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The release features minor updates to documentation, and addresses bugs affecting export of multiple images for structure views, trackpad scrolling, sequence ID margin width, and extraction of secondary structure for imported models. It also includes two new alignment editing operations - Left and Right justify, which can be applied to the whole alignment or current selection.

New Features

  • Left/Right justify the alignment or current selection (with Undo)
  • Minimum versions of Jalview’s build toolchain are explicitly specified in doc/building.md

development and deployment

  • timeout for test tasks to prevent hanging builds

Issues Resolved

  • Secondary structure not available after dragging a 3D structure onto a sequence to associate it when ‘Process secondary structure’ flag is true in preferences
  • Clustal colourscheme documentation not consistent with implementation
  • Handles to adjust ID panel width or annotation panel height can be dragged out of the Alignment window
  • Trackpad scrolling not proportional to gesture velocity
  • Cannot output individual images of more than one structure view attached to one open alignment
  • –jvmempc and –jvmemmax don’t work for jalview installed via conda or jar
  • User’s default colour scheme is erroneously applied to alignments in Jalview projects opened via command line when no –colour argument supplied
  • Headless alignment export with structure annotations doesn’t include secondary structure and temperature factor (Known defect since
  • Uniprot record retrieval not working in JalviewJS (affects all versions)
  • bio.tools record version number updated
  • Miscellaneous patches to fix hangs in 2.11.3 test suite
  • Jalview archive build getdown doesn’t include wrapper scripts

New Known Issues

  • Protein structure derived annotation tracks not available as reference annotation unless ‘add to alignment’ preference is enabled
  • Enabling just “Add Secondary Structure” Structure preference when importing structure via CLI results in temperature factor being shown in alignment