jbrowse-plugin-mafviewer 1.0.8 → 1.1.2

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Files changed (126) hide show
  1. package/README.md +54 -20
  2. package/dist/{TaffyAdapter/TaffyAdapter.d.ts → BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts} +11 -7
  3. package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js +204 -0
  4. package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js.map +1 -0
  5. package/dist/{TaffyAdapter → BgzipTaffyAdapter}/configSchema.d.ts +14 -1
  6. package/dist/{TaffyAdapter → BgzipTaffyAdapter}/configSchema.js +21 -6
  7. package/dist/BgzipTaffyAdapter/configSchema.js.map +1 -0
  8. package/dist/BgzipTaffyAdapter/index.d.ts +2 -0
  9. package/dist/BgzipTaffyAdapter/index.js +11 -0
  10. package/dist/BgzipTaffyAdapter/index.js.map +1 -0
  11. package/dist/BgzipTaffyAdapter/rowInstructions.d.ts +35 -0
  12. package/dist/BgzipTaffyAdapter/rowInstructions.js +55 -0
  13. package/dist/BgzipTaffyAdapter/rowInstructions.js.map +1 -0
  14. package/dist/BgzipTaffyAdapter/types.d.ts +13 -0
  15. package/dist/BgzipTaffyAdapter/types.js +2 -0
  16. package/dist/BgzipTaffyAdapter/types.js.map +1 -0
  17. package/dist/BgzipTaffyAdapter/virtualOffset.d.ts +8 -0
  18. package/dist/BgzipTaffyAdapter/virtualOffset.js +23 -0
  19. package/dist/BgzipTaffyAdapter/virtualOffset.js.map +1 -0
  20. package/dist/BigMafAdapter/BigMafAdapter.js +1 -1
  21. package/dist/BigMafAdapter/BigMafAdapter.js.map +1 -1
  22. package/dist/BigMafAdapter/configSchema.d.ts +11 -0
  23. package/dist/BigMafAdapter/configSchema.js +11 -0
  24. package/dist/BigMafAdapter/configSchema.js.map +1 -1
  25. package/dist/BigMafAdapter/index.js +1 -1
  26. package/dist/BigMafAdapter/index.js.map +1 -1
  27. package/dist/LinearMafDisplay/components/ColorLegend.js +10 -6
  28. package/dist/LinearMafDisplay/components/ColorLegend.js.map +1 -1
  29. package/dist/LinearMafDisplay/components/ReactComponent.js +39 -4
  30. package/dist/LinearMafDisplay/components/ReactComponent.js.map +1 -1
  31. package/dist/LinearMafDisplay/components/SetRowHeight.js +7 -7
  32. package/dist/LinearMafDisplay/components/SetRowHeight.js.map +1 -1
  33. package/dist/LinearMafDisplay/components/SvgWrapper.d.ts +8 -0
  34. package/dist/LinearMafDisplay/components/SvgWrapper.js +21 -0
  35. package/dist/LinearMafDisplay/components/SvgWrapper.js.map +1 -0
  36. package/dist/LinearMafDisplay/components/Tree.d.ts +5 -0
  37. package/dist/LinearMafDisplay/components/Tree.js +22 -0
  38. package/dist/LinearMafDisplay/components/Tree.js.map +1 -0
  39. package/dist/LinearMafDisplay/components/YScaleBars.d.ts +0 -1
  40. package/dist/LinearMafDisplay/components/YScaleBars.js +6 -27
  41. package/dist/LinearMafDisplay/components/YScaleBars.js.map +1 -1
  42. package/dist/LinearMafDisplay/components/util.d.ts +1 -0
  43. package/dist/LinearMafDisplay/components/util.js +8 -0
  44. package/dist/LinearMafDisplay/components/util.js.map +1 -0
  45. package/dist/LinearMafDisplay/index.js +1 -1
  46. package/dist/LinearMafDisplay/index.js.map +1 -1
  47. package/dist/LinearMafDisplay/renderSvg.js +1 -0
  48. package/dist/LinearMafDisplay/renderSvg.js.map +1 -1
  49. package/dist/LinearMafDisplay/stateModel.d.ts +76 -14
  50. package/dist/LinearMafDisplay/stateModel.js +118 -18
  51. package/dist/LinearMafDisplay/stateModel.js.map +1 -1
  52. package/dist/LinearMafDisplay/types.d.ts +17 -0
  53. package/dist/LinearMafDisplay/types.js +16 -0
  54. package/dist/LinearMafDisplay/types.js.map +1 -0
  55. package/dist/LinearMafRenderer/LinearMafRenderer.d.ts +3 -3
  56. package/dist/LinearMafRenderer/LinearMafRenderer.js +11 -9
  57. package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -1
  58. package/dist/LinearMafRenderer/components/ReactComponent.js +1 -1
  59. package/dist/LinearMafRenderer/components/ReactComponent.js.map +1 -1
  60. package/dist/LinearMafRenderer/index.js +1 -1
  61. package/dist/LinearMafRenderer/index.js.map +1 -1
  62. package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js +42 -25
  63. package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map +1 -1
  64. package/dist/MafRPC/index.d.ts +16 -0
  65. package/dist/MafRPC/index.js +19 -0
  66. package/dist/MafRPC/index.js.map +1 -0
  67. package/dist/MafTabixAdapter/MafTabixAdapter.d.ts +8 -0
  68. package/dist/MafTabixAdapter/MafTabixAdapter.js +18 -19
  69. package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -1
  70. package/dist/MafTabixAdapter/configSchema.d.ts +17 -0
  71. package/dist/MafTabixAdapter/configSchema.js +17 -1
  72. package/dist/MafTabixAdapter/configSchema.js.map +1 -1
  73. package/dist/MafTabixAdapter/index.js +1 -1
  74. package/dist/MafTabixAdapter/index.js.map +1 -1
  75. package/dist/MafTrack/index.js.map +1 -1
  76. package/dist/index.js +6 -4
  77. package/dist/index.js.map +1 -1
  78. package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +65 -4
  79. package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +4 -4
  80. package/dist/parseNewick.d.ts +60 -0
  81. package/dist/parseNewick.js +95 -0
  82. package/dist/parseNewick.js.map +1 -0
  83. package/dist/util.d.ts +9 -0
  84. package/dist/util.js +9 -0
  85. package/dist/util.js.map +1 -0
  86. package/package.json +18 -5
  87. package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts +235 -0
  88. package/src/{TaffyAdapter → BgzipTaffyAdapter}/configSchema.ts +21 -6
  89. package/src/{TaffyAdapter → BgzipTaffyAdapter}/index.ts +5 -4
  90. package/src/BgzipTaffyAdapter/rowInstructions.ts +91 -0
  91. package/src/BgzipTaffyAdapter/types.ts +16 -0
  92. package/src/BgzipTaffyAdapter/virtualOffset.ts +29 -0
  93. package/src/BigMafAdapter/BigMafAdapter.ts +11 -11
  94. package/src/BigMafAdapter/configSchema.ts +11 -0
  95. package/src/BigMafAdapter/index.ts +2 -1
  96. package/src/LinearMafDisplay/components/ColorLegend.tsx +36 -25
  97. package/src/LinearMafDisplay/components/ReactComponent.tsx +68 -3
  98. package/src/LinearMafDisplay/components/SetRowHeight.tsx +6 -5
  99. package/src/LinearMafDisplay/components/SvgWrapper.tsx +39 -0
  100. package/src/LinearMafDisplay/components/Tree.tsx +33 -0
  101. package/src/LinearMafDisplay/components/YScaleBars.tsx +8 -43
  102. package/src/LinearMafDisplay/components/util.ts +7 -0
  103. package/src/LinearMafDisplay/index.ts +2 -1
  104. package/src/LinearMafDisplay/renderSvg.tsx +2 -1
  105. package/src/LinearMafDisplay/stateModel.ts +139 -18
  106. package/src/LinearMafDisplay/types.ts +41 -0
  107. package/src/LinearMafRenderer/LinearMafRenderer.ts +13 -10
  108. package/src/LinearMafRenderer/components/ReactComponent.tsx +2 -1
  109. package/src/LinearMafRenderer/index.ts +2 -1
  110. package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx +109 -65
  111. package/src/MafRPC/index.ts +39 -0
  112. package/src/MafTabixAdapter/MafTabixAdapter.ts +31 -25
  113. package/src/MafTabixAdapter/configSchema.ts +17 -1
  114. package/src/MafTabixAdapter/index.ts +2 -1
  115. package/src/MafTrack/index.ts +1 -0
  116. package/src/index.ts +6 -4
  117. package/src/parseNewick.ts +94 -0
  118. package/src/util.ts +11 -0
  119. package/LICENSE +0 -201
  120. package/dist/TaffyAdapter/TaffyAdapter.js +0 -89
  121. package/dist/TaffyAdapter/TaffyAdapter.js.map +0 -1
  122. package/dist/TaffyAdapter/configSchema.js.map +0 -1
  123. package/dist/TaffyAdapter/index.d.ts +0 -2
  124. package/dist/TaffyAdapter/index.js +0 -11
  125. package/dist/TaffyAdapter/index.js.map +0 -1
  126. package/src/TaffyAdapter/TaffyAdapter.ts +0 -112

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