--- /dev/null
+---
+channel: release
+version: 2.11.2.0
+date: 2022-03-10
+---
+
+## New Features
+
+- <!-- JAL-3616 JAL-3551 JAL-2322 --> Support for viewing 3D structures with ChimeraX and Pymol in addition to Jmol and Chimera.
+- <!-- JAL-3829 --> Discover 3D structure data for sequences with Uniprot references via 3D-Beacons
+- <!-- JAL-3391 --> Rank and select available structures for Uniprot sequences according to number of residues in structure mapped to positions involved in the alignment
+- <!-- JAL-2226 --> Structure annotation rows for all mapped chains in 3D structures are included in the 'Reference Annotation' for a sequence
+- <!-- JAL-1260 --> Import Genbank and EMBL format flatfiles
+- <!-- JAL-3821 --> ENA record's mol_type honoured so RNA molecules imported from ENA records are shown as RNA
+- <!-- JAL-3863 --> Support for Canonical Uniprot IDs
+- <!-- JAL-3503 --> New Preferences tab for adjusting Jalview's memory settings at launch
+- <!-- JAL-3881 --> Sequence IDs split on '_' as well as other non-alphanumerics when discovering database references with 'Fetch DB Refs'
+- <!-- JAL-3884 --> Suppressed harmless exceptions output to Console whilst discovering database references for a sequence
+- <!-- JAL-3204 --> Updated Jalview bindings for Uniprot XML schema
+- <!-- JAL-3926 --> Uniprot and PDBe autosearch option is disabled by default
+- <!-- JAL-3144 --> Reverted to Jalview 'classic' drop-down menu for selecting which database to fetch from in sequence fetcher dialog.
+- <!-- 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)
+- <!-- JAL-3530 --> -nowebservicediscovery command line argument to prevent automatic discovery of analysis webservices on launch
+- <!-- 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
+- <!-- JAL-3632 JAL-3633 --> support for HTTP/S access via proxies that require authentication
+- <!-- JAL-3103 --> New mechanism for opening URLs with system default browser (works on OSX and Linux as well as Windows)
+- <!-- JAL-3871 JAL-3874 --> Upgraded bundled version of Jmol to 14.31.53
+- <!-- JAL-3837 --> GPL license info on splash screen and About text
+
+
+### Jalview Native App
+- <!-- 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/>
+ *This is the recommended workaround for known issue about working directory preservation when running native application from command line.*
+- Notarized MacOS installer for compliance with latest OSX releases (Monterey)
+- <!-- JAL-3805 --> Uninstaller application for old (InstallAnywhere based) Jalview installations removed from the OSX disk image
+- <!-- JAL-3608 --> Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
+- <!-- 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 [JAL-3137](https://issues.jalview.org/browse/JAL-3137))
+- <!-- JAL-3633 --> Getdown launcher inherits HTTP/S proxy configuration from jalview_properties
+- <!-- JAL- --> New Jalview Develop app - making it even easier to get at Jalview's development builds
+- <!-- JAL-3594 --> New splashscreens for Jalview, Jalview Test and Jalview Develop applications.
+- <!-- JAL-3728 --> Jalview logos shown for Jalview Java Console and other window widgets in taskbar and dock rather than anonymous 'Java' icons
+
+
+### JalviewJS
+- <!-- JAL-3624 --> PDB structures mapped to Uniprot Sequences with SIFTS
+- <!-- JAL-3208 --> setprop commandline argument reinstated for JalviewJS only
+- <!-- JAL-3163 --> Missing message bundle keys are only reported once per key (avoids excessive log output in js console)
+- <!-- JAL-3168 --> Feature type is included in the title of the Feature Settings' Colour Chooser dialog
+- <!-- JAL-3279 --> Build details reported in About window
+- <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 --> Numerous minor GUI additions and improvements in sync with Java application.
+
+
+### Development
+- <!-- --> First integrated JalviewJS and Jalview release
+- <!-- JAL-3841,JAL-3248 --> Updated README and doc/building.md
+- <!-- JAL-3789, JAL-3679 --> Improved JalviewJS/Jalview build process, added support for system package provided eclipse installs on linux
+- Install4j 9.0.x used for installer packaging
+- <!-- JAL-3930 --> Improved use of installers for unattended installation with a customizedId of "JALVIEW" in install4j's Jalview Launcher
+- <!-- JAL-3907 --> Improved compatibility of Jalview build with Java 17 (next LTS target)
+
+
+## Issues Resolved
+
+- <!-- JAL-3674 --> Slow structure commands can block Jalview execution
+- <!-- JAL-3904 --> Structure window's viewer-specific menu disappears when only one structure is shown (and many sequences:one chain mappings are present)
+- <!-- JAL-3779 --> Annotation file: PROPERTIES apply only to the first SEQUENCE_GROUP defined
+- <!-- 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)
+- <!-- JAL-3761 --> Not all codon positions highlighted for overlapping exon splice sites (e.g due to RNA slippage)
+- <!-- JAL-3794 --> X was not being recognised as the unknown base in DNA sequences
+- <!-- JAL-3915 --> Removed RNAview checkbox and logic from Structure Preferences
+- <!-- JAL-3583 --> Tooltip behaviour improved (slightly)
+- <!-- JAL-3162 --> Can edit a feature so that start > end
+- <!-- JAL-2848 --> Cancel from Amend Features doesn't reset a modified graduated colour
+- <!-- JAL-3788 --> New View with automatic 'Show Overview' preference enabled results in Null Pointer Exceptions when clustal colouring is enabled
+- <!-- JAL-3275 --> Can open multiple Preferences panels
+- <!-- JAL-3633 --> Properly configure HTTPS proxy settings from Preferences
+- <!-- JAL-3949 --> Standard out logging broken: messages only routing to stderr and appear as a raw template
+- <!-- JAL-3739 --> Entering web service parameter values in numerical field doesn't update the value of the parameter until return is pressed.
+- <!-- 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
+
+
+### JalviewJS
+- <!-- JAL-3202 --> Consensus profile may include zero (rounded down) percentage values causing a divide by zero
+- <!-- JAL-3762 --> JalviewJS doesn't honour arguments passed via Info.args when there are arguments on the URL
+- <!-- JAL-3602 --> gradle closure-compiler not using UTF-8
+- <!-- JAL-3603 --> Annotation file fails to load from URL in JalviewJS
+
+
+### Development
+- Gradle
+ - Fixed non-fatal gradle errors during build
+ - <!-- JAL-3745 --> Updated build.gradle for use with Gradle v.6.6+
+
+
+### Known Issues
+- <!-- 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)
git://source.jalview.org / jalview.git / blobdiff