+ id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.1">.1</a><br />
+ <em>05/04/2022</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3973 -->Distribution Tarball includes git commit
+ and branch details
+ </li>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3975 -->Keyboard mode (F2) stops working after
+ using the "Create sequence feature" dialog
+ </li>
+ <li>
+ <!-- JAL-3976 -->3D Structure chooser fails to select
+ structures from 3D-beacons and pops up a 'null' dialog
+ </li>
+ <li>
+ <!-- JAL-3985 -->PDB FTS query results in error dialog
+ containing '414' [URL too long]
+ </li>
+ <li>
+ <!-- JAL-3980 JAL-3981 -->Sequence ID tooltip not shown during
+ long running retrieval/crossref operations (affects at least
+ 2.11.1 onwards)
+ </li>
+ <li>
+ <!-- JAL-3973 -->Cannot build Jalview 2.11.2.0 via gradle
+ from its source tarball
+ </li>
+ </ul> <em>New Known Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-3984 -->Keyboard mode (F2) stops working after
+ using the "Text Colour" dialog
+ </li>
+ <li>
+ <!-- JAL-3873 -->Colour by->all views doesn't allow
+ colouring same structure from different views (since
+ 2.11.2.0)
+ </li>
+ <li>
+ <!-- JAL-3981 --> Sequence Details report can take a long
+ time to be displayed for heavily annotated sequences (such
+ as single genome contigs for highly studied organisms)
+ </li>
+ <li>
+ <!-- JAL-3886 -->Pfam and Rfam alignment retrieval as
+ gzipped stockholm doesn't work on JalviewJS build of 2.11.2
+ </li>
+ <li>
+ <!-- JAL-3972 -->Java 11 Only: Jalview 2.11.2.0 OSX install
+ not working due to VAqua requiring
+ sun.awt.image.MultiResolutionImage
+ </li>
+ <li>
+ <!-- JAL-3981 -->Sequence Details can take a long time to be
+ displayed for heavily annotated sequences (all versions)
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
+ <em>10/03/2022</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
+ structures with ChimeraX and Pymol in addition to Jmol and
+ Chimera.
+ </li>
+ <li>
+ <!-- JAL-3829 -->Discover 3D structure data for sequences
+ with Uniprot references via 3D-Beacons
+ </li>
+ <li>
+ <!-- JAL-3391 -->Rank and select available structures for
+ Uniprot sequences according to number of residues in
+ structure mapped to positions involved in the alignment
+ </li>
+ <li>
+ <!-- JAL-2226 -->Structure annotation rows for all mapped
+ chains in 3D structures are included in the 'Reference
+ Annotation' for a sequence
+ </li>
+ <li>
+ <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
+ </li>
+ <li>
+ <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
+ molecules imported from ENA records are shown as RNA
+ <li>
+ <!-- JAL-3863 -->Support for Canonical Uniprot IDs
+ </li>
+ <li>
+ <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
+ memory settings at launch
+ </li>
+ <li>
+ <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
+ non-alphanumerics when discovering database references with
+ 'Fetch DB Refs'
+ </li>
+ <li>
+ <!-- JAL-3884 -->Suppressed harmless exceptions output to
+ Console whilst discovering database references for a
+ sequence
+ </li>
+ <li>
+ <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
+ schema
+ </li>
+ <li>
+ <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
+ disabled by default
+ </li>
+ <li>
+ <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
+ menu for selecting which database to fetch from in sequence
+ fetcher dialog.
+ </li>
+ <li>
+ <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
+ to 15.2 and revised model organism names (rat, xenopus,
+ dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
+ drosophila_melanogaster)
+ </li>
+ <li>
+ <!-- JAL-3530 -->-nowebservicediscovery command line
+ argument to prevent automatic discovery of analysis
+ webservices on launch
+ </li>
+ <li>
+ <!-- JAL-3618 -->Allow 'App' directories to be opened when
+ locating Chimera, ChimeraX or Pymol binaries via filechooser
+ opened by double clicking the Structure Preferences' path
+ textbox
+ </li>
+ <li>
+ <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
+ proxies that require authentication
+ </li>
+ <li>
+ <!-- JAL-3103 -->New mechanism for opening URLs with system
+ default browser (works on OSX and Linux as well as Windows)
+ </li>
+ <li>
+ <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
+ to 14.31.53
+ </li>
+ <li>
+ <!-- JAL-3837 -->GPL license info on splash screen and About
+ text
+ </li>
+ </ul> <em>Jalview Native App</em>
+ <ul>
+ <li>
+ <!-- JAL-3830 -->New command line launcher scripts (.sh,
+ .ps1, .bat) usable on macOS, Linux/Unix, Windows and
+ documentation in Help. Installer wizard has option to add
+ this to PATH, or link to it in your PATH.<br /> <em>This
+ is the recommended workaround for known issue about
+ working directory preservation when running native
+ application from command line. <!-- JAL-3523 -->
+ </em>
+ </li>
+ <li>Notarized MacOS installer for compliance with latest
+ OSX releases (Monterey)</li>
+ <li>
+ <!-- JAL-3805 -->Uninstaller application for old
+ (InstallAnywhere based) Jalview installations removed from
+ the OSX disk image
+ </li>
+ <li>
+ <!-- JAL-3608 -->Options to allow user to choose the (Swing)
+ Look and Feel (LaF) used by Jalview
+ </li>
+ <li>
+ <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
+ operation on Linux Ubuntu with HiDPI display in Java 11
+ (still known issues with HiDPI screens in java 8 and 11. see
+ <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
+ </li>
+ <li>
+ <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
+ configuration from jalview_properties
+ </li>
+ <li>
+ <!-- JAL- -->New Jalview Develop app - making it even easier
+ to get at Jalview's development builds
+ </li>
+ <li>
+ <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
+ and Jalview Develop applications.
+ </li>
+ <li>
+ <!-- JAL-3728 -->Jalview logos shown for Jalview Java
+ Console and other window widgets in taskbar and dock rather
+ than anonymous 'Java' icons
+ </li>
+ </ul> <em>JalviewJS</em>
+ <ul>
+ <li>
+ <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
+ with SIFTS
+ </li>
+ <li>
+ <!-- JAL-3208 -->setprop commandline argument reinstated for
+ JalviewJS only
+ </li>
+ <li>
+ <!-- JAL-3163 -->Missing message bundle keys are only
+ reported once per key (avoids excessive log output in js
+ console)
+ </li>
+ <li>
+ <!-- JAL-3168 -->Feature type is included in the title of
+ the Feature Settings' Colour Chooser dialog
+ </li>
+ <li>
+ <!-- JAL-3279 -->Build details reported in About window
+ </li>
+ <li>
+ <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
+ GUI additions and improvements in sync with Java
+ application.
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>
+ <!-- -->First integrated JalviewJS and Jalview release
+ </li>
+ <li>
+ <!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md
+ </li>
+ <li>
+ <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
+ process, added support for system package provided eclipse
+ installs on linux
+ </li>
+ <li>Install4j 9.0.x used for installer packaging</li>
+ <li>
+ <!-- JAL-3930 -->Improved use of installers for unattended
+ installation with a customizedId of "JALVIEW" in install4j's
+ Jalview Launcher
+ </li>
+ <li>
+ <!-- JAL-3907 -->Improved compatibility of Jalview build
+ with Java 17 (next LTS target)
+ </li>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3674 -->Slow structure commands can block Jalview
+ execution
+ </li>
+ <li>
+ <!-- JAL-3904 -->Structure window's viewer-specific menu
+ disappears when only one structure is shown (and many
+ sequences:one chain mappings are present)
+ </li>
+ <li>
+ <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
+ the first SEQUENCE_GROUP defined
+ </li>
+
+ <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-3794 -->X was not being recognised as the unknown
+ base in DNA sequences
+ </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>
+ <li>
+ <!-- JAL-3788 -->New View with automatic 'Show Overview'
+ preference enabled results in Null Pointer Exceptions when
+ clustal colouring is enabled
+ </li>
+ <li>
+ <!-- JAL-3275 -->Can open multiple Preferences panels
+ </li>
+ <li>
+ <!-- JAL-3633 -->Properly configure HTTPS proxy settings
+ from Preferences
+ </li>
+ <li>
+ <!-- JAL-3949 -->Standard out logging broken: messages only
+ routing to stderr and appear as a raw template
+ </li>
+ <li>
+ <!-- JAL-3739 -->Entering web service parameter values in
+ numerical field doesn't update the value of the parameter
+ until return is pressed.
+ </li>
+ <li>
+ <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
+ concerning duplicate CDS sequences generated when protein
+ products for certain ENA records are repeatedly shown via
+ Calculate->Show Cross Refs
+ </li>
+ </ul> <em>JalviewJS</em>
+ <ul>
+ <li>
+ <!-- JAL-3202 -->Consensus profile may include zero (rounded
+ down) percentage values causing a divide by zero
+ </li>
+ <li>
+ <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
+ via Info.args when there are arguments on the URL
+ </li>
+ <li>
+ <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
+ </li>
+ <li>
+ <!-- JAL-3603 -->Annotation file fails to load from URL in
+ JalviewJS
+ </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> <em>Known Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-3764 -->Display of RESNUM sequence features are not
+ suppressed when structures associated with a sequence are
+ viewed with an external viewer (Regression from 2.11.1
+ series)
+ </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