Jalview 2.11.1.0

Version Date: 
22-04-2020

Jalview 2.11.1.0 is the first minor release in the 2.11 series, and introduces a new 'point release' versioning model. The release includes a range of improvements including 'virtual features', which provide a more flexible way of mapping sequence features between protein products and their coding regions. This release also features an updated Jalview installer which adds improved memory management on OSX and Windows for large memory systems, and for linux users - a bundled Java installation and file associations for common filetypes handled by the Jalview application.

New Features

  • 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.
  • Feature attributes from VCF files can be exported and re-imported as GFF3 files
  • Capture VCF "fixed column" values POS, ID, QUAL, FILTER as Feature Attributes
  • More robust VCF numeric data field validation while parsing
  • Feature Settings dialog keeps same screen position if reopened
  • Feature Settings dialog title includes name of associated view
  • Font anti-aliasing in alignment views enabled by default
  • Very long feature descriptions truncated in tooltips and menus
  • Warn if Sort by Score or Density attempted with no feature types visible
  • Improved support for filtering feature attributes with large integer values

Jalview Installer

  • Versions for install4j and getdown and installer template version reported in console (may be null when Jalview launched as executable jar or via conda)
  • Layout improvements for OSX .dmg Finder and higher quality background images
  • New installer/application launcher generated with install4j 8.0.4
  • Jalview File Associations shown for Unix Platforms
  • Improved defaults for maximum memory setting when running on large memory machines

Release processes

  • New point release version scheme - 2.11.1.0
  • 'Jalview Test' installers/apps for easier access to test-release channel builds

Build System

  • Clover updated to 4.4.1
  • Test code included in Clover coverage report

Groovy Scripts

  • exportconsensus.groovy prints a FASTA file to stdout containing the consensus sequence for each alignment in a Jalview session

  • ComputePeptideVariants.groovy to translate genomic sequence_variant annotation from CDS as missense_variant or synonymous_variant on protein products.

Issues Resolved

  • Hidden sequence markers still visible when 'Show hidden markers' option is not ticked
  • Hidden sequence markers not shown in EPS and PNG output when 'Automatically set ID width' is set in jalview preferences or properties file
  • Feature Editor dialog can be opened when 'Show Sequence Features' option is not ticked
  • Undo 'Null' operation shown after sort by buttons in Feature Settings dialog are clicked when no features are visible
  • ID margins for CDS and Protein views not equal when split frame is first opened
  • Sequence position numbers in status bar not correct after editing a sequence's start position
  • Alignment is misaligned in wrapped mode with annotation and exceptions thrown when only a few columns shown in wrapped mode
  • Sequence IDs missing in headless export of wrapped alignment figure with annotations
  • Sorting Structure Chooser table by Sequence ID fails with ClassCastException
  • Chimera session not restored from Jalview Project
  • Double-click on 'Show feature' checkbox in feature settings dialog also selects columns
  • SpinnerNumberModel causes IllegalArgumentException in some circumstances
  • Multiple feature settings dialogs can be opened for a view
  • Feature Settings dialog is orphaned if alignment window is closed
  • Credits missing some authors in Jalview help documentation for 2.11.0 release
  • Export of Pfam alignment as Stockholm includes Pfam ID as sequence's accession rather than its Uniprot Accession

Java 11 Compatibility issues

  • OSX - Can't view some search results in PDB/Uniprot search panel

Installer

  • Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)

Repository and Source Release

  • removed obsolete .cvsignore files from repository
  • Clover report generation running out of memory

New Known Issues

  • OSX - Current working directory not preserved when Jalview.app launched with parameters from command line
  • Sequence IDs aligned to wrong margin and clipped in headless figure export when Right Align option enabled
  • Jalview Installation type always reports 'Source' in console output
  • Test Suite: Certain Functional tests fail on jalview's bamboo server but run fine locally.