-->
<head>
<title>Release History</title>
+<style>
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+ /* remove bullets, narrower indent */
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+ padding-left: 10px;
+ padding-bottom: 4px;
+}
+
+li {
+ /* separate the items from eachother */
+ margin-left: -3px;
+ padding-bottom: 3px;
+ padding-left: 6px;
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+ /* doesnt get processed in javahelp */
+ content: '\00b7 ';
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</head>
<body>
<p>
<tr>
<td width="60" nowrap>
<div align="center">
+ <strong><a name="Jalview.2.10.2">2.10.2</a><br />
+ <em>30/5/2017</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em>General</em>
+ <ul>
+ <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
+ <li><!-- JAL-384 -->Custom BLOSUM/Clustal type shading schemes can be created via groovy scripts</li>
+
+ <li><!-- JAL-2314, -->Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li><!-- --></li>
+ <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>
+ <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
+
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li><!-- --></li>
+ </ul>
+ </div></td><td><div align="left">
+ <em>General</em>
+ <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-2430 -->Hidden regions in alignment views are not coloured in linked structure views</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-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
+ <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
+ <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-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <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-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
+ <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</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-2461 -->DAS registry not found exceptions removed from console output</li>
+
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <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>
+ </ul>
+ <em>New Known Issues</em>
+ <ul>
+ <li></li>
+ </ul>
+
+ </div>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
<strong><a name="Jalview.2.10.1">2.10.1</a><br />
- <em>24/11/2016</em></strong>
+ <em>29/11/2016</em></strong>
</div>
</td>
<td><div align="left">
for all consensus calculations
</li>
<li>
- <!-- JAL-2177 -->Updated Jmol shipped with applet and
- desktop to 14.6.4
+ <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
</li>
- <li>
- <!-- -->
- </li>
-
+ <li>Updated Jalview's Certum code signing certificate
+ for 2016-2017</li>
</ul>
<em>Application</em>
<ul>
<li>
- <!-- JAL-1723 -->Sequence ID tool tips have been tamed
- (databases sorted alphabetically, abridged ID sets)
+ <!-- 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>
Chimera session
</li>
<li>
- <!-- JAL-2320-->Jalview's chimera control window closes if
+ <!-- JAL-2320-->Jalview's Chimera control window closes if
the Chimera it is connected to is shut down
</li>
<li>
- <!-- JAL-2281-->Custom URL links for database
- cross-references are matched to database name regardless
- of case
- </li>
- <li>
- <!-- JAL-1738-->Select highlighted columns menu item and
- keystroke (B) to mark columns containing highlighted
- regions from structure selections or results of a Find
- operation
+ <!-- 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>
-
-
- </ul>
- <em>Applet</em>
- <ul>
- </ul>
- <em>Build and deployment</em>
- <ul>
- <li>Updated Jalview's Certum code signing certificate
- for 2016-2017</li>
</ul>
</div></td>
<td>
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>
</ul>
<em>Application</em>
<!--JAL-2332 -->Attempting to view structure for Hen
lysozyme results in a PDB Client error dialog box
</li>
- </ul>
- <em>Applet</em>
- <ul>
- </ul>
- <em>Build and deployment</em>
- <ul>
<li>
- <!-- JAL-2308, -->Failing/passing unit tests
- </li>
+ <!-- JAL-2319 -->Structure View's mapping report switched ranges for PDB and sequence for SIFTS</li>
+ <!-- JAL-2319 -->SIFTS 'Not_Observed' residues mapped to non-existant coordindate data</li>
</ul>
- <em>New Known Issues</em>
+<!-- <em>New Known Issues</em>
<ul>
<li></li>
- </ul>
+ </ul> -->
</div>
</td>
</tr>