Jalview 2.11.1.1

Version Date: 
17-09-2020

Jalview 2.11.1.1 is the first patch release in the 2.11.1 series. It includes fixes for critical bugs, and brings some new features suggested by the Jalview community. 

Critical Known Issues

  • We've had reports from a small number of windows 10 users who see a warning dialog pop up when Jalview tries to save a new version of an existing file. If you are affected by this bug and this latest version of Jalview doesn't fix it, please let us know!
  • 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
  • Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0)
  • Linked CDS/Protein alignment of genes sharing the same ENA accession doesn't work as expected.

New Features

  • Shift+arrow keys navigate to next gap or residue in cursor mode
  • Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23
  • IntervalStore library updated to v.1.1: optimisations and improvements suggested by Bob Hanson and improved compatibility with JalviewJS
  • Retrieve GZipped stockholm formatted alignments from Pfam and Rfam
  • Recognise GZipped content for URLs and File import (no longer based on .gz extension)
  • Updated Spanish Translation for 2.11.1
  • Migrate EMBL record retrieval to use latest ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and EMBL flat file
  • Improved warning messages, debug logging and fixed Retry action when Jalview encounters errors when saving or making backup files.
  • Enhanced Jalview Java Console:
    • Jalview's logging level can be configured
    • Copy to Clipboard Buttion
  • Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+)

Launching Jalview

  • Configure Jalview Desktop's look and feel through a system property
  • Improved built-in documentation and command line help for configuring Jalview's memory

Issues Resolved

  • 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
  • Escape does not clear highlights on the alignment (Since Jalview 2.10.3)
  • Alt+Left or Right arrow in cursor mode doesn't slide selected sequences, just sequence under cursor
  • Alt+Up/Down in cursor mode doesn't move sequence under the cursor
  • Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig
  • Errors encountered when processing variants from VCF files yield "Error processing VCF: Format specifier '%s'" on the console
  • Count of features not shown can be wrong when there are both local and complementary features mapped to the position under the cursor
  • Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled
  • Slider with negative range values not rendered correctly in VAqua4 (Since 2.10.4)
  • Single quotes not displayed correctly in internationalised text for some messages and log output
  • Find doesn't report matches that span hidden gapped columns
  • Resolved memory leaks in Tree and PCA panels, Alignment viewport and annotation renderer.
  • Jalview ignores file format parameter specifying output format when exporting an alignment via the command line
  • 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.)
  • Cannot process alignments from HTTPS urls via command line
  • References to https://www.jalview.org in program and documentation

Issues Resolved with Launching Jalview

  • Jalview application fails when launched the first time for a version that has different jars to the previous launched version.

Issues Resolved with Developing Jalview

  • Fixed issue with cleaning up old coverage data, causing cloverReport gradle task to fail with an OutOfMemory error.
  • Migrated the Jalview Version Checker to monitor the release channel

New Known defects

  • 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)
  • Co-located features exported and re-imported are ordered differently when shown on alignment and in tooltips. (Also affects v2.11.1.0)
  • 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
  • Stale build data in jalview standalone jar builds (only affects 2.11.1.1 branch)
  • Sequence ID colourscheme not re-applied when alignment view restored from project (since Jalview 2.11.0)