jbrowse-plugin-mafviewer 1.4.3 → 1.4.6

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Files changed (204) hide show
  1. package/README.md +1 -1
  2. package/dist/BigMafAdapter/BigMafAdapter.js +4 -5
  3. package/dist/BigMafAdapter/BigMafAdapter.js.map +1 -1
  4. package/dist/BigMafAdapter/configSchema.d.ts +2 -2
  5. package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js +39 -109
  6. package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js.map +1 -1
  7. package/dist/LinearMafDisplay/components/MAFTooltip.d.ts +0 -3
  8. package/dist/LinearMafDisplay/components/MAFTooltip.js.map +1 -1
  9. package/dist/LinearMafDisplay/components/MsaHighlightOverlay.d.ts +9 -0
  10. package/dist/LinearMafDisplay/components/MsaHighlightOverlay.js +34 -0
  11. package/dist/LinearMafDisplay/components/MsaHighlightOverlay.js.map +1 -0
  12. package/dist/LinearMafDisplay/components/Sidebar/ColorLegend.js +2 -2
  13. package/dist/LinearMafDisplay/components/Sidebar/ColorLegend.js.map +1 -1
  14. package/dist/LinearMafDisplay/components/Sidebar/RectBg.d.ts +1 -1
  15. package/dist/LinearMafDisplay/components/Sidebar/RectBg.js +2 -3
  16. package/dist/LinearMafDisplay/components/Sidebar/RectBg.js.map +1 -1
  17. package/dist/LinearMafDisplay/components/Sidebar/SvgWrapper.js +81 -11
  18. package/dist/LinearMafDisplay/components/Sidebar/SvgWrapper.js.map +1 -1
  19. package/dist/LinearMafDisplay/components/Sidebar/Tree.js +30 -9
  20. package/dist/LinearMafDisplay/components/Sidebar/Tree.js.map +1 -1
  21. package/dist/LinearMafDisplay/components/Sidebar/YScaleBars.d.ts +0 -1
  22. package/dist/LinearMafDisplay/components/Sidebar/YScaleBars.js.map +1 -1
  23. package/dist/LinearMafDisplay/components/useDragSelection.d.ts +25 -0
  24. package/dist/LinearMafDisplay/components/useDragSelection.js +103 -0
  25. package/dist/LinearMafDisplay/components/useDragSelection.js.map +1 -0
  26. package/dist/LinearMafDisplay/configSchema.d.ts +3 -30
  27. package/dist/LinearMafDisplay/renderSvg.js +1 -1
  28. package/dist/LinearMafDisplay/renderSvg.js.map +1 -1
  29. package/dist/LinearMafDisplay/stateModel.d.ts +1090 -102
  30. package/dist/LinearMafDisplay/stateModel.js +156 -17
  31. package/dist/LinearMafDisplay/stateModel.js.map +1 -1
  32. package/dist/LinearMafDisplay/types.d.ts +2 -2
  33. package/dist/LinearMafDisplay/util.d.ts +6 -0
  34. package/dist/LinearMafDisplay/util.js +28 -6
  35. package/dist/LinearMafDisplay/util.js.map +1 -1
  36. package/dist/LinearMafRenderer/LinearMafRenderer.d.ts +43 -10
  37. package/dist/LinearMafRenderer/LinearMafRenderer.js +1 -1
  38. package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -1
  39. package/dist/LinearMafRenderer/components/LinearMafRendering.d.ts +14 -5
  40. package/dist/LinearMafRenderer/components/LinearMafRendering.js +40 -20
  41. package/dist/LinearMafRenderer/components/LinearMafRendering.js.map +1 -1
  42. package/dist/LinearMafRenderer/configSchema.d.ts +1 -6
  43. package/dist/LinearMafRenderer/configSchema.js +1 -6
  44. package/dist/LinearMafRenderer/configSchema.js.map +1 -1
  45. package/dist/LinearMafRenderer/makeImageData.js +6 -7
  46. package/dist/LinearMafRenderer/makeImageData.js.map +1 -1
  47. package/dist/LinearMafRenderer/rendering/features.d.ts +0 -1
  48. package/dist/LinearMafRenderer/rendering/features.js +1 -14
  49. package/dist/LinearMafRenderer/rendering/features.js.map +1 -1
  50. package/dist/LinearMafRenderer/rendering/insertions.d.ts +1 -1
  51. package/dist/LinearMafRenderer/rendering/insertions.js +10 -8
  52. package/dist/LinearMafRenderer/rendering/insertions.js.map +1 -1
  53. package/dist/LinearMafRenderer/rendering/matches.d.ts +1 -1
  54. package/dist/LinearMafRenderer/rendering/matches.js +3 -15
  55. package/dist/LinearMafRenderer/rendering/matches.js.map +1 -1
  56. package/dist/LinearMafRenderer/rendering/mismatches.d.ts +1 -1
  57. package/dist/LinearMafRenderer/rendering/mismatches.js +3 -3
  58. package/dist/LinearMafRenderer/rendering/spatialIndex.js +8 -2
  59. package/dist/LinearMafRenderer/rendering/spatialIndex.js.map +1 -1
  60. package/dist/LinearMafRenderer/rendering/text.js +1 -3
  61. package/dist/LinearMafRenderer/rendering/text.js.map +1 -1
  62. package/dist/LinearMafRenderer/rendering/types.d.ts +6 -5
  63. package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js +1 -1
  64. package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map +1 -1
  65. package/dist/MafAddTrackWorkflow/index.js +1 -1
  66. package/dist/MafAddTrackWorkflow/index.js.map +1 -1
  67. package/dist/MafGetSequences/MafGetSequences.d.ts +1 -0
  68. package/dist/MafGetSequences/MafGetSequences.js +2 -1
  69. package/dist/MafGetSequences/MafGetSequences.js.map +1 -1
  70. package/dist/MafSequenceWidget/LabelsCanvas.d.ts +8 -0
  71. package/dist/MafSequenceWidget/LabelsCanvas.js +37 -0
  72. package/dist/MafSequenceWidget/LabelsCanvas.js.map +1 -0
  73. package/dist/MafSequenceWidget/MafSequenceHoverHighlight.d.ts +6 -0
  74. package/dist/MafSequenceWidget/MafSequenceHoverHighlight.js +52 -0
  75. package/dist/MafSequenceWidget/MafSequenceHoverHighlight.js.map +1 -0
  76. package/dist/MafSequenceWidget/MafSequenceHoverHighlightExtension.d.ts +2 -0
  77. package/dist/MafSequenceWidget/MafSequenceHoverHighlightExtension.js +12 -0
  78. package/dist/MafSequenceWidget/MafSequenceHoverHighlightExtension.js.map +1 -0
  79. package/dist/MafSequenceWidget/MafSequenceWidget.d.ts +6 -0
  80. package/dist/MafSequenceWidget/MafSequenceWidget.js +189 -0
  81. package/dist/MafSequenceWidget/MafSequenceWidget.js.map +1 -0
  82. package/dist/MafSequenceWidget/SequenceCanvas.d.ts +12 -0
  83. package/dist/MafSequenceWidget/SequenceCanvas.js +86 -0
  84. package/dist/MafSequenceWidget/SequenceCanvas.js.map +1 -0
  85. package/dist/MafSequenceWidget/SequenceDisplay.d.ts +12 -0
  86. package/dist/MafSequenceWidget/SequenceDisplay.js +117 -0
  87. package/dist/MafSequenceWidget/SequenceDisplay.js.map +1 -0
  88. package/dist/MafSequenceWidget/SequenceTooltip.d.ts +11 -0
  89. package/dist/MafSequenceWidget/SequenceTooltip.js +39 -0
  90. package/dist/MafSequenceWidget/SequenceTooltip.js.map +1 -0
  91. package/dist/MafSequenceWidget/baseColors.d.ts +3 -0
  92. package/dist/MafSequenceWidget/baseColors.js +64 -0
  93. package/dist/MafSequenceWidget/baseColors.js.map +1 -0
  94. package/dist/MafSequenceWidget/colToGenomePos.d.ts +13 -0
  95. package/dist/MafSequenceWidget/colToGenomePos.js +32 -0
  96. package/dist/MafSequenceWidget/colToGenomePos.js.map +1 -0
  97. package/dist/MafSequenceWidget/colToGenomePos.test.d.ts +1 -0
  98. package/dist/MafSequenceWidget/colToGenomePos.test.js +136 -0
  99. package/dist/MafSequenceWidget/colToGenomePos.test.js.map +1 -0
  100. package/dist/MafSequenceWidget/configSchema.d.ts +1 -0
  101. package/dist/MafSequenceWidget/configSchema.js +3 -0
  102. package/dist/MafSequenceWidget/configSchema.js.map +1 -0
  103. package/dist/MafSequenceWidget/constants.d.ts +4 -0
  104. package/dist/MafSequenceWidget/constants.js +5 -0
  105. package/dist/MafSequenceWidget/constants.js.map +1 -0
  106. package/dist/MafSequenceWidget/index.d.ts +2 -0
  107. package/dist/MafSequenceWidget/index.js +16 -0
  108. package/dist/MafSequenceWidget/index.js.map +1 -0
  109. package/dist/MafSequenceWidget/stateModelFactory.d.ts +67 -0
  110. package/dist/MafSequenceWidget/stateModelFactory.js +21 -0
  111. package/dist/MafSequenceWidget/stateModelFactory.js.map +1 -0
  112. package/dist/MafTabixAdapter/MafTabixAdapter.js +4 -35
  113. package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -1
  114. package/dist/MafTabixAdapter/configSchema.d.ts +4 -4
  115. package/dist/MafTrack/configSchema.d.ts +16 -11
  116. package/dist/index.js +2 -0
  117. package/dist/index.js.map +1 -1
  118. package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +12 -24
  119. package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +4 -4
  120. package/dist/util/clipboard.d.ts +2 -0
  121. package/dist/util/clipboard.js +28 -0
  122. package/dist/util/clipboard.js.map +1 -0
  123. package/dist/util/fastaUtils.d.ts +2 -1
  124. package/dist/util/fastaUtils.js +93 -50
  125. package/dist/util/fastaUtils.js.map +1 -1
  126. package/dist/util/fastaUtils.test.js +190 -0
  127. package/dist/util/fastaUtils.test.js.map +1 -1
  128. package/dist/util/parseAssemblyName.d.ts +32 -0
  129. package/dist/util/parseAssemblyName.js +87 -0
  130. package/dist/util/parseAssemblyName.js.map +1 -0
  131. package/dist/util/parseAssemblyName.test.d.ts +1 -0
  132. package/dist/util/parseAssemblyName.test.js +269 -0
  133. package/dist/util/parseAssemblyName.test.js.map +1 -0
  134. package/package.json +12 -12
  135. package/src/BigMafAdapter/BigMafAdapter.ts +5 -5
  136. package/src/LinearMafDisplay/components/LinearMafDisplayComponent.tsx +63 -145
  137. package/src/LinearMafDisplay/components/MAFTooltip.tsx +0 -3
  138. package/src/LinearMafDisplay/components/MsaHighlightOverlay.tsx +62 -0
  139. package/src/LinearMafDisplay/components/Sidebar/ColorLegend.tsx +2 -6
  140. package/src/LinearMafDisplay/components/Sidebar/RectBg.tsx +8 -3
  141. package/src/LinearMafDisplay/components/Sidebar/SvgWrapper.tsx +117 -15
  142. package/src/LinearMafDisplay/components/Sidebar/Tree.tsx +53 -8
  143. package/src/LinearMafDisplay/components/Sidebar/YScaleBars.tsx +0 -1
  144. package/src/LinearMafDisplay/components/useDragSelection.ts +159 -0
  145. package/src/LinearMafDisplay/renderSvg.tsx +1 -1
  146. package/src/LinearMafDisplay/stateModel.ts +215 -20
  147. package/src/LinearMafDisplay/types.ts +2 -2
  148. package/src/LinearMafDisplay/util.ts +35 -7
  149. package/src/LinearMafRenderer/LinearMafRenderer.ts +3 -5
  150. package/src/LinearMafRenderer/components/LinearMafRendering.tsx +67 -33
  151. package/src/LinearMafRenderer/configSchema.ts +1 -6
  152. package/src/LinearMafRenderer/makeImageData.ts +5 -14
  153. package/src/LinearMafRenderer/rendering/features.ts +2 -36
  154. package/src/LinearMafRenderer/rendering/insertions.ts +13 -8
  155. package/src/LinearMafRenderer/rendering/matches.ts +2 -27
  156. package/src/LinearMafRenderer/rendering/mismatches.ts +3 -3
  157. package/src/LinearMafRenderer/rendering/spatialIndex.ts +9 -2
  158. package/src/LinearMafRenderer/rendering/text.ts +1 -2
  159. package/src/LinearMafRenderer/rendering/types.ts +8 -5
  160. package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx +1 -1
  161. package/src/MafAddTrackWorkflow/index.ts +1 -1
  162. package/src/MafGetSequences/MafGetSequences.ts +10 -2
  163. package/src/MafSequenceWidget/LabelsCanvas.tsx +58 -0
  164. package/src/MafSequenceWidget/MafSequenceHoverHighlight.tsx +83 -0
  165. package/src/MafSequenceWidget/MafSequenceHoverHighlightExtension.tsx +24 -0
  166. package/src/MafSequenceWidget/MafSequenceWidget.tsx +294 -0
  167. package/src/MafSequenceWidget/SequenceCanvas.tsx +136 -0
  168. package/src/MafSequenceWidget/SequenceDisplay.tsx +188 -0
  169. package/src/MafSequenceWidget/SequenceTooltip.tsx +70 -0
  170. package/src/MafSequenceWidget/baseColors.ts +76 -0
  171. package/src/MafSequenceWidget/colToGenomePos.test.ts +166 -0
  172. package/src/MafSequenceWidget/colToGenomePos.ts +40 -0
  173. package/src/MafSequenceWidget/configSchema.ts +3 -0
  174. package/src/MafSequenceWidget/constants.ts +4 -0
  175. package/src/MafSequenceWidget/index.ts +24 -0
  176. package/src/MafSequenceWidget/stateModelFactory.ts +43 -0
  177. package/src/MafTabixAdapter/MafTabixAdapter.ts +12 -51
  178. package/src/index.ts +2 -0
  179. package/src/util/__snapshots__/fastaUtils.test.ts.snap +35 -0
  180. package/src/util/clipboard.ts +35 -0
  181. package/src/util/fastaUtils.test.ts +199 -0
  182. package/src/util/fastaUtils.ts +118 -51
  183. package/src/util/parseAssemblyName.test.ts +350 -0
  184. package/src/util/parseAssemblyName.ts +106 -0
  185. package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.d.ts +0 -11
  186. package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js +0 -97
  187. package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js.map +0 -1
  188. package/dist/LinearMafDisplay/components/util.d.ts +0 -1
  189. package/dist/LinearMafDisplay/components/util.js +0 -8
  190. package/dist/LinearMafDisplay/components/util.js.map +0 -1
  191. package/dist/LinearMafRenderer/components/util.d.ts +0 -1
  192. package/dist/LinearMafRenderer/components/util.js +0 -13
  193. package/dist/LinearMafRenderer/components/util.js.map +0 -1
  194. package/dist/util/fetchSequences.d.ts +0 -18
  195. package/dist/util/fetchSequences.js +0 -39
  196. package/dist/util/fetchSequences.js.map +0 -1
  197. package/dist/util/useSequences.d.ts +0 -21
  198. package/dist/util/useSequences.js +0 -64
  199. package/dist/util/useSequences.js.map +0 -1
  200. package/src/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.tsx +0 -175
  201. package/src/LinearMafDisplay/components/util.ts +0 -7
  202. package/src/LinearMafRenderer/components/util.ts +0 -13
  203. package/src/util/fetchSequences.ts +0 -57
  204. package/src/util/useSequences.ts +0 -90

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