Release processes</em></p>
<ul>
-<li><!-- JAL-3508 --> New point release version scheme - 2.11.1.0</li>
-<li><!-- JAL-3577 --> 'Jalview Test' installers/apps for easier access to test-release channel builds</li>
+<li>New point release version scheme - 2.11.1.0 <!-- JAL-3508 --></li>
+<li>'Jalview Test' installers/apps for easier access to test-release channel builds <!-- JAL-3577 --></li>
</ul>
-<h3>Build System</h3>
+<p><em>Build System</em></p>
<ul>
-<li><!-- JAL-3510 --> Clover updated to 4.4.1</li>
-<li><!-- JAL-3513 --> Test code included in Clover coverage report</li>
+<li>Clover updated to 4.4.1 <!-- JAL-3510 --></li>
+<li>Test code included in Clover coverage report <!-- JAL-3513 --></li>
</ul>
-<h3>Groovy Scripts</h3>
+<p><em>Groovy Scripts</em></p>
<ul>
-<li><!-- JAL-3547 --> exportconsensus.groovy prints a FASTA file to stdout containing the consensus sequence for each alignment in a Jalview session</li>
-<li><!-- JAL-3578 --> ComputePeptideVariants.groovy to translate genomic sequence_variant annotation from CDS as missense_variant or synonymous_variant on protein products.</li>
+<li>exportconsensus.groovy prints a FASTA file to stdout containing the consensus sequence for each alignment in a Jalview session <!-- JAL-3547 --></li>
+<li>ComputePeptideVariants.groovy to translate genomic sequence_variant annotation from CDS as missense_variant or synonymous_variant on protein products. <!-- JAL-3578 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3581 --> Hidden sequence markers still visible when 'Show hidden markers' option is not ticked</li>
-<li><!-- JAL-247 --> Hidden sequence markers not shown in EPS and PNG output when 'Automatically set ID width' is set in jalview preferences or properties file</li>
-<li><!-- JAL-3571 --> Feature Editor dialog can be opened when 'Show Sequence Features' option is not ticked</li>
-<li><!-- JAL-3549 --> Undo 'Null' operation shown after sort by buttons in Feature Settings dialog are clicked when no features are visible</li>
-<li><!-- JAL-3412 --> ID margins for CDS and Protein views not equal when split frame is first opened</li>
-<li><!-- JAL-3296 --> Sequence position numbers in status bar not correct after editing a sequence's start position</li>
-<li><!-- JAL-3377 --> Alignment is misaligned in wrapped mode with annotation and exceptions thrown when only a few columns shown in wrapped mode</li>
-<li><!-- JAL-3386 --> Sequence IDs missing in headless export of wrapped alignment figure with annotations</li>
-<li><!-- JAL-3388--> Sorting Structure Chooser table by Sequence ID fails with ClassCastException</li>
-<li><!-- JAL-3389 --> Chimera session not restored from Jalview Project</li>
-<li><!-- JAL-3441 --> Double-click on 'Show feature' checkbox in feature settings dialog also selects columns</li>
-<li><!-- JAL-3473 --> SpinnerNumberModel causes IllegalArgumentException in some circumstances</li>
-<li><!-- JAL-3534 --> Multiple feature settings dialogs can be opened for a view</li>
-<li><!-- JAL-2764 --> Feature Settings dialog is orphaned if alignment window is closed</li>
-<li><!-- JAL-3406 --> Credits missing some authors in Jalview help documentation for 2.11.0 release</li>
-<li><!-- JAL-3529 --> Export of Pfam alignment as Stockholm includes Pfam ID as sequence's accession rather than its Uniprot Accession</li>
+<li>Hidden sequence markers still visible when 'Show hidden markers' option is not ticked <!-- JAL-3581 --></li>
+<li>Hidden sequence markers not shown in EPS and PNG output when 'Automatically set ID width' is set in jalview preferences or properties file <!-- JAL-247 --></li>
+<li>Feature Editor dialog can be opened when 'Show Sequence Features' option is not ticked <!-- JAL-3571 --></li>
+<li>Undo 'Null' operation shown after sort by buttons in Feature Settings dialog are clicked when no features are visible <!-- JAL-3549 --></li>
+<li>ID margins for CDS and Protein views not equal when split frame is first opened <!-- JAL-3412 --></li>
+<li>Sequence position numbers in status bar not correct after editing a sequence's start position <!-- JAL-3296 --></li>
+<li>Alignment is misaligned in wrapped mode with annotation and exceptions thrown when only a few columns shown in wrapped mode <!-- JAL-3377 --></li>
+<li>Sequence IDs missing in headless export of wrapped alignment figure with annotations <!-- JAL-3386 --></li>
+<li>Sorting Structure Chooser table by Sequence ID fails with ClassCastException <!-- JAL-3388--></li>
+<li>Chimera session not restored from Jalview Project <!-- JAL-3389 --></li>
+<li>Double-click on 'Show feature' checkbox in feature settings dialog also selects columns <!-- JAL-3441 --></li>
+<li>SpinnerNumberModel causes IllegalArgumentException in some circumstances <!-- JAL-3473 --></li>
+<li>Multiple feature settings dialogs can be opened for a view <!-- JAL-3534 --></li>
+<li>Feature Settings dialog is orphaned if alignment window is closed <!-- JAL-2764 --></li>
+<li>Credits missing some authors in Jalview help documentation for 2.11.0 release <!-- JAL-3406 --></li>
+<li>Export of Pfam alignment as Stockholm includes Pfam ID as sequence's accession rather than its Uniprot Accession <!-- JAL-3529 --></li>
</ul>
-<h3>Java 11 Compatibility issues</h3>
+<p><em>Java 11 Compatibility issues</em></p>
<ul>
-<li><!-- JAL-2987 --> OSX - Can't view some search results in PDB/Uniprot search panel</li>
+<li>OSX - Can't view some search results in PDB/Uniprot search panel <!-- JAL-2987 --></li>
</ul>
-<h3>Installer</h3>
+<p><em>Installer</em></p>
<ul>
-<li><!-- JAL-3447 --> Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)</li>
+<li>Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif) <!-- JAL-3447 --></li>
</ul>
-<h3>Repository and Source Release</h3>
+<p><em>Repository and Source Release</em></p>
<ul>
-<li><!-- JAL-3474 --> removed obsolete .cvsignore files from repository</li>
-<li><!-- JAL-3541 --> Clover report generation running out of memory</li>
+<li>removed obsolete .cvsignore files from repository <!-- JAL-3474 --></li>
+<li>Clover report generation running out of memory <!-- JAL-3541 --></li>
</ul>
-<h3>New Known Issues</h3>
+<p><em>New Known Issues</em></p>
<ul>
-<li><!-- JAL-3523 --> OSX - Current working directory not preserved when Jalview.app launched with parameters from command line</li>
-<li><!-- JAL-3525 --> Sequence IDs aligned to wrong margin and clipped in headless figure export when Right Align option enabled</li>
-<li><!-- JAL-3542 --> Jalview Installation type always reports 'Source' in console output</li>
-<li><!-- JAL-3562 --> Test Suite: Certain Functional tests fail on jalview's bamboo server but run fine locally.</li>
+<li>OSX - Current working directory not preserved when Jalview.app launched with parameters from command line <!-- JAL-3523 --></li>
+<li>Sequence IDs aligned to wrong margin and clipped in headless figure export when Right Align option enabled <!-- JAL-3525 --></li>
+<li>Jalview Installation type always reports 'Source' in console output <!-- JAL-3542 --></li>
+<li>Test Suite: Certain Functional tests fail on jalview's bamboo server but run fine locally. <!-- JAL-3562 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.11<a id="Jalview.2.11.0">.0</a></strong>
<br />
<em>4 July 2019</em>
</td>
<td class="new_features" align="left" valign="top">
<ul>
-<li><!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 --> Jalview Native Application and Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open source project) rather than InstallAnywhere</li>
-<li><!-- JAL-1929 --> Jalview Launcher System to auto-configure memory settings, receive over the air updates and launch specific versions via (<a href="https://github.com/threerings/getdown">Three Rings' GetDown</a>)</li>
-<li><!-- JAL-1839,JAL-3254,JAL-3260 --> File type associations for formats supported by Jalview (including .jvp project files)</li>
-<li><!-- JAL-3260 --> Jalview launch files (.jvl) to pass command line arguments and switch between different getdown channels</li>
-<li><!-- JAL-3141 --> Backup files created when saving Jalview project or alignment files</li>
-<li><!-- JAL-1793 --> Annotate nucleotide alignments from VCF data files</li>
-<li><!-- JAL-2753 --> Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
-<li><!-- JAL-2620 --> Alternative genetic code tables for 'Translate as cDNA'</li>
-<li><!-- JAL-3018 --> Update of Ensembl Rest Client to API v10.0</li>
+<li>Jalview Native Application and Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open source project) rather than InstallAnywhere <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 --></li>
+<li>Jalview Launcher System to auto-configure memory settings, receive over the air updates and launch specific versions via (<a href="https://github.com/threerings/getdown">Three Rings' GetDown</a>) <!-- JAL-1929 --></li>
+<li>File type associations for formats supported by Jalview (including .jvp project files) <!-- JAL-1839,JAL-3254,JAL-3260 --></li>
+<li>Jalview launch files (.jvl) to pass command line arguments and switch between different getdown channels <!-- JAL-3260 --></li>
+<li>Backup files created when saving Jalview project or alignment files <!-- JAL-3141 --></li>
+<li>Annotate nucleotide alignments from VCF data files <!-- JAL-1793 --></li>
+<li>Version of HTSJDK shipped with Jalview updated to version 2.12.0 <!-- JAL-2753 --></li>
+<li>Alternative genetic code tables for 'Translate as cDNA' <!-- JAL-2620 --></li>
+<li>Update of Ensembl Rest Client to API v10.0 <!-- JAL-3018 --></li>
<li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
<ul>
-<li><!-- JAL-3140 JAL-2446 --> IntervalStoreJ (NCList implementation that allows updates) used for Sequence Feature collections</li>
-<li><!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 --> 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-2879 --> Feature Attributes and shading schemes stored and restored from Jalview Projects</li>
-<li><!-- JAL-3334 --> Use full Sequence Ontology (via BioJava) to recognise variant features</li>
-<li><!-- JAL-2897,JAL-3330 --> Show synonymous codon variants on peptide sequences (also coloured red by default)</li>
-<li><!-- JAL-2792 --> Popup window to show full report for a selected sequence feature's details</li>
-<li><!-- JAL-3139,JAL-2816,JAL-1117 --> More efficient sequence feature render algorithm (Z-sort/transparency and filter aware)</li>
-<li><!-- JAL-3049,JAL-3054 --> Improved tooltips in Feature Settings dialog</li>
+<li>IntervalStoreJ (NCList implementation that allows updates) used for Sequence Feature collections <!-- JAL-3140 JAL-2446 --></li>
+<li>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) <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 --></li>
+<li>Feature Attributes and shading schemes stored and restored from Jalview Projects <!-- JAL-2879 --></li>
+<li>Use full Sequence Ontology (via BioJava) to recognise variant features <!-- JAL-3334 --></li>
+<li>Show synonymous codon variants on peptide sequences (also coloured red by default) <!-- JAL-2897,JAL-3330 --></li>
+<li>Popup window to show full report for a selected sequence feature's details <!-- JAL-2792 --></li>
+<li>More efficient sequence feature render algorithm (Z-sort/transparency and filter aware) <!-- JAL-3139,JAL-2816,JAL-1117 --></li>
+<li>Improved tooltips in Feature Settings dialog <!-- JAL-3049,JAL-3054 --></li>
</ul>
</li>
-<li><!-- JAL-3205 --> Symmetric score matrices for faster tree and PCA calculations</li>
+<li>Symmetric score matrices for faster tree and PCA calculations <!-- JAL-3205 --></li>
<li><strong>Principal Components Analysis Viewer</strong>
<ul>
-<li><!-- JAL-1767,JAL-2647 --> Principal Components Analysis results and Viewer state saved in Jalview Project</li>
-<li><!-- JAL-2962 --> 'Change parameters' option removed from viewer's drop-down menus</li>
-<li><!-- JAL-2975 --> Can use shift + arrow keys to rotate PCA image incrementally</li>
-<li><!-- JAL-2965, JAL-1285 --> PCA plot is depth cued</li>
+<li>Principal Components Analysis results and Viewer state saved in Jalview Project <!-- JAL-1767,JAL-2647 --></li>
+<li>'Change parameters' option removed from viewer's drop-down menus <!-- JAL-2962 --></li>
+<li>Can use shift + arrow keys to rotate PCA image incrementally <!-- JAL-2975 --></li>
+<li>PCA plot is depth cued <!-- JAL-2965, JAL-1285 --></li>
</ul>
</li>
-<li><!-- JAL-3127 --> New 'Colour by Sequence ID' option</li>
+<li>New 'Colour by Sequence ID' option <!-- JAL-3127 --></li>
<li><strong>Speed and Efficiency</strong>
<ul>
-<li><!-- JAL-2185,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>More efficient creation of selections and multiple groups when working with large alignments <!-- JAL-2185,JAL-3198 --></li>
+<li>Speedier import of annotation rows when parsing Stockholm files <!-- JAL-3200 --></li>
</ul>
</li>
<li><strong>User Interface</strong>
<ul>
-<li><!-- JAL-2933 --> Finder panel remembers last position in each view</li>
-<li><!-- JAL-2527 JAL-3203 --> Alignment Overview now WYSIWIS (What you see is what is shown)<br/>
+<li>Finder panel remembers last position in each view <!-- JAL-2933 --></li>
+<li>Alignment Overview now WYSIWIS (What you see is what is shown)<br/> <!-- JAL-2527 JAL-3203 -->
Only visible regions of alignment are shown by default (can be changed in user preferences)</li>
-<li><!-- JAL-3169 --> File Chooser stays open after responding Cancel to the Overwrite Dialog</li>
-<li><!-- JAL-2420,JAL-3166 --> Better popup menu behaviour when all sequences are hidden</li>
-<li><!-- JAL-1244 --> Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps</li>
-<li><!-- JAL-3132 --> Status bar updates over sequence and annotation labels</li>
-<li><!-- JAL-3093 --> Annotation tooltips and popup menus are shown when in wrapped mode</li>
-<li><!-- JAL-3073 --> Can select columns by dragging left/right in a graph or histogram annotation</li>
-<li><!-- JAL-2814,JAL-437 --> Help button on Uniprot and PDB search panels</li>
-<li><!-- JAL-2621 --> Cursor changes over draggable box in Overview panel</li>
-<li><!-- JAL-3181 --> Consistent ordering of links in sequence id popup menu</li>
-<li><!-- JAL-3080 --> Red line indicating tree-cut position not shown if no subgroups are created</li>
-<li><!-- JAL-3042 --> Removed ability to configure length of search history by right-clicking search box</li>
+<li>File Chooser stays open after responding Cancel to the Overwrite Dialog <!-- JAL-3169 --></li>
+<li>Better popup menu behaviour when all sequences are hidden <!-- JAL-2420,JAL-3166 --></li>
+<li>Status bar shows bounds when dragging a selection region, and gap count when inserting or deleting gaps <!-- JAL-1244 --></li>
+<li>Status bar updates over sequence and annotation labels <!-- JAL-3132 --></li>
+<li>Annotation tooltips and popup menus are shown when in wrapped mode <!-- JAL-3093 --></li>
+<li>Can select columns by dragging left/right in a graph or histogram annotation <!-- JAL-3073 --></li>
+<li>Help button on Uniprot and PDB search panels <!-- JAL-2814,JAL-437 --></li>
+<li>Cursor changes over draggable box in Overview panel <!-- JAL-2621 --></li>
+<li>Consistent ordering of links in sequence id popup menu <!-- JAL-3181 --></li>
+<li>Red line indicating tree-cut position not shown if no subgroups are created <!-- JAL-3080 --></li>
+<li>Removed ability to configure length of search history by right-clicking search box <!-- JAL-3042 --></li>
</ul>
</li>
-<li><!-- JAL-3232 --> Jalview Groovy Scripting Console updated to Groovy v2.5</li>
+<li>Jalview Groovy Scripting Console updated to Groovy v2.5 <!-- JAL-3232 --></li>
<li><strong>Java 11 Support (not yet on general release)</strong>
<ul>
-<li><!-- --> OSX GUI integrations for App menu's 'About' entry and trapping CMD-Q</li>
+<li>OSX GUI integrations for App menu's 'About' entry and trapping CMD-Q <!-- --></li>
</ul>
</li>
</ul>
-<h3>Deprecations</h3>
+<p><em>Deprecations</em></p>
<ul>
-<li><!-- JAL-3035 --> DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop</li>
-<li><!-- JAL-3063,JAL-3116 --> Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients</li>
-<li><!-- JAL-3311 --> Disable VAMSAS menu in preparation for removal</li>
-<li><!-- --> Jalview Desktop no longer distributed via Java Web Start</li>
+<li>DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop <!-- JAL-3035 --></li>
+<li>Castor library for XML marshalling and unmarshalling has been replaced by JAXB for Jalview projects and XML based data retrieval clients <!-- JAL-3063,JAL-3116 --></li>
+<li>Disable VAMSAS menu in preparation for removal <!-- JAL-3311 --></li>
+<li>Jalview Desktop no longer distributed via Java Web Start <!-- --></li>
</ul>
-<h3>Documentation</h3>
+<p><em>Documentation</em></p>
<ul>
-<li><!-- JAL-3003 --> Added remarks about transparent rendering effects not supported in EPS figure export</li>
-<li><!-- JAL-2903 --> Typos in documentation for Preferences dialog</li>
+<li>Added remarks about transparent rendering effects not supported in EPS figure export <!-- JAL-3003 --></li>
+<li>Typos in documentation for Preferences dialog <!-- JAL-2903 --></li>
</ul>
-<h3>Development and Release Processes</h3>
+<p><em>Development and Release Processes</em></p>
<ul>
-<li><!-- JAL-3196,JAL-3179.JAL-2671 --> Build system migrated from Ant to Gradle</li>
-<li><!-- JAL-1424 --> Enhanced checks for missing and duplicated keys in Message bundles</li>
-<li><!-- JAL-3225 --> Eclipse project configuration managed with gradle-eclipse</li>
-<li><!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --> Atlassian Bamboo continuous integration for unattended Test Suite execution</li>
-<li><!-- JAL-2864 --> Memory test suite to detect leaks in common operations</li>
-<li><!-- JAL-2360,JAL-2416 --> More unit test coverage, and minor issues resolved</li>
-<li><!-- JAL-3248 --> Developer documentation migrated to markdown (with HTML rendering)</li>
-<li><!-- JAL-3287 --> HelpLinksChecker runs on Windows</li>
-<li><!-- JAL-3289 --> New URLs for publishing development versions of Jalview</li>
+<li>Build system migrated from Ant to Gradle <!-- JAL-3196,JAL-3179.JAL-2671 --></li>
+<li>Enhanced checks for missing and duplicated keys in Message bundles <!-- JAL-1424 --></li>
+<li>Eclipse project configuration managed with gradle-eclipse <!-- JAL-3225 --></li>
+<li>Atlassian Bamboo continuous integration for unattended Test Suite execution <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --></li>
+<li>Memory test suite to detect leaks in common operations <!-- JAL-2864 --></li>
+<li>More unit test coverage, and minor issues resolved <!-- JAL-2360,JAL-2416 --></li>
+<li>Developer documentation migrated to markdown (with HTML rendering) <!-- JAL-3248 --></li>
+<li>HelpLinksChecker runs on Windows <!-- JAL-3287 --></li>
+<li>New URLs for publishing development versions of Jalview <!-- JAL-3289 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-3143 --> Timeouts when retrieving data from Ensembl</li>
-<li><!-- JAL-3244 --> 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows</li>
-<li><!-- JAL-3286 --> Blank error dialog is displayed when discovering structures for sequences with lots of PDB structures</li>
-<li><!-- JAL-3239 --> Text misaligned in EPS or SVG image export with monospaced font</li>
-<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 redrawing the overview with large alignments</li>
-<li><!-- JAL-2750 --> 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-3218 --> Couldn't hide selected columns adjacent to a hidden column marker via scale popup menu</li>
-<li><!-- JAL-2846 --> Error message for trying to load in invalid URLs doesn't tell users the invalid URL</li>
-<li><!-- JAL-2816 --> Tooltips displayed for features filtered by score from view</li>
-<li><!-- JAL-3330 --> Sequence Variants retrieved from Ensembl during show cross references or Fetch Database References are shown in red in original view</li>
-<li><!-- JAL-2898,JAL-2207 --> stop_gained variants not shown correctly on peptide sequence (computed variant shown as p.Res.null)</li>
-<li><!-- JAL-2060 --> 'Graduated colour' option not offered for manually created features (where feature score is Float.NaN)</li>
-<li><!-- JAL-3097,JAL-3099 --> Blank extra columns drawn or printed when columns are hidden</li>
-<li><!-- JAL-3082 --> Regular expression error for '(' in Select Columns by Annotation description</li>
-<li><!-- JAL-3072 --> Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel</li>
-<li><!-- JAL-3075 --> Column selection incorrect after scrolling out of scale panel</li>
-<li><!-- JAL-3074 --> Left/right drag in annotation can scroll alignment down</li>
-<li><!-- JAL-3108 --> Error if mouse moved before clicking Reveal in scale panel</li>
-<li><!-- JAL-3002 --> Column display is out by one after Page Down, Page Up in wrapped mode</li>
-<li><!-- JAL-2839,JAL-781 --> Finder doesn't skip hidden regions</li>
-<li><!-- JAL-2932 --> Finder searches in minimised alignments</li>
-<li><!-- JAL-2250 --> 'Apply Colour to All Groups' not always selected on opening an alignment</li>
-<li><!-- JAL-3180 --> 'Colour by Annotation' not marked selected in Colour menu</li>
-<li><!-- JAL-3201 --> Per-group Clustal colour scheme changes when different groups in the alignment are selected</li>
-<li><!-- JAL-2717 --> Internationalised colour scheme names not shown correctly in menu</li>
-<li><!-- JAL-3206 --> Colour by Annotation can go black at min/max threshold limit</li>
-<li><!-- JAL-3125 --> Value input for graduated feature colour threshold gets 'unrounded'</li>
-<li><!-- JAL-2982 --> PCA image export doesn't respect background colour</li>
-<li><!-- JAL-2963 --> PCA points don't dim when rotated about y axis</li>
-<li><!-- JAL-2959 --> PCA Print dialog continues after Cancel</li>
-<li><!-- JAL-3078 --> Cancel in Tree Font dialog resets alignment, not Tree font</li>
-<li><!-- JAL-2964 --> Associate Tree with All Views not restored from project file</li>
-<li><!-- JAL-2915 --> Scrolling of split frame is sluggish if Overview shown in complementary view</li>
-<li><!-- JAL-3313 --> Codon consensus incorrectly scaled when shown without normalisation</li>
-<li><!-- JAL-3021 --> Sequence Details report should open positioned at top of report</li>
-<li><!-- JAL-914 --> Help page can be opened twice</li>
-<li><!-- JAL-3333 --> Fuzzy text in web service status menu on OSX Mojave</li>
-</ul>
-<h3>Editing</h3>
-<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,JAL-2684 (tests) --> Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10)</li>
-<li><!-- JAL-2830 --> Inserting gap sequence via the Edit Sequence dialog corrupts dataset sequence</li>
-<li><!-- JAL-868 --> Structure colours not updated when associated tree repartitions the alignment view (Regression in 2.10.5)</li>
-</ul>
-<h3>Datamodel</h3>
-<ul>
-<li><!-- JAL-2986 --> Sequence.findIndex returns wrong value when sequence's End is greater than its length</li>
-</ul>
-<h3>Bugs fixed for Java 11 Support (not yet on general release)</h3>
-<ul>
-<li><!-- JAL-3288 --> Menus work properly in split-screen</li>
-</ul>
-<h3>New Known Defects</h3>
-<ul>
-<li><!-- JAL-3340 --> Select columns containing feature by double clicking ignores bounds of an existing selected region</li>
-<li><!-- JAL-3313 --> Codon consensus logo incorrectly scaled in gapped regions of protein alignment.</li>
-<li><!-- JAL-2647 --> Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project</li>
-<li><!-- JAL-3213 --> Alignment panel height can be too small after 'New View'</li>
-<li><!-- JAL-3240 --> Display is incorrect after removing gapped columns within hidden columns</li>
-<li><!-- JAL-3314 --> Rightmost selection is lost when mouse re-enters window after dragging left to select columns to left of visible region</li>
-<li><!-- JAL-2876 --> Features coloured according to their description string and thresholded by score in earlier versions of Jalview are not shown as thresholded features in 2.11. To workaround please create a Score filter instead.</li>
-<li><!-- JAL-3184 --> Cancel on Feature Settings dialog doesn't reset group visibility</li>
-<li><!-- JAL-3338 --> F2 doesn't enable/disable keyboard mode in linked CDS/Protein view</li>
-<li><!-- JAL-797 --> Closing tree windows with CMD/CTRL-W for alignments with multiple views can close views unexpectedly</li>
-</ul>
-<h3>Java 11 Specific defects</h3>
-<ul>
-<li><!-- JAL-3235 --> Jalview Properties file is not sorted alphabetically when saved</li>
+<li>Timeouts when retrieving data from Ensembl <!-- JAL-3143 --></li>
+<li>'View [Structure] Mappings' and structure superposition in Jmol fail on Windows <!-- JAL-3244 --></li>
+<li>Blank error dialog is displayed when discovering structures for sequences with lots of PDB structures <!-- JAL-3286 --></li>
+<li>Text misaligned in EPS or SVG image export with monospaced font <!-- JAL-3239 --></li>
+<li>Warning of 'Duplicate entry' when saving Jalview project involving multiple views <!-- JAL-3171 --></li>
+<li>Overview for complementary view in a linked CDS/Protein alignment is not updated when Hide Columns by Annotation dialog hides columns <!-- JAL-3164 --></li>
+<li>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 <!-- JAL-3158 --></li>
+<li>Annotations tooltip changes beyond visible columns <!-- JAL-3161 --></li>
+<li>Table Columns could be re-ordered in Feature Settings and Jalview Preferences panels <!-- JAL-3154 --></li>
+<li>Jalview hangs when closing windows, or redrawing the overview with large alignments <!-- JAL-2865 --></li>
+<li>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 <!-- JAL-2750 --></li>
+<li>Couldn't hide selected columns adjacent to a hidden column marker via scale popup menu <!-- JAL-3218 --></li>
+<li>Error message for trying to load in invalid URLs doesn't tell users the invalid URL <!-- JAL-2846 --></li>
+<li>Tooltips displayed for features filtered by score from view <!-- JAL-2816 --></li>
+<li>Sequence Variants retrieved from Ensembl during show cross references or Fetch Database References are shown in red in original view <!-- JAL-3330 --></li>
+<li>stop_gained variants not shown correctly on peptide sequence (computed variant shown as p.Res.null) <!-- JAL-2898,JAL-2207 --></li>
+<li>'Graduated colour' option not offered for manually created features (where feature score is Float.NaN) <!-- JAL-2060 --></li>
+<li>Blank extra columns drawn or printed when columns are hidden <!-- JAL-3097,JAL-3099 --></li>
+<li>Regular expression error for '(' in Select Columns by Annotation description <!-- JAL-3082 --></li>
+<li>Scroll doesn't stop on mouse up after dragging out of Scale or Annotation Panel <!-- JAL-3072 --></li>
+<li>Column selection incorrect after scrolling out of scale panel <!-- JAL-3075 --></li>
+<li>Left/right drag in annotation can scroll alignment down <!-- JAL-3074 --></li>
+<li>Error if mouse moved before clicking Reveal in scale panel <!-- JAL-3108 --></li>
+<li>Column display is out by one after Page Down, Page Up in wrapped mode <!-- JAL-3002 --></li>
+<li>Finder doesn't skip hidden regions <!-- JAL-2839,JAL-781 --></li>
+<li>Finder searches in minimised alignments <!-- JAL-2932 --></li>
+<li>'Apply Colour to All Groups' not always selected on opening an alignment <!-- JAL-2250 --></li>
+<li>'Colour by Annotation' not marked selected in Colour menu <!-- JAL-3180 --></li>
+<li>Per-group Clustal colour scheme changes when different groups in the alignment are selected <!-- JAL-3201 --></li>
+<li>Internationalised colour scheme names not shown correctly in menu <!-- JAL-2717 --></li>
+<li>Colour by Annotation can go black at min/max threshold limit <!-- JAL-3206 --></li>
+<li>Value input for graduated feature colour threshold gets 'unrounded' <!-- JAL-3125 --></li>
+<li>PCA image export doesn't respect background colour <!-- JAL-2982 --></li>
+<li>PCA points don't dim when rotated about y axis <!-- JAL-2963 --></li>
+<li>PCA Print dialog continues after Cancel <!-- JAL-2959 --></li>
+<li>Cancel in Tree Font dialog resets alignment, not Tree font <!-- JAL-3078 --></li>
+<li>Associate Tree with All Views not restored from project file <!-- JAL-2964 --></li>
+<li>Scrolling of split frame is sluggish if Overview shown in complementary view <!-- JAL-2915 --></li>
+<li>Codon consensus incorrectly scaled when shown without normalisation <!-- JAL-3313 --></li>
+<li>Sequence Details report should open positioned at top of report <!-- JAL-3021 --></li>
+<li>Help page can be opened twice <!-- JAL-914 --></li>
+<li>Fuzzy text in web service status menu on OSX Mojave <!-- JAL-3333 --></li>
+</ul>
+<p><em>Editing</em></p>
+<ul>
+<li>Start and End should be updated when sequence data at beginning or end of alignment added/removed via 'Edit' sequence <!-- JAL-2822 --></li>
+<li>Delete/Cut selection doesn't relocate sequence features correctly when start of sequence is removed (Known defect since 2.10) <!-- JAL-2541,JAL-2684 (tests) --></li>
+<li>Inserting gap sequence via the Edit Sequence dialog corrupts dataset sequence <!-- JAL-2830 --></li>
+<li>Structure colours not updated when associated tree repartitions the alignment view (Regression in 2.10.5) <!-- JAL-868 --></li>
+</ul>
+<p><em>Datamodel</em></p>
+<ul>
+<li>Sequence.findIndex returns wrong value when sequence's End is greater than its length <!-- JAL-2986 --></li>
+</ul>
+<p><em>Bugs fixed for Java 11 Support (not yet on general release)</em></p>
+<ul>
+<li>Menus work properly in split-screen <!-- JAL-3288 --></li>
+</ul>
+<p><em>New Known Defects</em></p>
+<ul>
+<li>Select columns containing feature by double clicking ignores bounds of an existing selected region <!-- JAL-3340 --></li>
+<li>Codon consensus logo incorrectly scaled in gapped regions of protein alignment. <!-- JAL-3313 --></li>
+<li>Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project <!-- JAL-2647 --></li>
+<li>Alignment panel height can be too small after 'New View' <!-- JAL-3213 --></li>
+<li>Display is incorrect after removing gapped columns within hidden columns <!-- JAL-3240 --></li>
+<li>Rightmost selection is lost when mouse re-enters window after dragging left to select columns to left of visible region <!-- JAL-3314 --></li>
+<li>Features coloured according to their description string and thresholded by score in earlier versions of Jalview are not shown as thresholded features in 2.11. To workaround please create a Score filter instead. <!-- JAL-2876 --></li>
+<li>Cancel on Feature Settings dialog doesn't reset group visibility <!-- JAL-3184 --></li>
+<li>F2 doesn't enable/disable keyboard mode in linked CDS/Protein view <!-- JAL-3338 --></li>
+<li>Closing tree windows with CMD/CTRL-W for alignments with multiple views can close views unexpectedly <!-- JAL-797 --></li>
+</ul>
+<p><em>Java 11 Specific defects</em></p>
+<ul>
+<li>Jalview Properties file is not sorted alphabetically when saved <!-- JAL-3235 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.10">.10</a><a id="Jalview.2.10.5">.5</a></strong>
<br />
<em>10 September 2018</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3></h3>
<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>
+<li>Default memory for Jalview webstart and InstallAnywhere increased to 1G. <!-- JAL-3101 --></li>
+<li>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> <!-- JAL-247 --></li>
+<li>Ensembl client updated to Version 7 REST API and sequence data now imported as JSON. <!-- JAL-3076 --></li>
+<li>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. <!-- JAL-3065 --></li>
</ul>
-<h3>Development</h3>
+<p><em>Development</em></p>
<ul>
-<li><!-- JAL-3047 --> Support added to execute test suite instrumented with <a href="http://openclover.org/">Open Clover</a></li>
+<li>Support added to execute test suite instrumented with <a href="http://openclover.org/">Open Clover</a> <!-- JAL-3047 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3></h3>
<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.</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>
+<li>Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example alignment. <!-- JAL-3104 --></li>
+<li>Annotation obscures sequences if lots of annotation displayed. <!-- JAL-2854 --></li>
+<li>Group conservation/consensus not shown for newly created group when 'Apply to all groups' selected <!-- JAL-3107 --></li>
+<li>Corrupted display when switching to wrapped mode when sequence panel's vertical scrollbar is visible. <!-- JAL-3087 --></li>
+<li>Alignment is black in exported EPS file when sequences are selected in exported view. <!-- JAL-3003 --></li>
+<li>Groups with different coloured borders aren't rendered with correct colour. <!-- JAL-3059 --></li>
+<li>Jalview could hang when importing certain types of knotted RNA secondary structure. <!-- JAL-3092 --></li>
+<li>Sequence highlight and selection in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1. <!-- JAL-3095 --></li>
+<li>'.' inserted into RNA secondary structure annotation when columns are inserted into an alignment, and when exporting as Stockholm flatfile. <!-- JAL-3061 --></li>
+<li>Jalview annotation rows containing upper and lower-case 'E' and 'H' do not automatically get treated as RNA secondary structure. <!-- JAL-3053 --></li>
+<li>.jvp should be used as default extension (not .jar) when saving a Jalview project file. <!-- JAL-3106 --></li>
+<li>Mac Users: closing a window correctly transfers focus to previous window on OSX <!-- JAL-3105 --></li>
</ul>
-<h3>Java 10 Issues Resolved</h3>
+<p><em>Java 10 Issues Resolved</em></p>
<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>
+<li>OSX - Can't save new files via the File or export menus by typing in a name into the Save dialog box. <!-- JAL-2988 --></li>
+<li>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. <!-- JAL-2988 JAL-2968 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.4b1">.4b1</a></strong>
<br />
<em>7 June 2018</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3></h3>
<ul>
-<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>
+<li>Use HGVS nomenclature for variant annotation retrieved from Uniprot <!-- JAL-2920 --></li>
+<li>Windows File Shortcuts can be dragged onto the Jalview Desktop <!-- JAL-1460 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3></h3>
-<ul>
-<li><!-- JAL-3017 --> Cannot import features with multiple variant elements (blocks import of some Uniprot records)</li>
-<li><!-- JAL-2997 --> Clustal files with sequence positions in right-hand column parsed correctly</li>
-<li><!-- JAL-2991 --> Wrap view - export to SVG - IDs shown but 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 (Windows)</li>
-<li><!-- 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 Jalview desktop on Windows doesn't open file<br/>
+<ul>
+<li>Cannot import features with multiple variant elements (blocks import of some Uniprot records) <!-- JAL-3017 --></li>
+<li>Clustal files with sequence positions in right-hand column parsed correctly <!-- JAL-2997 --></li>
+<li>Wrap view - export to SVG - IDs shown but not alignment area in exported graphic <!-- JAL-2991 --></li>
+<li>F2/Keyboard mode edits work when Overview window has input focus <!-- JAL-2993 --></li>
+<li>Annotation panel set too high when annotation added to view (Windows) <!-- JAL-2992 --></li>
+<li>Jalview Desktop is slow to start up when network connectivity is poor <!-- JAL-3009 --></li>
+<li>Drag URL from chrome, firefox, IE to Jalview desktop on Windows doesn't open file<br/> <!-- JAL-1460 -->
<em>Dragging the currently open URL and links from a page viewed in Firefox or Chrome on Windows is now fully supported. If you are using Edge, only links in the page can be dragged, and with Internet Explorer, only the currently open URL in the browser can be dropped onto Jalview.</em></li>
</ul>
-<h3>New Known Defects</h3>
+<p><em>New Known Defects</em></p>
<ul>
-<li><!-- JAL-3083 --> Cancel option doesn't reset Colour by Annotation</li>
+<li>Cancel option doesn't reset Colour by Annotation <!-- JAL-3083 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.4">.4</a></strong>
<br />
<em>10 May 2018</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3></h3>
<ul>
-<li><!-- JAL-1847 JAL-2944 --> New Structure Chooser control for disabling automatic superposition of multiple structures and open structures in existing views</li>
-<li><!-- JAL-984 --> Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li>
-<li><!-- JAL-2885 --> Jalview uses HTTPS for Uniprot, Xfam and Ensembl services</li>
-<li><!-- JAL-2759 --> Improved performance for large alignments and lots of hidden columns</li>
-<li><!-- JAL-2593 --> Improved performance when rendering lots of features (particularly when transparency is disabled)</li>
-<li><!-- JAL-2296,JAL-2295 --> Experimental features in 2.10.2 for exchange of Jalview features and Chimera attributes made generally available</li>
+<li>New Structure Chooser control for disabling automatic superposition of multiple structures and open structures in existing views <!-- JAL-1847 JAL-2944 --></li>
+<li>Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them. <!-- JAL-984 --></li>
+<li>Jalview uses HTTPS for Uniprot, Xfam and Ensembl services <!-- JAL-2885 --></li>
+<li>Improved performance for large alignments and lots of hidden columns <!-- JAL-2759 --></li>
+<li>Improved performance when rendering lots of features (particularly when transparency is disabled) <!-- JAL-2593 --></li>
+<li>Experimental features in 2.10.2 for exchange of Jalview features and Chimera attributes made generally available <!-- JAL-2296,JAL-2295 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
<ul>
-<li><!-- JAL-2899 --> Structure and Overview aren't updated when Colour By Annotation threshold slider is adjusted</li>
-<li><!-- JAL-2778 --> Slow redraw when Overview panel shown overlapping alignment panel</li>
-<li><!-- JAL-2929 --> Overview doesn't show end of unpadded sequence as gaps</li>
-<li><!-- JAL-2789, JAL-2893 --> Cross-reference handling improved: CDS not handled correctly if transcript has no UTR</li>
-<li><!-- JAL-2321 --> Secondary structure and temperature factor annotation not added to sequence when local PDB file associated with it by drag'n'drop or structure chooser</li>
-<li><!-- JAL-2984 --> Answering 'No' to PDB Autoassociate dialog doesn't import PDB files dropped on an alignment</li>
-<li><!-- JAL-2666 --> Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views</li>
-<li><!-- JAL-2930 --> Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.</li>
-<li><!-- JAL-2924 --> Tooltip shouldn't be displayed for empty columns in annotation row</li>
-<li><!-- JAL-2913 --> Preferences panel's ID Width control is not honored in batch mode</li>
-<li><!-- JAL-2945 --> Linked sequence highlighting doesn't work for structures added to existing Jmol view</li>
-<li><!-- JAL-2223 --> 'View Mappings' includes duplicate entries after importing project with multiple views</li>
-<li><!-- JAL-2781 JAL-2780 --> Viewing or annotating Uniprot protein sequences via SIFTS from associated PDB entries with negative residue numbers or missing residues fails</li>
-<li><!-- JAL-2952 --> Exception when shading sequence with negative Temperature Factor values from annotated PDB files (e.g. as generated by CONSURF)</li>
-<li><!-- JAL-2920 --> Uniprot 'sequence variant' features tooltip doesn't include a text description of mutation</li>
-<li><!-- JAL-2922 --> Invert displayed features very slow when structure and/or overview windows are also shown</li>
-<li><!-- JAL-2954 --> Selecting columns from highlighted regions very slow for alignments with large numbers of sequences</li>
-<li><!-- JAL-2925 --> Copy Consensus fails for group consensus with 'StringIndexOutOfBounds'</li>
-<li><!-- JAL-2976 --> VAqua(4) provided as fallback Look and Feel for OSX platforms running Java 10</li>
-<li><!-- JAL-2960 --> Adding a structure to existing structure view appears to do nothing because the view is hidden behind the alignment view</li>
+<li>Structure and Overview aren't updated when Colour By Annotation threshold slider is adjusted <!-- JAL-2899 --></li>
+<li>Slow redraw when Overview panel shown overlapping alignment panel <!-- JAL-2778 --></li>
+<li>Overview doesn't show end of unpadded sequence as gaps <!-- JAL-2929 --></li>
+<li>Cross-reference handling improved: CDS not handled correctly if transcript has no UTR <!-- JAL-2789, JAL-2893 --></li>
+<li>Secondary structure and temperature factor annotation not added to sequence when local PDB file associated with it by drag'n'drop or structure chooser <!-- JAL-2321 --></li>
+<li>Answering 'No' to PDB Autoassociate dialog doesn't import PDB files dropped on an alignment <!-- JAL-2984 --></li>
+<li>Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views <!-- JAL-2666 --></li>
+<li>Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+. <!-- JAL-2930 --></li>
+<li>Tooltip shouldn't be displayed for empty columns in annotation row <!-- JAL-2924 --></li>
+<li>Preferences panel's ID Width control is not honored in batch mode <!-- JAL-2913 --></li>
+<li>Linked sequence highlighting doesn't work for structures added to existing Jmol view <!-- JAL-2945 --></li>
+<li>'View Mappings' includes duplicate entries after importing project with multiple views <!-- JAL-2223 --></li>
+<li>Viewing or annotating Uniprot protein sequences via SIFTS from associated PDB entries with negative residue numbers or missing residues fails <!-- JAL-2781 JAL-2780 --></li>
+<li>Exception when shading sequence with negative Temperature Factor values from annotated PDB files (e.g. as generated by CONSURF) <!-- JAL-2952 --></li>
+<li>Uniprot 'sequence variant' features tooltip doesn't include a text description of mutation <!-- JAL-2920 --></li>
+<li>Invert displayed features very slow when structure and/or overview windows are also shown <!-- JAL-2922 --></li>
+<li>Selecting columns from highlighted regions very slow for alignments with large numbers of sequences <!-- JAL-2954 --></li>
+<li>Copy Consensus fails for group consensus with 'StringIndexOutOfBounds' <!-- JAL-2925 --></li>
+<li>VAqua(4) provided as fallback Look and Feel for OSX platforms running Java 10 <!-- JAL-2976 --></li>
+<li>Adding a structure to existing structure view appears to do nothing because the view is hidden behind the alignment view <!-- JAL-2960 --></li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
-<li><!-- JAL-2926 --> Copy consensus sequence option in applet should copy the group consensus when popup is opened on it</li>
+<li>Copy consensus sequence option in applet should copy the group consensus when popup is opened on it <!-- JAL-2926 --></li>
</ul>
-<h3>Batch Mode</h3>
+<p><em>Batch Mode</em></p>
<ul>
-<li><!-- JAL-2913 --> Fixed ID width preference is not respected</li>
+<li>Fixed ID width preference is not respected <!-- JAL-2913 --></li>
</ul>
-<h3>New Known Defects</h3>
+<p><em>New Known Defects</em></p>
<ul>
-<li><!-- JAL-2973 --> Exceptions occasionally raised when editing a large alignment and overview is displayed</li>
-<li><!-- JAL-2974 --> 'Overview updating' progress bar is shown repeatedly after a series of edits even when the overview is no longer reflecting updates</li>
-<li><!-- JAL-2946 --> 'SIFTS Mapping Error' when viewing structures for protein subsequence (if 'Trim Retrieved Sequences' enabled) or Ensembl isoforms (Workaround in 2.10.4 is to fail back to N&W mapping)</li>
-<li><!-- JAL-2990 --> Export Annotations from File Menu with CSV option gives blank output</li>
+<li>Exceptions occasionally raised when editing a large alignment and overview is displayed <!-- JAL-2973 --></li>
+<li>'Overview updating' progress bar is shown repeatedly after a series of edits even when the overview is no longer reflecting updates <!-- JAL-2974 --></li>
+<li>'SIFTS Mapping Error' when viewing structures for protein subsequence (if 'Trim Retrieved Sequences' enabled) or Ensembl isoforms (Workaround in 2.10.4 is to fail back to N&W mapping) <!-- JAL-2946 --></li>
+<li>Export Annotations from File Menu with CSV option gives blank output <!-- JAL-2990 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.3b1">.3b1</a></strong>
<br />
<em>24 January 2018</em>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>Desktop</h3>
+<p><em>Desktop</em></p>
<ul>
-<li><!-- JAL-2859--> Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
-<li><!-- JAL-2851--> Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
-<li><!-- JAL-2842--> Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
-<li><!-- JAL-2827--> Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
-<li><!-- JAL-2740--> Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
-<li><!-- JAL-2849--> User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
-<li><!-- JAL-2679--> Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
+<li>Only one structure is loaded when several sequences and structures are selected for viewing/superposing <!-- JAL-2859--></li>
+<li>Alignment doesn't appear to scroll vertically via trackpad and scrollwheel <!-- JAL-2851--></li>
+<li>Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment <!-- JAL-2842--></li>
+<li>Helix annotation has 'notches' when scrolled into view if columns are hidden <!-- JAL-2827--></li>
+<li>Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns <!-- JAL-2740--></li>
+<li>User preference for disabling inclusion of sequence limits when exporting as flat file has no effect <!-- JAL-2849--></li>
+<li>Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes <!-- JAL-2679--></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.3">.3</a></strong>
<br />
<em>17 November 2017</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3></h3>
<ul>
-<li><!-- JAL-2446 --> Faster and more efficient management and rendering of sequence features</li>
-<li><!-- JAL 2523--> More reliable Ensembl fetching with HTTP 429 rate limit request hander</li>
-<li><!-- JAL-2773 --> Structure views don't get updated unless their colours have changed</li>
-<li><!-- JAL-2495 --> All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
-<li><!-- JAL-2790 --> 'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs</li>
-<li><!-- JAL-2617 --> Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
-<li><!-- JAL-2685 --> Start/End limits are shown in Pairwise Alignment report</li>
-<li><!-- JAL-2810 --> Sequence fetcher's Free text 'autosearch' feature can be disabled</li>
-<li><!-- JAL-2810 --> Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs</li>
-<li><!-- JAL-2758 --> Short names for sequences retrieved from Uniprot</li>
+<li>Faster and more efficient management and rendering of sequence features <!-- JAL-2446 --></li>
+<li>More reliable Ensembl fetching with HTTP 429 rate limit request hander <!-- JAL 2523--></li>
+<li>Structure views don't get updated unless their colours have changed <!-- JAL-2773 --></li>
+<li>All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera) <!-- JAL-2495 --></li>
+<li>'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs <!-- JAL-2790 --></li>
+<li>Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references <!-- JAL-2617 --></li>
+<li>Start/End limits are shown in Pairwise Alignment report <!-- JAL-2685 --></li>
+<li>Sequence fetcher's Free text 'autosearch' feature can be disabled <!-- JAL-2810 --></li>
+<li>Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs <!-- JAL-2810 --></li>
+<li>Short names for sequences retrieved from Uniprot <!-- JAL-2758 --></li>
</ul>
-<h3>Scripting</h3>
+<p><em>Scripting</em></p>
<ul>
<li>Groovy interpreter updated to 2.4.12</li>
<li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li>
</ul>
-<h3>Testing and Deployment</h3>
+<p><em>Testing and Deployment</em></p>
<ul>
-<li><!-- JAL-2727 --> Test to catch memory leaks in Jalview UI</li>
+<li>Test to catch memory leaks in Jalview UI <!-- JAL-2727 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
-<li><!-- JAL-2643 --> Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
-<li><!-- JAL-2682 --> Race condition when parsing sequence ID strings in parallel</li>
-<li><!-- JAL-2608 --> Overview windows are also closed when alignment window is closed</li>
-<li><!-- JAL-2548 --> Export of features doesn't always respect group visibility</li>
-<li><!-- JAL-2831 --> Jumping from column 1 to column 100,000 takes a long time in Cursor mode</li>
+<li>Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view <!-- JAL-2643 --></li>
+<li>Race condition when parsing sequence ID strings in parallel <!-- JAL-2682 --></li>
+<li>Overview windows are also closed when alignment window is closed <!-- JAL-2608 --></li>
+<li>Export of features doesn't always respect group visibility <!-- JAL-2548 --></li>
+<li>Jumping from column 1 to column 100,000 takes a long time in Cursor mode <!-- JAL-2831 --></li>
</ul>
-<h3>Desktop</h3>
+<p><em>Desktop</em></p>
<ul>
-<li><!-- JAL-2777 --> Structures with whitespace chainCode cannot be viewed in Chimera</li>
-<li><!-- JAL-2728 --> Protein annotation panel too high in CDS/Protein view</li>
-<li><!-- JAL-2757 --> Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs</li>
-<li><!-- JAL-2253 --> Slow EnsemblGenome ID lookup</li>
-<li><!-- JAL-2529 --> Revised Ensembl REST API CDNA query</li>
-<li><!-- JAL-2739 --> Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
-<li><!-- JAL-2768 --> Annotation display corrupted when scrolling right in unwapped alignment view</li>
-<li><!-- JAL-2542 --> Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
-<li><!-- JAL-2733 --> Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
-<li><!-- JAL-2658 --> Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
-<li><!-- JAL-2524 --> Jalview becomes sluggish in wide alignments when hidden columns are present</li>
-<li><!-- JAL-2392 --> Jalview freezes when loading and displaying several structures</li>
-<li><!-- JAL-2732 --> Black outlines left after resizing or moving a window</li>
-<li><!-- JAL-1900,JAL-1625 --> Unable to minimise windows within the Jalview desktop on OSX</li>
-<li><!-- JAL-2667 --> Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
-<li><!-- JAL-2636 --> Scale mark not shown when close to right hand end of alignment</li>
-<li><!-- JAL-2684 --> Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions</li>
-<li><!-- JAL-2793 --> Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
-<li><!-- JAL-2036 --> Show cross-references not enabled after restoring project until a new view is created</li>
-<li><!-- JAL-2756 --> Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)</li>
-<li><!-- JAL-2775 --> Overview redraws whole window when box position is adjusted</li>
-<li><!-- JAL-2225 --> Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)</li>
-<li><!-- JAL-2811 --> Double residue highlights in cursor mode if new selection moves alignment window</li>
-<li><!-- JAL-2837,JAL-2840 --> Alignment vanishes when using arrow key in cursor mode to pass hidden column marker</li>
-<li><!-- JAL-2679 --> Ensembl Genomes example ID changed to one that produces correctly annotated transcripts and products</li>
-<li><!-- JAL-2776 --> Toggling a feature group after first time doesn't update associated structure view</li>
+<li>Structures with whitespace chainCode cannot be viewed in Chimera <!-- JAL-2777 --></li>
+<li>Protein annotation panel too high in CDS/Protein view <!-- JAL-2728 --></li>
+<li>Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs <!-- JAL-2757 --></li>
+<li>Slow EnsemblGenome ID lookup <!-- JAL-2253 --></li>
+<li>Revised Ensembl REST API CDNA query <!-- JAL-2529 --></li>
+<li>Hidden column marker in last column not rendered when switching back from Wrapped to normal view <!-- JAL-2739 --></li>
+<li>Annotation display corrupted when scrolling right in unwapped alignment view <!-- JAL-2768 --></li>
+<li>Existing features on subsequence incorrectly relocated when full sequence retrieved from database <!-- JAL-2542 --></li>
+<li>Last reported memory still shown when Desktop->Show Memory is unticked (OSX only) <!-- JAL-2733 --></li>
+<li>Amend Features dialog doesn't allow features of same type and group to be selected for amending <!-- JAL-2658 --></li>
+<li>Jalview becomes sluggish in wide alignments when hidden columns are present <!-- JAL-2524 --></li>
+<li>Jalview freezes when loading and displaying several structures <!-- JAL-2392 --></li>
+<li>Black outlines left after resizing or moving a window <!-- JAL-2732 --></li>
+<li>Unable to minimise windows within the Jalview desktop on OSX <!-- JAL-1900,JAL-1625 --></li>
+<li>Mouse wheel doesn't scroll vertically when in wrapped alignment mode <!-- JAL-2667 --></li>
+<li>Scale mark not shown when close to right hand end of alignment <!-- JAL-2636 --></li>
+<li>Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions <!-- JAL-2684 --></li>
+<li>Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog <!-- JAL-2793 --></li>
+<li>Show cross-references not enabled after restoring project until a new view is created <!-- JAL-2036 --></li>
+<li>Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2) <!-- JAL-2756 --></li>
+<li>Overview redraws whole window when box position is adjusted <!-- JAL-2775 --></li>
+<li>Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10) <!-- JAL-2225 --></li>
+<li>Double residue highlights in cursor mode if new selection moves alignment window <!-- JAL-2811 --></li>
+<li>Alignment vanishes when using arrow key in cursor mode to pass hidden column marker <!-- JAL-2837,JAL-2840 --></li>
+<li>Ensembl Genomes example ID changed to one that produces correctly annotated transcripts and products <!-- JAL-2679 --></li>
+<li>Toggling a feature group after first time doesn't update associated structure view <!-- JAL-2776 --></li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
-<li><!-- JAL-2687 --> Concurrent modification exception when closing alignment panel</li>
+<li>Concurrent modification exception when closing alignment panel <!-- JAL-2687 --></li>
</ul>
-<h3>BioJSON</h3>
+<p><em>BioJSON</em></p>
<ul>
-<li><!-- JAL-2546 --> BioJSON export does not preserve non-positional features</li>
+<li>BioJSON export does not preserve non-positional features <!-- JAL-2546 --></li>
</ul>
-<h3>New Known Issues</h3>
+<p><em>New Known Issues</em></p>
<ul>
-<li><!-- JAL-2541 --> Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview)</li>
-<li><!-- JAL-2841 --> Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top</li>
-<li><!-- JAL-2791 --> Select columns containing feature ignores graduated colour threshold</li>
-<li><!-- JAL-2822,JAL-2823 --> Edit sequence operation doesn't always preserve numbering and sequence features</li>
+<li>Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview) <!-- JAL-2541 --></li>
+<li>Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top <!-- JAL-2841 --></li>
+<li>Select columns containing feature ignores graduated colour threshold <!-- JAL-2791 --></li>
+<li>Edit sequence operation doesn't always preserve numbering and sequence features <!-- JAL-2822,JAL-2823 --></li>
</ul>
-<h3>Known Java 9 Issues</h3>
+<p><em>Known Java 9 Issues</em></p>
<ul>
-<li><!-- JAL-2902 --> Groovy Console very slow to open and is not responsive when entering characters (Webstart, Java 9.01, OSX 10.10)</li>
+<li>Groovy Console very slow to open and is not responsive when entering characters (Webstart, Java 9.01, OSX 10.10) <!-- JAL-2902 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.2b2">.2b2</a></strong>
<br />
<em>2 October 2017</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>New features in Jalview Desktop</h3>
+<p><em>New features in Jalview Desktop</em></p>
<ul>
-<li><!-- JAL-2748 --> Uniprot Sequence Fetcher now uses web API at uniprot.org</li>
-<li><!-- JAL-2745 --> HTTPS used for all connections to ebi.ac.uk</li>
+<li>Uniprot Sequence Fetcher now uses web API at uniprot.org <!-- JAL-2748 --></li>
+<li>HTTPS used for all connections to ebi.ac.uk <!-- JAL-2745 --></li>
</ul>
</td>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.2b1">.2b1</a></strong>
<br />
<em>7 September 2017</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3></h3>
<ul>
-<li><!-- JAL-2588 --> Show gaps in overview window by colouring in grey (sequences used to be coloured grey, and gaps were white)</li>
-<li><!-- JAL-2588,JAL-2527 --> Overview tab in Jalview Desktop Preferences</li>
-<li><!-- JAL-2587 --> Overview updates immediately on increase in size and progress bar shown as higher resolution overview is recalculated</li>
+<li>Show gaps in overview window by colouring in grey (sequences used to be coloured grey, and gaps were white) <!-- JAL-2588 --></li>
+<li>Overview tab in Jalview Desktop Preferences <!-- JAL-2588,JAL-2527 --></li>
+<li>Overview updates immediately on increase in size and progress bar shown as higher resolution overview is recalculated <!-- JAL-2587 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3></h3>
<ul>
-<li><!-- JAL-2664 --> Overview window redraws every hidden column region row by row</li>
-<li><!-- JAL-2681 --> duplicate protein sequences shown after retrieving Ensembl crossrefs for sequences from Uniprot</li>
-<li><!-- JAL-2603 --> Overview window throws NPE if show boxes format setting is unticked</li>
-<li><!-- JAL-2610 --> Groups are coloured wrongly in overview if group has show boxes format setting unticked</li>
-<li><!-- JAL-2672,JAL-2665 --> Redraw problems when autoscrolling whilst dragging current selection group to include sequences and columns not currently displayed</li>
-<li><!-- JAL-2691 --> Not all chains are mapped when multimeric assemblies are imported via CIF file</li>
-<li><!-- JAL-2704 --> Gap colour in custom colourscheme is not displayed when threshold or conservation colouring is also enabled.</li>
-<li><!-- JAL-2549 --> JABAWS 2.2 services report wrong JABAWS server version</li>
-<li><!-- JAL-2673 --> Jalview continues to scroll after dragging a selected region off the visible region of the alignment</li>
-<li><!-- JAL-2724 --> Cannot apply annotation based colourscheme to all groups in a view</li>
-<li><!-- JAL-2511 --> IDs don't line up with sequences initially after font size change using the Font chooser or middle-mouse zoom</li>
+<li>Overview window redraws every hidden column region row by row <!-- JAL-2664 --></li>
+<li>duplicate protein sequences shown after retrieving Ensembl crossrefs for sequences from Uniprot <!-- JAL-2681 --></li>
+<li>Overview window throws NPE if show boxes format setting is unticked <!-- JAL-2603 --></li>
+<li>Groups are coloured wrongly in overview if group has show boxes format setting unticked <!-- JAL-2610 --></li>
+<li>Redraw problems when autoscrolling whilst dragging current selection group to include sequences and columns not currently displayed <!-- JAL-2672,JAL-2665 --></li>
+<li>Not all chains are mapped when multimeric assemblies are imported via CIF file <!-- JAL-2691 --></li>
+<li>Gap colour in custom colourscheme is not displayed when threshold or conservation colouring is also enabled. <!-- JAL-2704 --></li>
+<li>JABAWS 2.2 services report wrong JABAWS server version <!-- JAL-2549 --></li>
+<li>Jalview continues to scroll after dragging a selected region off the visible region of the alignment <!-- JAL-2673 --></li>
+<li>Cannot apply annotation based colourscheme to all groups in a view <!-- JAL-2724 --></li>
+<li>IDs don't line up with sequences initially after font size change using the Font chooser or middle-mouse zoom <!-- JAL-2511 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.2">.2</a></strong>
<br />
<em>17 August 2017</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Calculations</h3>
+<p><em>Calculations</em></p>
<ul>
-<li><!-- JAL-1933 --> Occupancy annotation row shows number of ungapped positions in each column of the alignment.</li>
-<li><!-- JAL-1632 --> Tree/PCA calculation menu items merged to a calculation dialog box</li>
-<li><!-- JAL-2379 --> Revised implementation of PCA for speed and memory efficiency (~30x faster)</li>
-<li><!-- JAL-2403 --> Revised implementation of sequence similarity scores as used by Tree, PCA, Shading Consensus and other calculations</li>
-<li><!-- JAL-2416 --> Score matrices are stored as resource files within the Jalview codebase</li>
-<li><!-- JAL-2500 --> Trees computed on Sequence Feature Similarity may have different topology due to increased precision</li>
+<li>Occupancy annotation row shows number of ungapped positions in each column of the alignment. <!-- JAL-1933 --></li>
+<li>Tree/PCA calculation menu items merged to a calculation dialog box <!-- JAL-1632 --></li>
+<li>Revised implementation of PCA for speed and memory efficiency (~30x faster) <!-- JAL-2379 --></li>
+<li>Revised implementation of sequence similarity scores as used by Tree, PCA, Shading Consensus and other calculations <!-- JAL-2403 --></li>
+<li>Score matrices are stored as resource files within the Jalview codebase <!-- JAL-2416 --></li>
+<li>Trees computed on Sequence Feature Similarity may have different topology due to increased precision <!-- JAL-2500 --></li>
</ul>
-<h3>Rendering</h3>
+<p><em>Rendering</em></p>
<ul>
-<li><!-- JAL-2360,JAL-2371, --> More robust colours and shader model for alignments and groups</li>
-<li><!-- JAL-384 --> Custom shading schemes created via groovy scripts</li>
+<li>More robust colours and shader model for alignments and groups <!-- JAL-2360,JAL-2371, --></li>
+<li>Custom shading schemes created via groovy scripts <!-- JAL-384 --></li>
</ul>
-<h3>Overview</h3>
+<p><em>Overview</em></p>
<ul>
-<li><!-- JAL-2526 --> Efficiency improvements for interacting with alignment and overview windows</li>
-<li><!-- JAL-2514 --> Scrolling of wrapped alignment views via overview</li>
-<li><!-- JAL-2388 --> Hidden columns and sequences can be omitted in Overview</li>
-<li><!-- JAL-2611 --> Click-drag in visible area allows fine adjustment of visible position</li>
+<li>Efficiency improvements for interacting with alignment and overview windows <!-- JAL-2526 --></li>
+<li>Scrolling of wrapped alignment views via overview <!-- JAL-2514 --></li>
+<li>Hidden columns and sequences can be omitted in Overview <!-- JAL-2388 --></li>
+<li>Click-drag in visible area allows fine adjustment of visible position <!-- JAL-2611 --></li>
</ul>
-<h3>Data import/export</h3>
+<p><em>Data import/export</em></p>
<ul>
-<li><!-- JAL-2535 --> Posterior probability annotation from Stockholm files imported as sequence associated annotation</li>
-<li><!-- JAL-2507 --> More robust per-sequence positional annotation input/output via stockholm flatfile</li>
-<li><!-- JAL-2533 --> Sequence names don't include file extension when importing structure files without embedded names or PDB accessions</li>
-<li><!-- JAL-2416 --> Drag and drop load of AAIndex and NCBI format sequence substitution matrices</li>
+<li>Posterior probability annotation from Stockholm files imported as sequence associated annotation <!-- JAL-2535 --></li>
+<li>More robust per-sequence positional annotation input/output via stockholm flatfile <!-- JAL-2507 --></li>
+<li>Sequence names don't include file extension when importing structure files without embedded names or PDB accessions <!-- JAL-2533 --></li>
+<li>Drag and drop load of AAIndex and NCBI format sequence substitution matrices <!-- JAL-2416 --></li>
</ul>
-<h3>User Interface</h3>
+<p><em>User Interface</em></p>
<ul>
-<li><!-- JAL-2447 --> Experimental Features Checkbox in Desktop's Tools menu to hide or show untested features in the application.</li>
-<li><!-- JAL-2491 --> Linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
-<li><!-- JAL-2547 --> Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent</li>
-<li><!-- JAL-1476 --> Status bar message shown when not enough aligned positions were available to create a 3D structure superposition.</li>
+<li>Experimental Features Checkbox in Desktop's Tools menu to hide or show untested features in the application. <!-- JAL-2447 --></li>
+<li>Linked scrolling of CDS/Protein views via Overview or sequence motif search operations <!-- JAL-2491 --></li>
+<li>Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent <!-- JAL-2547 --></li>
+<li>Status bar message shown when not enough aligned positions were available to create a 3D structure superposition. <!-- JAL-1476 --></li>
</ul>
-<h3>3D Structure</h3>
+<p><em>3D Structure</em></p>
<ul>
-<li><!-- JAL-2430 --> Hidden regions in alignment views are not coloured in linked structure views</li>
-<li><!-- JAL-1596 --> Faster Chimera/Jalview communication by file-based command exchange</li>
-<li><!-- JAL-2375 --> Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences</li>
-<li><!-- JAL-2520 --> Structures imported via URL are cached in the Jalview project rather than downloaded again when the project is reopened.</li>
-<li><!-- JAL-2295, JAL-2296 --> New entries in the Chimera menu to transfer Chimera's structure attributes as Jalview features, and vice-versa (<strong>Experimental Feature</strong>)</li>
+<li>Hidden regions in alignment views are not coloured in linked structure views <!-- JAL-2430 --></li>
+<li>Faster Chimera/Jalview communication by file-based command exchange <!-- JAL-1596 --></li>
+<li>Structure chooser automatically shows Cached Structures rather than querying the PDBe if structures are already available for sequences <!-- JAL-2375 --></li>
+<li>Structures imported via URL are cached in the Jalview project rather than downloaded again when the project is reopened. <!-- JAL-2520 --></li>
+<li>New entries in the Chimera menu to transfer Chimera's structure attributes as Jalview features, and vice-versa (<strong>Experimental Feature</strong>) <!-- JAL-2295, JAL-2296 --></li>
</ul>
-<h3>Web Services</h3>
+<p><em>Web Services</em></p>
<ul>
-<li><!-- JAL-2549 --> Updated JABAWS client to v2.2</li>
-<li><!-- JAL-2335 --> Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services</li>
-<li><!-- JAL-2316, --> URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
+<li>Updated JABAWS client to v2.2 <!-- JAL-2549 --></li>
+<li>Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services <!-- JAL-2335 --></li>
+<li>URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB <!-- JAL-2316, --></li>
</ul>
-<h3>Scripting</h3>
+<p><em>Scripting</em></p>
<ul>
-<li><!-- JAL-2344 --> FileFormatI interface for describing and identifying file formats (instead of String constants)</li>
-<li><!-- JAL-2228 --> FeatureCounter script refactored for efficiency when counting all displayed features (not backwards compatible with 2.10.1)</li>
+<li>FileFormatI interface for describing and identifying file formats (instead of String constants) <!-- JAL-2344 --></li>
+<li>FeatureCounter script refactored for efficiency when counting all displayed features (not backwards compatible with 2.10.1) <!-- JAL-2228 --></li>
</ul>
-<h3>Example files</h3>
+<p><em>Example files</em></p>
<ul>
-<li><!-- JAL-2631 --> Graduated feature colour style example included in the example feature file</li>
+<li>Graduated feature colour style example included in the example feature file <!-- JAL-2631 --></li>
</ul>
-<h3>Documentation</h3>
+<p><em>Documentation</em></p>
<ul>
-<li><!-- JAL-2339 --> Release notes reformatted for readability with the built-in Java help viewer</li>
-<li><!-- JAL-1644 --> Find documentation updated with 'search sequence description' option</li>
+<li>Release notes reformatted for readability with the built-in Java help viewer <!-- JAL-2339 --></li>
+<li>Find documentation updated with 'search sequence description' option <!-- JAL-1644 --></li>
</ul>
-<h3>Test Suite</h3>
+<p><em>Test Suite</em></p>
<ul>
-<li><!-- JAL-2485, --> External service integration tests for Uniprot REST Free Text Search Client</li>
-<li><!-- JAL-2474 --> Added PrivilegedAccessor to test suite</li>
-<li><!-- JAL-2326 --> Prevent or clear modal dialogs raised during tests</li>
+<li>External service integration tests for Uniprot REST Free Text Search Client <!-- JAL-2485, --></li>
+<li>Added PrivilegedAccessor to test suite <!-- JAL-2474 --></li>
+<li>Prevent or clear modal dialogs raised during tests <!-- JAL-2326 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>Calculations</h3>
+<p><em>Calculations</em></p>
<ul>
-<li><!-- JAL-2398, --> Fixed incorrect value in BLOSUM 62 score matrix - C->R should be '-3'<br/>
+<li>Fixed incorrect value in BLOSUM 62 score matrix - C->R should be '-3'<br/> <!-- JAL-2398, -->
Old matrix restored with this one-line groovy script:<br/>
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3</li>
-<li><!-- JAL-2397 --> <a href=""></a> Fixed Jalview's treatment of gaps in PCA and substitution matrix based Tree calculations.<br/></li>
+<li><a href=""></a> Fixed Jalview's treatment of gaps in PCA and substitution matrix based Tree calculations.<br/> <!-- JAL-2397 --></li>
</ul>
<br/>
In earlier versions of Jalview, gaps matching gaps were penalised, and gaps matching non-gaps penalised even more. In the PCA calculation, gaps were actually treated as non-gaps - so different costs were applied, which meant Jalview's PCAs were different to those produced by SeqSpace.<br/>
jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false // to restore 2.10.2 mode <br/>
<br/>
*Note: these settings will affect all subsequent tree and PCA calculations (not recommended)*
- - <!-- JAL-2424 --> Fixed off-by-one bug that affected scaling of branch lengths for trees computed using Sequence Feature Similarity.
- - <!-- JAL-2377 --> PCA calculation could hang when generating output report when working with highly redundant alignments
- - <!-- JAL-2544 --> Sort by features includes features to right of selected region when gaps present on right-hand boundary
-<h3>User Interface</h3>
-<ul>
-<li><!-- JAL-2346 --> Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view</li>
-<li><!-- JAL-2419 --> Current selection lost if popup menu opened on a region of alignment without groups</li>
-<li><!-- JAL-2374 --> Popup menu not always shown for regions of an alignment with overlapping groups</li>
-<li><!-- JAL-2310 --> Finder double counts if both a sequence's name and description match</li>
-<li><!-- JAL-2370 --> Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
-<li><!-- JAL-2386 --> 'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
-<li><!-- JAL-2373 --> Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
-<li><!-- JAL-2385 --> Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
-<li><!-- JAL-2547 --> Sequence features shown in tooltip for gaps before start of features</li>
-<li><!-- JAL-2623 --> Graduated feature colour threshold not restored to UI when feature colour is edited</li>
-<li><!-- JAL-147 --> Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.</li>
-<li><!-- JAL-2630 --> Structure and alignment overview update as graduate feature colour settings are modified via the dialog box</li>
-<li><!-- JAL-2034 --> Overview window doesn't always update when a group defined on the alignment is resized</li>
-<li><!-- JAL-2605 --> Mouseovers on left/right scale region in wrapped view result in positional status updates</li>
-<li><!-- JAL-2563 --> Status bar doesn't show position for ambiguous amino acid and nucleotide symbols</li>
-<li><!-- JAL-2602 --> Copy consensus sequence failed if alignment included gapped columns</li>
-<li><!-- JAL-2473 --> Minimum size set for Jalview windows so widgets don't permanently disappear</li>
-<li><!-- JAL-2503 --> Cannot select or filter quantitative annotation that are shown only as column labels (e.g. T-Coffee column reliability scores)</li>
-<li><!-- JAL-2594 --> Exception thrown if trying to create a sequence feature on gaps only</li>
-<li><!-- JAL-2504 --> Features created with 'New feature' button from a Find inherit previously defined feature type rather than the Find query string</li>
-<li><!-- JAL-2423 --> incorrect title in output window when exporting tree calculated in Jalview</li>
-<li><!-- JAL-2437 --> Hiding sequences at bottom of alignment and then revealing them reorders sequences on the alignment</li>
-<li><!-- JAL-964 --> Group panel in sequence feature settings doesn't update to reflect available set of groups after interactively adding or modifying features</li>
-<li><!-- JAL-2225 --> Sequence Database chooser unusable on Linux</li>
-<li><!-- JAL-2291 --> Hide insertions in PopUp->Selection menu only excluded gaps in current sequence and ignored selection.</li>
-</ul>
-<h3>Rendering</h3>
-<ul>
-<li><!-- JAL-2421 --> Overview window visible region moves erratically when hidden rows or columns are present</li>
-<li><!-- JAL-2362 --> Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
-<li><!-- JAL-2405 --> Protein specific colours only offered in colour and group colour menu for protein alignments</li>
-<li><!-- JAL-2385 --> Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
-<li><!-- JAL-2624 --> Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%</li>
-<li><!-- JAL-2589 --> User defined gap colour not shown in overview when features overlaid on alignment</li>
-<li><!-- JAL-2567 --> Feature settings for different views not recovered correctly from Jalview project file</li>
-<li><!-- JAL-2256 --> Feature colours in overview when first opened (automatically via preferences) are different to the main alignment panel</li>
-</ul>
-<h3>Data import/export</h3>
-<ul>
-<li><!-- JAL-2576 --> Very large alignments take a long time to load</li>
-<li><!-- JAL-2507 --> Per-sequence RNA secondary structures added after a sequence was imported are not written to Stockholm File</li>
-<li><!-- JAL-2509 --> WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm</li>
-<li><!-- JAL-2509 --> Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots</li>
-<li><!-- JAL-2365,JAL-2642 --> Cannot configure feature colours with lightGray or darkGray via features file (but can specify lightgray)</li>
-<li><!-- JAL-2383 --> Above PID colour threshold not recovered when alignment view imported from project</li>
-<li><!-- JAL-2520,JAL-2465 --> No mappings generated between structure and sequences extracted from structure files imported via URL and viewed in Jmol</li>
-<li><!-- JAL-2520 --> Structures loaded via URL are saved in Jalview Projects rather than fetched via URL again when the project is loaded and the structure viewed</li>
-</ul>
-<h3>Web Services</h3>
-<ul>
-<li><!-- JAL-2519 --> EnsemblGenomes example failing after release of Ensembl v.88</li>
-<li><!-- JAL-2366 --> Proxy server address and port always appear enabled in Preferences->Connections</li>
-<li><!-- JAL-2461 --> DAS registry not found exceptions removed from console output</li>
-<li><!-- JAL-2582 --> Cannot retrieve protein products from Ensembl by Peptide ID</li>
-<li><!-- JAL-2482, JAL-2487 --> Incorrect PDB-Uniprot mappings created from SIFTs, and spurious 'Couldn't open structure in Chimera' errors raised after April 2017 update (problem due to 'null' string rather than empty string used for residues with no corresponding PDB mapping).</li>
-</ul>
-<h3>Application UI</h3>
-<ul>
-<li><!-- JAL-2361 --> User Defined Colours not added to Colour menu</li>
-<li><!-- JAL-2401 --> Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
-<li><!-- JAL-2399--> Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
-<li><!-- JAL-2243 --> Feature settings panel does not update as new features are added to alignment</li>
-<li><!-- JAL-2532 --> Cancel in feature settings reverts changes to feature colours via the Amend features dialog</li>
-<li><!-- JAL-2506 --> Null pointer exception when attempting to edit graduated feature colour via amend features dialog box</li>
-<li><!-- JAL-2436 --> Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
-<li><!-- JAL-2426 --> Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
-<li><!-- JAL-1608 --> Typo in selection popup menu - Create groups now 'Create Group'</li>
-<li><!-- JAL-1608 --> CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
-<li><!-- JAL-2464 --> Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
-<li><!-- JAL-1256 --> Trackpad horizontal scroll gesture adjusts start position in wrap mode</li>
-<li><!-- JAL-2563 --> Status bar doesn't show positions for ambiguous amino acids</li>
-<li><!-- JAL-2431 --> cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins</li>
-<li><!-- JAL-2592 --> User defined colourschemes called 'User Defined' don't appear in Colours menu</li>
-</ul>
-<h3>Applet</h3>
-<ul>
-<li><!-- JAL-2468 --> Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot</li>
-<li><!-- JAL-2442 --> Features not rendered as transparent on overview or linked structure view</li>
-<li><!-- JAL-2372 --> Colour group by conservation doesn't work (since 2.8)</li>
-<li><!-- JAL-2517 --> Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
-</ul>
-<h3>Test Suite</h3>
-<ul>
-<li><!-- JAL-2314 --> Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails</li>
-<li><!-- JAL-2307 --> Unit test failure: jalview.ws.sifts.SiftsClientTest due to compatibility problems with deep array comparison equality asserts in successive versions of TestNG</li>
-<li><!-- JAL-2479 --> Relocated StructureChooserTest and ParameterUtilsTest Unit tests to Network suite</li>
-</ul>
-<h3>New Known Issues</h3>
-<ul>
-<li><!-- JAL-2566 --> Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
-<li><!-- JAL-2550 --> Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS RNA secondary structure symbols</li>
-<li><!-- JAL-2590 --> Cannot load and display Newick trees reliably from eggnog Ortholog database</li>
-<li><!-- JAL-2468 --> Status bar shows 'Marked x columns containing features of type Highlight' when 'B' is pressed to mark columns containing highlighted regions.</li>
-<li><!-- JAL-2321 --> Dropping a PDB file onto a sequence doesn't always add secondary structure annotation.</li>
+ - Fixed off-by-one bug that affected scaling of branch lengths for trees computed using Sequence Feature Similarity. <!-- JAL-2424 -->
+ - PCA calculation could hang when generating output report when working with highly redundant alignments <!-- JAL-2377 -->
+ - Sort by features includes features to right of selected region when gaps present on right-hand boundary <!-- JAL-2544 -->
+<p><em>User Interface</em></p>
+<ul>
+<li>Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view <!-- JAL-2346 --></li>
+<li>Current selection lost if popup menu opened on a region of alignment without groups <!-- JAL-2419 --></li>
+<li>Popup menu not always shown for regions of an alignment with overlapping groups <!-- JAL-2374 --></li>
+<li>Finder double counts if both a sequence's name and description match <!-- JAL-2310 --></li>
+<li>Hiding column selection containing two hidden regions results in incorrect hidden regions <!-- JAL-2370 --></li>
+<li>'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups <!-- JAL-2386 --></li>
+<li>Percentage identity and conservation menu items do not show a tick or allow shading to be disabled <!-- JAL-2373 --></li>
+<li>Conservation shading or PID threshold lost when base colourscheme changed if slider not visible <!-- JAL-2385 --></li>
+<li>Sequence features shown in tooltip for gaps before start of features <!-- JAL-2547 --></li>
+<li>Graduated feature colour threshold not restored to UI when feature colour is edited <!-- JAL-2623 --></li>
+<li>Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode. <!-- JAL-147 --></li>
+<li>Structure and alignment overview update as graduate feature colour settings are modified via the dialog box <!-- JAL-2630 --></li>
+<li>Overview window doesn't always update when a group defined on the alignment is resized <!-- JAL-2034 --></li>
+<li>Mouseovers on left/right scale region in wrapped view result in positional status updates <!-- JAL-2605 --></li>
+<li>Status bar doesn't show position for ambiguous amino acid and nucleotide symbols <!-- JAL-2563 --></li>
+<li>Copy consensus sequence failed if alignment included gapped columns <!-- JAL-2602 --></li>
+<li>Minimum size set for Jalview windows so widgets don't permanently disappear <!-- JAL-2473 --></li>
+<li>Cannot select or filter quantitative annotation that are shown only as column labels (e.g. T-Coffee column reliability scores) <!-- JAL-2503 --></li>
+<li>Exception thrown if trying to create a sequence feature on gaps only <!-- JAL-2594 --></li>
+<li>Features created with 'New feature' button from a Find inherit previously defined feature type rather than the Find query string <!-- JAL-2504 --></li>
+<li>incorrect title in output window when exporting tree calculated in Jalview <!-- JAL-2423 --></li>
+<li>Hiding sequences at bottom of alignment and then revealing them reorders sequences on the alignment <!-- JAL-2437 --></li>
+<li>Group panel in sequence feature settings doesn't update to reflect available set of groups after interactively adding or modifying features <!-- JAL-964 --></li>
+<li>Sequence Database chooser unusable on Linux <!-- JAL-2225 --></li>
+<li>Hide insertions in PopUp->Selection menu only excluded gaps in current sequence and ignored selection. <!-- JAL-2291 --></li>
+</ul>
+<p><em>Rendering</em></p>
+<ul>
+<li>Overview window visible region moves erratically when hidden rows or columns are present <!-- JAL-2421 --></li>
+<li>Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring <!-- JAL-2362 --></li>
+<li>Protein specific colours only offered in colour and group colour menu for protein alignments <!-- JAL-2405 --></li>
+<li>Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds <!-- JAL-2385 --></li>
+<li>Feature colour thresholds not respected when rendered on overview and structures when opacity at 100% <!-- JAL-2624 --></li>
+<li>User defined gap colour not shown in overview when features overlaid on alignment <!-- JAL-2589 --></li>
+<li>Feature settings for different views not recovered correctly from Jalview project file <!-- JAL-2567 --></li>
+<li>Feature colours in overview when first opened (automatically via preferences) are different to the main alignment panel <!-- JAL-2256 --></li>
+</ul>
+<p><em>Data import/export</em></p>
+<ul>
+<li>Very large alignments take a long time to load <!-- JAL-2576 --></li>
+<li>Per-sequence RNA secondary structures added after a sequence was imported are not written to Stockholm File <!-- JAL-2507 --></li>
+<li>WUSS notation for simple pseudoknots lost when importing RNA secondary structure via Stockholm <!-- JAL-2509 --></li>
+<li>Secondary structure arrows for [] and {} not shown in correct direction for simple pseudoknots <!-- JAL-2509 --></li>
+<li>Cannot configure feature colours with lightGray or darkGray via features file (but can specify lightgray) <!-- JAL-2365,JAL-2642 --></li>
+<li>Above PID colour threshold not recovered when alignment view imported from project <!-- JAL-2383 --></li>
+<li>No mappings generated between structure and sequences extracted from structure files imported via URL and viewed in Jmol <!-- JAL-2520,JAL-2465 --></li>
+<li>Structures loaded via URL are saved in Jalview Projects rather than fetched via URL again when the project is loaded and the structure viewed <!-- JAL-2520 --></li>
+</ul>
+<p><em>Web Services</em></p>
+<ul>
+<li>EnsemblGenomes example failing after release of Ensembl v.88 <!-- JAL-2519 --></li>
+<li>Proxy server address and port always appear enabled in Preferences->Connections <!-- JAL-2366 --></li>
+<li>DAS registry not found exceptions removed from console output <!-- JAL-2461 --></li>
+<li>Cannot retrieve protein products from Ensembl by Peptide ID <!-- JAL-2582 --></li>
+<li>Incorrect PDB-Uniprot mappings created from SIFTs, and spurious 'Couldn't open structure in Chimera' errors raised after April 2017 update (problem due to 'null' string rather than empty string used for residues with no corresponding PDB mapping). <!-- JAL-2482, JAL-2487 --></li>
+</ul>
+<p><em>Application UI</em></p>
+<ul>
+<li>User Defined Colours not added to Colour menu <!-- JAL-2361 --></li>
+<li>Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added) <!-- JAL-2401 --></li>
+<li>Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds <!-- JAL-2399--></li>
+<li>Feature settings panel does not update as new features are added to alignment <!-- JAL-2243 --></li>
+<li>Cancel in feature settings reverts changes to feature colours via the Amend features dialog <!-- JAL-2532 --></li>
+<li>Null pointer exception when attempting to edit graduated feature colour via amend features dialog box <!-- JAL-2506 --></li>
+<li>Structure viewer's View -> Colour By view selection menu changes colours of alignment views <!-- JAL-2436 --></li>
+<li>Spurious exceptions in console raised from alignment calculation workers after alignment has been closed <!-- JAL-2426 --></li>
+<li>Typo in selection popup menu - Create groups now 'Create Group' <!-- JAL-1608 --></li>
+<li>CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work <!-- JAL-1608 --></li>
+<li>Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel' <!-- JAL-2464 --></li>
+<li>Trackpad horizontal scroll gesture adjusts start position in wrap mode <!-- JAL-1256 --></li>
+<li>Status bar doesn't show positions for ambiguous amino acids <!-- JAL-2563 --></li>
+<li>cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins <!-- JAL-2431 --></li>
+<li>User defined colourschemes called 'User Defined' don't appear in Colours menu <!-- JAL-2592 --></li>
+</ul>
+<p><em>Applet</em></p>
+<ul>
+<li>Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot <!-- JAL-2468 --></li>
+<li>Features not rendered as transparent on overview or linked structure view <!-- JAL-2442 --></li>
+<li>Colour group by conservation doesn't work (since 2.8) <!-- JAL-2372 --></li>
+<li>Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme <!-- JAL-2517 --></li>
+</ul>
+<p><em>Test Suite</em></p>
+<ul>
+<li>Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails <!-- JAL-2314 --></li>
+<li>Unit test failure: jalview.ws.sifts.SiftsClientTest due to compatibility problems with deep array comparison equality asserts in successive versions of TestNG <!-- JAL-2307 --></li>
+<li>Relocated StructureChooserTest and ParameterUtilsTest Unit tests to Network suite <!-- JAL-2479 --></li>
+</ul>
+<p><em>New Known Issues</em></p>
+<ul>
+<li>Protein/CDS view scrolling not always in phase after a sequence motif find operation <!-- JAL-2566 --></li>
+<li>Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS RNA secondary structure symbols <!-- JAL-2550 --></li>
+<li>Cannot load and display Newick trees reliably from eggnog Ortholog database <!-- JAL-2590 --></li>
+<li>Status bar shows 'Marked x columns containing features of type Highlight' when 'B' is pressed to mark columns containing highlighted regions. <!-- JAL-2468 --></li>
+<li>Dropping a PDB file onto a sequence doesn't always add secondary structure annotation. <!-- JAL-2321 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.1">.1</a></strong>
<br />
<em>29 November 2016</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
-<li><!-- JAL-98 --> Improved memory usage: sparse arrays used for all consensus calculations</li>
-<li><!-- JAL-2177 --> Jmol updated to version 14.6.4 (released 3rd Oct 2016)</li>
+<li>Improved memory usage: sparse arrays used for all consensus calculations <!-- JAL-98 --></li>
+<li>Jmol updated to version 14.6.4 (released 3rd Oct 2016) <!-- JAL-2177 --></li>
<li>Updated Jalview's Certum code signing certificate for 2016-2017</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
-<li><!-- JAL-1723 --> Sequence ID tool tip presents abridged set of database cross-references, sorted alphabetically</li>
-<li><!-- JAL-2282--> New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a <a href="webServices/urllinks.html#warning">warning dialog</a> asking them to update their preferences.</li>
-<li><!-- JAL-2287--> Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session</li>
-<li><!-- JAL-2320--> Jalview's Chimera control window closes if the Chimera it is connected to is shut down</li>
-<li><!-- JAL-1738--> New keystroke (B) and Select highlighted columns menu item to mark columns containing highlighted regions (e.g. from structure selections or results of a Find operation)</li>
-<li><!-- JAL-2284--> Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer</li>
+<li>Sequence ID tool tip presents abridged set of database cross-references, sorted alphabetically <!-- JAL-1723 --></li>
+<li>New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a <a href="webServices/urllinks.html#warning">warning dialog</a> asking them to update their preferences. <!-- JAL-2282--></li>
+<li>Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session <!-- JAL-2287--></li>
+<li>Jalview's Chimera control window closes if the Chimera it is connected to is shut down <!-- JAL-2320--></li>
+<li>New keystroke (B) and Select highlighted columns menu item to mark columns containing highlighted regions (e.g. from structure selections or results of a Find operation) <!-- JAL-1738--></li>
+<li>Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer <!-- JAL-2284--></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
-<li><!-- JAL-2286 --> Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2)</li>
-<li><!-- JAL-2301 --> Threonine incorrectly reported as not hydrophobic</li>
-<li><!-- JAL-2318 --> Updates to documentation pages (above PID threshold, amino acid properties)</li>
-<li><!-- JAL-2292 --> Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report</li>
-<li><!--JAL-2324 --> Identical features with non-numeric scores could be added multiple times to a sequence</li>
-<li><!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 --> Disulphide bond features shown as two highlighted residues rather than a range in linked structure views, and treated correctly when selecting and computing trees from features</li>
-<li><!-- JAL-2281--> Custom URL links for database cross-references are matched to database name regardless of case</li>
+<li>Columns with more than one modal residue are not coloured or thresholded according to percent identity (first observed in Jalview 2.8.2) <!-- JAL-2286 --></li>
+<li>Threonine incorrectly reported as not hydrophobic <!-- JAL-2301 --></li>
+<li>Updates to documentation pages (above PID threshold, amino acid properties) <!-- JAL-2318 --></li>
+<li>Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report <!-- JAL-2292 --></li>
+<li>Identical features with non-numeric scores could be added multiple times to a sequence <!--JAL-2324 --></li>
+<li>Disulphide bond features shown as two highlighted residues rather than a range in linked structure views, and treated correctly when selecting and computing trees from features <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 --></li>
+<li>Custom URL links for database cross-references are matched to database name regardless of case <!-- JAL-2281--></li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
-<li><!-- JAL-2282--> Custom URL links for specific database names without regular expressions also offer links from Sequence ID</li>
-<li><!-- JAL-2315--> Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration</li>
-<li><!-- JAL-2272--> CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan</li>
-<li><!-- JAL-2280 --> Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment</li>
-<li><!-- JAL-2312 --> Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file</li>
-<li><!-- JAL-2317--> Certain structures do not get mapped to the structure view when displayed with Chimera</li>
-<li><!-- JAL-2317--> No chains shown in the Chimera view panel's View->Show Chains submenu</li>
-<li><!--JAL-2277 --> Export as HTML with embedded SVG doesn't work for wrapped alignment views</li>
-<li><!--JAL-2197 --> Rename UI components for running JPred predictions from 'JNet' to 'JPred'</li>
-<li><!-- JAL-2337,JAL-2277 --> Export as PNG or SVG is corrupted when annotation panel vertical scroll is not at first annotation row</li>
-<li><!--JAL-2332 --> Attempting to view structure for Hen lysozyme results in a PDB Client error dialog box</li>
-<li><!-- JAL-2319 --> Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
+<li>Custom URL links for specific database names without regular expressions also offer links from Sequence ID <!-- JAL-2282--></li>
+<li>Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration <!-- JAL-2315--></li>
+<li>CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan <!-- JAL-2272--></li>
+<li>Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment <!-- JAL-2280 --></li>
+<li>Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file <!-- JAL-2312 --></li>
+<li>Certain structures do not get mapped to the structure view when displayed with Chimera <!-- JAL-2317--></li>
+<li>No chains shown in the Chimera view panel's View->Show Chains submenu <!-- JAL-2317--></li>
+<li>Export as HTML with embedded SVG doesn't work for wrapped alignment views <!--JAL-2277 --></li>
+<li>Rename UI components for running JPred predictions from 'JNet' to 'JPred' <!--JAL-2197 --></li>
+<li>Export as PNG or SVG is corrupted when annotation panel vertical scroll is not at first annotation row <!-- JAL-2337,JAL-2277 --></li>
+<li>Attempting to view structure for Hen lysozyme results in a PDB Client error dialog box <!--JAL-2332 --></li>
+<li>Structure View's mapping report switched ranges for PDB and sequence for SIFTS <!-- JAL-2319 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.0b1">.0b1</a></strong>
<br />
<em>25 October 2016</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>3D Structure chooser opens with 'Cached structures' view if structures already loaded</li>
<li>Progress bar reports models as they are loaded to structure views</li>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Colour by conservation always enabled and no tick shown in menu when BLOSUM or PID shading applied</li>
<li>FER1_ARATH and FER2_ARATH labels were switched in example sequences/projects/trees</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Jalview projects with views of local PDB structure files saved on Windows cannot be opened on OSX</li>
<li>Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment</li>
<li>Exceptions are not raised in console when a new view is created on the alignment</li>
<li>OSX right-click fixed for group selections: CMD-click to insert/remove gaps in groups and CTRL-click to open group pop-up menu</li>
</ul>
-<h3>Build and deployment</h3>
+<p><em>Build and deployment</em></p>
<ul>
<li>URL link checker now copes with multi-line anchor tags</li>
</ul>
-<h3>New Known Issues</h3>
+<p><em>New Known Issues</em></p>
<ul>
<li>Drag and drop from URL links in browsers do not work on Windows</li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.10<a id="Jalview.2.10.0">.0</a></strong>
<br />
<em>6 October 2016</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>General</h3>
-<ul>
-<li><!-- JAL-2124 --> Updated Spanish translations.</li>
-<li><!-- JAL-2164,JAL-1919,JAL-2148 --> Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
-<li><!-- JAL-192 ---> Alignment ruler shows positions relative to reference sequence</li>
-<li><!-- JAL-2202 --> Position/residue shown in status bar when mousing over sequence associated annotation</li>
-<li><!-- JAL-2171 --> Default RNA SS symbol to 'matching bracket' for manual entry</li>
-<li><!-- JAL-2214 --> RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
-<li><!-- JAL-2092 --> Feature settings popup menu options for showing or hiding columns containing a feature</li>
-<li><!-- JAL-1557 --> Edit selected group by double clicking on group and sequence associated annotation labels</li>
-<li><!-- JAL-2236 --> Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs</li>
-</ul>
-<h3>Application</h3>
-<ul>
-<li><!-- JAL-2050--> Automatically hide introns when opening a gene/transcript view</li>
-<li><!-- JAL-1563 --> Uniprot Sequence fetcher Free Text Search dialog</li>
-<li><!-- JAL-1957, JAL-1479 JAL-1491 --> UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database</li>
-<li><!-- JAL-2079 --> Updated download sites used for Rfam and Pfam sources to xfam.org</li>
-<li><!-- JAL-2084 --> Disabled Rfam(Full) in the sequence fetcher</li>
-<li><!-- JAL-2123 --> Show residue labels in Chimera when mousing over sequences in Jalview</li>
-<li><!-- JAL-2027--> Support for reverse-complement coding regions in ENA and EMBL</li>
-<li><!-- JAL-1855, JAL-2113, JAL-2114--> Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API</li>
-<li><!-- JAL-2027 --> Support for ENA CDS records with reverse complement operator</li>
-<li><!-- JAL-1812 --> Update to groovy-2.4.6-indy - for faster groovy script execution</li>
-<li><!-- JAL-1812 --> New 'execute Groovy script' option in an alignment window's Calculate menu</li>
-<li><!-- JAL-1812 --> Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
-<li><!-- JAL-2068 --> Support for creating new alignment calculation workers from groovy scripts</li>
-<li><!-- JAL-1369 ---> Store/restore reference sequence in Jalview projects</li>
-<li><!-- JAL-1803 --> Chain codes for a sequence's PDB associations are now saved/restored from project</li>
-<li><!-- JAL-1993 --> Database selection dialog always shown before sequence fetcher is opened</li>
-<li><!-- JAL-2183 --> Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
-<li><!-- JAL-1563 --> Free-text search client for UniProt using the UniProt REST API</li>
-<li><!-- JAL-2168 --> -nonews command line parameter to prevent the news reader opening</li>
-<li><!-- JAL-2028 --> Displayed columns for PDBe and Uniprot querying stored in preferences</li>
-<li><!-- JAL-2091 --> Pagination for displaying PDBe and Uniprot search results</li>
-<li><!-- JAL-1977--> Tooltips shown on database chooser</li>
-<li><!-- JAL-391 --> Reverse complement function in calculate menu for nucleotide sequences</li>
-<li><!-- JAL-2005, JAL-599 --> Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).</li>
-<li><!-- JAL-2152--> Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10</li>
-<li><!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 --> Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API</li>
-<li><!-- JAL-2049 --> Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)</li>
-<li><!-- JAL-2232 --> ENA CDS 'show cross references' for Uniprot sequences</li>
-<li><!-- JAL-2213,JAL-1856 --> Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.</li>
-<li><!-- JAL-2154 --> Revised Jalview Project format for efficient recovery of sequence coding and alignment annotation relationships.</li>
+<p><em>General</em></p>
+<ul>
+<li>Updated Spanish translations. <!-- JAL-2124 --></li>
+<li>Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing. <!-- JAL-2164,JAL-1919,JAL-2148 --></li>
+<li>Alignment ruler shows positions relative to reference sequence <!-- JAL-192 ---></li>
+<li>Position/residue shown in status bar when mousing over sequence associated annotation <!-- JAL-2202 --></li>
+<li>Default RNA SS symbol to 'matching bracket' for manual entry <!-- JAL-2171 --></li>
+<li>RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column <!-- JAL-2214 --></li>
+<li>Feature settings popup menu options for showing or hiding columns containing a feature <!-- JAL-2092 --></li>
+<li>Edit selected group by double clicking on group and sequence associated annotation labels <!-- JAL-1557 --></li>
+<li>Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs <!-- JAL-2236 --></li>
+</ul>
+<p><em>Application</em></p>
+<ul>
+<li>Automatically hide introns when opening a gene/transcript view <!-- JAL-2050--></li>
+<li>Uniprot Sequence fetcher Free Text Search dialog <!-- JAL-1563 --></li>
+<li>UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database <!-- JAL-1957, JAL-1479 JAL-1491 --></li>
+<li>Updated download sites used for Rfam and Pfam sources to xfam.org <!-- JAL-2079 --></li>
+<li>Disabled Rfam(Full) in the sequence fetcher <!-- JAL-2084 --></li>
+<li>Show residue labels in Chimera when mousing over sequences in Jalview <!-- JAL-2123 --></li>
+<li>Support for reverse-complement coding regions in ENA and EMBL <!-- JAL-2027--></li>
+<li>Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API <!-- JAL-1855, JAL-2113, JAL-2114--></li>
+<li>Support for ENA CDS records with reverse complement operator <!-- JAL-2027 --></li>
+<li>Update to groovy-2.4.6-indy - for faster groovy script execution <!-- JAL-1812 --></li>
+<li>New 'execute Groovy script' option in an alignment window's Calculate menu <!-- JAL-1812 --></li>
+<li>Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode <!-- JAL-1812 --></li>
+<li>Support for creating new alignment calculation workers from groovy scripts <!-- JAL-2068 --></li>
+<li>Store/restore reference sequence in Jalview projects <!-- JAL-1369 ---></li>
+<li>Chain codes for a sequence's PDB associations are now saved/restored from project <!-- JAL-1803 --></li>
+<li>Database selection dialog always shown before sequence fetcher is opened <!-- JAL-1993 --></li>
+<li>Double click on an entry in Jalview's database chooser opens a sequence fetcher <!-- JAL-2183 --></li>
+<li>Free-text search client for UniProt using the UniProt REST API <!-- JAL-1563 --></li>
+<li>-nonews command line parameter to prevent the news reader opening <!-- JAL-2168 --></li>
+<li>Displayed columns for PDBe and Uniprot querying stored in preferences <!-- JAL-2028 --></li>
+<li>Pagination for displaying PDBe and Uniprot search results <!-- JAL-2091 --></li>
+<li>Tooltips shown on database chooser <!-- JAL-1977--></li>
+<li>Reverse complement function in calculate menu for nucleotide sequences <!-- JAL-391 --></li>
+<li>Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets). <!-- JAL-2005, JAL-599 --></li>
+<li>Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10 <!-- JAL-2152--></li>
+<li>Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 --></li>
+<li>Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl) <!-- JAL-2049 --></li>
+<li>ENA CDS 'show cross references' for Uniprot sequences <!-- JAL-2232 --></li>
+<li>Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records. <!-- JAL-2213,JAL-1856 --></li>
+<li>Revised Jalview Project format for efficient recovery of sequence coding and alignment annotation relationships. <!-- JAL-2154 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>General</h3>
-<ul>
-<li><!-- JAL-2077 --> reinstate CTRL-click for opening pop-up menu on OSX</li>
-<li><!-- JAL-2018--> Export features in Jalview format (again) includes graduated colourschemes</li>
-<li><!-- JAL-2172,JAL-1722, JAL-2001--> More responsive when working with big alignments and lots of hidden columns</li>
-<li><!-- JAL-2053--> Hidden column markers not always rendered at right of alignment window</li>
-<li><!-- JAL-2067 --> Tidied up links in help file table of contents</li>
-<li><!-- JAL-2072 --> Feature based tree calculation not shown for DNA alignments</li>
-<li><!-- JAL-2075 --> Hidden columns ignored during feature based tree calculation</li>
-<li><!-- JAL-2065 --> Alignment view stops updating when show unconserved enabled for group on alignment</li>
-<li><!-- JAL-2086 --> Cannot insert gaps into sequence when set as reference</li>
-<li><!-- JAL-2146 --> Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation</li>
-<li><!-- JAL-2099 --> Incorrect column numbers in ruler when hidden columns present</li>
-<li><!-- JAL-1577 --> Colour by RNA Helices not enabled when user created annotation added to alignment</li>
-<li><!-- JAL-1841 --> RNA Structure consensus only computed for '()' base pair annotation</li>
-<li><!-- JAL-2215, JAL-1841 --> Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus</li>
-<li><!-- JAL-2174--> Extend selection with columns containing feature not working</li>
-<li><!-- JAL-2275 --> Pfam format writer puts extra space at beginning of sequence</li>
-<li><!-- JAL-1827 --> Incomplete sequence extracted from pdb entry 3a6s</li>
-<li><!-- JAL-2238 --> Cannot create groups on an alignment from from a tree when t-coffee scores are shown</li>
-<li><!-- JAL-1836,1967 --> Cannot import and view PDB structures with chains containing negative resnums (4q4h)</li>
-<li><!-- JAL-1998 --> ArithmeticExceptions raised when parsing some structures</li>
-<li><!-- JAL-1991, JAl-1952 --> 'Empty' alignment blocks added to Clustal, PIR and PileUp output</li>
-<li><!-- JAL-2008 --> Reordering sequence features that are not visible causes alignment window to repaint</li>
-<li><!-- JAL-2006 --> Threshold sliders don't work in graduated colour and colour by annotation row for e-value scores associated with features and annotation rows</li>
-<li><!-- JAL-1797 --> amino acid physicochemical conservation calculation should be case independent</li>
-<li><!-- JAL-2173 --> Remove annotation also updates hidden columns</li>
-<li><!-- JAL-2234 --> FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)</li>
-<li><!-- JAL-2065 --> Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled</li>
-<li><!-- JAL-1306 --> Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
-<li><!-- JAL-1932 --> Remove right on penultimate column of alignment does nothing</li>
-</ul>
-<h3>Application</h3>
-<ul>
-<li><!-- JAL-1552--> URLs and links can't be imported by drag'n'drop on OSX when launched via webstart (note - not yet fixed for El Capitan)</li>
-<li><!-- JAL-1911--> Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
-<li><!-- JAL-1944 --> Error thrown when exporting a view with hidden sequences as flat-file alignment</li>
-<li><!-- JAL-2030--> InstallAnywhere distribution fails when launching Chimera</li>
-<li><!-- JAL-2080--> Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
-<li><!-- JAL-2085 --> Cannot save project when view has a reference sequence defined</li>
-<li><!-- JAL-1011 --> Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
-<li><!-- JAL-1989 --> Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
-<li><!-- JAL-1369 --> Cannot save/restore representative sequence from project when only one sequence is represented</li>
-<li><!-- JAL-2002 --> Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
-<li><!-- JAL-2215 --> Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
-<li><!-- JAL-1962 --> View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>
-<li><!-- JAL-2102, JAL-2101, JAL-2102, --> PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type</li>
-<li><!-- JAL-1975 --> Export complete shown after destination file chooser is cancelled during an image export</li>
-<li><!-- JAL-2025 --> Error when querying PDB Service with sequence name containing special characters</li>
-<li><!-- JAL-2024 --> Manual PDB structure querying should be case insensitive</li>
-<li><!-- JAL-2104 --> Large tooltips with broken HTML formatting don't wrap</li>
-<li><!-- JAL-1128 --> Figures exported from wrapped view are truncated so L looks like I in consensus annotation</li>
-<li><!-- JAL-2003 --> Export features should only export the currently displayed features for the current selection or view</li>
-<li><!-- JAL-2036 --> Enable 'Get Cross-References' in menu after fetching cross-references, and restoring from project</li>
-<li><!-- JAL-2032 --> Mouseover of a copy of a sequence is not followed in the structure viewer</li>
-<li><!-- JAL-2163 --> Titles for individual alignments in splitframe not restored from project</li>
-<li><!-- JAL-2145 --> missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default</li>
-<li><!-- JAL-1797 --> amino acid physicochemical conservation is case dependent</li>
-<li><!-- JAL-1448 --> RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)</li>
-<li><!-- JAL-1960 --> Only offer PDB structures in structure viewer based on sequence name, PDB and UniProt cross-references</li>
-<li><!-- JAL-1976 --> No progress bar shown during export of alignment as HTML</li>
-<li><!-- JAL-2213 --> Structures not always superimposed after multiple structures are shown for one or more sequences.</li>
-<li><!-- JAL-1370 --> Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.</li>
-<li><!-- JAL-1823 --> Cannot specify chain code when entering specific PDB id for sequence</li>
-<li><!-- JAL-1944 --> File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.</li>
-<li><!--JAL-2026--> Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence</li>
-<li><!-- JAL-1887 --> Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report</li>
-<li><!-- JAL-2284 --> Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project.</li>
-<li><!-- JAL-2118 --> Newly created annotation row reorders after clicking on it to create new annotation for a column.</li>
-<li><!-- JAL-1980 --> Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window.</li>
-</ul>
-<h3>Applet</h3>
-<ul>
-<li><!-- JAL-2151 --> Incorrect columns are selected when hidden columns present before start of sequence</li>
-<li><!-- JAL-1986 --> Missing dependencies on applet pages (JSON jars)</li>
-<li><!-- JAL-1947 --> Overview pixel size changes when sequences are hidden in applet</li>
-<li><!-- JAL-1996 --> Updated instructions for applet deployment on examples pages.</li>
+<p><em>General</em></p>
+<ul>
+<li>reinstate CTRL-click for opening pop-up menu on OSX <!-- JAL-2077 --></li>
+<li>Export features in Jalview format (again) includes graduated colourschemes <!-- JAL-2018--></li>
+<li>More responsive when working with big alignments and lots of hidden columns <!-- JAL-2172,JAL-1722, JAL-2001--></li>
+<li>Hidden column markers not always rendered at right of alignment window <!-- JAL-2053--></li>
+<li>Tidied up links in help file table of contents <!-- JAL-2067 --></li>
+<li>Feature based tree calculation not shown for DNA alignments <!-- JAL-2072 --></li>
+<li>Hidden columns ignored during feature based tree calculation <!-- JAL-2075 --></li>
+<li>Alignment view stops updating when show unconserved enabled for group on alignment <!-- JAL-2065 --></li>
+<li>Cannot insert gaps into sequence when set as reference <!-- JAL-2086 --></li>
+<li>Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation <!-- JAL-2146 --></li>
+<li>Incorrect column numbers in ruler when hidden columns present <!-- JAL-2099 --></li>
+<li>Colour by RNA Helices not enabled when user created annotation added to alignment <!-- JAL-1577 --></li>
+<li>RNA Structure consensus only computed for '()' base pair annotation <!-- JAL-1841 --></li>
+<li>Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus <!-- JAL-2215, JAL-1841 --></li>
+<li>Extend selection with columns containing feature not working <!-- JAL-2174--></li>
+<li>Pfam format writer puts extra space at beginning of sequence <!-- JAL-2275 --></li>
+<li>Incomplete sequence extracted from pdb entry 3a6s <!-- JAL-1827 --></li>
+<li>Cannot create groups on an alignment from from a tree when t-coffee scores are shown <!-- JAL-2238 --></li>
+<li>Cannot import and view PDB structures with chains containing negative resnums (4q4h) <!-- JAL-1836,1967 --></li>
+<li>ArithmeticExceptions raised when parsing some structures <!-- JAL-1998 --></li>
+<li>'Empty' alignment blocks added to Clustal, PIR and PileUp output <!-- JAL-1991, JAl-1952 --></li>
+<li>Reordering sequence features that are not visible causes alignment window to repaint <!-- JAL-2008 --></li>
+<li>Threshold sliders don't work in graduated colour and colour by annotation row for e-value scores associated with features and annotation rows <!-- JAL-2006 --></li>
+<li>amino acid physicochemical conservation calculation should be case independent <!-- JAL-1797 --></li>
+<li>Remove annotation also updates hidden columns <!-- JAL-2173 --></li>
+<li>FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) <!-- JAL-2234 --></li>
+<li>Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled <!-- JAL-2065 --></li>
+<li>Quality and Conservation are now shown on load even when Consensus calculation is disabled <!-- JAL-1306 --></li>
+<li>Remove right on penultimate column of alignment does nothing <!-- JAL-1932 --></li>
+</ul>
+<p><em>Application</em></p>
+<ul>
+<li>URLs and links can't be imported by drag'n'drop on OSX when launched via webstart (note - not yet fixed for El Capitan) <!-- JAL-1552--></li>
+<li>Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms <!-- JAL-1911--></li>
+<li>Error thrown when exporting a view with hidden sequences as flat-file alignment <!-- JAL-1944 --></li>
+<li>InstallAnywhere distribution fails when launching Chimera <!-- JAL-2030--></li>
+<li>Jalview very slow to launch via webstart (also hotfix for 2.9.0b2) <!-- JAL-2080--></li>
+<li>Cannot save project when view has a reference sequence defined <!-- JAL-2085 --></li>
+<li>Columns are suddenly selected in other alignments and views when revealing hidden columns <!-- JAL-1011 --></li>
+<li>Hide columns not mirrored in complement view in a cDNA/Protein splitframe <!-- JAL-1989 --></li>
+<li>Cannot save/restore representative sequence from project when only one sequence is represented <!-- JAL-1369 --></li>
+<li>Disabled 'Best Uniprot Coverage' option in Structure Chooser <!-- JAL-2002 --></li>
+<li>Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel <!-- JAL-2215 --></li>
+<li>View mapping in structure view shows mappings between sequence and all chains in a PDB file <!-- JAL-1962 --></li>
+<li>PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type <!-- JAL-2102, JAL-2101, JAL-2102, --></li>
+<li>Export complete shown after destination file chooser is cancelled during an image export <!-- JAL-1975 --></li>
+<li>Error when querying PDB Service with sequence name containing special characters <!-- JAL-2025 --></li>
+<li>Manual PDB structure querying should be case insensitive <!-- JAL-2024 --></li>
+<li>Large tooltips with broken HTML formatting don't wrap <!-- JAL-2104 --></li>
+<li>Figures exported from wrapped view are truncated so L looks like I in consensus annotation <!-- JAL-1128 --></li>
+<li>Export features should only export the currently displayed features for the current selection or view <!-- JAL-2003 --></li>
+<li>Enable 'Get Cross-References' in menu after fetching cross-references, and restoring from project <!-- JAL-2036 --></li>
+<li>Mouseover of a copy of a sequence is not followed in the structure viewer <!-- JAL-2032 --></li>
+<li>Titles for individual alignments in splitframe not restored from project <!-- JAL-2163 --></li>
+<li>missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default <!-- JAL-2145 --></li>
+<li>amino acid physicochemical conservation is case dependent <!-- JAL-1797 --></li>
+<li>RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems) <!-- JAL-1448 --></li>
+<li>Only offer PDB structures in structure viewer based on sequence name, PDB and UniProt cross-references <!-- JAL-1960 --></li>
+<li>No progress bar shown during export of alignment as HTML <!-- JAL-1976 --></li>
+<li>Structures not always superimposed after multiple structures are shown for one or more sequences. <!-- JAL-2213 --></li>
+<li>Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled. <!-- JAL-1370 --></li>
+<li>Cannot specify chain code when entering specific PDB id for sequence <!-- JAL-1823 --></li>
+<li>File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled. <!-- JAL-1944 --></li>
+<li>Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence <!--JAL-2026--></li>
+<li>Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report <!-- JAL-1887 --></li>
+<li>Unable to read old Jalview projects that contain non-XML data added after Jalvew wrote project. <!-- JAL-2284 --></li>
+<li>Newly created annotation row reorders after clicking on it to create new annotation for a column. <!-- JAL-2118 --></li>
+<li>Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window. <!-- JAL-1980 --></li>
+</ul>
+<p><em>Applet</em></p>
+<ul>
+<li>Incorrect columns are selected when hidden columns present before start of sequence <!-- JAL-2151 --></li>
+<li>Missing dependencies on applet pages (JSON jars) <!-- JAL-1986 --></li>
+<li>Overview pixel size changes when sequences are hidden in applet <!-- JAL-1947 --></li>
+<li>Updated instructions for applet deployment on examples pages. <!-- JAL-1996 --></li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.9<a id="Jalview.2.9.0b2">.0b2</a></strong>
<br />
<em>16 October 2015</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Time stamps for signed Jalview application and applet jars</li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Duplicate group consensus and conservation rows shown when tree is partitioned</li>
<li>Erratic behaviour when tree partitions made with multiple cDNA/Protein split views</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.9<a id="Jalview.2.9.0b1">.0b1</a></strong>
<br />
<em>8 October 2015</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Updated Spanish translations of localized text for 2.9</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Signed OSX InstallAnywhere installer<br/></li>
<li>Support for per-sequence based annotations in BioJSON</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Split frame example added to applet examples page</li>
</ul>
-<h3>Build and Deployment</h3>
+<p><em>Build and Deployment</em></p>
<ul>
-<li><!-- JAL-1888 --> New ant target for running Jalview's test suite</li>
+<li>New ant target for running Jalview's test suite <!-- JAL-1888 --></li>
</ul>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Mapping of cDNA to protein in split frames incorrect when sequence start > 1</li>
<li>Broken images in filter column by annotation dialog documentation</li>
<li>Feature colours not parsed from features file</li>
<li>Exceptions and incomplete link URLs recovered when loading a features file containing HTML tags in feature description</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Annotations corrupted after BioJS export and reimport</li>
<li>Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'</li>
<li>Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view</li>
<li>Restoring of Clustal, RNA Helices and T-Coffee color schemes from BioJSON</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Reorder sequences mirrored in cDNA/Protein split frame</li>
<li>Applet with Jmol examples not loading correctly</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.9">.9</a></strong>
<br />
<em>10 September 2015</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Linked visualisation and analysis of DNA and Protein alignments:
<ul>
<li>Conserved physicochemical properties shown in amino acid conservation row</li>
<li>Alignments can be sorted by number of RNA helices</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>New cDNA/Protein analysis capabilities
<ul>
<li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
<li>change "View protein structure" menu option to "3D Structure ..."</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>New layout for applet example pages</li>
<li>New parameters to enable SplitFrame view (file2,enableSplitFrame, scaleProteinAsCdna)</li>
<li>New example demonstrating linked viewing of cDNA and Protein alignments</li>
</ul>
-<h3>Development and deployment</h3>
+<p><em>Development and deployment</em></p>
<ul>
<li>Java 1.7 minimum requirement for Jalview 2.9</li>
<li>Include installation type and git revision in build properties and console log output</li>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Escape should close any open find dialogs</li>
<li>Typo in select-by-features status report</li>
<li>Cannot show linked products for EMBL / ENA records</li>
<li>Jalview's tooltip wraps long texts containing no spaces</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Jmol to JalviewLite mouseover/link not working</li>
<li>JalviewLite can't import sequences with ID descriptions containing angle brackets</li>
</ul>
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Cannot export and reimport RNA secondary structure via jalview annotation file</li>
<li>Random helix colour palette for colour by annotation with RNA secondary structure</li>
<li>'Show unconserved' doesn't work for lower case sequences</li>
<li>Nucleotide ambiguity codes involving R not recognised</li>
</ul>
-<h3>Deployment and Documentation</h3>
+<p><em>Deployment and Documentation</em></p>
<ul>
<li>Applet example pages appear different to the rest of www.jalview.org</li>
</ul>
-<h3>Application Known issues</h3>
+<p><em>Application Known issues</em></p>
<ul>
<li>Incomplete sequence extracted from PDB entry 3a6s</li>
<li>Misleading message appears after trying to delete solid column.</li>
<li>Cannot disable consensus calculation independently of quality and conservation</li>
<li>Mouseover highlighting between cDNA and protein can become sluggish with more than one splitframe shown</li>
</ul>
-<h3>Applet Known Issues</h3>
+<p><em>Applet Known Issues</em></p>
<ul>
<li>Core PDB parsing code requires Jmol</li>
<li>Sequence canvas panel goes white when alignment window is being resized</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.8<a id="Jalview.2.8.2b1">.2b1</a></strong>
<br />
<em>15 December 2014</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.8<a id="Jalview.2.8.2">.2</a></strong>
<br />
<em>3 December 2014</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Updated Java code signing certificate donated by Certum.PL.</li>
<li>Features and annotation preserved when performing pairwise alignment</li>
<li>'colour by annotation' can colour by RNA and protein secondary structure</li>
<li>Warn user if 'Find' regular expression is invalid (<em>mentioned post-hoc with 2.9 release</em>)</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Extract and display secondary structure for sequences with 3D structures</li>
<li>Support for parsing RNAML</li>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Distinguish alignment and sequence associated RNA structure in structure->view->VARNA</li>
<li>Raise dialog box if user deletes all sequences in an alignment</li>
<li>Jalview cannot contact DAS Registy when running on Java 8</li>
<li><!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] --> 'Superpose with' submenu not shown when new view created</li>
</ul>
-<h3>Deployment and Documentation</h3>
+<p><em>Deployment and Documentation</em></p>
<ul>
<li>2G and 1G options in launchApp have no effect on memory allocation</li>
<li>launchApp service doesn't automatically open www.jalview.org/examples/exampleFile.jar if no file is given</li>
<li><!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] --> InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is available</li>
</ul>
-<h3>Application Known issues</h3>
+<p><em>Application Known issues</em></p>
<ul>
<li><!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] --> corrupted or unreadable alignment display when scrolling alignment to right</li>
<li><!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] --> retrieval fails but progress bar continues for DAS retrieval with large number of ID</li>
<li><!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] --> colour by RNA Helices not enabled when user created annotation added to alignment</li>
<li><!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] --> Jalview icon not shown on dock in Mountain Lion/Webstart</li>
</ul>
-<h3>Applet Known Issues</h3>
+<p><em>Applet Known Issues</em></p>
<ul>
<li><!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] --> JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies</li>
<li><!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] --> Jalview and Jmol example not compatible with IE9</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.8<a id="Jalview.2.8.1">.1</a></strong>
<br />
<em>4 June 2014</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Internationalisation of user interface (usually called i18n support) and translation for Spanish locale</li>
<li>Define/Undefine group on current selection with Ctrl-G/Shift Ctrl-G</li>
<li>Sensible precision for symbol distribution percentages shown in logo tooltip.</li>
<li>Annotation panel height set according to amount of annotation when alignment first opened</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service</li>
<li>Select columns containing particular features from Feature Settings dialog</li>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>logo keeps spinning and status remains at queued or running after job is cancelled</li>
<li>cannot export features from alignments imported from Jalview/VAMSAS projects</li>
<li>Disorder thresholds rendered incorrectly after performing IUPred disorder prediction</li>
<li>Multiple group annotated consensus rows shown when changing 'normalise logo' display setting</li>
<li>Find shows blank dialog after 'finished searching' if nothing matches query</li>
-<li><!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 --> Null Pointer Exceptions raised when sorting by feature with lots of groups</li>
-<li><!-- JAL-1476 Work in progress - don't send junk to Jmol --> Errors in Jmol console when structures in alignment don't overlap</li>
+<li>Null Pointer Exceptions raised when sorting by feature with lots of groups <!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 --></li>
+<li>Errors in Jmol console when structures in alignment don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol --></li>
<li>Not all working JABAWS services are shown in Jalview's menu</li>
<li>JAVAWS version of Jalview fails to launch with 'invalid literal/length code'</li>
<li>Annotation/RNA Helix colourschemes cannot be applied to alignment with groups (actually fixed in 2.8.0b1)</li>
<li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Remove group option is shown even when selection is not a group</li>
<li>Apply to all groups ticked but colourscheme changes don't affect groups</li>
<li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
<li>Increased font size for dropdown menus on OSX and embedded windows</li>
</ul>
-<h3>Other</h3>
+<p><em>Other</em></p>
<ul>
<li>Consensus sequence for alignments/groups with a single sequence were not calculated</li>
<li>annotation files that contain only groups imported as annotation and junk sequences</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.8<a id="Jalview.2.8.0b1">.0b1</a></strong>
<br />
<em>30 January 2014</em>
<li>Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works</li>
<li>Groovy scripting for headless Jalview operation</li>
</ul>
-<h3>Other improvements</h3>
+<p><em>Other improvements</em></p>
<ul>
<li>Upgrade desktop installer to InstallAnywhere 2013</li>
<li>COMBINE statement uses current SEQUENCE_REF and GROUP_REF scope to group annotation rows</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.8">.8</a></strong>
<br />
<em>12 November 2012</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega)</li>
<li>JABAWS server status indicator in Web Services preferences</li>
<li>DAS 1.6 and DAS 2.0 source support using new JDAS client library</li>
<li>Examples directory and Groovy library included in InstallAnywhere distribution</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>RNA alignment and secondary structure annotation visualization applet example</li>
</ul>
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Normalise option for consensus sequence logo</li>
<li>Reset button in PCA window to return dimensions to defaults</li>
<li>'colour by annotation' per sequence option to shade each sequence according to its associated alignment annotation</li>
<li>New Jalview Logo</li>
</ul>
-<h3>Documentation and Development</h3>
+<p><em>Documentation and Development</em></p>
<ul>
<li>documentation for score matrices used in Jalview</li>
<li>New Website!</li>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service</li>
<li>Stop windows being moved outside desktop on OSX</li>
<li>NPE with v2.7 example when clicking on Tree associated with all views</li>
<li>Exceptions when copy/paste sequences with grouped annotation rows to new window</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter</li>
<li>loading features via javascript API automatically enables feature display</li>
<li>scrollToColumnIn javascript API method doesn't work</li>
</ul>
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Redundancy removal fails for rna alignment</li>
<li>PCA calculation fails when sequence has been selected and then deselected</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.7">.7</a></strong>
<br />
<em>27 September 2011</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Jalview Desktop News Reader</li>
<li>Tweaked default layout of web services menu</li>
<li>Sort associated views menu option for tree panel</li>
<li>Group all JABA and non-JABA services for a particular analysis function in its own submenu</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Userdefined and autogenerated annotation rows for groups</li>
<li>Adjustment of alignment annotation pane height</li>
</ul>
</li>
</ul>
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>Enable Jmol displays to be associated with multiple multiple alignments</li>
<li>Option to automatically sort alignment with new tree</li>
<li>Configurable newline string when writing alignment and other flat files</li>
<li>Allow alignment annotation description lines to contain html tags</li>
</ul>
-<h3>Documentation and Development</h3>
+<p><em>Documentation and Development</em></p>
<ul>
<li>Add groovy test harness for bulk load testing to examples</li>
<li>Groovy script to load and align a set of sequences using a web service before displaying the result in the Jalview desktop</li>
</td>
<td class="issues_resolved" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>User defined colourscheme throws exception when current built in colourscheme is saved as new scheme</li>
<li>AlignFrame->Save in application pops up save dialog for valid filename/format</li>
<li>Structures imported from file and saved in project get name like jalview_pdb1234.txt when reloaded</li>
<li>Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Alignment height set incorrectly when lots of annotation rows are displayed</li>
<li>Relative URLs in feature HTML text not resolved to codebase</li>
<li>Hover tooltip and mouseover of position on structure not sent from Jmol in applet</li>
<li>Certain sequences of javascript method calls to applet API fatally hang browser</li>
</ul>
-<h3>General</h3>
+<p><em>General</em></p>
<ul>
<li>View follows structure mouseover scrolls beyond position with wrapped view and hidden regions</li>
<li>Find sequence position moves to wrong residue with/without hidden columns</li>
<li>Hiding (nearly) all sequences doesn't work properly</li>
<li>Sequences containing lowercase letters are not properly associated with their pdb files</li>
</ul>
-<h3>Documentation and Development</h3>
+<p><em>Documentation and Development</em></p>
<ul>
<li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright tool</li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.6<a id="Jalview.2.6.1">.1</a></strong>
<br />
<em>15 November 2010</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>New warning dialog when the Jalview Desktop cannot contact web services</li>
<li>JABA service parameters for a preset are shown in service job window</li>
<li>Consensus and conservation annotation rows occasionally become blank for all new windows</li>
<li>Exception raised when right clicking above sequences in wrapped view mode</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>multiple multiply aligned structure views cause cpu usage to hit 100% and computer to hang</li>
<li>Web Service parameter layout breaks for long user parameter names</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.6">.6</a></strong>
<br />
<em>26 September 2010</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
<li>Web Services preference tab</li>
<li>Superpose structures using associated sequence alignment</li>
<li>Export coordinates and projection as CSV from PCA viewer</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>enable javascript: execution by the applet via the link out mechanism</li>
</ul>
-<h3>Other</h3>
+<p><em>Other</em></p>
<ul>
<li>Updated the Jmol Jalview interface to work with Jmol series 12</li>
<li>The Jalview Desktop and JalviewLite applet now require Java 1.5</li>
<ul>
<li>clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>typo in AlignmentFrame->View->Hide->all but selected Regions menu item</li>
<li>sequence fetcher replaces ',' for ';' when the ',' is part of a valid accession ID</li>
<li>InstallAnywhere builds fail to launch on OS X java 10.5 update 4 (due to apple Java 1.6 update)</li>
<li>Installanywhere Jalview silently fails to launch</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Jalview.getFeatureGroups() raises an ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
</ul>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.5<a id="Jalview.2.5.1">.1</a></strong>
<br />
<em>14 June 2010</em>
<li>Stockholm format shown in list of readable formats, and parser copes better with alignments from RFAM.</li>
<li>CSV output of consensus only includes the percentage of all symbols if sequence logo display is enabled</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>annotation panel disappears when annotation is hidden/removed</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Alignment view not redrawn properly when new alignment opened where annotation panel is visible but no annotations are present on alignment</li>
<li>pasted region containing hidden columns is incorrectly displayed in new alignment window</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.5">.5</a></strong>
<br />
<em>30 April 2010</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>New Capabilities</h3>
+<p><em>New Capabilities</em></p>
<ul>
<li>URL links generated from description line for regular-expression based URL links (applet and application)</li>
<li>Non-positional feature URL links are shown in link menu</li>
<li>Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).</li>
<li>New hide/show options including Shift+Control+H to hide everything but the currently selected region.</li>
</ul>
-<h3>Application</h3>
+<p><em>Application</em></p>
<ul>
<li>Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources</li>
<li>Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.</li>
<li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.</li>
<li>Group-associated consensus, sequence logos and conservation plots</li>
<li>Symbol distributions for each column can be exported and visualized as sequence logos</li>
-<li><!-- todo for applet --> Optionally scale multi-character column labels to fit within each column of annotation row</li>
+<li>Optionally scale multi-character column labels to fit within each column of annotation row <!-- todo for applet --></li>
<li>Optional automatic sort of associated alignment view when a new tree is opened.</li>
<li>Jalview Java Console</li>
<li>Better placement of desktop window when moving between different screens.</li>
</ul>
</li>
</ul>
-<h3>Applet</h3>
+<p><em>Applet</em></p>
<ul>
<li>Middle button resizes annotation row height</li>
<li>New Parameters
</li>
<li>Non-positional features displayed in sequence ID tooltip</li>
</ul>
-<h3>Other</h3>
+<p><em>Other</em></p>
<ul>
<li>Features format: graduated colour definitions and specification of feature scores</li>
<li>Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES)</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.4<a id="Jalview.2.4.0">.0</a><a id="Jalview.2.4.0.b2">.b2</a></strong>
<br />
<em>28 October 2009</em>
<li>Find function matches case-insensitively for sequence ID string searches</li>
<li>Non-standard characters do not cause pairwise alignment to fail with exception</li>
</ul>
-<h3>Application Issues</h3>
+<p><em>Application Issues</em></p>
<ul>
<li>Sequences are now validated against EMBL database</li>
<li>Sequence fetcher fetches multiple records for all data sources</li>
</ul>
-<h3>InstallAnywhere Issues</h3>
+<p><em>InstallAnywhere Issues</em></p>
<ul>
<li>Dock icon works for Mac OS X java (Mac 1.6 update issue with installAnywhere mechanism)</li>
<li>Command line launching of JARs from InstallAnywhere version (java class versioning error fixed)</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.4">.4</a></strong>
<br />
<em>27 August 2008</em>
</td>
<td class="new_features" align="left" valign="top">
-<h3>User Interface</h3>
+<p><em>User Interface</em></p>
<ul>
<li>Linked highlighting of codon and amino acid from translation and protein products</li>
<li>Linked highlighting of structure associated with residue mapping to codon position</li>
<li>Column labels in alignment annotation can be centred.</li>
<li>Tooltip for sequence associated annotation give name of sequence</li>
</ul>
-<h3>Web Services and URL fetching</h3>
+<p><em>Web Services and URL fetching</em></p>
<ul>
<li>JPred3 web service</li>
<li>Prototype sequence search client (no public services available yet)</li>
<li>URL Links created for matching database cross references as well as sequence ID</li>
<li>URL Links can be created using regular-expressions</li>
</ul>
-<h3>Sequence Database Connectivity</h3>
+<p><em>Sequence Database Connectivity</em></p>
<ul>
<li>Retrieval of cross-referenced sequences from other databases</li>
<li>Generalised database reference retrieval and validation to all fetchable databases</li>
<li>Fetch sequences from DAS sources supporting the sequence command</li>
</ul>
-<h3>Import and Export</h3>
+<p><em>Import and Export</em></p>
<ul>
<li>export annotation rows as CSV for spreadsheet import</li>
<li>Jalview projects record alignment dataset associations, EMBL products, and cDNA sequence mappings</li>
<li>Sequence Group colour can be specified in Annotation File</li>
<li>Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme</li>
</ul>
-<h3>VAMSAS Client capabilities (Experimental)</h3>
+<p><em>VAMSAS Client capabilities (Experimental)</em></p>
<ul>
<li>treenode binding for VAMSAS tree exchange</li>
<li>local editing and update of sequences in VAMSAS alignments (experimental)</li>
<li>Create new or select existing session to join</li>
<li>load and save of vamsas documents</li>
</ul>
-<h3>Application command line</h3>
+<p><em>Application command line</em></p>
<ul>
<li>-tree parameter to open trees (introduced for passing from applet)</li>
<li>-fetchfrom command line argument to specify nicknames of DAS servers to query for alignment features</li>
<li>-dasserver command line argument to add new servers that are also automatically queried for features</li>
<li>-groovy command line argument executes a given groovy script after all input data has been loaded and parsed</li>
</ul>
-<h3>Applet-Application data exchange</h3>
+<p><em>Applet-Application data exchange</em></p>
<ul>
<li>Trees passed as applet parameters can be passed to application (when using "View in full application")</li>
</ul>
-<h3>Applet Parameters</h3>
+<p><em>Applet Parameters</em></p>
<ul>
<li>feature group display control parameter</li>
<li>debug parameter</li>
<li>showbutton parameter</li>
</ul>
-<h3>Applet API methods</h3>
+<p><em>Applet API methods</em></p>
<ul>
<li>newView public method</li>
<li>Window (current view) specific get/set public methods</li>
<li>Feature display control methods</li>
<li>get list of currently selected sequences</li>
</ul>
-<h3>New Jalview distribution features</h3>
+<p><em>New Jalview distribution features</em></p>
<ul>
<li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
<li>RELEASE file gives build properties for the latest Jalview release.</li>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.3">.3</a></strong>
<br />
<em>9 May 2007</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.2<a id="Jalview.2.2.1">.1</a></strong>
<br />
<em>12 February 2007</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.2">.2</a></strong>
<br />
<em>27 November 2006</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.1<a id="Jalview.2.1.1">.1</a></strong>
<br />
<em>12 September 2006</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.1">.1</a></strong>
<br />
<em>22 August 2006</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2.08<a id="Jalview.2.08.1">.1</a></strong>
<br />
<em>2 May 2006</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.08b">.08b</a></strong>
<br />
<em>18 April 2006</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.08">.08</a></strong>
<br />
<em>10 April 2006</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.07">.07</a></strong>
<br />
<em>12 December 2005</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.06">.06</a></strong>
<br />
<em>28 September 2005</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.05b">.05b</a></strong>
<br />
<em>15 September 2005</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.05">.05</a></strong>
<br />
<em>30 August 2005</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.04">.04</a></strong>
<br />
<em>24 August 2005</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.03">.03</a></strong>
<br />
<em>18 August 2005</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.02">.02</a></strong>
<br />
<em>18 July 2005</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.01">.01</a></strong>
<br />
<em>12 July 2005</em>
</td>
</tr>
- <td class="release" align="left" valign="top" nowrap>
+ <td class="release" align="center" valign="top" nowrap>
<strong>2<a id="Jalview.2.0">.0</a></strong>
<br />
<em>20 June 2005</em>
git://source.jalview.org / jalview.git / commitdiff