<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>
+ </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>
+
+ </ul>
+ <em>Application</em>
+ <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>
+ </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>
+ <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-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>
+
+ </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-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>
+ </ul>
+ <!--
+ <em>Applet</em>
+ <ul>
+ </ul> -->
+ <em>Build and deployment</em>
+ <ul>
+ <li>
+ <!-- JAL-2308, -->Failing/passing unit tests
+ </li>
+ </ul>
+ <em>New Known Issues</em>
+ <ul>
+ <li></li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <td width="60" nowrap>
+ <div align="center">
<strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
<em>25/10/2016</em></strong>
</div>
<em>General</em>
<ul>
<li>Colour by conservation always enabled and no tick
- shown in menu when BLOSUM or PID shading applied</li>
+ 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>
<em>Application</em>
<ul>
<!-- 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>
<em>Application</em>
<ul>
<!-- 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>
<!-- may exclude, this is an external service stability issue JAL-1941
-- > RNA 3D structure not added via DSSR service</li> -->
</ul>
</ul> <em>Applet</em>
<ul>
<li>Split frame example added to applet examples page</li>
+ </ul><em>Build and Deployment</em>
+ <ul>
+ <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
</ul></td>
<td>
<div align="left">
git://source.jalview.org / jalview.git / blobdiff