<em>General</em>
<ul>
<li><!-- JAL-98 -->Improved memory usage: sparse arrays used for all consensus calculations</li>
- <li><!-- JAL- --></li>
+ <li><!-- JAL-2177 -->Updated Jmol shipped with applet and desktop to 14.6.4</li>
+ <li><!-- --></li>
+
</ul>
<em>Application</em>
<ul>
<li><!-- JAL-2282-->New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a warning dialog 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-2281-->Custom URL links for database cross-references are matched to database name regardless of case</li>
- <li></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</li>
+ <li><!-- JAL-2284-->Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer</li>
</ul>
<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>
+
</ul>
<em>Application</em>
<ul>
- <li><!-- JAL-2282-->Custom URL links for specific database names without regular expressions also offer invalid links from Sequence ID</li>
+ <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-2335 -->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-2197 -->Rename UI components for running JPred predictions from 'JNet' to 'JPred'</li>
+
+ <li><!--JAL- --></li>
<li><!-- --></li>
<li><!-- --></li>