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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. Improvement JAL-4526
    Update jalview webservices documentation page
  2. Bug JAL-4524
    Input sequences returned as alignment result if job fails on server
  3. Bug JAL-4519
    Jalview reports that input data didn't have enough sequences if slivka rejects an MSA job
  4. Bug JAL-4503
    Location of structure viewer not faithfully saved and restored in project
  5. Epic JAL-4488
    routine service and program integration tests
  6. Improvement JAL-4484
    Temporarily configure 3d structure viewer via CLI for a jalview session
  7. Improvement JAL-4466
    allow pairwise alignment gap parameters to be adjusted
  8. Improvement JAL-4459
    Progress bars for PCA, trees and pairwise alignments, and cancel buttons.
  9. Improvement JAL-4452
    highlight positions in structures associated with many aligned transcripts
  10. Improvement JAL-4443
    Add support for PaSiMap analysis in JalviewJS
  11. Improvement JAL-4438
    refactor ResidueShaderI to support new types of data-dependent shading
  12. Epic JAL-4399
    Consensus annotations and Tree visualisations for sequence annotation
  13. Task JAL-4361
    Convert loadFileWaitTillLoaded to a promise
  14. Task JAL-4357
    update getdown/jre updater for apple silicon
  15. Improvement JAL-4352
    Reduce load on structure viewer when moving mouse over ruler
  16. Bug JAL-4346
    Sonoma 14.1.1 permissions issue
  17. Improvement JAL-4339
    Some files in a linux desktop installation are not deleted when uninstalling
  18. Bug JAL-4329
    CMD+W closes the tree viewer rather than Jmol when viewing example 2.7 project
  19. New Feature JAL-4326
    gui controls for configuring bitmap export preferences
  20. Improvement JAL-4324
    Option to align after retrieval of sequences before display
  21. Bug JAL-4323
    scripts adding new fileformats or colourschemes do not work when run via command line
  22. Improvement JAL-4322
    Optimise Console <> GUI threads to ensure minimal work on GUI thread and minimal blocking of operations on gui thread producing output
  23. Improvement JAL-4309
    Redesign sequence ID tooltip to improve user experience
  24. Improvement JAL-4305
    unify behaviour of groovy scripts when called via CLI, run from Groovy console and calculate 'run script' menu
  25. New Feature JAL-4300
    New alignment windows from aligment webservices inherit feature settings and layout from input
  26. Bug JAL-4291
    Fix failing AlignPanelTest.testCalculateIdWidth_withMaxWidth()
  27. Improvement JAL-4287
    Automatically discover and import alphaFold or best PDBe model when retrieving proteins from Uniprot
  28. Improvement JAL-4286
    Allow command line / programmatic export of images from external structure viewers
  29. Improvement JAL-4283
    Focus on specific regions of RNA structure when viewing in VARNA
  30. New Feature JAL-4267
    Allow injection of custom structure viewer script when viewing 3D data from Jalview
  31. Improvement JAL-4264
    Allow specific format to be specified when importing a file via GUI and CLI
  32. Task JAL-4263
    Test and squash memory leaks when working with lots of files via Jalview's NG-CLI
  33. Task JAL-4249
    New documentation: extending.md linked from building.md
  34. Improvement JAL-4245
    Return null from getRootDatasetSequence if there is no dataset sequence
  35. New Feature JAL-4244
    Support import of foldseek's m8 alignment files
  36. Bug JAL-4241
    Annotation analysis results not aligned to selection.
  37. Bug JAL-4232
    RNA specific services are enabled for protein sequences.
  38. Improvement JAL-4231
    make it easier to pick preferred experimental modalities for structure data
  39. Bug JAL-4229
    off by one in displayed VARNA secondary structure
  40. Bug JAL-4178
    Cannot cancel structure view open action once it has been started...
  41. Story JAL-4175
    Allow masking when visualising and analysing PAE matrices
  42. New Feature JAL-4162
    Read (and write) Relaxed PHYLIP formatted data
  43. Bug JAL-4155
    ScalePanelTest fails when run after AlignViewportTest and PaintRefresherTest
  44. Bug JAL-4142
    example JVP files no longer have distinct locations for expanded windows
  45. Bug JAL-4139
    Multi-Harmony service parsing error at JalviewJS launch
  46. 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
  47. Task JAL-4129
    Migrate semantics for DBRefEntry version string to support versioned sources and cross-references
  48. Bug JAL-4127
    'Reload' for a jalview project results in all windows being duplicated
  49. Improvement JAL-4122
    Interactive Matrix Viewer for PAE and other matrix objects
  50. New Feature JAL-4113
    Recipe for embedding a Jalview MSA in a JavaFX app
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