<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
+ </li>
+ <li>
+ <!-- JAL-3376 -->Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
</li>
<li>
- <!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
+ <!-- JAL-3375 -->More robust VCF numeric data field
+ validation while parsing
</li>
<li>
- <!-- JAL-3376 -->Capture VCF "fixed column" values POS,
- ID, QUAL, FILTER as Feature Attributes
+ <!-- JAL-3533 -->Feature Settings dialog keeps same screen
+ position if reopened
</li>
<li>
- <!-- JAL-3375 -->More robust VCF numeric data field validation while parsing
+ <!-- JAL-3535 -->Feature Settings dialog title includes name
+ of associated view
</li>
<li>
- <!-- JAL-3533 -->Feature Settings dialog keeps same screen position if reopened
- </li>
+ <!-- JAL-3538 -->Font anti-aliasing in alignment views
+ enabled by default
+ </li>
<li>
- <!-- JAL-3538 -->Font anti-aliasing in alignment views enabled by default
- </li>
+ <!-- JAL-3468 -->Very long feature descriptions truncated in
+ tooltips and menus
+ </li>
<li>
- <!-- JAL-3468 -->Very long feature descriptions truncated in tooltips and menus
- </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-3412 -->ID margins for CDS and Protein views not equal when split frame is first opened
+ <!-- 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
</li>
<li>
- <!-- JAL-3296 -->Sequence position numbers in status bar not correct after editing a sequence's start position
+ <!-- JAL-3412 -->ID margins for CDS and Protein views not
+ equal when split frame is first opened
+ </li>
+ <li>
+ <!-- JAL-3296 -->Sequence position numbers in status bar not
+ correct after editing a sequence's start position
</li>
<li>
<!-- JAL-3377 -->Alignment is misaligned in wrapped mode
IllegalArgumentException in some circumstances
</li>
<li>
- <!-- JAL-3534 -->Multiple feature settings dialogs can be opened for a view
+ <!-- JAL-3534 -->Multiple feature settings dialogs can be
+ opened for a view
</li>
<li>
- <!-- JAL-2764 -->Feature Settings dialog is orphaned if alignment window is closed
+ <!-- JAL-2764 -->Feature Settings dialog is orphaned if
+ alignment window is closed
</li>
<li>
<!-- 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-2987 -->OSX - Can't view some search results in PDB/Uniprot search panel
+ <!-- JAL-2987 -->OSX - Can't view some search results in
+ PDB/Uniprot search panel
</li>
- </ul> <em>Installer</em>
+ </ul> <em>Installer</em>
<ul>
- <li><!-- JAL-3447 -->Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
+ <li>
+ <!-- JAL-3447 -->Jalview should not create file associations
+ for 3D structure files (.pdb, .mmcif. .cif)
</li>
</ul> <em>Repository and Source Release</em>
<ul>
<li>
- <!-- JAL-3474 -->removed obsolete .cvsignore files from repository
+ <!-- JAL-3474 -->removed obsolete .cvsignore files from
+ repository
</li>
<li>
- <!-- JAL-3541 -->Clover report generation running out of memory
+ <!-- JAL-3541 -->Clover report generation running out of
+ memory
</li>
- </ul>
- <em>New Known Issues</em>
+ </ul> <em>New Known Issues</em>
<ul>
<li>
<!-- JAL-3523 -->OSX - Current working directory not
enabled
</li>
<li>
- <!-- JAL-3542 -->Jalview Installation type always reports 'Source' in console output
+ <!-- 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>