@jbrowse/plugin-wiggle 2.4.2 → 2.6.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (220) hide show
  1. package/dist/BigWigAdapter/BigWigAdapter.d.ts +2 -2
  2. package/dist/BigWigAdapter/BigWigAdapter.js +4 -3
  3. package/dist/BigWigAdapter/BigWigAdapter.js.map +1 -1
  4. package/dist/BigWigAdapter/configSchema.d.ts +20 -1
  5. package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts +2 -2
  6. package/dist/DensityRenderer/configSchema.d.ts +33 -1
  7. package/dist/LinePlotRenderer/configSchema.d.ts +44 -1
  8. package/dist/LinearWiggleDisplay/components/SetColorDialog.d.ts +2 -2
  9. package/dist/LinearWiggleDisplay/components/Tooltip.d.ts +1 -1
  10. package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +2 -2
  11. package/dist/LinearWiggleDisplay/index.js +27 -4
  12. package/dist/LinearWiggleDisplay/index.js.map +1 -1
  13. package/dist/LinearWiggleDisplay/models/configSchema.d.ts +81 -1
  14. package/dist/LinearWiggleDisplay/models/configSchema.js +6 -67
  15. package/dist/LinearWiggleDisplay/models/configSchema.js.map +1 -1
  16. package/dist/LinearWiggleDisplay/models/model.d.ts +172 -320
  17. package/dist/LinearWiggleDisplay/models/model.js +18 -450
  18. package/dist/LinearWiggleDisplay/models/model.js.map +1 -1
  19. package/dist/LinearWiggleDisplay/models/renderSvg.d.ts +4 -0
  20. package/dist/LinearWiggleDisplay/models/renderSvg.js +21 -0
  21. package/dist/LinearWiggleDisplay/models/renderSvg.js.map +1 -0
  22. package/dist/MultiDensityRenderer/MultiDensityRenderer.js +1 -1
  23. package/dist/MultiDensityRenderer/MultiDensityRenderer.js.map +1 -1
  24. package/dist/MultiDensityRenderer/configSchema.d.ts +33 -1
  25. package/dist/MultiLineRenderer/MultiLineRenderer.js +1 -1
  26. package/dist/MultiLineRenderer/MultiLineRenderer.js.map +1 -1
  27. package/dist/MultiLineRenderer/configSchema.d.ts +51 -1
  28. package/dist/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts +2 -2
  29. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +2 -2
  30. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js +37 -38
  31. package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js.map +1 -1
  32. package/dist/MultiLinearWiggleDisplay/components/Tooltip.d.ts +1 -1
  33. package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +3 -3
  34. package/dist/MultiLinearWiggleDisplay/index.js +25 -2
  35. package/dist/MultiLinearWiggleDisplay/index.js.map +1 -1
  36. package/dist/MultiLinearWiggleDisplay/models/configSchema.d.ts +87 -1
  37. package/dist/MultiLinearWiggleDisplay/models/configSchema.js +6 -66
  38. package/dist/MultiLinearWiggleDisplay/models/configSchema.js.map +1 -1
  39. package/dist/MultiLinearWiggleDisplay/models/model.d.ts +288 -153
  40. package/dist/MultiLinearWiggleDisplay/models/model.js +334 -523
  41. package/dist/MultiLinearWiggleDisplay/models/model.js.map +1 -1
  42. package/dist/MultiLinearWiggleDisplay/models/renderSvg.d.ts +4 -0
  43. package/dist/MultiLinearWiggleDisplay/models/renderSvg.js +20 -0
  44. package/dist/MultiLinearWiggleDisplay/models/renderSvg.js.map +1 -0
  45. package/dist/MultiQuantitativeTrack/configSchema.d.ts +73 -1
  46. package/dist/MultiRowLineRenderer/MultiRowLineRenderer.js +1 -1
  47. package/dist/MultiRowLineRenderer/MultiRowLineRenderer.js.map +1 -1
  48. package/dist/MultiRowLineRenderer/configSchema.d.ts +51 -1
  49. package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +1 -1
  50. package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js.map +1 -1
  51. package/dist/MultiRowXYPlotRenderer/configSchema.d.ts +68 -1
  52. package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +1 -1
  53. package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js +2 -2
  54. package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js.map +1 -1
  55. package/dist/MultiWiggleAdapter/configSchema.d.ts +18 -1
  56. package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts +2 -2
  57. package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js +1 -1
  58. package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map +1 -1
  59. package/dist/MultiWiggleRendering.d.ts +2 -2
  60. package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.js +3 -2
  61. package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.js.map +1 -1
  62. package/dist/MultiXYPlotRenderer/configSchema.d.ts +65 -1
  63. package/dist/QuantitativeTrack/configSchema.d.ts +73 -1
  64. package/dist/Tooltip.d.ts +1 -1
  65. package/dist/WiggleBaseRenderer.d.ts +1 -1
  66. package/dist/WiggleRPC/MultiWiggleGetSources.d.ts +21 -0
  67. package/dist/WiggleRPC/MultiWiggleGetSources.js +51 -0
  68. package/dist/WiggleRPC/MultiWiggleGetSources.js.map +1 -0
  69. package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts +14 -0
  70. package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +37 -0
  71. package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js.map +1 -0
  72. package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +20 -0
  73. package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +54 -0
  74. package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js.map +1 -0
  75. package/dist/WiggleRPC/rpcMethods.d.ts +3 -47
  76. package/dist/WiggleRPC/rpcMethods.js +16 -117
  77. package/dist/WiggleRPC/rpcMethods.js.map +1 -1
  78. package/dist/WiggleRendering.d.ts +2 -2
  79. package/dist/XYPlotRenderer/configSchema.d.ts +65 -1
  80. package/dist/configSchema.d.ts +51 -1
  81. package/dist/index.d.ts +329 -180
  82. package/dist/index.js +2 -2
  83. package/dist/index.js.map +1 -1
  84. package/dist/shared/SetMinMaxDialog.d.ts +2 -2
  85. package/dist/shared/YScaleBar.d.ts +4 -3
  86. package/dist/shared/YScaleBar.js +1 -1
  87. package/dist/shared/YScaleBar.js.map +1 -1
  88. package/dist/shared/configShared.d.ts +85 -0
  89. package/dist/shared/configShared.js +84 -0
  90. package/dist/shared/configShared.js.map +1 -0
  91. package/dist/shared/modelShared.d.ts +576 -0
  92. package/dist/shared/modelShared.js +480 -0
  93. package/dist/shared/modelShared.js.map +1 -0
  94. package/dist/util.d.ts +9 -9
  95. package/dist/util.js +13 -22
  96. package/dist/util.js.map +1 -1
  97. package/esm/BigWigAdapter/BigWigAdapter.d.ts +2 -2
  98. package/esm/BigWigAdapter/BigWigAdapter.js +6 -4
  99. package/esm/BigWigAdapter/BigWigAdapter.js.map +1 -1
  100. package/esm/BigWigAdapter/configSchema.d.ts +20 -1
  101. package/esm/CreateMultiWiggleExtension/ConfirmDialog.d.ts +2 -2
  102. package/esm/DensityRenderer/configSchema.d.ts +33 -1
  103. package/esm/LinePlotRenderer/configSchema.d.ts +44 -1
  104. package/esm/LinearWiggleDisplay/components/SetColorDialog.d.ts +2 -2
  105. package/esm/LinearWiggleDisplay/components/Tooltip.d.ts +1 -1
  106. package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +2 -2
  107. package/esm/LinearWiggleDisplay/index.js +2 -2
  108. package/esm/LinearWiggleDisplay/index.js.map +1 -1
  109. package/esm/LinearWiggleDisplay/models/configSchema.d.ts +81 -1
  110. package/esm/LinearWiggleDisplay/models/configSchema.js +3 -67
  111. package/esm/LinearWiggleDisplay/models/configSchema.js.map +1 -1
  112. package/esm/LinearWiggleDisplay/models/model.d.ts +172 -320
  113. package/esm/LinearWiggleDisplay/models/model.js +22 -454
  114. package/esm/LinearWiggleDisplay/models/model.js.map +1 -1
  115. package/esm/LinearWiggleDisplay/models/renderSvg.d.ts +4 -0
  116. package/esm/LinearWiggleDisplay/models/renderSvg.js +14 -0
  117. package/esm/LinearWiggleDisplay/models/renderSvg.js.map +1 -0
  118. package/esm/MultiDensityRenderer/MultiDensityRenderer.js +1 -1
  119. package/esm/MultiDensityRenderer/MultiDensityRenderer.js.map +1 -1
  120. package/esm/MultiDensityRenderer/configSchema.d.ts +33 -1
  121. package/esm/MultiLineRenderer/MultiLineRenderer.js +1 -1
  122. package/esm/MultiLineRenderer/MultiLineRenderer.js.map +1 -1
  123. package/esm/MultiLineRenderer/configSchema.d.ts +51 -1
  124. package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts +2 -2
  125. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +2 -2
  126. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js +37 -38
  127. package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js.map +1 -1
  128. package/esm/MultiLinearWiggleDisplay/components/Tooltip.d.ts +1 -1
  129. package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +3 -3
  130. package/esm/MultiLinearWiggleDisplay/index.js +2 -2
  131. package/esm/MultiLinearWiggleDisplay/index.js.map +1 -1
  132. package/esm/MultiLinearWiggleDisplay/models/configSchema.d.ts +87 -1
  133. package/esm/MultiLinearWiggleDisplay/models/configSchema.js +3 -66
  134. package/esm/MultiLinearWiggleDisplay/models/configSchema.js.map +1 -1
  135. package/esm/MultiLinearWiggleDisplay/models/model.d.ts +288 -153
  136. package/esm/MultiLinearWiggleDisplay/models/model.js +336 -527
  137. package/esm/MultiLinearWiggleDisplay/models/model.js.map +1 -1
  138. package/esm/MultiLinearWiggleDisplay/models/renderSvg.d.ts +4 -0
  139. package/esm/MultiLinearWiggleDisplay/models/renderSvg.js +13 -0
  140. package/esm/MultiLinearWiggleDisplay/models/renderSvg.js.map +1 -0
  141. package/esm/MultiQuantitativeTrack/configSchema.d.ts +73 -1
  142. package/esm/MultiRowLineRenderer/MultiRowLineRenderer.js +1 -1
  143. package/esm/MultiRowLineRenderer/MultiRowLineRenderer.js.map +1 -1
  144. package/esm/MultiRowLineRenderer/configSchema.d.ts +51 -1
  145. package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +1 -1
  146. package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js.map +1 -1
  147. package/esm/MultiRowXYPlotRenderer/configSchema.d.ts +68 -1
  148. package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +1 -1
  149. package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js +3 -2
  150. package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js.map +1 -1
  151. package/esm/MultiWiggleAdapter/configSchema.d.ts +18 -1
  152. package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts +2 -2
  153. package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js +1 -1
  154. package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map +1 -1
  155. package/esm/MultiWiggleRendering.d.ts +2 -2
  156. package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js +2 -1
  157. package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js.map +1 -1
  158. package/esm/MultiXYPlotRenderer/configSchema.d.ts +65 -1
  159. package/esm/QuantitativeTrack/configSchema.d.ts +73 -1
  160. package/esm/Tooltip.d.ts +1 -1
  161. package/esm/WiggleBaseRenderer.d.ts +1 -1
  162. package/esm/WiggleRPC/MultiWiggleGetSources.d.ts +21 -0
  163. package/esm/WiggleRPC/MultiWiggleGetSources.js +44 -0
  164. package/esm/WiggleRPC/MultiWiggleGetSources.js.map +1 -0
  165. package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts +14 -0
  166. package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +30 -0
  167. package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js.map +1 -0
  168. package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +20 -0
  169. package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +47 -0
  170. package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js.map +1 -0
  171. package/esm/WiggleRPC/rpcMethods.d.ts +3 -47
  172. package/esm/WiggleRPC/rpcMethods.js +3 -111
  173. package/esm/WiggleRPC/rpcMethods.js.map +1 -1
  174. package/esm/WiggleRendering.d.ts +2 -2
  175. package/esm/XYPlotRenderer/configSchema.d.ts +65 -1
  176. package/esm/configSchema.d.ts +51 -1
  177. package/esm/index.d.ts +329 -180
  178. package/esm/index.js +3 -3
  179. package/esm/index.js.map +1 -1
  180. package/esm/shared/SetMinMaxDialog.d.ts +2 -2
  181. package/esm/shared/YScaleBar.d.ts +4 -3
  182. package/esm/shared/YScaleBar.js +1 -1
  183. package/esm/shared/YScaleBar.js.map +1 -1
  184. package/esm/shared/configShared.d.ts +85 -0
  185. package/esm/shared/configShared.js +81 -0
  186. package/esm/shared/configShared.js.map +1 -0
  187. package/esm/shared/modelShared.d.ts +576 -0
  188. package/esm/shared/modelShared.js +454 -0
  189. package/esm/shared/modelShared.js.map +1 -0
  190. package/esm/util.d.ts +9 -9
  191. package/esm/util.js +10 -18
  192. package/esm/util.js.map +1 -1
  193. package/package.json +4 -4
  194. package/src/BigWigAdapter/BigWigAdapter.test.ts +8 -3
  195. package/src/BigWigAdapter/BigWigAdapter.ts +8 -7
  196. package/src/LinearWiggleDisplay/index.ts +2 -2
  197. package/src/LinearWiggleDisplay/models/configSchema.ts +4 -73
  198. package/src/LinearWiggleDisplay/models/model.tsx +25 -524
  199. package/src/LinearWiggleDisplay/models/renderSvg.tsx +29 -0
  200. package/src/MultiDensityRenderer/MultiDensityRenderer.ts +1 -2
  201. package/src/MultiLineRenderer/MultiLineRenderer.ts +1 -2
  202. package/src/MultiLinearWiggleDisplay/components/SetColorDialog.tsx +54 -51
  203. package/src/MultiLinearWiggleDisplay/index.ts +2 -2
  204. package/src/MultiLinearWiggleDisplay/models/configSchema.ts +4 -72
  205. package/src/MultiLinearWiggleDisplay/models/model.tsx +134 -389
  206. package/src/MultiLinearWiggleDisplay/models/renderSvg.tsx +26 -0
  207. package/src/MultiRowLineRenderer/MultiRowLineRenderer.ts +1 -2
  208. package/src/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.ts +1 -2
  209. package/src/MultiWiggleAdapter/MultiWiggleAdapter.ts +1 -1
  210. package/src/MultiWiggleAddTrackWidget/AddTrackWorkflow.tsx +1 -1
  211. package/src/MultiXYPlotRenderer/MultiXYPlotRenderer.ts +2 -2
  212. package/src/WiggleRPC/MultiWiggleGetSources.ts +68 -0
  213. package/src/WiggleRPC/WiggleGetGlobalQuantitativeStats.ts +44 -0
  214. package/src/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.ts +73 -0
  215. package/src/WiggleRPC/rpcMethods.ts +3 -170
  216. package/src/index.ts +4 -4
  217. package/src/shared/YScaleBar.tsx +4 -2
  218. package/src/shared/configShared.ts +90 -0
  219. package/src/shared/modelShared.ts +510 -0
  220. package/src/util.ts +24 -26
@@ -3,17 +3,26 @@ import { Instance } from 'mobx-state-tree';
3
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  import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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  import { Feature } from '@jbrowse/core/util';
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  import PluginManager from '@jbrowse/core/PluginManager';
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+ import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
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  interface Source {
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  name: string;
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  color?: string;
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  group?: string;
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  }
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- declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
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+ /**
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+ * #stateModel MultiLinearWiggleDisplay
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+ * extends `SharedWiggleMixin`
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+ */
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+ export declare function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("mobx-state-tree").ISimpleType<string>;
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  } & {
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  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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+ } & {
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+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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+ } & {
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  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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  key: import("mobx-state-tree").ISimpleType<string>;
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  region: import("mobx-state-tree").IModelType<{
@@ -51,6 +60,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
51
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  setMessage(messageText: string): void;
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  setRendered(props: {
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  reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
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+ /**
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+ * #getter
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+ */
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  features: Map<string, Feature>;
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  layout: any;
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  maxHeightReached: boolean;
@@ -60,11 +72,30 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
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  reload(): void;
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  beforeDestroy(): void;
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74
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
75
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
76
+ maxFeatureScreenDensity: {
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+ type: string;
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+ description: string;
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+ defaultValue: number;
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+ };
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+ fetchSizeLimit: {
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+ type: string;
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+ defaultValue: number;
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+ description: string;
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+ };
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+ height: {
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+ type: string;
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+ defaultValue: number;
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+ description: string;
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+ };
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+ mouseover: {
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+ type: string;
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+ description: string;
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+ defaultValue: string;
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+ contextVariable: string[];
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+ };
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
65
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  } & {
66
- type: import("mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
67
- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
68
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  selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
69
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  resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
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  fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -75,16 +106,30 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
75
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  summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
76
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  rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
77
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  scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
78
- autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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- displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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- layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
109
+ autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
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+ * #property
111
+ */
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+ displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
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+ * #property
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+ */
81
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  constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
82
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  max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
83
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  min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
84
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  }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
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+ configuration: AnyConfigurationSchemaType;
120
+ } & {
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+ /**
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+ * #property
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+ */
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+ type: import("mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
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+ /**
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+ * #property
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+ */
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+ layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
85
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  }, {
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  rendererTypeName: string;
87
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  error: unknown;
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+ message: string | undefined;
88
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  } & {
89
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  readonly RenderingComponent: React.FC<{
90
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  model: {
@@ -94,6 +139,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
94
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
95
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  rendererTypeName: string;
96
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  error: unknown;
142
+ message: string | undefined;
97
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  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
98
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
99
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  type: import("mobx-state-tree").ISimpleType<string>;
@@ -101,8 +147,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
101
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  }, {
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  rendererTypeName: string;
103
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  error: unknown;
150
+ message: string | undefined;
104
151
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
105
- onHorizontalScroll?: Function | undefined;
152
+ onHorizontalScroll?: Function | undefined; /**
153
+ * #property
154
+ */
106
155
  blockState?: Record<string, any> | undefined;
107
156
  }>;
108
157
  readonly DisplayBlurb: React.FC<{
@@ -113,6 +162,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
113
162
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
114
163
  rendererTypeName: string;
115
164
  error: unknown;
165
+ message: string | undefined;
116
166
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
117
167
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
118
168
  type: import("mobx-state-tree").ISimpleType<string>;
@@ -120,6 +170,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
120
170
  }, {
121
171
  rendererTypeName: string;
122
172
  error: unknown;
173
+ message: string | undefined;
123
174
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
124
175
  }> | null;
125
176
  readonly adapterConfig: any;
@@ -129,21 +180,49 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
129
180
  readonly DisplayMessageComponent: React.FC<any> | undefined;
130
181
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
131
182
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
132
- regionCannotBeRendered(): undefined;
183
+ regionCannotBeRendered(): null;
133
184
  } & {
185
+ setMessage(arg?: string | undefined): void;
134
186
  setError(error?: unknown): void;
135
187
  setRpcDriverName(rpcDriverName: string): void;
136
188
  reload(): void;
137
189
  } & {
138
- currBpPerPx: number;
139
190
  scrollTop: number;
140
- message: string;
191
+ } & {
192
+ readonly height: number;
193
+ } & {
194
+ setScrollTop(scrollTop: number): void;
195
+ setHeight(displayHeight: number): number;
196
+ resizeHeight(distance: number): number;
197
+ } & {
198
+ featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
199
+ featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
200
+ currStatsBpPerPx: number;
201
+ } & {
202
+ readonly currentBytesRequested: number;
203
+ readonly currentFeatureScreenDensity: number;
204
+ readonly maxFeatureScreenDensity: any;
205
+ readonly featureDensityStatsReady: boolean;
206
+ readonly maxAllowableBytes: number;
207
+ } & {
208
+ afterAttach(): void;
209
+ } & {
210
+ setCurrStatsBpPerPx(n: number): void;
211
+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
212
+ getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
213
+ setFeatureDensityStatsP(arg: any): void;
214
+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
215
+ clearFeatureDensityStats(): void;
216
+ } & {
217
+ readonly regionTooLarge: boolean;
218
+ readonly regionTooLargeReason: string;
219
+ } & {
220
+ regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
221
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
222
+ } & {
141
223
  featureIdUnderMouse: string | undefined;
142
224
  contextMenuFeature: Feature | undefined;
143
- estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
144
- estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
145
225
  } & {
146
- readonly height: number;
147
226
  readonly blockType: "dynamicBlocks" | "staticBlocks";
148
227
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
149
228
  } & {
@@ -152,153 +231,273 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
152
231
  readonly selectedFeatureId: string | undefined;
153
232
  readonly DisplayMessageComponent: React.FC<any> | undefined;
154
233
  } & {
155
- readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
234
+ readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>; /**
235
+ * #getter
236
+ * can be used to give it a "color scale" like a R heatmap, not
237
+ * implemented like this yet but flag can be used for this
238
+ */
156
239
  readonly featureUnderMouse: Feature | undefined;
157
240
  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
158
241
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
159
242
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
160
- readonly currentBytesRequested: number;
161
- readonly currentFeatureScreenDensity: number;
162
- readonly maxFeatureScreenDensity: any;
163
- readonly estimatedStatsReady: boolean;
164
- readonly maxAllowableBytes: number;
165
- } & {
166
- setMessage(message: string): void;
167
243
  } & {
168
- afterAttach(): void;
169
- estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
170
- setRegionsStatsP(arg: any): void;
171
- setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
172
- clearRegionsStats(): void;
173
- setHeight(displayHeight: number): number;
174
- resizeHeight(distance: number): number;
175
- setScrollTop(scrollTop: number): void;
176
- updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
177
244
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
178
- setCurrBpPerPx(n: number): void;
179
245
  deleteBlock(key: string): void;
180
246
  selectFeature(feature: Feature): void;
181
247
  clearFeatureSelection(): void;
182
- setFeatureIdUnderMouse(feature: string | undefined): void;
183
- reload(): void;
248
+ setFeatureIdUnderMouse(feature?: string | undefined): void;
184
249
  setContextMenuFeature(feature?: Feature | undefined): void;
185
- } & {
186
- readonly regionTooLarge: boolean;
187
- readonly regionTooLargeReason: string;
188
250
  } & {
189
251
  reload(): Promise<void>;
190
252
  } & {
191
- afterAttach(): void;
192
- } & {
193
- regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
194
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
195
253
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
196
254
  contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
197
- renderProps(): any;
255
+ renderProps(): any; /**
256
+ * #method
257
+ */
198
258
  } & {
199
- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
200
- overrideHeight: number;
201
- theme: import("@mui/material").ThemeOptions;
202
- }): Promise<JSX.Element>;
259
+ renderSvg(opts: ExportSvgDisplayOptions): Promise<React.JSX.Element>;
260
+ afterAttach(): void;
203
261
  } & {
204
262
  message: string | undefined;
205
263
  stats: {
206
264
  scoreMin: number;
207
265
  scoreMax: number;
208
266
  } | undefined;
209
- statsRegion: string | undefined;
267
+ /**
268
+ * #action
269
+ */
210
270
  statsFetchInProgress: AbortController | undefined;
211
- featureUnderMouseVolatile: Feature | undefined;
212
- sourcesVolatile: Source[] | undefined;
213
271
  } & {
214
- setLayout(layout: Source[]): void;
215
- clearLayout(): void;
216
- updateStats(stats: {
217
- scoreMin: number;
272
+ updateQuantitativeStats(stats: {
273
+ scoreMin: number; /**
274
+ * #action
275
+ */
218
276
  scoreMax: number;
219
277
  }): void;
220
- setSources(sources: Source[]): void;
221
- setColor(color: string): void;
222
- setPosColor(color: string): void;
223
- setNegColor(color: string): void;
278
+ setColor(color?: string | undefined): void;
279
+ setPosColor(color?: string | undefined): void;
280
+ setNegColor(color?: string | undefined): void;
224
281
  setLoading(aborter: AbortController): void;
225
282
  selectFeature(feature: Feature): void;
226
- setFeatureUnderMouse(f?: Feature): void;
227
283
  setResolution(res: number): void;
228
284
  setFill(fill: number): void;
229
285
  toggleLogScale(): void;
230
- setScaleType(scale?: string): void;
286
+ setScaleType(scale?: string | undefined): void;
231
287
  setSummaryScoreMode(val: string): void;
232
288
  setAutoscale(val: string): void;
233
- setMaxScore(val?: number): void;
289
+ setMaxScore(val?: number | undefined): void;
234
290
  setRendererType(val: string): void;
235
- setMinScore(val?: number): void;
291
+ setMinScore(val?: number | undefined): void;
236
292
  toggleCrossHatches(): void;
237
293
  setCrossHatches(cross: boolean): void;
238
294
  } & {
239
- readonly featureUnderMouse: Feature | undefined;
240
- readonly TooltipComponent: React.FC<{}>;
241
295
  readonly adapterTypeName: any;
242
296
  readonly rendererTypeNameSimple: any;
243
- readonly rendererTypeName: string;
244
297
  readonly filters: undefined;
245
- readonly scaleType: string;
246
- readonly maxScore: number;
247
- readonly minScore: number;
298
+ readonly scaleType: any;
299
+ readonly maxScore: any;
300
+ readonly minScore: any;
248
301
  } & {
302
+ readonly adapterCapabilities: string[];
249
303
  readonly rendererConfig: {
250
304
  [x: string]: any;
251
305
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
252
306
  setSubschema(slotName: string, data: unknown): any;
253
307
  } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
308
+ readonly autoscaleType: any;
309
+ } & {
310
+ readonly domain: number[] | undefined;
311
+ } & {
312
+ readonly filled: boolean;
313
+ readonly summaryScoreModeSetting: string;
314
+ readonly scaleOpts: {
315
+ domain: number[] | undefined;
316
+ stats: {
317
+ scoreMin: number;
318
+ scoreMax: number;
319
+ } | undefined;
320
+ autoscaleType: any;
321
+ scaleType: any;
322
+ inverted: any;
323
+ };
324
+ readonly canHaveFill: boolean;
325
+ readonly displayCrossHatchesSetting: boolean;
326
+ readonly hasResolution: boolean;
327
+ readonly hasGlobalStats: boolean;
328
+ } & {
329
+ scoreTrackMenuItems(): ({
330
+ label: string;
331
+ subMenu: {
332
+ label: string;
333
+ onClick: () => void;
334
+ }[];
335
+ onClick?: undefined;
336
+ } | {
337
+ label: string;
338
+ subMenu: {
339
+ label: string;
340
+ type: string;
341
+ checked: boolean;
342
+ onClick: () => void;
343
+ }[];
344
+ onClick?: undefined;
345
+ } | {
346
+ label: string;
347
+ onClick: () => void;
348
+ subMenu?: undefined;
349
+ })[];
254
350
  } & {
351
+ reload(): Promise<void>;
352
+ } & {
353
+ featureUnderMouseVolatile: Feature | undefined;
354
+ sourcesVolatile: Source[] | undefined;
355
+ } & {
356
+ /**
357
+ * #action
358
+ */
359
+ setLayout(layout: Source[]): void;
360
+ /**
361
+ * #action
362
+ */
363
+ clearLayout(): void;
364
+ /**
365
+ * #action
366
+ */
367
+ setSources(sources: Source[]): void;
368
+ /**
369
+ * #action
370
+ */
371
+ setFeatureUnderMouse(f?: Feature): void;
372
+ } & {
373
+ /**
374
+ * #getter
375
+ */
376
+ readonly featureUnderMouse: Feature | undefined;
377
+ /**
378
+ * #getter
379
+ */
380
+ readonly TooltipComponent: React.FC<{}>;
381
+ /**
382
+ * #getter
383
+ */
384
+ readonly rendererTypeName: string;
385
+ } & {
386
+ /**
387
+ * #getter
388
+ */
255
389
  readonly needsScalebar: boolean;
390
+ /**
391
+ * #getter
392
+ */
256
393
  readonly needsFullHeightScalebar: boolean;
394
+ /**
395
+ * #getter
396
+ */
257
397
  readonly isMultiRow: boolean;
398
+ /**
399
+ * #getter
400
+ * can be used to give it a "color scale" like a R heatmap, not
401
+ * implemented like this yet but flag can be used for this
402
+ */
258
403
  readonly needsCustomLegend: boolean;
259
404
  readonly canHaveFill: boolean;
405
+ /**
406
+ * #getter
407
+ * the multirowxy and multiline don't need to use colors on the legend
408
+ * boxes since their track is drawn with the color. sort of a stylistic
409
+ * choice
410
+ */
260
411
  readonly renderColorBoxes: boolean;
412
+ /**
413
+ * #getter
414
+ * positions multi-row below the tracklabel even if using overlap
415
+ * tracklabels for everything else
416
+ */
261
417
  readonly prefersOffset: boolean;
418
+ /**
419
+ * #getter
420
+ */
262
421
  readonly sources: {
263
422
  color: string;
264
423
  name: string;
265
424
  group?: string | undefined;
266
425
  }[] | undefined;
267
426
  } & {
268
- readonly filled: boolean;
269
- readonly summaryScoreModeSetting: string;
270
- readonly domain: number[] | undefined;
271
- readonly scaleOpts: {
272
- autoscaleType: string;
273
- domain: number[] | undefined;
274
- stats: {
275
- scoreMin: number;
276
- scoreMax: number;
277
- } | undefined;
278
- scaleType: string;
279
- inverted: any;
280
- };
281
- readonly autoscaleType: string;
282
- readonly displayCrossHatchesSetting: boolean;
427
+ /**
428
+ * #getter
429
+ */
283
430
  readonly rowHeight: number;
431
+ /**
432
+ * #getter
433
+ */
284
434
  readonly rowHeightTooSmallForScalebar: boolean;
435
+ /**
436
+ * #getter
437
+ */
285
438
  readonly useMinimalTicks: any;
286
439
  } & {
440
+ /**
441
+ * #getter
442
+ */
287
443
  readonly ticks: {
288
444
  range: number[];
289
445
  values: number[];
290
446
  format: (d: import("d3-scale").NumberValue) => string;
291
447
  position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
292
448
  } | undefined;
449
+ /**
450
+ * #getter
451
+ */
293
452
  readonly colors: string[];
294
- readonly adapterCapabilities: string[];
295
453
  } & {
454
+ /**
455
+ * #method
456
+ */
296
457
  renderProps(): any;
458
+ /**
459
+ * #getter
460
+ */
297
461
  readonly hasResolution: boolean;
462
+ /**
463
+ * #getter
464
+ */
298
465
  readonly hasGlobalStats: boolean;
466
+ /**
467
+ * #getter
468
+ */
299
469
  readonly fillSetting: 2 | 0 | 1;
300
470
  } & {
471
+ /**
472
+ * #method
473
+ */
301
474
  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 | {
475
+ label: string;
476
+ subMenu: ({
477
+ label: string;
478
+ subMenu: {
479
+ label: string;
480
+ onClick: () => void;
481
+ }[];
482
+ onClick?: undefined;
483
+ } | {
484
+ label: string;
485
+ subMenu: {
486
+ label: string;
487
+ type: string;
488
+ checked: boolean;
489
+ onClick: () => void;
490
+ }[];
491
+ onClick?: undefined;
492
+ } | {
493
+ label: string;
494
+ onClick: () => void;
495
+ subMenu?: undefined;
496
+ })[];
497
+ type?: undefined;
498
+ checked?: undefined;
499
+ onClick?: undefined;
500
+ } | {
302
501
  label: string;
303
502
  subMenu: {
304
503
  label: string;
@@ -317,76 +516,12 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
317
516
  subMenu?: undefined;
318
517
  })[];
319
518
  } & {
320
- reload(): Promise<void>;
321
519
  afterAttach(): void;
322
- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
323
- overrideHeight: number;
324
- theme: import("@mui/material").ThemeOptions;
325
- }): Promise<JSX.Element>;
326
- }, {
327
- type: string;
328
- } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
329
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
330
- type: import("mobx-state-tree").ISimpleType<string>;
331
- rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
332
- } & {
333
- heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
334
- blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
335
- key: import("mobx-state-tree").ISimpleType<string>;
336
- region: import("mobx-state-tree").IModelType<{
337
- refName: import("mobx-state-tree").ISimpleType<string>;
338
- start: import("mobx-state-tree").ISimpleType<number>;
339
- end: import("mobx-state-tree").ISimpleType<number>;
340
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
341
- } & {
342
- assemblyName: import("mobx-state-tree").ISimpleType<string>;
343
- }, {
344
- setRefName(newRefName: string): void;
345
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
346
- reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
347
- isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
348
- isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
349
- }, {
350
- renderInProgress: AbortController | undefined;
351
- filled: boolean;
352
- reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
353
- features: Map<string, Feature> | undefined;
354
- layout: any;
355
- status: string;
356
- error: unknown;
357
- message: string | undefined;
358
- maxHeightReached: boolean;
359
- ReactComponent: ({ model, }: {
360
- model: any;
361
- }) => any;
362
- renderProps: any;
363
- } & {
364
- doReload(): void;
365
- afterAttach(): void;
366
- setStatus(message: string): void;
367
- setLoading(abortController: AbortController): void;
368
- setMessage(messageText: string): void;
369
- setRendered(props: {
370
- reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
371
- features: Map<string, Feature>;
372
- layout: any;
373
- maxHeightReached: boolean;
374
- renderProps: any;
375
- } | undefined): void;
376
- setError(error: unknown): void;
377
- reload(): void;
378
- beforeDestroy(): void;
379
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
380
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
381
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
382
- }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
383
- type: string;
384
- id: string;
385
- rpcDriverName: string | undefined;
386
- heightPreConfig: number | undefined;
387
- userBpPerPxLimit: number | undefined;
388
- userByteSizeLimit: number | undefined;
389
- } & import("mobx-state-tree")._NotCustomized>;
520
+ /**
521
+ * #action
522
+ */
523
+ renderSvg(opts: ExportSvgDisplayOptions): Promise<React.JSX.Element>;
524
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
390
525
  export type WiggleDisplayStateModel = ReturnType<typeof stateModelFactory>;
391
526
  export type WiggleDisplayModel = Instance<WiggleDisplayStateModel>;
392
527
  export default stateModelFactory;