Jalview 2.11.2.0

Version Date: 
10-03-2022

Jalview 2.11.2.0 is a minor version release, with a considerable number of improvements and new features for working with 3D structure data.

This version introduces new support for two popular 3D structure visualisation tools - ChimeraX and Pymol, an integrated client for EMBL-EBI's 3D-Beacons Network for discovery of protein 3D structures, a new Jalview Desktop installation package that provides improved platform integration and a new command line tool allowing Jalview to be more easily called from scripts.

New Features

  • Support for viewing 3D structures with ChimeraX and Pymol in addition to Jmol and Chimera.
  • Discover 3D structure data for sequences with Uniprot references via 3D-Beacons
  • Rank and select available structures for Uniprot sequences according to number of residues in structure mapped to positions involved in the alignment
  • Structure annotation rows for all mapped chains in 3D structures are included in the 'Reference Annotation' for a sequence
  • Import Genbank and EMBL format flatfiles
  • ENA record's mol_type honoured so RNA molecules imported from ENA records are shown as RNA
  • Support for Canonical Uniprot IDs
  • New Preferences tab for adjusting Jalview's memory settings at launch
  • Sequence IDs split on '_' as well as other non-alphanumerics when discovering database references with 'Fetch DB Refs'
  • Suppressed harmless exceptions output to Console whilst discovering database references for a sequence
  • Updated Jalview bindings for Uniprot XML schema
  • Uniprot and PDBe autosearch option is disabled by default
  • Reverted to Jalview 'classic' drop-down menu for selecting which database to fetch from in sequence fetcher dialog.
  • Updated Ensembl REST Client compatibility to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster)
  • -nowebservicediscovery command line argument to prevent automatic discovery of analysis webservices on launch
  • Allow 'App' directories to be opened when locating Chimera, ChimeraX or Pymol binaries via filechooser opened by double clicking the Structure Preferences' path textbox
  • support for HTTP/S access via proxies that require authentication
  • New mechanism for opening URLs with system default browser (works on OSX and Linux as well as Windows)
  • Upgraded bundled version of Jmol to 14.31.53
  • GPL license info on splash screen and About text

Jalview Native App

  • 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.
    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)
  • Uninstaller application for old (InstallAnywhere based) Jalview installations removed from the OSX disk image
  • Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
  • 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)
  • Getdown launcher inherits HTTP/S proxy configuration from jalview_properties
  • New Jalview Develop app - making it even easier to get at Jalview's development builds
  • New splashscreens for Jalview, Jalview Test and Jalview Develop applications.
  • Jalview logos shown for Jalview Java Console and other window widgets in taskbar and dock rather than anonymous 'Java' icons

JalviewJS

  • PDB structures mapped to Uniprot Sequences with SIFTS
  • setprop commandline argument reinstated for JalviewJS only
  • Missing message bundle keys are only reported once per key (avoids excessive log output in js console)
  • Feature type is included in the title of the Feature Settings' Colour Chooser dialog
  • Build details reported in About window
  • Numerous minor GUI additions and improvements in sync with Java application.

Development

  • First integrated JalviewJS and Jalview release
  • Updated README and doc/building.md
  • Improved JalviewJS/Jalview build process, added support for system package provided eclipse installs on linux
  • Install4j 9.0.x used for installer packaging
  • Improved use of installers for unattended installation with a customizedId of "JALVIEW" in install4j's Jalview Launcher
  • Improved compatibility of Jalview build with Java 17 (next LTS target)

Issues Resolved

  • Slow structure commands can block Jalview execution
  • Structure window's viewer-specific menu disappears when only one structure is shown (and many sequences:one chain mappings are present)
  • Annotation file: PROPERTIES apply only to the first SEQUENCE_GROUP defined
  • Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3)
  • Not all codon positions highlighted for overlapping exon splice sites (e.g due to RNA slippage)
  • X was not being recognised as the unknown base in DNA sequences
  • Removed RNAview checkbox and logic from Structure Preferences
  • Tooltip behaviour improved (slightly)
  • Can edit a feature so that start > end
  • Cancel from Amend Features doesn't reset a modified graduated colour
  • New View with automatic 'Show Overview' preference enabled results in Null Pointer Exceptions when clustal colouring is enabled
  • Can open multiple Preferences panels
  • Properly configure HTTPS proxy settings from Preferences
  • Standard out logging broken: messages only routing to stderr and appear as a raw template
  • Entering web service parameter values in numerical field doesn't update the value of the parameter until return is pressed.
  • 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

  • Consensus profile may include zero (rounded down) percentage values causing a divide by zero
  • JalviewJS doesn't honour arguments passed via Info.args when there are arguments on the URL
  • gradle closure-compiler not using UTF-8
  • Annotation file fails to load from URL in JalviewJS

Development

  • Gradle
    • Fixed non-fatal gradle errors during build
    • Updated build.gradle for use with Gradle v.6.6+

Known Issues

  • 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)