+
<html>
<!--
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
</p>
<table border="1">
<tr>
- <th nowrap><em>Release</em></th>
+ <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
<th><em>New Features</em></th>
<th><em>Issues Resolved</em></th>
</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
- name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
- <em>25/2/2020</em></strong></td>
+ id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
+ <em>24/02/2022</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL-3863 -->Support for Canonical Uniprot IDs
+ </li>
+ </ul> <em>JalviewJS</em>
+ <ul><li><!-- 3624 -->PDB structures mapped to Uniprot Sequences with SIFTS</li>
+ <li></li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Updated building instructions</li>
+ <li>First integrated JalviewJS and Jalview release</li>
+ </ul>
+
+ </td>
+ <td>
+ <ul>
+ <li>
+ <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3)
+ </li>
+ <li>
+ <!-- JAL-3761 -->Not all codon positions highlighted for
+ overlapping exon splice sites (e.g due to RNA slippage)
+ </li>
+ <li>
+ <!-- JAL-3915 -->Removed RNAview checkbox and logic from
+ Structure Preferences
+ </li>
+ <li><!-- JAL-3583 -->Tooltip behaviour improved (slightly)</li>
+ <li><!-- JAL-3162 -->Can edit a feature so that start > end</li>
+ <li><!-- JAL-2848 -->Cancel from Amend Features doesn't reset a modified graduated colour</li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Gradle<ul><li>Fixed non-fatal gradle errors during build</li>
+ <li><!-- JAL-3745 -->Updated build.gradle for use with Gradle v.6.6+</li></ul></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.2.11.1.7">.7</a><br />
+ <em>18/01/2022</em></strong></td>
+ <td></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
+ updated by Jalview or other applications (Windows, other non
+ Unix/BSD OSs)
+ </li>
+ </ul> <em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
+ certificates.
+ </li>
+ </ul>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
+ <em>6/01/2022</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
+ </li>
+ </ul></td>
+ <td>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
+ <em>20/12/2021</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
+ (was log4j 1.2.x).
+ </ul> <em>Development</em>
+ <ul>
+ <li>Updated building instructions</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>
+ <!-- JAL-3840 -->Occupancy calculation is incorrect for
+ alignment columns with over -1+2^32 gaps (breaking filtering
+ and display)
+ </li>
+ <li>
+ <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
+ scale factors being set with buggy window-managers (linux
+ only)
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Fixed non-fatal gradle errors during build</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.2.11.1.4">.4</a><br />
+ <em>09/03/2021</em></strong></td>
+ <td align="left" valign="top"><em>Improved control of
+ Jalview's use of network services via jalview_properties</em>
+ <ul>
+ <li>
+ <!-- JAL-3814 -->New .jalview_properties token controlling
+ launch of the news browser (like -nonews argument)
+ </li>
+ <li>
+ <!-- JAL-3813 -->New .jalview_properties token controlling
+ download of linkout URLs from
+ www.jalview.org/services/identifiers
+ </li>
+ <li>
+ <!-- JAL-3812 -->New .jalview_properties token controlling
+ download of BIOJSHTML templates
+ </li>
+ <li>
+ <!-- JAL-3811 -->New 'Discover Web Services' option to
+ trigger a one off JABAWS discovery if autodiscovery was
+ disabled
+ </li>
+ </ul></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3818 -->Intermittent deadlock opening structure in
+ Jmol
+ </li>
+ </ul> <em>New Known defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
+ always restored from project (since 2.10.3)
+ </li>
+ <li>
+ <!-- JAL-3806 -->Selections from tree built from CDS aren't
+ propagated to Protein alignment (since 2.11.1.3)
+ </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.2.11.1.3">.3</a><br />
+ <em>29/10/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3765 -->Find doesn't always highlight all matching
+ positions in a sequence (bug introduced in 2.11.1.2)
+ </li>
+ <li>
+ <!-- JAL-3760 -->Alignments containing one or more protein
+ sequences can be classed as nucleotide
+ </li>
+ <li>
+ <!-- JAL-3748 -->CDS alignment doesn't match original CDS
+ sequences after alignment of protein products (known defect
+ first reported for 2.11.1.0)
+ </li>
+ <li>
+ <!-- JAL-3725 -->No tooltip or popup menu for genomic
+ features outwith CDS shown overlaid on protein
+ </li>
+ <li>
+ <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
+ correctly mapped by Jalview (e.g. affects viral CDS with
+ ribosomal slippage, since 2.9.0)
+ </li>
+ <li>
+ <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
+ CDS features
+ </li>
+ <li>
+ <!-- JAL-3700 -->Selections in CDS sequence panel don't
+ always select corresponding protein sequences
+ </li>
+ <li>
+ <!-- JAL-3759 --> <em>Make groups from selection</em> for a
+ column selection doesn't always ignore hidden columns
+ </li>
+ </ul> <em>Installer</em>
+ <ul>
+ <li>
+ <!-- JAL-3611 -->Space character in Jalview install path on
+ Windows prevents install4j launching getdown
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3248 -->Fixed typos and specified compatible gradle
+ version numbers in doc/building.md
+ </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.2.11.1.2">.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-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>Jalview's logging level can be configured</li>
+ <li>Copy to Clipboard Buttion</li>
+ </ul>
+ </li>
+ <li>
+ <!-- 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-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
+ <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-3376 -->Record "fixed column" values POS,
- ID, QUAL, FILTER from VCF as Feature Attributes
+ <!-- JAL-3493 -->Escape does not clear highlights on the
+ alignment (Since Jalview 2.10.3)
+ </li>
+ <li>
+ <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
+ doesn't slide selected sequences, just sequence under cursor
+ </li>
+ <li>
+ <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
+ sequence under the cursor
+ </li>
+ <li>
+ <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
+ multiple EMBL gene products shown forĀ a single contig
+ </li>
+ <li>
+ <!-- JAL-3696 -->Errors encountered when processing variants
+ from VCF files yield "Error processing VCF: Format specifier
+ '%s'" on the console
+ </li>
+ <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-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>
+ <li>
+ <!-- JAL-3749 -->Duplicate CDS sequences are generated when
+ protein products for certain ENA records are repeatedly
+ shown via Calculate->Show Cross Refs
+ </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 (e.g. AF* attributes)
+ 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 -->
+ <!-- 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>
+ <ul>
<li>
<!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
in console (may be null when Jalview launched as executable jar or via conda)
</li>
<li>
<!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
- </li>
+ </li>
<li>
- <!-- JAL-3393 -->New installer/application launcher generated with install4j 8.0.4
+ <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
</li>
- <li><!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
- <li><!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
+ <li>
+ <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
+ <li>
+ <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
</ul> <em>Release processes</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>
<!-- JAL-3513 -->Test code included in Clover coverage
report
</li>
- </ul> <em>Deprecations</em>
+ </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-3412 -->ID margin for CDS and Protein views not equal when split frame is first opened
+ <!-- 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 via GUI
+ <!-- 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
feature settings dialog also selects columns
</li>
<li>
- <!-- JAL-3473 -->SpinnerNumberModel causing
+ <!-- JAL-3473 -->SpinnerNumberModel causes
IllegalArgumentException in some circumstances
</li>
<li>
+ <!-- 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
+ </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 results in PDB/Uniprot FTS
+ <!-- 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 does not automatically create file associations for 3D structure files (.pdb, .mmcif. .cif)</li>
+ <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 redundant .gitignore files from
+ <!-- JAL-3474 -->removed obsolete .cvsignore files from
repository
</li>
- </ul>
- <em>New Known Issues</em>
+ <li>
+ <!-- JAL-3541 -->Clover report generation running out of
+ memory
+ </li>
+ </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>