</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>
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
+ <em>25/09/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
+ "Encountered problems opening
+ https://www.jalview.org/examples/exampleFile_2_7.jvp"
+ </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.2.11.1.1">.1</a><br />
+ <em>17/09/2020</em></strong></td>
<td align="left" valign="top">
<ul>
<li>
- <!-- JAL-3187 -->Option to show 'virtual' codon features on
- protein (or vice versa)
+ <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
+ residue in cursor mode
+ </li>
+ <li>
+ <!-- JAL-3695 -->Support import of VCF 4.3 by updating
+ HTSJDK from 2.12 to 2.23
+ </li>
+ <li>
+ <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
+ optimisations and improvements suggested by Bob Hanson and
+ improved compatibility with JalviewJS
+ </li>
+ <li>
+ <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
+ alignments from Pfam and Rfam
+ </li>
+ <li>
+ <!-- JAL-2656 -->Recognise GZipped content for URLs and File
+ import (no longer based on .gz extension)
+ </li>
+ <li>
+ <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
+ </li>
+ <li>
+ <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
+ ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
+ EMBL flat file
+ </li>
+ <li>
+ <!-- JAL-3667 -->Improved warning messages, debug logging
+ and fixed Retry action when Jalview encounters errors when
+ saving or making backup files.
+ </li>
+ <li>
+ <!-- JAL-3676 -->Enhanced Jalview Java Console:
<ul>
- <li>
- <!-- JAL-3304 -->Option to export virtual features if
- shown
- </li>
- <li>
- <!-- JAL-3302 -->Option to transfer virtual features to
- Chimera
- </li>
+ <li>Jalview's logging level can be configured</li>
+ <li>Copy to Clipboard Buttion</li>
</ul>
</li>
<li>
- <!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
+ <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
+ when running on Linux (Requires Java 11+)
+ </li>
+ </ul> <em>Launching Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
+ through a system property
+ </li>
+ <li>
+ <!-- JAL-3477 -->Improved built-in documentation and command
+ line help for configuring Jalview's memory
+ </li>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3691 -->Conservation and Quality tracks are shown
+ but not calculated and no protein or DNA score models are
+ available for tree/PCA calculation when launched with
+ Turkish language locale
+ </li>
+ <li>
+ <!-- JAL-3493 -->Escape does not clear highlights on the
+ alignment (Since Jalview 2.10.3)
</li>
<li>
- <!-- JAL-3376 -->Capture VCF "fixed column" values POS,
- ID, QUAL, FILTER as Feature Attributes
+ <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
+ doesn't slide selected sequences, just sequence under cursor
</li>
<li>
- <!-- JAL-3375 -->More robust VCF numeric data field validation while parsing
+ <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
+ sequence under the cursor
</li>
<li>
- <!-- JAL-3533 -->Feature Settings dialog keeps same screen position if reopened
- </li>
+ <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
+ multiple EMBL gene products shown for a single contig
+ </li>
<li>
- <!-- JAL-3538 -->Font anti-aliasing in alignment views enabled by default
- </li>
+ <!-- JAL-3696 -->Errors encountered when processing variants
+ from VCF files yield "Error processing VCF: Format specifier
+ '%s'" on the console
+ </li>
<li>
- <!-- JAL-3468 -->Very long feature descriptions truncated in tooltips and menus
- </li>
+ <!-- JAL-3697 -->Count of features not shown can be wrong
+ when there are both local and complementary features mapped
+ to the position under the cursor
+ </li>
+ <li>
+ <!-- JAL-3673 -->Sequence ID for reference sequence is
+ clipped when Right align Sequence IDs enabled
+ </li>
+ <li>
+ <!-- JAL-2983 -->Slider with negative range values not
+ rendered correctly in VAqua4 (Since 2.10.4)
+ </li>
<li>
- <!-- JAL-3549 -->Warn if Sort by Score or Density attempted with no feature types visible
+ <!-- JAL-3685 -->Single quotes not displayed correctly in
+ internationalised text for some messages and log output
+ </li>
+ <li>
+ <!-- JAL-3490 -->Find doesn't report matches that span
+ hidden gapped columns
+ </li>
+ <li>
+ <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
+ panels, Alignment viewport and annotation renderer.
+ </li>
+ <li>
+ <!-- JAL-3561 -->Jalview ignores file format parameter
+ specifying output format when exporting an alignment via the
+ command line
+ </li>
+ <li>
+ <!-- JAL-3667 -->Windows 10: For a minority of users, if
+ backups are not enabled, Jalview sometimes fails to
+ overwrite an existing file and raises a warning dialog. (in
+ 2.11.0, and 2.11.1.0, the workaround is to try to save the
+ file again, and if that fails, delete the original file and
+ save in place.)
+ </li>
+ <li>
+ <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
+ via command line
+ </li>
+ <li>
+ <!-- JAL-3741 -->References to http://www.jalview.org in
+ program and documentation
+ </li>
+ </ul> <em>Launching Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3718 -->Jalview application fails when launched the
+ first time for a version that has different jars to the
+ previous launched version.
+ </li>
+ </ul> <em>Developing Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
+ data, causing cloverReport gradle task to fail with an
+ OutOfMemory error.
+ </li>
+ <li>
+ <!-- JAL-3280 -->Migrated the Jalview Version Checker to
+ monitor the release channel
+ </li>
+ </ul> <em>New Known defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3748 -->CDS shown in result of submitting proteins
+ in a CDS/Protein alignment to a web service is wrong when
+ proteins share a common transcript sequence (e.g.
+ genome of RNA viruses)
+ </li>
+ <li>
+ <!-- JAL-3576 -->Co-located features exported and re-imported
+ are ordered differently when shown on alignment and in
+ tooltips. (Also affects v2.11.1.0)
+ </li>
+ <li>
+ <!-- JAL-3702 -->Drag and drop of alignment file onto
+ alignment window when in a HiDPI scaled mode in Linux only
+ works for the top left quadrant of the alignment window
+ </li>
+ <li>
+ <!-- JAL-3701 -->Stale build data in jalview standalone jar
+ builds (only affects 2.11.1.1 branch)
+ </li>
+ <li>
+ <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
+ when alignment view restored from project (since Jalview 2.11.0)
+ </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>22/04/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- 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-3375 -->More robust VCF numeric data field
+ validation while parsing
+ </li>
+ <li>
+ <!-- JAL-3533 -->Feature Settings dialog keeps same screen
+ position if reopened
+ </li>
+ <li>
+ <!-- JAL-3535 -->Feature Settings dialog title includes name
+ of associated view
+ </li>
+ <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-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-3296 -->Sequence position numbers in status bar not correct after editing a sequence's start position
+ <!-- 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-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>
git://source.jalview.org / jalview.git / blobdiff