jbrowse-plugin-mafviewer 1.3.1 → 1.4.0

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Files changed (101) hide show
  1. package/README.md +1 -48
  2. package/dist/BigMafAdapter/BigMafAdapter.js +39 -28
  3. package/dist/BigMafAdapter/BigMafAdapter.js.map +1 -1
  4. package/dist/LinearMafDisplay/components/Crosshairs.js +1 -1
  5. package/dist/LinearMafDisplay/components/Crosshairs.js.map +1 -1
  6. package/dist/LinearMafDisplay/components/MAFTooltip.d.ts +2 -3
  7. package/dist/LinearMafDisplay/components/MAFTooltip.js +6 -19
  8. package/dist/LinearMafDisplay/components/MAFTooltip.js.map +1 -1
  9. package/dist/LinearMafDisplay/stateModel.d.ts +8 -0
  10. package/dist/LinearMafDisplay/stateModel.js +10 -0
  11. package/dist/LinearMafDisplay/stateModel.js.map +1 -1
  12. package/dist/LinearMafDisplay/util.d.ts +20 -0
  13. package/dist/LinearMafDisplay/util.js +29 -0
  14. package/dist/LinearMafDisplay/util.js.map +1 -1
  15. package/dist/LinearMafRenderer/LinearMafRenderer.d.ts +9 -0
  16. package/dist/LinearMafRenderer/LinearMafRenderer.js +1 -2
  17. package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -1
  18. package/dist/LinearMafRenderer/components/LinearMafRendering.d.ts +13 -0
  19. package/dist/LinearMafRenderer/components/LinearMafRendering.js +46 -0
  20. package/dist/LinearMafRenderer/components/LinearMafRendering.js.map +1 -0
  21. package/dist/LinearMafRenderer/components/ReactComponent.d.ts +3 -0
  22. package/dist/LinearMafRenderer/components/ReactComponent.js +41 -2
  23. package/dist/LinearMafRenderer/components/ReactComponent.js.map +1 -1
  24. package/dist/LinearMafRenderer/components/util.d.ts +1 -0
  25. package/dist/LinearMafRenderer/components/util.js +13 -0
  26. package/dist/LinearMafRenderer/components/util.js.map +1 -0
  27. package/dist/LinearMafRenderer/index.js +1 -1
  28. package/dist/LinearMafRenderer/index.js.map +1 -1
  29. package/dist/LinearMafRenderer/makeImageData.d.ts +6 -5
  30. package/dist/LinearMafRenderer/makeImageData.js +35 -146
  31. package/dist/LinearMafRenderer/makeImageData.js.map +1 -1
  32. package/dist/LinearMafRenderer/rendering/features.d.ts +4 -0
  33. package/dist/LinearMafRenderer/rendering/features.js +41 -0
  34. package/dist/LinearMafRenderer/rendering/features.js.map +1 -0
  35. package/dist/LinearMafRenderer/rendering/gaps.d.ts +2 -0
  36. package/dist/LinearMafRenderer/rendering/gaps.js +19 -0
  37. package/dist/LinearMafRenderer/rendering/gaps.js.map +1 -0
  38. package/dist/LinearMafRenderer/rendering/index.d.ts +8 -0
  39. package/dist/LinearMafRenderer/rendering/index.js +10 -0
  40. package/dist/LinearMafRenderer/rendering/index.js.map +1 -0
  41. package/dist/LinearMafRenderer/rendering/insertions.d.ts +2 -0
  42. package/dist/LinearMafRenderer/rendering/insertions.js +78 -0
  43. package/dist/LinearMafRenderer/rendering/insertions.js.map +1 -0
  44. package/dist/LinearMafRenderer/rendering/matches.d.ts +2 -0
  45. package/dist/LinearMafRenderer/rendering/matches.js +34 -0
  46. package/dist/LinearMafRenderer/rendering/matches.js.map +1 -0
  47. package/dist/LinearMafRenderer/rendering/mismatches.d.ts +13 -0
  48. package/dist/LinearMafRenderer/rendering/mismatches.js +57 -0
  49. package/dist/LinearMafRenderer/rendering/mismatches.js.map +1 -0
  50. package/dist/LinearMafRenderer/rendering/spatialIndex.d.ts +9 -0
  51. package/dist/LinearMafRenderer/rendering/spatialIndex.js +19 -0
  52. package/dist/LinearMafRenderer/rendering/spatialIndex.js.map +1 -0
  53. package/dist/LinearMafRenderer/rendering/text.d.ts +12 -0
  54. package/dist/LinearMafRenderer/rendering/text.js +42 -0
  55. package/dist/LinearMafRenderer/rendering/text.js.map +1 -0
  56. package/dist/LinearMafRenderer/rendering/types.d.ts +55 -0
  57. package/dist/LinearMafRenderer/rendering/types.js +15 -0
  58. package/dist/LinearMafRenderer/rendering/types.js.map +1 -0
  59. package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js +37 -35
  60. package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map +1 -1
  61. package/dist/MafTabixAdapter/MafTabixAdapter.js +48 -22
  62. package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -1
  63. package/dist/index.js +0 -2
  64. package/dist/index.js.map +1 -1
  65. package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +5 -29
  66. package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +4 -4
  67. package/dist/out.js +32310 -0
  68. package/dist/out.js.map +7 -0
  69. package/dist/util/fastaUtils.js.map +1 -1
  70. package/package.json +3 -2
  71. package/src/BigMafAdapter/BigMafAdapter.ts +49 -28
  72. package/src/LinearMafDisplay/components/Crosshairs.tsx +1 -7
  73. package/src/LinearMafDisplay/components/MAFTooltip.tsx +14 -33
  74. package/src/LinearMafDisplay/stateModel.ts +10 -0
  75. package/src/LinearMafDisplay/util.ts +57 -0
  76. package/src/LinearMafRenderer/LinearMafRenderer.ts +1 -2
  77. package/src/LinearMafRenderer/components/LinearMafRendering.tsx +76 -0
  78. package/src/LinearMafRenderer/components/util.ts +13 -0
  79. package/src/LinearMafRenderer/index.ts +1 -1
  80. package/src/LinearMafRenderer/makeImageData.ts +64 -196
  81. package/src/LinearMafRenderer/rendering/features.ts +111 -0
  82. package/src/LinearMafRenderer/rendering/gaps.ts +33 -0
  83. package/src/LinearMafRenderer/rendering/index.ts +9 -0
  84. package/src/LinearMafRenderer/rendering/insertions.ts +154 -0
  85. package/src/LinearMafRenderer/rendering/matches.ts +62 -0
  86. package/src/LinearMafRenderer/rendering/mismatches.ts +113 -0
  87. package/src/LinearMafRenderer/rendering/spatialIndex.ts +40 -0
  88. package/src/LinearMafRenderer/rendering/text.ts +72 -0
  89. package/src/LinearMafRenderer/rendering/types.ts +65 -0
  90. package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx +5 -6
  91. package/src/MafTabixAdapter/MafTabixAdapter.ts +77 -22
  92. package/src/index.ts +0 -2
  93. package/src/util/fastaUtils.ts +2 -1
  94. package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts +0 -307
  95. package/src/BgzipTaffyAdapter/configSchema.ts +0 -59
  96. package/src/BgzipTaffyAdapter/index.ts +0 -16
  97. package/src/BgzipTaffyAdapter/rowInstructions.ts +0 -91
  98. package/src/BgzipTaffyAdapter/types.ts +0 -16
  99. package/src/BgzipTaffyAdapter/util.ts +0 -25
  100. package/src/BgzipTaffyAdapter/virtualOffset.ts +0 -29
  101. package/src/LinearMafRenderer/components/ReactComponent.tsx +0 -13

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