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Welcome to the Jalview project's issue tracker.
If you experience any problems, please contact James (Jim) Procter.

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  1. Bug JAL-4439
    Multiple pseudo windows
  2. Improvement JAL-4422
    improve space and time efficiency for comparison and redundancy calculations
  3. Bug JAL-4421
    Release installer DMG does not display the background image
  4. Bug JAL-4415
    Enabling just "Add Secondary Structure" Structure preference when importing structure via CLI results in temperature factor being shown in alignment
  5. Improvement JAL-4410
    Recognise and map multimeric models from swissmodel via 3d-beacons
  6. Improvement JAL-4402
    Friendlier names for automatically created groups
  7. Epic JAL-4399
    Consensus annotations and Tree visualisations for sequence annotation
  8. Improvement JAL-4395
    Allow local_eclipse.properties to be read by buildship
  9. Bug JAL-4374
    The jalview:// (or jalviewx://) scheme does not work when a port is specified
  10. Task JAL-4359
    patch JalviewJS to correctly handle relative and absolute paths from page rather than j2s directory
  11. Bug JAL-4329
    CMD+W closes the tree viewer rather than Jmol when viewing example 2.7 project
  12. Bug JAL-4327
    When the Groovy console is opened Jalview does not prompt to save before quitting
  13. Improvement JAL-4311
    properly handle 3d-beacons sources other than alphafold providing PLDDT confidence scores & shading from model quality score type response
  14. Bug JAL-4302
    tree vertical scale not correct when shown in tree viewer (but fine when exported)
  15. Bug JAL-4240
    sequence ID tooltip in JalviewJS has double line spacing
  16. Bug JAL-4239
    java.util.Random.NextLong not implemented
  17. Bug JAL-4238
    PAEs not being shown in JalviewJS
  18. Epic JAL-4147
    sub-labels for annotation rows
  19. New Feature JAL-4138
    user preferences and structure chooser controls for automatically showing PAE annotation row along side pLDDT when loading structure from alphafold, and control secondary structure and temp factor display
  20. New Feature JAL-4123
    Configure how temperature factor column should be interpreted when loading a 3D structure for a sequence
  21. Bug JAL-4059
    update swingJS for JalviewJS 2.11.2,2.11.3, and 2.11.4
  22. Bug JAL-4058
    Disable startup preferences and other irrelevant widgets for JalviewJS
  23. Improvement JAL-3914
    Import model reliability scores encoded as temperature factor annotation with their correct name and semantics
  24. New Feature JAL-3860
    propagate mouseover, region highlights and selection events on reference to transcripts and products
  25. Improvement JAL-3576
    IntervalStore should preserve order of addition of co-located features
  26. Improvement JAL-3329
    Automatically hide alignment calculation rows when only one sequence is present
  27. Improvement JAL-3209
    Make it easier to modify colour for a group or all groups via the Colours menu
  28. Task JAL-2880
    no binding between derived annotation rows and original structure data file parsed via Jmol
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