@jbrowse/plugin-variants 2.18.0 → 3.0.0

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Files changed (272) hide show
  1. package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts +1 -1
  2. package/dist/LinearVariantDisplay/model.d.ts +5 -5
  3. package/dist/MultiLinearVariantDisplay/components/Crosshair.d.ts +7 -0
  4. package/dist/MultiLinearVariantDisplay/components/Crosshair.js +35 -0
  5. package/dist/MultiLinearVariantDisplay/components/VariantDisplayComponent.d.ts +1 -2
  6. package/dist/MultiLinearVariantDisplay/components/VariantDisplayComponent.js +5 -49
  7. package/dist/MultiLinearVariantDisplay/index.js +18 -8
  8. package/dist/MultiLinearVariantDisplay/model.d.ts +113 -40
  9. package/dist/MultiLinearVariantDisplay/model.js +24 -176
  10. package/dist/MultiLinearVariantDisplay/renderSvg.d.ts +1 -2
  11. package/dist/MultiLinearVariantDisplay/renderSvg.js +2 -5
  12. package/dist/MultiLinearVariantMatrixDisplay/components/Crosshair.d.ts +7 -0
  13. package/dist/MultiLinearVariantMatrixDisplay/components/Crosshair.js +28 -0
  14. package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts +1 -2
  15. package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js +13 -16
  16. package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.d.ts +1 -2
  17. package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js +6 -56
  18. package/dist/MultiLinearVariantMatrixDisplay/model.d.ts +109 -27
  19. package/dist/MultiLinearVariantMatrixDisplay/model.js +31 -136
  20. package/dist/MultiLinearVariantMatrixDisplay/renderSvg.d.ts +1 -2
  21. package/dist/MultiLinearVariantMatrixDisplay/renderSvg.js +3 -7
  22. package/dist/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.d.ts +4 -32
  23. package/dist/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js +44 -63
  24. package/dist/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.d.ts +3 -2
  25. package/dist/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.js +31 -5
  26. package/dist/MultiLinearVariantMatrixRenderer/index.js +2 -2
  27. package/dist/MultiLinearVariantMatrixRenderer/makeImageData.d.ts +10 -0
  28. package/dist/MultiLinearVariantMatrixRenderer/makeImageData.js +100 -0
  29. package/dist/MultiLinearVariantMatrixRenderer/types.d.ts +15 -0
  30. package/dist/MultiLinearVariantMatrixRenderer/types.js +2 -0
  31. package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts +4 -21
  32. package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.js +38 -25
  33. package/dist/MultiLinearVariantRenderer/MultiVariantRendering.d.ts +7 -3
  34. package/dist/MultiLinearVariantRenderer/MultiVariantRendering.js +36 -27
  35. package/dist/MultiLinearVariantRenderer/configSchema.d.ts +1 -33
  36. package/dist/MultiLinearVariantRenderer/configSchema.js +0 -5
  37. package/dist/MultiLinearVariantRenderer/makeImageData.d.ts +4 -0
  38. package/dist/MultiLinearVariantRenderer/makeImageData.js +67 -0
  39. package/dist/MultiLinearVariantRenderer/types.d.ts +19 -0
  40. package/dist/MultiLinearVariantRenderer/types.js +2 -0
  41. package/dist/MultiVariantBaseRenderer.d.ts +4 -4
  42. package/dist/StructuralVariantChordRenderer/Chord.d.ts +2 -19
  43. package/dist/StructuralVariantChordRenderer/Chord.js +3 -25
  44. package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +2 -3
  45. package/dist/StructuralVariantChordRenderer/ReactComponent.js +7 -29
  46. package/dist/StructuralVariantChordRenderer/types.d.ts +17 -0
  47. package/dist/StructuralVariantChordRenderer/types.js +2 -0
  48. package/dist/Tooltip.d.ts +2 -2
  49. package/dist/Tooltip.js +6 -32
  50. package/dist/VariantFeatureWidget/Checkbox2.d.ts +1 -2
  51. package/dist/VariantFeatureWidget/Checkbox2.js +2 -5
  52. package/dist/VariantFeatureWidget/LaunchBreakendPanel.d.ts +2 -3
  53. package/dist/VariantFeatureWidget/LaunchBreakendPanel.js +66 -69
  54. package/dist/VariantFeatureWidget/LaunchBreakendWidgetArea.d.ts +4 -0
  55. package/dist/VariantFeatureWidget/LaunchBreakendWidgetArea.js +60 -0
  56. package/dist/VariantFeatureWidget/VariantConsequenceDataGrid.d.ts +5 -0
  57. package/dist/VariantFeatureWidget/VariantConsequenceDataGrid.js +15 -0
  58. package/dist/VariantFeatureWidget/VariantConsequenceDataGridWrapper.d.ts +5 -0
  59. package/dist/VariantFeatureWidget/VariantConsequenceDataGridWrapper.js +20 -0
  60. package/dist/VariantFeatureWidget/VariantConsequencePanel.d.ts +5 -0
  61. package/dist/VariantFeatureWidget/VariantConsequencePanel.js +15 -0
  62. package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts +1 -2
  63. package/dist/VariantFeatureWidget/VariantFeatureWidget.js +47 -36
  64. package/dist/VariantFeatureWidget/VariantSampleFilters.d.ts +9 -0
  65. package/dist/VariantFeatureWidget/VariantSampleFilters.js +10 -0
  66. package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts +9 -7
  67. package/dist/VariantFeatureWidget/VariantSampleGrid.js +14 -44
  68. package/dist/VariantFeatureWidget/index.js +17 -7
  69. package/dist/VariantFeatureWidget/types.d.ts +16 -0
  70. package/dist/VariantFeatureWidget/types.js +2 -0
  71. package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.js +10 -27
  72. package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts +12 -7
  73. package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js +27 -37
  74. package/dist/VcfAdapter/VcfAdapter.d.ts +7 -0
  75. package/dist/VcfAdapter/VcfAdapter.js +29 -3
  76. package/dist/VcfAdapter/configSchema.d.ts +8 -0
  77. package/dist/VcfAdapter/configSchema.js +12 -1
  78. package/dist/VcfAdapter/index.js +17 -7
  79. package/dist/VcfFeature/index.js +2 -1
  80. package/dist/VcfFeature/util.js +3 -4
  81. package/dist/VcfTabixAdapter/VcfTabixAdapter.js +38 -12
  82. package/dist/VcfTabixAdapter/configSchema.d.ts +8 -0
  83. package/dist/VcfTabixAdapter/configSchema.js +8 -0
  84. package/dist/VcfTabixAdapter/index.js +17 -7
  85. package/dist/extensionPoints.js +21 -33
  86. package/dist/getMultiVariantFeaturesAutorun.d.ts +4 -7
  87. package/dist/getMultiVariantFeaturesAutorun.js +16 -15
  88. package/dist/getMultiVariantSourcesAutorun.d.ts +1 -6
  89. package/dist/shared/BulkEditPanel.d.ts +4 -5
  90. package/dist/shared/BulkEditPanel.js +69 -88
  91. package/dist/shared/ClusterDialog.d.ts +4 -5
  92. package/dist/shared/ClusterDialog.js +45 -86
  93. package/dist/shared/ColorLegend.d.ts +2 -3
  94. package/dist/shared/ColorLegend.js +8 -10
  95. package/dist/shared/HelpfulTips.d.ts +1 -0
  96. package/dist/shared/HelpfulTips.js +7 -0
  97. package/dist/shared/LegendBar.d.ts +3 -3
  98. package/dist/shared/LegendBar.js +6 -12
  99. package/dist/shared/MAFFilterDialog.d.ts +2 -3
  100. package/dist/shared/MAFFilterDialog.js +14 -42
  101. package/dist/shared/MultiVariantBaseModel.d.ts +341 -0
  102. package/dist/shared/MultiVariantBaseModel.js +316 -0
  103. package/dist/shared/MultiVariantTooltip.d.ts +6 -0
  104. package/dist/shared/MultiVariantTooltip.js +23 -0
  105. package/dist/shared/RectBg.d.ts +2 -3
  106. package/dist/shared/RectBg.js +3 -7
  107. package/dist/shared/RowPalettizer.d.ts +2 -3
  108. package/dist/shared/RowPalettizer.js +30 -28
  109. package/dist/shared/SetColorDialog.d.ts +2 -3
  110. package/dist/shared/SetColorDialog.js +26 -65
  111. package/dist/shared/SetMinMaxDialog.d.ts +1 -2
  112. package/dist/shared/SetMinMaxDialog.js +11 -41
  113. package/dist/shared/SetRowHeightDialog.d.ts +8 -0
  114. package/dist/shared/SetRowHeightDialog.js +18 -0
  115. package/dist/shared/SharedVariantMixin.d.ts +7 -7
  116. package/dist/shared/SourcesDataGrid.d.ts +6 -0
  117. package/dist/shared/SourcesDataGrid.js +68 -0
  118. package/dist/shared/SourcesGrid.d.ts +2 -3
  119. package/dist/shared/SourcesGrid.js +5 -134
  120. package/dist/shared/SourcesGridHeader.d.ts +7 -0
  121. package/dist/shared/SourcesGridHeader.js +41 -0
  122. package/dist/shared/multiVariantColor.d.ts +3 -0
  123. package/dist/shared/multiVariantColor.js +50 -0
  124. package/dist/types.d.ts +14 -0
  125. package/dist/types.js +2 -0
  126. package/dist/util.d.ts +6 -9
  127. package/dist/util.js +47 -14
  128. package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts +1 -1
  129. package/esm/LinearVariantDisplay/model.d.ts +5 -5
  130. package/esm/MultiLinearVariantDisplay/components/Crosshair.d.ts +7 -0
  131. package/esm/MultiLinearVariantDisplay/components/Crosshair.js +30 -0
  132. package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.d.ts +1 -2
  133. package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.js +5 -26
  134. package/esm/MultiLinearVariantDisplay/index.js +1 -1
  135. package/esm/MultiLinearVariantDisplay/model.d.ts +113 -40
  136. package/esm/MultiLinearVariantDisplay/model.js +7 -169
  137. package/esm/MultiLinearVariantDisplay/renderSvg.d.ts +1 -2
  138. package/esm/MultiLinearVariantDisplay/renderSvg.js +2 -5
  139. package/esm/MultiLinearVariantMatrixDisplay/components/Crosshair.d.ts +7 -0
  140. package/esm/MultiLinearVariantMatrixDisplay/components/Crosshair.js +23 -0
  141. package/esm/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts +1 -2
  142. package/esm/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js +13 -13
  143. package/esm/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.d.ts +1 -2
  144. package/esm/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js +6 -33
  145. package/esm/MultiLinearVariantMatrixDisplay/model.d.ts +109 -27
  146. package/esm/MultiLinearVariantMatrixDisplay/model.js +14 -129
  147. package/esm/MultiLinearVariantMatrixDisplay/renderSvg.d.ts +1 -2
  148. package/esm/MultiLinearVariantMatrixDisplay/renderSvg.js +3 -7
  149. package/esm/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.d.ts +4 -32
  150. package/esm/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js +11 -63
  151. package/esm/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.d.ts +3 -2
  152. package/esm/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.js +31 -2
  153. package/esm/MultiLinearVariantMatrixRenderer/index.js +1 -1
  154. package/esm/MultiLinearVariantMatrixRenderer/makeImageData.d.ts +10 -0
  155. package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js +97 -0
  156. package/esm/MultiLinearVariantMatrixRenderer/types.d.ts +15 -0
  157. package/esm/MultiLinearVariantMatrixRenderer/types.js +1 -0
  158. package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts +4 -21
  159. package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.js +6 -26
  160. package/esm/MultiLinearVariantRenderer/MultiVariantRendering.d.ts +7 -3
  161. package/esm/MultiLinearVariantRenderer/MultiVariantRendering.js +34 -5
  162. package/esm/MultiLinearVariantRenderer/configSchema.d.ts +1 -33
  163. package/esm/MultiLinearVariantRenderer/configSchema.js +0 -2
  164. package/esm/MultiLinearVariantRenderer/makeImageData.d.ts +4 -0
  165. package/esm/MultiLinearVariantRenderer/makeImageData.js +61 -0
  166. package/esm/MultiLinearVariantRenderer/types.d.ts +19 -0
  167. package/esm/MultiLinearVariantRenderer/types.js +1 -0
  168. package/esm/MultiVariantBaseRenderer.d.ts +4 -4
  169. package/esm/StructuralVariantChordRenderer/Chord.d.ts +2 -19
  170. package/esm/StructuralVariantChordRenderer/Chord.js +3 -2
  171. package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +2 -3
  172. package/esm/StructuralVariantChordRenderer/ReactComponent.js +7 -6
  173. package/esm/StructuralVariantChordRenderer/types.d.ts +17 -0
  174. package/esm/StructuralVariantChordRenderer/types.js +1 -0
  175. package/esm/Tooltip.d.ts +2 -2
  176. package/esm/Tooltip.js +6 -9
  177. package/esm/VariantFeatureWidget/Checkbox2.d.ts +1 -2
  178. package/esm/VariantFeatureWidget/Checkbox2.js +2 -2
  179. package/esm/VariantFeatureWidget/LaunchBreakendPanel.d.ts +2 -3
  180. package/esm/VariantFeatureWidget/LaunchBreakendPanel.js +48 -61
  181. package/esm/VariantFeatureWidget/LaunchBreakendWidgetArea.d.ts +4 -0
  182. package/esm/VariantFeatureWidget/LaunchBreakendWidgetArea.js +24 -0
  183. package/esm/VariantFeatureWidget/VariantConsequenceDataGrid.d.ts +5 -0
  184. package/esm/VariantFeatureWidget/VariantConsequenceDataGrid.js +9 -0
  185. package/esm/VariantFeatureWidget/VariantConsequenceDataGridWrapper.d.ts +5 -0
  186. package/esm/VariantFeatureWidget/VariantConsequenceDataGridWrapper.js +17 -0
  187. package/esm/VariantFeatureWidget/VariantConsequencePanel.d.ts +5 -0
  188. package/esm/VariantFeatureWidget/VariantConsequencePanel.js +9 -0
  189. package/esm/VariantFeatureWidget/VariantFeatureWidget.d.ts +1 -2
  190. package/esm/VariantFeatureWidget/VariantFeatureWidget.js +30 -29
  191. package/esm/VariantFeatureWidget/VariantSampleFilters.d.ts +9 -0
  192. package/esm/VariantFeatureWidget/VariantSampleFilters.js +7 -0
  193. package/esm/VariantFeatureWidget/VariantSampleGrid.d.ts +9 -7
  194. package/esm/VariantFeatureWidget/VariantSampleGrid.js +15 -22
  195. package/esm/VariantFeatureWidget/types.d.ts +16 -0
  196. package/esm/VariantFeatureWidget/types.js +1 -0
  197. package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js +10 -27
  198. package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts +12 -7
  199. package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js +27 -37
  200. package/esm/VcfAdapter/VcfAdapter.d.ts +7 -0
  201. package/esm/VcfAdapter/VcfAdapter.js +31 -5
  202. package/esm/VcfAdapter/configSchema.d.ts +8 -0
  203. package/esm/VcfAdapter/configSchema.js +12 -1
  204. package/esm/VcfFeature/index.js +2 -1
  205. package/esm/VcfFeature/util.js +3 -4
  206. package/esm/VcfTabixAdapter/VcfTabixAdapter.js +38 -12
  207. package/esm/VcfTabixAdapter/configSchema.d.ts +8 -0
  208. package/esm/VcfTabixAdapter/configSchema.js +8 -0
  209. package/esm/extensionPoints.js +21 -33
  210. package/esm/getMultiVariantFeaturesAutorun.d.ts +4 -7
  211. package/esm/getMultiVariantFeaturesAutorun.js +16 -15
  212. package/esm/getMultiVariantSourcesAutorun.d.ts +1 -6
  213. package/esm/shared/BulkEditPanel.d.ts +4 -5
  214. package/esm/shared/BulkEditPanel.js +70 -66
  215. package/esm/shared/ClusterDialog.d.ts +4 -5
  216. package/esm/shared/ClusterDialog.js +44 -62
  217. package/esm/shared/ColorLegend.d.ts +2 -3
  218. package/esm/shared/ColorLegend.js +8 -10
  219. package/esm/shared/HelpfulTips.d.ts +1 -0
  220. package/esm/shared/HelpfulTips.js +4 -0
  221. package/esm/shared/LegendBar.d.ts +3 -3
  222. package/esm/shared/LegendBar.js +7 -13
  223. package/esm/shared/MAFFilterDialog.d.ts +2 -3
  224. package/esm/shared/MAFFilterDialog.js +14 -19
  225. package/esm/shared/MultiVariantBaseModel.d.ts +341 -0
  226. package/esm/shared/MultiVariantBaseModel.js +277 -0
  227. package/esm/shared/MultiVariantTooltip.d.ts +6 -0
  228. package/esm/shared/MultiVariantTooltip.js +17 -0
  229. package/esm/shared/RectBg.d.ts +2 -3
  230. package/esm/shared/RectBg.js +3 -4
  231. package/esm/shared/RowPalettizer.d.ts +2 -3
  232. package/esm/shared/RowPalettizer.js +30 -25
  233. package/esm/shared/SetColorDialog.d.ts +2 -3
  234. package/esm/shared/SetColorDialog.js +26 -42
  235. package/esm/shared/SetMinMaxDialog.d.ts +1 -2
  236. package/esm/shared/SetMinMaxDialog.js +11 -18
  237. package/esm/shared/SetRowHeightDialog.d.ts +8 -0
  238. package/esm/shared/SetRowHeightDialog.js +15 -0
  239. package/esm/shared/SharedVariantMixin.d.ts +7 -7
  240. package/esm/shared/SourcesDataGrid.d.ts +6 -0
  241. package/esm/shared/SourcesDataGrid.js +62 -0
  242. package/esm/shared/SourcesGrid.d.ts +2 -3
  243. package/esm/shared/SourcesGrid.js +5 -111
  244. package/esm/shared/SourcesGridHeader.d.ts +7 -0
  245. package/esm/shared/SourcesGridHeader.js +35 -0
  246. package/esm/shared/multiVariantColor.d.ts +3 -0
  247. package/esm/shared/multiVariantColor.js +45 -0
  248. package/esm/types.d.ts +14 -0
  249. package/esm/types.js +1 -0
  250. package/esm/util.d.ts +6 -9
  251. package/esm/util.js +43 -13
  252. package/package.json +6 -7
  253. package/dist/VariantFeatureWidget/AnnotGrid.d.ts +0 -6
  254. package/dist/VariantFeatureWidget/AnnotGrid.js +0 -39
  255. package/dist/VariantFeatureWidget/VariantAnnotationTable.d.ts +0 -6
  256. package/dist/VariantFeatureWidget/VariantAnnotationTable.js +0 -16
  257. package/dist/configSchema.d.ts +0 -34
  258. package/dist/configSchema.js +0 -44
  259. package/dist/shared/DraggableDialog.d.ts +0 -6
  260. package/dist/shared/DraggableDialog.js +0 -62
  261. package/dist/shared/Tooltip.d.ts +0 -18
  262. package/dist/shared/Tooltip.js +0 -38
  263. package/esm/VariantFeatureWidget/AnnotGrid.d.ts +0 -6
  264. package/esm/VariantFeatureWidget/AnnotGrid.js +0 -13
  265. package/esm/VariantFeatureWidget/VariantAnnotationTable.d.ts +0 -6
  266. package/esm/VariantFeatureWidget/VariantAnnotationTable.js +0 -10
  267. package/esm/configSchema.d.ts +0 -34
  268. package/esm/configSchema.js +0 -42
  269. package/esm/shared/DraggableDialog.d.ts +0 -6
  270. package/esm/shared/DraggableDialog.js +0 -34
  271. package/esm/shared/Tooltip.d.ts +0 -18
  272. package/esm/shared/Tooltip.js +0 -33
@@ -107,7 +107,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
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  } & {
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  renderSvg(opts: import("@jbrowse/plugin-circular-view/src/CircularView/model").ExportSvgOptions & {
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  theme?: import("@mui/material").ThemeOptions;
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- }): Promise<import("react").JSX.Element>;
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+ }): Promise<import("react/jsx-runtime").JSX.Element>;
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  } & {
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  readonly rendererTypeName: any;
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  renderProps(): Record<string, unknown>;
@@ -36,7 +36,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  status?: string;
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  reactElement?: React.ReactElement;
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  };
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- }) => import("react").JSX.Element | undefined;
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+ }) => import("react/jsx-runtime").JSX.Element | undefined;
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  renderProps: any;
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  } & {
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  doReload(): void;
@@ -179,13 +179,13 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  } & {
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  readonly statsReadyAndRegionNotTooLarge: boolean;
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  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
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+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
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  } & {
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  featureIdUnderMouse: undefined | string;
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  contextMenuFeature: undefined | Feature;
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  } & {
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- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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- readonly blockType: "dynamicBlocks" | "staticBlocks";
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+ readonly DisplayMessageComponent: undefined | React.FC<any>;
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+ readonly blockType: "staticBlocks" | "dynamicBlocks";
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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  } & {
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  readonly renderDelay: number;
@@ -212,7 +212,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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  renderProps(): any;
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  } & {
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- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
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+ renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
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  afterAttach(): void;
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  } & {
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  readonly activeFilters: any;
@@ -0,0 +1,7 @@
1
+ import type { MultiLinearVariantDisplayModel } from '../model';
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+ declare const Crosshair: ({ mouseX, mouseY, model, }: {
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+ mouseX: number;
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+ mouseY: number;
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+ model: MultiLinearVariantDisplayModel;
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+ }) => import("react/jsx-runtime").JSX.Element | null;
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+ export default Crosshair;
@@ -0,0 +1,35 @@
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+ "use strict";
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+ var __importDefault = (this && this.__importDefault) || function (mod) {
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+ return (mod && mod.__esModule) ? mod : { "default": mod };
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+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ const jsx_runtime_1 = require("react/jsx-runtime");
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+ const util_1 = require("@jbrowse/core/util");
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+ const mobx_react_1 = require("mobx-react");
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+ const mui_1 = require("tss-react/mui");
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+ const MultiVariantTooltip_1 = __importDefault(require("../../shared/MultiVariantTooltip"));
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+ const useStyles = (0, mui_1.makeStyles)()({
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+ rel: {
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+ position: 'relative',
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+ },
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+ cursor: {
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+ pointerEvents: 'none',
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+ zIndex: 1000,
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+ position: 'absolute',
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+ },
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+ color: {
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+ width: 10,
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+ height: 10,
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+ },
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+ });
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+ const Crosshair = (0, mobx_react_1.observer)(function ({ mouseX, mouseY, model, }) {
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+ const { classes } = useStyles();
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+ const { hoveredGenotype, height, scrollTop, rowHeight, sources } = model;
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+ const { width } = (0, util_1.getContainingView)(model);
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+ const source = sources === null || sources === void 0 ? void 0 : sources[Math.floor(mouseY / rowHeight)];
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+ const y = mouseY - scrollTop;
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+ return source ? ((0, jsx_runtime_1.jsxs)("div", { className: classes.rel, children: [(0, jsx_runtime_1.jsxs)("svg", { className: classes.cursor, width: width, height: height, style: {
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+ top: scrollTop,
33
+ }, children: [(0, jsx_runtime_1.jsx)("line", { x1: 0, x2: width, y1: y, y2: y, stroke: "black" }), (0, jsx_runtime_1.jsx)("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })] }), (0, jsx_runtime_1.jsx)(MultiVariantTooltip_1.default, { source: { ...source, hoveredGenotype } })] })) : null;
34
+ });
35
+ exports.default = Crosshair;
@@ -1,6 +1,5 @@
1
- import React from 'react';
2
1
  import type { MultiLinearVariantDisplayModel } from '../model';
3
2
  declare const MultiLinearVariantDisplayComponent: (props: {
4
3
  model: MultiLinearVariantDisplayModel;
5
- }) => React.JSX.Element;
4
+ }) => import("react/jsx-runtime").JSX.Element;
6
5
  export default MultiLinearVariantDisplayComponent;
@@ -1,53 +1,20 @@
1
1
  "use strict";
2
- var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
- if (k2 === undefined) k2 = k;
4
- var desc = Object.getOwnPropertyDescriptor(m, k);
5
- if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
- desc = { enumerable: true, get: function() { return m[k]; } };
7
- }
8
- Object.defineProperty(o, k2, desc);
9
- }) : (function(o, m, k, k2) {
10
- if (k2 === undefined) k2 = k;
11
- o[k2] = m[k];
12
- }));
13
- var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
14
- Object.defineProperty(o, "default", { enumerable: true, value: v });
15
- }) : function(o, v) {
16
- o["default"] = v;
17
- });
18
- var __importStar = (this && this.__importStar) || function (mod) {
19
- if (mod && mod.__esModule) return mod;
20
- var result = {};
21
- if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
- __setModuleDefault(result, mod);
23
- return result;
24
- };
25
2
  var __importDefault = (this && this.__importDefault) || function (mod) {
26
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
27
4
  };
28
5
  Object.defineProperty(exports, "__esModule", { value: true });
29
- const react_1 = __importStar(require("react"));
30
- const ui_1 = require("@jbrowse/core/ui");
31
- const BaseTooltip_1 = __importDefault(require("@jbrowse/core/ui/BaseTooltip"));
32
- const util_1 = require("@jbrowse/core/util");
6
+ const jsx_runtime_1 = require("react/jsx-runtime");
7
+ const react_1 = require("react");
33
8
  const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
34
9
  const mobx_react_1 = require("mobx-react");
35
- const mui_1 = require("tss-react/mui");
10
+ const Crosshair_1 = __importDefault(require("./Crosshair"));
36
11
  const LegendBar_1 = __importDefault(require("../../shared/LegendBar"));
37
- const useStyles = (0, mui_1.makeStyles)()({
38
- cursor: {
39
- pointerEvents: 'none',
40
- },
41
- });
42
12
  const MultiLinearVariantDisplayComponent = (0, mobx_react_1.observer)(function (props) {
43
13
  const { model } = props;
44
- const { classes } = useStyles();
45
- const { height, sources, rowHeight, scrollTop } = model;
46
14
  const ref = (0, react_1.useRef)(null);
47
15
  const [mouseY, setMouseY] = (0, react_1.useState)();
48
16
  const [mouseX, setMouseX] = (0, react_1.useState)();
49
- const { width } = (0, util_1.getContainingView)(model);
50
- return (react_1.default.createElement("div", { ref: ref, onMouseMove: event => {
17
+ return ((0, jsx_runtime_1.jsxs)("div", { ref: ref, onMouseMove: event => {
51
18
  var _a;
52
19
  const rect = (_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect();
53
20
  const top = (rect === null || rect === void 0 ? void 0 : rect.top) || 0;
@@ -57,17 +24,6 @@ const MultiLinearVariantDisplayComponent = (0, mobx_react_1.observer)(function (
57
24
  }, onMouseLeave: () => {
58
25
  setMouseY(undefined);
59
26
  setMouseX(undefined);
60
- } },
61
- react_1.default.createElement(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }),
62
- react_1.default.createElement(LegendBar_1.default, { model: model }),
63
- mouseY && sources ? (react_1.default.createElement("div", { style: { position: 'relative' } },
64
- react_1.default.createElement("svg", { className: classes.cursor, width: width, height: height, style: { position: 'absolute', top: scrollTop } },
65
- react_1.default.createElement("line", { x1: 0, x2: width, y1: mouseY - scrollTop, y2: mouseY - scrollTop, stroke: "black" }),
66
- react_1.default.createElement("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })),
67
- react_1.default.createElement(BaseTooltip_1.default, null,
68
- react_1.default.createElement(ui_1.SanitizedHTML, { html: Object.entries(sources[Math.floor(mouseY / rowHeight)] || {})
69
- .filter(([key]) => key !== 'color')
70
- .map(([key, value]) => `${key}:${value}`)
71
- .join('\n') })))) : null));
27
+ }, children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }), (0, jsx_runtime_1.jsx)(LegendBar_1.default, { model: model }), mouseX && mouseY ? ((0, jsx_runtime_1.jsx)(Crosshair_1.default, { mouseX: mouseX, mouseY: mouseY, model: model })) : null] }));
72
28
  });
73
29
  exports.default = MultiLinearVariantDisplayComponent;
@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
15
15
  }) : function(o, v) {
16
16
  o["default"] = v;
17
17
  });
18
- var __importStar = (this && this.__importStar) || function (mod) {
19
- if (mod && mod.__esModule) return mod;
20
- var result = {};
21
- if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
- __setModuleDefault(result, mod);
23
- return result;
24
- };
18
+ var __importStar = (this && this.__importStar) || (function () {
19
+ var ownKeys = function(o) {
20
+ ownKeys = Object.getOwnPropertyNames || function (o) {
21
+ var ar = [];
22
+ for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
23
+ return ar;
24
+ };
25
+ return ownKeys(o);
26
+ };
27
+ return function (mod) {
28
+ if (mod && mod.__esModule) return mod;
29
+ var result = {};
30
+ if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
31
+ __setModuleDefault(result, mod);
32
+ return result;
33
+ };
34
+ })();
25
35
  var __importDefault = (this && this.__importDefault) || function (mod) {
26
36
  return (mod && mod.__esModule) ? mod : { "default": mod };
27
37
  };
@@ -38,7 +48,7 @@ function MultiLinearVariantDisplayF(pluginManager) {
38
48
  name: 'MultiLinearVariantDisplay',
39
49
  displayName: 'Multi-variant display (regular)',
40
50
  configSchema,
41
- stateModel: (0, model_1.default)(pluginManager, configSchema),
51
+ stateModel: (0, model_1.default)(configSchema),
42
52
  trackType: 'VariantTrack',
43
53
  viewType: 'LinearGenomeView',
44
54
  ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/VariantDisplayComponent')))),
@@ -1,10 +1,7 @@
1
- import { type ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
2
- import type { Source } from '../util';
3
- import type PluginManager from '@jbrowse/core/PluginManager';
4
1
  import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
5
- import type { AnyReactComponentType, Feature } from '@jbrowse/core/util';
2
+ import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
6
3
  import type { Instance } from 'mobx-state-tree';
7
- export declare function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
4
+ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
8
5
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
9
6
  type: import("mobx-state-tree").ISimpleType<string>;
10
7
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -24,7 +21,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
24
21
  stopToken: string | undefined;
25
22
  filled: boolean;
26
23
  reactElement: React.ReactElement | undefined;
27
- features: Map<string, Feature> | undefined;
24
+ features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
28
25
  layout: any;
29
26
  status: string;
30
27
  error: unknown;
@@ -39,7 +36,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
39
36
  status?: string;
40
37
  reactElement?: React.ReactElement;
41
38
  };
42
- }) => import("react").JSX.Element | undefined;
39
+ }) => import("react/jsx-runtime").JSX.Element | undefined;
43
40
  renderProps: any;
44
41
  } & {
45
42
  doReload(): void;
@@ -83,12 +80,20 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
83
80
  } & {
84
81
  type: import("mobx-state-tree").ISimpleType<"LinearBareDisplay">;
85
82
  configuration: AnyConfigurationSchemaType;
83
+ } & {
84
+ type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
85
+ layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../types").Source[], import("../types").Source[], import("../types").Source[]>, [undefined]>;
86
+ configuration: AnyConfigurationSchemaType;
87
+ minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
88
+ showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
89
+ renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
90
+ rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
91
+ autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
86
92
  } & {
87
93
  type: import("mobx-state-tree").ISimpleType<"MultiLinearVariantDisplay">;
88
- layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
89
94
  rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
95
+ minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
90
96
  autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
91
- showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
92
97
  }, {
93
98
  rendererTypeName: string;
94
99
  error: unknown;
@@ -180,32 +185,32 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
180
185
  } & {
181
186
  readonly statsReadyAndRegionNotTooLarge: boolean;
182
187
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
183
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
188
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
184
189
  } & {
185
190
  featureIdUnderMouse: undefined | string;
186
- contextMenuFeature: undefined | Feature;
191
+ contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
187
192
  } & {
188
- readonly DisplayMessageComponent: import("react").FC<any> | undefined;
189
- readonly blockType: "dynamicBlocks" | "staticBlocks";
193
+ readonly DisplayMessageComponent: undefined | React.FC<any>;
194
+ readonly blockType: "staticBlocks" | "dynamicBlocks";
190
195
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
191
196
  } & {
192
197
  readonly renderDelay: number;
193
- readonly TooltipComponent: AnyReactComponentType;
198
+ readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
194
199
  readonly selectedFeatureId: string | undefined;
195
200
  } & {
196
- readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
197
- readonly featureUnderMouse: Feature | undefined;
201
+ readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
202
+ readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
198
203
  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
199
204
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
200
205
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
201
206
  } & {
202
207
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
203
208
  deleteBlock(key: string): void;
204
- selectFeature(feature: Feature): void;
205
- navToFeature(feature: Feature): void;
209
+ selectFeature(feature: import("@jbrowse/core/util").Feature): void;
210
+ navToFeature(feature: import("@jbrowse/core/util").Feature): void;
206
211
  clearFeatureSelection(): void;
207
212
  setFeatureIdUnderMouse(feature?: string): void;
208
- setContextMenuFeature(feature?: Feature): void;
213
+ setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
209
214
  } & {
210
215
  reload(): Promise<void>;
211
216
  } & {
@@ -213,7 +218,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
213
218
  contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
214
219
  renderProps(): any;
215
220
  } & {
216
- renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
221
+ renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
217
222
  afterAttach(): void;
218
223
  } & {
219
224
  readonly rendererConfig: {
@@ -232,46 +237,114 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
232
237
  renderProps(): any;
233
238
  } & {
234
239
  sourcesLoadingStopToken: string | undefined;
235
- featureUnderMouseVolatile: Feature | undefined;
236
- sourcesVolatile: Source[] | undefined;
240
+ featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
241
+ sourcesVolatile: import("../types").Source[] | undefined;
242
+ featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
243
+ hasPhased: boolean;
244
+ sampleInfo: undefined | Record<string, import("../types").SampleInfo>;
245
+ hoveredGenotype: string | undefined;
237
246
  } & {
238
- setSourcesLoading(str: string): void;
239
- setLayout(layout: Source[]): void;
240
- clearLayout(): void;
241
- setSources(sources: Source[]): void;
242
- setFeatureUnderMouse(f?: Feature): void;
243
247
  setRowHeight(arg: number): void;
244
- setAutoHeight(arg: boolean): void;
248
+ setHoveredGenotype(arg: string): void;
249
+ setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
250
+ setLayout(layout: import("../types").Source[]): void;
251
+ clearLayout(): void;
252
+ setSourcesLoading(str: string): void;
253
+ setSources(sources: import("../types").Source[]): void;
254
+ setMafFilter(arg: number): void;
245
255
  setShowSidebarLabels(arg: boolean): void;
256
+ setPhasedMode(arg: string): void;
257
+ setAutoHeight(arg: boolean): void;
258
+ setHasPhased(arg: boolean): void;
259
+ setSampleInfo(arg: Record<string, import("../types").SampleInfo>): void;
246
260
  } & {
247
- readonly featureUnderMouse: Feature | undefined;
248
- readonly TooltipComponent: AnyReactComponentType;
249
- } & {
250
- readonly rendererTypeName: string;
261
+ readonly preSources: import("../types").Source[] | undefined;
251
262
  readonly sources: {
252
- color: string;
263
+ label: string;
264
+ id: string;
253
265
  baseUri?: string;
254
266
  name: string;
267
+ color?: string;
255
268
  group?: string;
269
+ HP?: number;
256
270
  }[] | undefined;
257
271
  } & {
258
272
  readonly rowHeight: number;
259
- } & {
260
- readonly canDisplayLabels: boolean;
261
- readonly totalHeight: number;
262
273
  adapterProps(): any;
263
- } & {
264
- renderProps(): any;
265
- } & {
266
274
  trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
267
275
  label: string;
276
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
277
+ muiName: string;
278
+ };
268
279
  type: string;
269
280
  checked: boolean;
270
281
  onClick: () => void;
282
+ subMenu?: undefined;
283
+ } | {
284
+ label: string;
285
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
286
+ muiName: string;
287
+ };
288
+ subMenu: ({
289
+ label: string;
290
+ disabled: boolean;
291
+ onClick: () => void;
292
+ type?: undefined;
293
+ checked?: undefined;
294
+ } | {
295
+ label: string;
296
+ type: string;
297
+ checked: boolean;
298
+ onClick: () => void;
299
+ disabled?: undefined;
300
+ })[];
301
+ type?: undefined;
302
+ checked?: undefined;
303
+ onClick?: undefined;
304
+ } | {
305
+ label: string;
306
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
307
+ muiName: string;
308
+ };
309
+ subMenu: ({
310
+ label: string;
311
+ type: string;
312
+ checked: boolean;
313
+ onClick: () => void;
314
+ disabled?: undefined;
315
+ } | {
316
+ label: string;
317
+ disabled: boolean;
318
+ checked: boolean;
319
+ type: string;
320
+ onClick: () => void;
321
+ })[];
322
+ type?: undefined;
323
+ checked?: undefined;
324
+ onClick?: undefined;
325
+ } | {
326
+ label: string;
327
+ icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
328
+ muiName: string;
329
+ };
330
+ subMenu: {
331
+ label: string;
332
+ onClick: () => void;
333
+ }[];
334
+ type?: undefined;
335
+ checked?: undefined;
336
+ onClick?: undefined;
271
337
  })[];
338
+ } & {
339
+ readonly canDisplayLabels: boolean;
340
+ readonly totalHeight: number;
341
+ } & {
342
+ renderProps(): any;
343
+ } & {
344
+ readonly rendererTypeName: string;
272
345
  } & {
273
346
  afterAttach(): void;
274
- renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
347
+ renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
275
348
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
276
349
  export type MultiLinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;
277
350
  export type MultiLinearVariantDisplayModel = Instance<MultiLinearVariantDisplayStateModel>;