Jalview 2.11.1.1

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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.

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+)
  • RESNUM sequence features (the green ones) are not automatically displayed when associated structures are displayed or for sequences retrieved from the PDB.

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.)
  • Dragging a PDB file onto an alignment with sequence features displayed causes displayed features to be hidden.
  • Cannot process alignments from HTTPS urls via command line
  • References to http://www.jalview.org in program and documentation

Launching Jalview

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

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)
  • Duplicate CDS sequences are generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs