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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-3259
    StockholmFileTest not portable: does not cope with platform specific line endings
  2. Bug JAL-3258
    FileLoader inappropriately uses System.getProperty("file.separator")
  3. Bug JAL-3257
    gffheader output with \n instead of System.getProperty("line.separator")
  4. Task JAL-3255
    install4j logo should be on the 2.11 downloads page
  5. Task JAL-3231
    Review FAQs for 2.11 release
  6. Task JAL-3230
    New FAQ for opening the 'System java console'
  7. Task JAL-3176
    Run 'Memory' test suite as Bamboo task during release process
  8. Bug JAL-3173
    fix JNetCONF definition in documentation
  9. Bug JAL-3160
    Sequence features and crossreferences lost if input linked CDNA/Protein view closed before MSA result shown
  10. Bug JAL-3159
    Sequences disappear when reducing height of alignment view
  11. Bug JAL-3157
    text color threshold not preserved across tree subgroup operations
  12. Improvement JAL-3137
    Support HiDPI scaling for hi-resolution displays
  13. Bug JAL-3133
    Colour by/Align with view selection menu loses focus on OSX/Java 11
  14. Improvement JAL-3128
    Sort group associated annotation rows in same way as ordering of groups in the alignment
  15. Bug JAL-3124
    Protein structure derived annotation tracks not automatically shown when 'add to alignment' preference is enabled (and not available unless it *is* ticked!)
  16. Bug JAL-3115
    Java 10 - Mac OSX - can't select from drop-down menu in linked cDNA/Protein splitview
  17. Bug JAL-3109
    Extra annotation rows appear when removing and recreating group in example project
  18. Bug JAL-3102
    Java 10 (OSX) - only see news from 7 Sept 2017 in news reader
  19. Bug JAL-3100
    Resize corners on bottom right of windows aren't visible on OSX/Java 10
  20. Task JAL-3067
    templating for integration of slivka client with Jalview
  21. Task JAL-3063
    Migrate from Castor to JAXB to enable Jalview project import/export in Jalview-js
  22. Improvement JAL-3057
    optimise calculations triggered by interactive operations
  23. Improvement JAL-3052
    tooltip does not jump when moved to right of window
  24. Improvement JAL-3051
    Add clustalx colour scheme reference to documentation
  25. New Feature JAL-3044
    Citation report
  26. Bug JAL-3036
    Fix image HTML5 Canvas scaling for hi-res screens
  27. Bug JAL-3029
    Groovy help page incorrect decription of variable binding / functions
  28. Bug JAL-3023
    Different terminology between Preferences and Format menu for show unconserved
  29. Bug JAL-3016
    Cannot reconstruct CDS alignment for alignment of several subsequences of a single dataset sequence
  30. Improvement JAL-2996
    treat '~' tilde as special gap character
  31. Improvement JAL-2995
    Make 'Input path' text fields easier to complete for novices
  32. Bug JAL-2987
    Can't view multiple-page results in PDB/Uniprot FTS on Java 10
  33. Bug JAL-2974
    Overview redraws multiple times for a series of edits
  34. Task JAL-2968
    migrate from Quaqua to a more widely supported OSX look and feel
  35. Bug JAL-2961
    Jmol view not always centred on structures when multiple structures are viewed
  36. Bug JAL-2951
    dont fetch dbrefs or SIFTS for file-based associations of 3D structures
  37. Task JAL-2950
    Resolve correct Ensembl REST API endpoint for Uniprot crossreferences to Ensembl
  38. New Feature JAL-2947
    Retrieve Uniprot entries for imported PDB structures
  39. Task JAL-2917
    verify compatibility and migrate jalview / compbio services to https
  40. New Feature JAL-2916
    Panning/zooming mode for alignment view
  41. Task JAL-2880
    no binding between derived annotation rows and original structure data file parsed via Jmol
  42. Improvement JAL-2863
    Refactor File format suffix export preferences
  43. Bug JAL-2862
    Jalview does not import reverse-strand RNA sequences via Stockholm
  44. Bug JAL-2833
    can't drag and drop URLs with spaces for import
  45. Bug JAL-2832
    Groovy 2.4.12 console doesn't echo StdOut
  46. New Feature JAL-2786
    Custom taxon lists for ensemblGenomes gene id lookup
  47. Bug JAL-2785
    Jalview Java Console appears during some functional tests
  48. Improvement JAL-2783
    Offer 'Open Groovy Console' as well as Run Groovy Script from Calculations
  49. Bug JAL-2765
    Short isoforms from Ensembl are expanded to full length Uniprot sequences
  50. Improvement JAL-2763
    Even smaller sequence ID tooltip !
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