@jbrowse/plugin-dotplot-view 2.16.1 → 2.18.0

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 (153) hide show
  1. package/dist/ComparativeRenderer/index.d.ts +3 -8
  2. package/dist/ComparativeRenderer/index.js +3 -8
  3. package/dist/DotplotDisplay/components/DotplotDisplay.d.ts +1 -1
  4. package/dist/DotplotDisplay/components/DotplotDisplay.js +1 -1
  5. package/dist/DotplotDisplay/index.d.ts +1 -7
  6. package/dist/DotplotDisplay/index.js +2 -12
  7. package/dist/DotplotDisplay/renderDotplotBlock.d.ts +1 -1
  8. package/dist/DotplotDisplay/renderDotplotBlock.js +3 -9
  9. package/dist/DotplotDisplay/stateModelFactory.d.ts +7 -43
  10. package/dist/DotplotDisplay/stateModelFactory.js +55 -97
  11. package/dist/DotplotReadVsRef/DotplotReadVsRef.d.ts +2 -2
  12. package/dist/DotplotReadVsRef/DotplotReadVsRef.js +16 -16
  13. package/dist/DotplotReadVsRef/index.d.ts +1 -1
  14. package/dist/DotplotReadVsRef/index.js +0 -2
  15. package/dist/DotplotRenderer/ComparativeRenderRpc.d.ts +3 -8
  16. package/dist/DotplotRenderer/ComparativeRenderRpc.js +3 -8
  17. package/dist/DotplotRenderer/DotplotRenderer.d.ts +5 -4
  18. package/dist/DotplotRenderer/DotplotRenderer.js +1 -2
  19. package/dist/DotplotRenderer/components/DotplotRendering.d.ts +1 -1
  20. package/dist/DotplotRenderer/configSchema.d.ts +0 -21
  21. package/dist/DotplotRenderer/configSchema.js +2 -27
  22. package/dist/DotplotRenderer/drawDotplot.d.ts +3 -3
  23. package/dist/DotplotRenderer/drawDotplot.js +3 -6
  24. package/dist/DotplotRenderer/index.d.ts +1 -1
  25. package/dist/DotplotRenderer/index.js +1 -1
  26. package/dist/DotplotView/1dview.d.ts +2 -77
  27. package/dist/DotplotView/1dview.js +4 -33
  28. package/dist/DotplotView/components/Axes.d.ts +1 -1
  29. package/dist/DotplotView/components/Axes.js +3 -4
  30. package/dist/DotplotView/components/CursorIcon.d.ts +1 -1
  31. package/dist/DotplotView/components/CursorIcon.js +1 -1
  32. package/dist/DotplotView/components/DotplotControls.d.ts +1 -1
  33. package/dist/DotplotView/components/DotplotControls.js +5 -6
  34. package/dist/DotplotView/components/DotplotTooltipClick.d.ts +1 -1
  35. package/dist/DotplotView/components/DotplotTooltipClick.js +1 -1
  36. package/dist/DotplotView/components/DotplotTooltipMouseover.d.ts +1 -1
  37. package/dist/DotplotView/components/DotplotTooltipMouseover.js +1 -1
  38. package/dist/DotplotView/components/DotplotView.d.ts +1 -1
  39. package/dist/DotplotView/components/DotplotView.js +5 -12
  40. package/dist/DotplotView/components/DotplotWarnings.d.ts +1 -1
  41. package/dist/DotplotView/components/DotplotWarnings.js +0 -1
  42. package/dist/DotplotView/components/ExportSvgDialog.d.ts +1 -1
  43. package/dist/DotplotView/components/ExportSvgDialog.js +2 -4
  44. package/dist/DotplotView/components/Grid.d.ts +1 -1
  45. package/dist/DotplotView/components/Grid.js +2 -4
  46. package/dist/DotplotView/components/Header.d.ts +1 -1
  47. package/dist/DotplotView/components/Header.js +2 -2
  48. package/dist/DotplotView/components/ImportForm/ImportCustomTrack.d.ts +2 -2
  49. package/dist/DotplotView/components/ImportForm/ImportCustomTrack.js +1 -1
  50. package/dist/DotplotView/components/ImportForm/ImportSyntenyTrackSelector.d.ts +1 -1
  51. package/dist/DotplotView/components/ImportForm/ImportSyntenyTrackSelector.js +5 -10
  52. package/dist/DotplotView/components/ImportForm/index.d.ts +1 -1
  53. package/dist/DotplotView/components/ImportForm/index.js +4 -5
  54. package/dist/DotplotView/components/ImportForm/util.js +1 -3
  55. package/dist/DotplotView/components/PanButtons.d.ts +1 -1
  56. package/dist/DotplotView/components/PanButtons.js +3 -4
  57. package/dist/DotplotView/components/WarningDialog.d.ts +6 -5
  58. package/dist/DotplotView/components/WarningDialog.js +10 -6
  59. package/dist/DotplotView/components/util.d.ts +2 -7
  60. package/dist/DotplotView/components/util.js +0 -5
  61. package/dist/DotplotView/index.d.ts +1 -1
  62. package/dist/DotplotView/index.js +0 -1
  63. package/dist/DotplotView/model.d.ts +5 -129
  64. package/dist/DotplotView/model.js +6 -192
  65. package/dist/DotplotView/svgcomponents/SVGBackground.js +1 -1
  66. package/dist/DotplotView/svgcomponents/SVGDotplotView.d.ts +1 -1
  67. package/dist/DotplotView/svgcomponents/SVGDotplotView.js +5 -9
  68. package/dist/LaunchDotplotView.d.ts +1 -1
  69. package/dist/LaunchDotplotView.js +1 -4
  70. package/dist/ServerSideRenderedBlockContent.d.ts +2 -1
  71. package/dist/ServerSideRenderedBlockContent.js +2 -3
  72. package/dist/ServerSideSyntenyRendering.d.ts +0 -4
  73. package/dist/ServerSideSyntenyRendering.js +1 -1
  74. package/dist/index.d.ts +1 -1
  75. package/dist/index.js +3 -6
  76. package/dist/util.d.ts +1 -1
  77. package/esm/ComparativeRenderer/index.d.ts +3 -8
  78. package/esm/ComparativeRenderer/index.js +3 -8
  79. package/esm/DotplotDisplay/components/DotplotDisplay.d.ts +1 -1
  80. package/esm/DotplotDisplay/components/DotplotDisplay.js +1 -1
  81. package/esm/DotplotDisplay/index.d.ts +1 -7
  82. package/esm/DotplotDisplay/index.js +2 -12
  83. package/esm/DotplotDisplay/renderDotplotBlock.d.ts +1 -1
  84. package/esm/DotplotDisplay/renderDotplotBlock.js +3 -6
  85. package/esm/DotplotDisplay/stateModelFactory.d.ts +7 -43
  86. package/esm/DotplotDisplay/stateModelFactory.js +56 -98
  87. package/esm/DotplotReadVsRef/DotplotReadVsRef.d.ts +2 -2
  88. package/esm/DotplotReadVsRef/DotplotReadVsRef.js +18 -18
  89. package/esm/DotplotReadVsRef/index.d.ts +1 -1
  90. package/esm/DotplotReadVsRef/index.js +0 -2
  91. package/esm/DotplotRenderer/ComparativeRenderRpc.d.ts +3 -8
  92. package/esm/DotplotRenderer/ComparativeRenderRpc.js +3 -8
  93. package/esm/DotplotRenderer/DotplotRenderer.d.ts +5 -4
  94. package/esm/DotplotRenderer/DotplotRenderer.js +1 -2
  95. package/esm/DotplotRenderer/components/DotplotRendering.d.ts +1 -1
  96. package/esm/DotplotRenderer/configSchema.d.ts +0 -21
  97. package/esm/DotplotRenderer/configSchema.js +2 -27
  98. package/esm/DotplotRenderer/drawDotplot.d.ts +3 -3
  99. package/esm/DotplotRenderer/drawDotplot.js +4 -7
  100. package/esm/DotplotRenderer/index.d.ts +1 -1
  101. package/esm/DotplotRenderer/index.js +1 -1
  102. package/esm/DotplotView/1dview.d.ts +2 -77
  103. package/esm/DotplotView/1dview.js +4 -33
  104. package/esm/DotplotView/components/Axes.d.ts +1 -1
  105. package/esm/DotplotView/components/Axes.js +3 -4
  106. package/esm/DotplotView/components/CursorIcon.d.ts +1 -1
  107. package/esm/DotplotView/components/CursorIcon.js +1 -1
  108. package/esm/DotplotView/components/DotplotControls.d.ts +1 -1
  109. package/esm/DotplotView/components/DotplotControls.js +5 -6
  110. package/esm/DotplotView/components/DotplotTooltipClick.d.ts +1 -1
  111. package/esm/DotplotView/components/DotplotTooltipClick.js +1 -1
  112. package/esm/DotplotView/components/DotplotTooltipMouseover.d.ts +1 -1
  113. package/esm/DotplotView/components/DotplotTooltipMouseover.js +1 -1
  114. package/esm/DotplotView/components/DotplotView.d.ts +1 -1
  115. package/esm/DotplotView/components/DotplotView.js +6 -13
  116. package/esm/DotplotView/components/DotplotWarnings.d.ts +1 -1
  117. package/esm/DotplotView/components/DotplotWarnings.js +0 -1
  118. package/esm/DotplotView/components/ExportSvgDialog.d.ts +1 -1
  119. package/esm/DotplotView/components/ExportSvgDialog.js +2 -4
  120. package/esm/DotplotView/components/Grid.d.ts +1 -1
  121. package/esm/DotplotView/components/Grid.js +2 -4
  122. package/esm/DotplotView/components/Header.d.ts +1 -1
  123. package/esm/DotplotView/components/Header.js +2 -2
  124. package/esm/DotplotView/components/ImportForm/ImportCustomTrack.d.ts +2 -2
  125. package/esm/DotplotView/components/ImportForm/ImportCustomTrack.js +2 -2
  126. package/esm/DotplotView/components/ImportForm/ImportSyntenyTrackSelector.d.ts +1 -1
  127. package/esm/DotplotView/components/ImportForm/ImportSyntenyTrackSelector.js +6 -11
  128. package/esm/DotplotView/components/ImportForm/index.d.ts +1 -1
  129. package/esm/DotplotView/components/ImportForm/index.js +6 -7
  130. package/esm/DotplotView/components/ImportForm/util.js +1 -3
  131. package/esm/DotplotView/components/PanButtons.d.ts +1 -1
  132. package/esm/DotplotView/components/PanButtons.js +3 -4
  133. package/esm/DotplotView/components/WarningDialog.d.ts +6 -5
  134. package/esm/DotplotView/components/WarningDialog.js +10 -6
  135. package/esm/DotplotView/components/util.d.ts +2 -7
  136. package/esm/DotplotView/components/util.js +0 -5
  137. package/esm/DotplotView/index.d.ts +1 -1
  138. package/esm/DotplotView/index.js +0 -1
  139. package/esm/DotplotView/model.d.ts +5 -129
  140. package/esm/DotplotView/model.js +7 -193
  141. package/esm/DotplotView/svgcomponents/SVGBackground.js +1 -1
  142. package/esm/DotplotView/svgcomponents/SVGDotplotView.d.ts +1 -1
  143. package/esm/DotplotView/svgcomponents/SVGDotplotView.js +5 -9
  144. package/esm/LaunchDotplotView.d.ts +1 -1
  145. package/esm/LaunchDotplotView.js +1 -4
  146. package/esm/ServerSideRenderedBlockContent.d.ts +2 -1
  147. package/esm/ServerSideRenderedBlockContent.js +2 -3
  148. package/esm/ServerSideSyntenyRendering.d.ts +0 -4
  149. package/esm/ServerSideSyntenyRendering.js +2 -2
  150. package/esm/index.d.ts +1 -1
  151. package/esm/index.js +3 -6
  152. package/esm/util.d.ts +1 -1
  153. package/package.json +2 -4
@@ -1,57 +1,36 @@
1
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  declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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- /**
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- * #slot
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- */
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  color: {
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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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- /**
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- * #slot
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- */
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  posColor: {
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  type: string;
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  description: string;
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  defaultValue: string;
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  };
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- /**
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- * #slot
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- */
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  negColor: {
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  type: string;
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  description: string;
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  defaultValue: string;
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  };
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- /**
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- * #slot
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- */
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  lineWidth: {
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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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- /**
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- * #slot
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- */
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  colorBy: {
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  type: string;
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  model: import("mobx-state-tree").ISimpleType<string>;
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  description: string;
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  defaultValue: string;
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  };
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- /**
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- * #slot
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- */
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  thresholdsPalette: {
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  type: string;
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  defaultValue: string[];
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  description: string;
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  };
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- /**
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- * #slot
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- */
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  thresholds: {
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  type: string;
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  defaultValue: string[];
@@ -2,48 +2,29 @@
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  Object.defineProperty(exports, "__esModule", { value: true });
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  const configuration_1 = require("@jbrowse/core/configuration");
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  const mobx_state_tree_1 = require("mobx-state-tree");
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- /**
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- * #config DotplotRenderer
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- * #category renderer
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- */
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- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
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+ function x() { }
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  exports.default = (0, configuration_1.ConfigurationSchema)('DotplotRenderer', {
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- /**
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- * #slot
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- */
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  color: {
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  type: 'color',
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  description: 'the color of each feature in a synteny, used with colorBy:default',
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  defaultValue: '#f0f',
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  contextVariable: ['feature'],
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  },
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- /**
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- * #slot
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- */
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  posColor: {
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  type: 'color',
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  description: 'the color for forward alignments, used with colorBy:strand',
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  defaultValue: 'blue',
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  },
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- /**
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- * #slot
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- */
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  negColor: {
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  type: 'color',
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  description: 'the color for reverse alignments, used with colorBy:strand',
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  defaultValue: 'red',
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  },
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- /**
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- * #slot
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- */
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  lineWidth: {
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  type: 'number',
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  description: 'width of the lines to be drawn',
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- defaultValue: 2.5, // 2.5 is similar to D-GENIES
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+ defaultValue: 2.5,
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  },
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- /**
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- * #slot
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- */
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  colorBy: {
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  type: 'stringEnum',
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  model: mobx_state_tree_1.types.enumeration('colorBy', [
@@ -63,17 +44,11 @@ exports.default = (0, configuration_1.ConfigurationSchema)('DotplotRenderer', {
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  </ul>`,
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  defaultValue: 'default',
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  },
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- /**
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- * #slot
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- */
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  thresholdsPalette: {
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  type: 'stringArray',
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  defaultValue: ['#094b09', '#2ebd40', '#d5670b', '#ffd84b'],
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  description: 'threshold colors, used with colorBy:identity',
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  },
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- /**
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- * #slot
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- */
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  thresholds: {
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  type: 'stringArray',
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  defaultValue: ['0.75', '0.5', '0.25', '0'],
@@ -1,6 +1,6 @@
1
- import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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- import { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
3
- import { Dotplot1DViewModel } from '../DotplotView/model';
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+ import type { Dotplot1DViewModel } from '../DotplotView/model';
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+ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
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+ import type { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType';
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  export interface DotplotRenderArgsDeserialized extends RenderArgsDeserialized {
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  adapterConfig: AnyConfigurationModel;
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  height: number;
@@ -2,15 +2,15 @@
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  Object.defineProperty(exports, "__esModule", { value: true });
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  exports.drawDotplot = drawDotplot;
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  const configuration_1 = require("@jbrowse/core/configuration");
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+ const ui_1 = require("@jbrowse/core/ui");
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  const Base1DUtils_1 = require("@jbrowse/core/util/Base1DUtils");
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- const mobx_state_tree_1 = require("mobx-state-tree");
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  const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
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- const ui_1 = require("@jbrowse/core/ui");
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+ const mobx_state_tree_1 = require("mobx-state-tree");
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  const { parseCigar } = plugin_alignments_1.MismatchParser;
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  const r = 'fell outside of range due to CIGAR string';
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  const lt = '(less than min coordinate of feature)';
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  const gt = '(greater than max coordinate of feature)';
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- const fudgeFactor = 1; // allow 1px fuzzyness before warn
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+ const fudgeFactor = 1;
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  function drawCir(ctx, x, y, r = 1) {
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  ctx.beginPath();
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  ctx.arc(x, y, r / 2, 0, 2 * Math.PI);
@@ -33,8 +33,6 @@ async function drawDotplot(ctx, props) {
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  const db2 = (_b = vview.dynamicBlocks.contentBlocks[0]) === null || _b === void 0 ? void 0 : _b.offsetPx;
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  const warnings = [];
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  ctx.lineWidth = lineWidth;
36
- // we operate on snapshots of these attributes of the hview/vview because
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- // it is significantly faster than accessing the mobx objects
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  const { bpPerPx: hBpPerPx } = hview;
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  const { bpPerPx: vBpPerPx } = vview;
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  function clampWithWarnX(num, min, max, feature) {
@@ -177,7 +175,6 @@ async function drawDotplot(ctx, props) {
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  }
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  currX = clampWithWarnX(currX, b1, b2, feature);
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  currY = clampWithWarnY(currY, e1, e2, feature);
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- // only draw a line segment if it is bigger than 0.5px
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  if (Math.abs(currX - lastDrawnX) > 0.5 ||
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  Math.abs(currY - lastDrawnY) > 0.5) {
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  ctx.lineTo(currX, height - currY);
@@ -1,2 +1,2 @@
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- import PluginManager from '@jbrowse/core/PluginManager';
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+ import type PluginManager from '@jbrowse/core/PluginManager';
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  export default function DotplotRendererF(pluginManager: PluginManager): void;
@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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  exports.default = DotplotRendererF;
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- const DotplotRendering_1 = __importDefault(require("./components/DotplotRendering"));
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  const DotplotRenderer_1 = __importDefault(require("./DotplotRenderer"));
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+ const DotplotRendering_1 = __importDefault(require("./components/DotplotRendering"));
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  const configSchema_1 = __importDefault(require("./configSchema"));
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  function DotplotRendererF(pluginManager) {
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  pluginManager.addRendererType(() => new DotplotRenderer_1.default({
@@ -1,4 +1,4 @@
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- import { Instance } from 'mobx-state-tree';
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+ import type { Instance } from 'mobx-state-tree';
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  declare const Dotplot1DView: 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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  displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
@@ -53,39 +53,14 @@ declare const Dotplot1DView: import("mobx-state-tree").IModelType<{
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  } & {
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  moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset): void;
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  } & {
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- /**
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- * #action
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- */
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  setScaleFactor(n: number): void;
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- /**
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- * #action
62
- */
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  center(): void;
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  } & {
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- /**
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- * #getter
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- * this uses padding=false and elision=false
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- */
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  readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
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- /**
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- * #getter
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- */
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  readonly scaleFactor: number;
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- /**
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- * #getter
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- */
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  readonly maxBpPerPx: number;
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- /**
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- * #getter
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- */
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  readonly minBpPerPx: number;
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- /**
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- * #getter
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- */
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  readonly maxOffset: number;
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- /**
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- * #getter
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- */
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  readonly minOffset: number;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
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  declare const DotplotHView: import("mobx-state-tree").IModelType<{
@@ -142,39 +117,14 @@ declare const DotplotHView: import("mobx-state-tree").IModelType<{
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  } & {
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  moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset): void;
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  } & {
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- /**
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- * #action
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- */
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  setScaleFactor(n: number): void;
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- /**
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- * #action
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- */
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  center(): void;
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  } & {
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- /**
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- * #getter
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- * this uses padding=false and elision=false
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- */
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  readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
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- /**
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- * #getter
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- */
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  readonly scaleFactor: number;
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- /**
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- * #getter
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- */
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  readonly maxBpPerPx: number;
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- /**
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- * #getter
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- */
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  readonly minBpPerPx: number;
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- /**
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- * #getter
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- */
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  readonly maxOffset: number;
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- /**
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- * #getter
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- */
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  readonly minOffset: number;
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  } & {
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  readonly width: any;
@@ -233,42 +183,17 @@ declare const DotplotVView: import("mobx-state-tree").IModelType<{
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  } & {
234
184
  moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset): void;
235
185
  } & {
236
- /**
237
- * #action
238
- */
239
186
  setScaleFactor(n: number): void;
240
- /**
241
- * #action
242
- */
243
187
  center(): void;
244
188
  } & {
245
- /**
246
- * #getter
247
- * this uses padding=false and elision=false
248
- */
249
189
  readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
250
- /**
251
- * #getter
252
- */
253
190
  readonly scaleFactor: number;
254
- /**
255
- * #getter
256
- */
257
191
  readonly maxBpPerPx: number;
258
- /**
259
- * #getter
260
- */
261
192
  readonly minBpPerPx: number;
262
- /**
263
- * #getter
264
- */
265
193
  readonly maxOffset: number;
266
- /**
267
- * #getter
268
- */
269
194
  readonly minOffset: number;
270
195
  } & {
271
196
  readonly width: any;
272
197
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
273
- export { DotplotVView, DotplotHView, Dotplot1DView };
198
+ export { Dotplot1DView, DotplotHView, DotplotVView };
274
199
  export type Dotplot1DViewModel = Instance<typeof Dotplot1DView>;
@@ -3,68 +3,39 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.Dotplot1DView = exports.DotplotHView = exports.DotplotVView = void 0;
7
- const mobx_state_tree_1 = require("mobx-state-tree");
8
- const mobx_1 = require("mobx");
6
+ exports.DotplotVView = exports.DotplotHView = exports.Dotplot1DView = void 0;
9
7
  const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
10
8
  const calculateDynamicBlocks_1 = __importDefault(require("@jbrowse/core/util/calculateDynamicBlocks"));
11
- /**
12
- * #stateModel Dotplot1DView
13
- * ref https://mobx-state-tree.js.org/concepts/volatiles on volatile state used here
14
- */
15
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
9
+ const mobx_1 = require("mobx");
10
+ const mobx_state_tree_1 = require("mobx-state-tree");
11
+ function x() { }
16
12
  const Dotplot1DView = Base1DViewModel_1.default.extend(self => {
17
13
  const scaleFactor = mobx_1.observable.box(1);
18
14
  return {
19
15
  views: {
20
- /**
21
- * #getter
22
- * this uses padding=false and elision=false
23
- */
24
16
  get dynamicBlocks() {
25
17
  return (0, calculateDynamicBlocks_1.default)(self, false, false);
26
18
  },
27
- /**
28
- * #getter
29
- */
30
19
  get scaleFactor() {
31
20
  return scaleFactor.get();
32
21
  },
33
- /**
34
- * #getter
35
- */
36
22
  get maxBpPerPx() {
37
23
  return self.totalBp / (self.width - 50);
38
24
  },
39
- /**
40
- * #getter
41
- */
42
25
  get minBpPerPx() {
43
26
  return 1 / 50;
44
27
  },
45
- /**
46
- * #getter
47
- */
48
28
  get maxOffset() {
49
29
  return self.displayedRegionsTotalPx - self.width * 0.2;
50
30
  },
51
- /**
52
- * #getter
53
- */
54
31
  get minOffset() {
55
32
  return -self.width * 0.8;
56
33
  },
57
34
  },
58
35
  actions: {
59
- /**
60
- * #action
61
- */
62
36
  setScaleFactor(n) {
63
37
  scaleFactor.set(n);
64
38
  },
65
- /**
66
- * #action
67
- */
68
39
  center() {
69
40
  const centerBp = self.totalBp / 2;
70
41
  const centerPx = centerBp / self.bpPerPx;
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { DotplotViewModel } from '../model';
2
+ import type { DotplotViewModel } from '../model';
3
3
  export declare const HorizontalAxis: ({ model, }: {
4
4
  model: DotplotViewModel;
5
5
  }) => React.JSX.Element;
@@ -5,13 +5,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  exports.VerticalAxisRaw = exports.VerticalAxis = exports.HorizontalAxisRaw = exports.HorizontalAxis = void 0;
7
7
  const react_1 = __importDefault(require("react"));
8
- const mui_1 = require("tss-react/mui");
9
- const mobx_react_1 = require("mobx-react");
10
- const mobx_state_tree_1 = require("mobx-state-tree");
11
8
  const util_1 = require("@jbrowse/core/util");
12
9
  const Base1DUtils_1 = require("@jbrowse/core/util/Base1DUtils");
13
10
  const material_1 = require("@mui/material");
14
- // locals
11
+ const mobx_react_1 = require("mobx-react");
12
+ const mobx_state_tree_1 = require("mobx-state-tree");
13
+ const mui_1 = require("tss-react/mui");
15
14
  const util_2 = require("./util");
16
15
  const useStyles = (0, mui_1.makeStyles)()(() => ({
17
16
  vtext: {
@@ -1,4 +1,4 @@
1
- import { SvgIconProps } from '@mui/material/SvgIcon';
2
1
  import React from 'react';
2
+ import type { SvgIconProps } from '@mui/material/SvgIcon';
3
3
  export declare function CursorMove(props: SvgIconProps): React.JSX.Element;
4
4
  export declare function CursorMouse(props: SvgIconProps): React.JSX.Element;
@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  exports.CursorMove = CursorMove;
7
7
  exports.CursorMouse = CursorMouse;
8
- const SvgIcon_1 = __importDefault(require("@mui/material/SvgIcon"));
9
8
  const react_1 = __importDefault(require("react"));
9
+ const SvgIcon_1 = __importDefault(require("@mui/material/SvgIcon"));
10
10
  function CursorMove(props) {
11
11
  return (react_1.default.createElement(SvgIcon_1.default, { ...props },
12
12
  react_1.default.createElement("path", { fill: "currentColor", d: "M13,6V11H18V7.75L22.25,12L18,16.25V13H13V18H16.25L12,22.25L7.75,18H11V13H6V16.25L1.75,12L6,7.75V11H11V6H7.75L12,1.75L16.25,6H13Z" })));
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { DotplotViewModel } from '../model';
2
+ import type { DotplotViewModel } from '../model';
3
3
  declare const DotplotControls: ({ model, }: {
4
4
  model: DotplotViewModel;
5
5
  }) => React.JSX.Element;
@@ -4,15 +4,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  const react_1 = __importDefault(require("react"));
7
- const material_1 = require("@mui/material");
8
- const mobx_react_1 = require("mobx-react");
9
7
  const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
10
- // icons
11
- const ZoomOut_1 = __importDefault(require("@mui/icons-material/ZoomOut"));
12
- const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
8
+ const Icons_1 = require("@jbrowse/core/ui/Icons");
13
9
  const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
10
+ const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
11
+ const ZoomOut_1 = __importDefault(require("@mui/icons-material/ZoomOut"));
12
+ const material_1 = require("@mui/material");
13
+ const mobx_react_1 = require("mobx-react");
14
14
  const CursorIcon_1 = require("./CursorIcon");
15
- const Icons_1 = require("@jbrowse/core/ui/Icons");
16
15
  const DotplotControls = (0, mobx_react_1.observer)(function ({ model, }) {
17
16
  return (react_1.default.createElement("div", null,
18
17
  react_1.default.createElement(material_1.IconButton, { onClick: () => {
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { DotplotViewModel } from '../model';
2
+ import type { DotplotViewModel } from '../model';
3
3
  type Coord = [number, number] | undefined;
4
4
  export declare const DotplotTooltipClick: ({ model, mousedown, mousedownClient, xdistance, ydistance, }: {
5
5
  model: DotplotViewModel;
@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  exports.DotplotTooltipClick = void 0;
7
7
  const react_1 = __importDefault(require("react"));
8
- const mobx_react_1 = require("mobx-react");
9
8
  const BaseTooltip_1 = __importDefault(require("@jbrowse/core/ui/BaseTooltip"));
9
+ const mobx_react_1 = require("mobx-react");
10
10
  const util_1 = require("./util");
11
11
  exports.DotplotTooltipClick = (0, mobx_react_1.observer)(function ({ model, mousedown, mousedownClient, xdistance, ydistance, }) {
12
12
  const { hview, vview, viewHeight } = model;
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { DotplotViewModel } from '../model';
2
+ import type { DotplotViewModel } from '../model';
3
3
  type Coord = [number, number] | undefined;
4
4
  declare const DotplotTooltipMouseover: ({ model, mouserect, mouserectClient, xdistance, }: {
5
5
  model: DotplotViewModel;
@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  const react_1 = __importDefault(require("react"));
7
- const mobx_react_1 = require("mobx-react");
8
7
  const BaseTooltip_1 = __importDefault(require("@jbrowse/core/ui/BaseTooltip"));
8
+ const mobx_react_1 = require("mobx-react");
9
9
  const util_1 = require("./util");
10
10
  const DotplotTooltipMouseover = (0, mobx_react_1.observer)(function ({ model, mouserect, mouserectClient, xdistance, }) {
11
11
  const { hview, vview, viewHeight } = model;
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { DotplotViewModel } from '../model';
2
+ import type { DotplotViewModel } from '../model';
3
3
  declare const DotplotView: ({ model }: {
4
4
  model: DotplotViewModel;
5
5
  }) => React.JSX.Element;
@@ -28,13 +28,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
28
28
  Object.defineProperty(exports, "__esModule", { value: true });
29
29
  const react_1 = __importStar(require("react"));
30
30
  const ui_1 = require("@jbrowse/core/ui");
31
- const mobx_react_1 = require("mobx-react");
32
31
  const mobx_1 = require("mobx");
32
+ const mobx_react_1 = require("mobx-react");
33
33
  const mui_1 = require("tss-react/mui");
34
- const ImportForm_1 = __importDefault(require("./ImportForm"));
35
- const Header_1 = __importDefault(require("./Header"));
36
- const Grid_1 = __importDefault(require("./Grid"));
37
34
  const Axes_1 = require("./Axes");
35
+ const Grid_1 = __importDefault(require("./Grid"));
36
+ const Header_1 = __importDefault(require("./Header"));
37
+ const ImportForm_1 = __importDefault(require("./ImportForm"));
38
38
  const TooltipWhereClicked = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./DotplotTooltipClick'))));
39
39
  const TooltipWhereMouseovered = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./DotplotTooltipMouseover'))));
40
40
  const blank = { left: 0, top: 0, width: 0, height: 0 };
@@ -60,7 +60,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
60
60
  width: '100%',
61
61
  gridRow: '1/2',
62
62
  gridColumn: '2/2',
63
- zIndex: 100, // needs to be below controls
63
+ zIndex: 100,
64
64
  '& path': {
65
65
  cursor: 'crosshair',
66
66
  fill: 'none',
@@ -78,8 +78,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
78
78
  borderTop: '1px solid #fafafa',
79
79
  },
80
80
  }));
81
- // produces offsetX/offsetY coordinates from a clientX and an element's
82
- // getBoundingClientRect
83
81
  function getOffset(coord, rect) {
84
82
  return coord && [coord[0] - rect.left, coord[1] - rect.top];
85
83
  }
@@ -119,7 +117,6 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
119
117
  (cursorMode === 'crosshair' && ctrlKeyWasUsed);
120
118
  const validSelect = (cursorMode === 'move' && ctrlKeyWasUsed) ||
121
119
  (cursorMode === 'crosshair' && !ctrlKeyWasUsed);
122
- // use non-React wheel handler to properly prevent body scrolling
123
120
  (0, react_1.useEffect)(() => {
124
121
  function onWheel(event) {
125
122
  event.preventDefault();
@@ -188,8 +185,6 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
188
185
  window.addEventListener('keyup', globalCtrlKeyUp);
189
186
  };
190
187
  }, []);
191
- // detect a mouseup after a mousedown was submitted, autoremoves mouseup once
192
- // that single mouseup is set
193
188
  (0, react_1.useEffect)(() => {
194
189
  function globalMouseUp(event) {
195
190
  if (Math.abs(xdistance) > 3 && Math.abs(ydistance) > 3 && validSelect) {
@@ -257,7 +252,6 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
257
252
  if (mousedown && mouseup) {
258
253
  model.zoomInToMouseCoords(mousedown, mouseup);
259
254
  }
260
- // below line is needed to prevent tooltip from sticking
261
255
  setMouseOvered(false);
262
256
  },
263
257
  },
@@ -267,7 +261,6 @@ const DotplotViewInternal = (0, mobx_react_1.observer)(function ({ model, }) {
267
261
  if (mousedown && mouseup) {
268
262
  model.onDotplotView(mousedown, mouseup);
269
263
  }
270
- // below line is needed to prevent tooltip from sticking
271
264
  setMouseOvered(false);
272
265
  },
273
266
  },
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { DotplotViewModel } from '../model';
2
+ import type { DotplotViewModel } from '../model';
3
3
  declare const DotplotWarnings: ({ model, }: {
4
4
  model: DotplotViewModel;
5
5
  }) => React.JSX.Element | null;
@@ -26,7 +26,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
26
26
  const react_1 = __importStar(require("react"));
27
27
  const material_1 = require("@mui/material");
28
28
  const mobx_react_1 = require("mobx-react");
29
- // lazy components
30
29
  const WarningDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./WarningDialog'))));
31
30
  const DotplotWarnings = (0, mobx_react_1.observer)(function ({ model, }) {
32
31
  const trackWarnings = model.tracks.filter(t => { var _a; return (_a = t.displays[0].warnings) === null || _a === void 0 ? void 0 : _a.length; });
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { ExportSvgOptions } from '../model';
2
+ import type { ExportSvgOptions } from '../model';
3
3
  export default function ExportSvgDialog({ model, handleClose, }: {
4
4
  model: {
5
5
  exportSvg(opts: ExportSvgOptions): Promise<void>;
@@ -25,9 +25,9 @@ var __importStar = (this && this.__importStar) || function (mod) {
25
25
  Object.defineProperty(exports, "__esModule", { value: true });
26
26
  exports.default = ExportSvgDialog;
27
27
  const react_1 = __importStar(require("react"));
28
- const material_1 = require("@mui/material");
29
28
  const ui_1 = require("@jbrowse/core/ui");
30
29
  const util_1 = require("@jbrowse/core/util");
30
+ const material_1 = require("@mui/material");
31
31
  function LoadingMessage() {
32
32
  return (react_1.default.createElement("div", null,
33
33
  react_1.default.createElement(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }),
@@ -56,9 +56,7 @@ function ExportSvgDialog({ model, handleClose, }) {
56
56
  } }),
57
57
  session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => {
58
58
  setThemeName(event.target.value);
59
- } }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key },
60
- // @ts-expect-error
61
- val.name || '(Unknown name)'))))) : null,
59
+ } }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, val.name || '(Unknown name)'))))) : null,
62
60
  offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => {
63
61
  setRasterizeLayers(val => !val);
64
62
  } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
@@ -1,5 +1,5 @@
1
1
  import React from 'react';
2
- import { DotplotViewModel } from '../model';
2
+ import type { DotplotViewModel } from '../model';
3
3
  export declare const GridRaw: ({ model, children, }: {
4
4
  model: DotplotViewModel;
5
5
  children?: React.ReactNode;