</div>
</td>
<td><div align="left">
- <em>General</em>
- <ul>
- <li><!-- JAL-98 -->Improved memory usage: sparse arrays used for all consensus calculations</li>
- <li><!-- JAL-2177 -->Updated Jmol shipped with applet and desktop to 14.6.4</li>
- <li><!-- --></li>
-
+ <em>General</em>
+ <ul>
+ <li>
+ <!-- JAL-98 -->Improved memory usage: sparse arrays used
+ for all consensus calculations
+ </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-1723 -->Sequence ID tool tips have been tamed (databases sorted alphabetically, abridged ID sets) </li>
- <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-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</li>
- <li><!-- JAL-2284-->Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer</li>
-
+ <li>
+ <!-- JAL-1723 -->Sequence ID tool tips have been tamed
+ (databases sorted alphabetically, abridged ID sets)
+ </li>
+ <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-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
+ </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>
<em>Build and deployment</em>
<ul>
- <li>Updated Jalview's Certum code signing certificate for 2016-2017</li>
+ <li>Updated Jalview's Certum code signing certificate
+ for 2016-2017</li>
</ul>
- </div>
- </td>
+ </div></td>
<td>
<div align="left">
<em>General</em>
<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-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>
+
</ul>
<em>Application</em>
<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-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-2337,JAL-2277 -->Export as PNG or SVG is corrupted when annotation panel vertical scroll is not at first annotation row</li>
- <li><!--JAL- --></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- -->
+ </li>
</ul>
<em>Applet</em>
<ul>
</ul>
<em>Build and deployment</em>
<ul>
- <li><!-- JAL-2308, -->Failing/passing unit tests</li>
+ <li>
+ <!-- JAL-2308, -->Failing/passing unit tests
+ </li>
</ul>
<em>New Known Issues</em>
<ul>
git://source.jalview.org / jalview.git / commitdiff