</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
+ <em>13/07/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <!-- -->
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li><!-- JAL-3493 -->Escape does not clear highlights on the alignment (Since Jalview 2.10.3)</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
- <em>27/03/2020</em></strong></td>
+ <em>22/04/2020</em></strong></td>
<td align="left" valign="top">
<ul>
<li>
- <!-- JAL-3187 -->Option to show 'virtual' codon features on
- protein (or vice versa)
- <ul>
- <li>
- <!-- JAL-3304 -->Option to export virtual features if
- shown
- </li>
- <li>
- <!-- JAL-3302 -->Option to transfer virtual features to
- Chimera
- </li>
- </ul>
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- 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>
+ <!-- JAL-3533 -->Feature Settings dialog keeps same screen
+ position if reopened
+ </li>
<li>
- <!-- JAL-3538 -->Font anti-aliasing in alignment views enabled by default
- </li>
+ <!-- JAL-3535 -->Feature Settings dialog title includes name
+ of associated view
+ </li>
<li>
- <!-- JAL-3468 -->Very long feature descriptions truncated in tooltips and menus
- </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-3549 -->Warn if Sort by Score or Density attempted with no feature types visible
+ <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
</li>
</ul><em>Jalview Installer</em>
<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>
</ul> <em>Build System</em>
<ul>
<li>
report
</li>
</ul>
- <ul>
- <em>Groovy Scripts</em>
- <ul>
- <li>
- <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA
- file to stdout containing the consensus sequence for each
- alignment in a Jalview session
- </li>
- </ul>
+ <em>Groovy Scripts</em>
+ <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>
</ul>
</td>
<td 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
<!-- 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>
</ul> <em>Java 11 Compatibility issues</em>
<ul>
<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>
</ul>
</td>
</tr>