@jbrowse/plugin-alignments 2.2.0 → 2.2.2

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Files changed (210) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -13
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  3. package/dist/BamAdapter/BamAdapter.d.ts +1 -1
  4. package/dist/BamAdapter/BamAdapter.js +1 -0
  5. package/dist/BamAdapter/BamAdapter.js.map +1 -1
  6. package/dist/BamAdapter/BamSlightlyLazyFeature.js +1 -0
  7. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  8. package/dist/BamAdapter/MismatchParser.d.ts +2 -2
  9. package/dist/BamAdapter/MismatchParser.js +4 -7
  10. package/dist/BamAdapter/MismatchParser.js.map +1 -1
  11. package/dist/BamAdapter/configSchema.js +1 -1
  12. package/dist/BamAdapter/configSchema.js.map +1 -1
  13. package/dist/BamAdapter/index.js +7 -5
  14. package/dist/BamAdapter/index.js.map +1 -1
  15. package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +1 -10
  16. package/dist/CramAdapter/CramSlightlyLazyFeature.js +5 -218
  17. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  18. package/dist/CramAdapter/CramTestAdapters.d.ts +1 -1
  19. package/dist/CramAdapter/CramTestAdapters.js +3 -2
  20. package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
  21. package/dist/CramAdapter/configSchema.js +2 -2
  22. package/dist/CramAdapter/configSchema.js.map +1 -1
  23. package/dist/CramAdapter/index.js +7 -5
  24. package/dist/CramAdapter/index.js.map +1 -1
  25. package/dist/CramAdapter/util.d.ts +18 -0
  26. package/dist/CramAdapter/util.js +241 -0
  27. package/dist/CramAdapter/util.js.map +1 -0
  28. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +1 -1
  29. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  30. package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +1 -1
  31. package/dist/LinearAlignmentsDisplay/models/model.d.ts +5 -5
  32. package/dist/LinearAlignmentsDisplay/models/model.js +7 -7
  33. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
  34. package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
  35. package/dist/LinearPileupDisplay/components/ColorByModifications.js +7 -22
  36. package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
  37. package/dist/LinearPileupDisplay/components/ColorByTag.js +2 -22
  38. package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
  39. package/dist/LinearPileupDisplay/components/FilterByTag.js +2 -15
  40. package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
  41. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +2 -19
  42. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  43. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +2 -18
  44. package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
  45. package/dist/LinearPileupDisplay/components/SortByTag.js +2 -23
  46. package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -1
  47. package/dist/LinearPileupDisplay/configSchema.d.ts +4 -4
  48. package/dist/LinearPileupDisplay/configSchema.js +2 -2
  49. package/dist/LinearPileupDisplay/configSchema.js.map +1 -1
  50. package/dist/LinearPileupDisplay/index.d.ts +3 -0
  51. package/dist/LinearPileupDisplay/index.js +3 -0
  52. package/dist/LinearPileupDisplay/index.js.map +1 -1
  53. package/dist/LinearPileupDisplay/model.d.ts +19 -9
  54. package/dist/LinearPileupDisplay/model.js +25 -30
  55. package/dist/LinearPileupDisplay/model.js.map +1 -1
  56. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  57. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +14 -10
  58. package/dist/LinearSNPCoverageDisplay/models/model.js +8 -6
  59. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  60. package/dist/PileupRPC/rpcMethods.d.ts +1 -1
  61. package/dist/PileupRPC/rpcMethods.js +12 -7
  62. package/dist/PileupRPC/rpcMethods.js.map +1 -1
  63. package/dist/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  64. package/dist/PileupRenderer/PileupRenderer.js +32 -28
  65. package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
  66. package/dist/PileupRenderer/configSchema.js +1 -1
  67. package/dist/PileupRenderer/configSchema.js.map +1 -1
  68. package/dist/PileupRenderer/index.js +8 -6
  69. package/dist/PileupRenderer/index.js.map +1 -1
  70. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
  71. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -182
  72. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
  73. package/dist/SNPCoverageAdapter/configSchema.d.ts +2 -3
  74. package/dist/SNPCoverageAdapter/configSchema.js +6 -3
  75. package/dist/SNPCoverageAdapter/configSchema.js.map +1 -1
  76. package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
  77. package/dist/SNPCoverageAdapter/generateCoverageBins.js +185 -0
  78. package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
  79. package/dist/SNPCoverageAdapter/index.d.ts +1 -2
  80. package/dist/SNPCoverageAdapter/index.js +17 -14
  81. package/dist/SNPCoverageAdapter/index.js.map +1 -1
  82. package/dist/index.d.ts +3 -2
  83. package/dist/index.js +4 -2
  84. package/dist/index.js.map +1 -1
  85. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -13
  86. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  87. package/esm/BamAdapter/BamAdapter.d.ts +1 -1
  88. package/esm/BamAdapter/BamAdapter.js +1 -0
  89. package/esm/BamAdapter/BamAdapter.js.map +1 -1
  90. package/esm/BamAdapter/BamSlightlyLazyFeature.js +1 -0
  91. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  92. package/esm/BamAdapter/MismatchParser.d.ts +2 -2
  93. package/esm/BamAdapter/MismatchParser.js +4 -7
  94. package/esm/BamAdapter/MismatchParser.js.map +1 -1
  95. package/esm/BamAdapter/configSchema.js +1 -1
  96. package/esm/BamAdapter/configSchema.js.map +1 -1
  97. package/esm/BamAdapter/index.js +7 -5
  98. package/esm/BamAdapter/index.js.map +1 -1
  99. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +1 -10
  100. package/esm/CramAdapter/CramSlightlyLazyFeature.js +5 -218
  101. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  102. package/esm/CramAdapter/CramTestAdapters.d.ts +1 -1
  103. package/esm/CramAdapter/CramTestAdapters.js +3 -2
  104. package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
  105. package/esm/CramAdapter/configSchema.js +2 -2
  106. package/esm/CramAdapter/configSchema.js.map +1 -1
  107. package/esm/CramAdapter/index.js +7 -5
  108. package/esm/CramAdapter/index.js.map +1 -1
  109. package/esm/CramAdapter/util.d.ts +18 -0
  110. package/esm/CramAdapter/util.js +236 -0
  111. package/esm/CramAdapter/util.js.map +1 -0
  112. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +1 -1
  113. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  114. package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +1 -1
  115. package/esm/LinearAlignmentsDisplay/models/model.d.ts +5 -5
  116. package/esm/LinearAlignmentsDisplay/models/model.js +7 -7
  117. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
  118. package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
  119. package/esm/LinearPileupDisplay/components/ColorByModifications.js +8 -23
  120. package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
  121. package/esm/LinearPileupDisplay/components/ColorByTag.js +3 -20
  122. package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
  123. package/esm/LinearPileupDisplay/components/FilterByTag.js +3 -13
  124. package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
  125. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +3 -17
  126. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  127. package/esm/LinearPileupDisplay/components/SetMaxHeight.js +3 -16
  128. package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
  129. package/esm/LinearPileupDisplay/components/SortByTag.js +3 -21
  130. package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -1
  131. package/esm/LinearPileupDisplay/configSchema.d.ts +4 -4
  132. package/esm/LinearPileupDisplay/configSchema.js +2 -2
  133. package/esm/LinearPileupDisplay/configSchema.js.map +1 -1
  134. package/esm/LinearPileupDisplay/index.d.ts +3 -0
  135. package/esm/LinearPileupDisplay/index.js +1 -0
  136. package/esm/LinearPileupDisplay/index.js.map +1 -1
  137. package/esm/LinearPileupDisplay/model.d.ts +19 -9
  138. package/esm/LinearPileupDisplay/model.js +25 -30
  139. package/esm/LinearPileupDisplay/model.js.map +1 -1
  140. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  141. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +14 -10
  142. package/esm/LinearSNPCoverageDisplay/models/model.js +9 -7
  143. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  144. package/esm/PileupRPC/rpcMethods.d.ts +1 -1
  145. package/esm/PileupRPC/rpcMethods.js +12 -7
  146. package/esm/PileupRPC/rpcMethods.js.map +1 -1
  147. package/esm/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  148. package/esm/PileupRenderer/PileupRenderer.js +32 -28
  149. package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
  150. package/esm/PileupRenderer/configSchema.js +1 -1
  151. package/esm/PileupRenderer/configSchema.js.map +1 -1
  152. package/esm/PileupRenderer/index.js +8 -6
  153. package/esm/PileupRenderer/index.js.map +1 -1
  154. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
  155. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -183
  156. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
  157. package/esm/SNPCoverageAdapter/configSchema.d.ts +2 -3
  158. package/esm/SNPCoverageAdapter/configSchema.js +6 -3
  159. package/esm/SNPCoverageAdapter/configSchema.js.map +1 -1
  160. package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
  161. package/esm/SNPCoverageAdapter/generateCoverageBins.js +182 -0
  162. package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
  163. package/esm/SNPCoverageAdapter/index.d.ts +1 -2
  164. package/esm/SNPCoverageAdapter/index.js +17 -15
  165. package/esm/SNPCoverageAdapter/index.js.map +1 -1
  166. package/esm/index.d.ts +3 -2
  167. package/esm/index.js +2 -2
  168. package/esm/index.js.map +1 -1
  169. package/package.json +4 -3
  170. package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +17 -16
  171. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +1 -473
  172. package/src/AlignmentsFeatureDetail/index.test.js +6 -4
  173. package/src/BamAdapter/BamAdapter.ts +3 -2
  174. package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -1
  175. package/src/BamAdapter/MismatchParser.test.ts +21 -12
  176. package/src/BamAdapter/MismatchParser.ts +7 -10
  177. package/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap +135 -135
  178. package/src/BamAdapter/configSchema.ts +1 -1
  179. package/src/BamAdapter/index.ts +7 -8
  180. package/src/CombinationTest.test.ts +107 -0
  181. package/src/CramAdapter/CramSlightlyLazyFeature.ts +10 -219
  182. package/src/CramAdapter/CramTestAdapters.ts +2 -1
  183. package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap +31 -31
  184. package/src/CramAdapter/__snapshots__/util.test.ts.snap +14 -0
  185. package/src/CramAdapter/configSchema.ts +2 -3
  186. package/src/CramAdapter/index.ts +7 -8
  187. package/src/CramAdapter/util.test.ts +26 -0
  188. package/src/CramAdapter/util.ts +251 -0
  189. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +3 -1
  190. package/src/LinearAlignmentsDisplay/models/model.tsx +8 -7
  191. package/src/LinearPileupDisplay/components/ColorByModifications.tsx +5 -34
  192. package/src/LinearPileupDisplay/components/ColorByTag.tsx +2 -29
  193. package/src/LinearPileupDisplay/components/FilterByTag.tsx +2 -22
  194. package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +2 -22
  195. package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +2 -24
  196. package/src/LinearPileupDisplay/components/SortByTag.tsx +2 -31
  197. package/src/LinearPileupDisplay/configSchema.ts +3 -5
  198. package/src/LinearPileupDisplay/index.ts +5 -0
  199. package/src/LinearPileupDisplay/model.ts +31 -30
  200. package/src/LinearSNPCoverageDisplay/models/model.ts +12 -8
  201. package/src/PileupRPC/rpcMethods.ts +15 -20
  202. package/src/PileupRenderer/{PileupRenderer.tsx → PileupRenderer.ts} +48 -54
  203. package/src/PileupRenderer/configSchema.ts +1 -1
  204. package/src/PileupRenderer/index.ts +8 -9
  205. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -249
  206. package/src/SNPCoverageAdapter/configSchema.ts +14 -13
  207. package/src/SNPCoverageAdapter/generateCoverageBins.ts +245 -0
  208. package/src/SNPCoverageAdapter/index.ts +17 -18
  209. package/src/__snapshots__/index.test.ts.snap +1 -1
  210. package/src/index.ts +11 -4
package/dist/LinearPileupDisplay/components/FilterByTag.js CHANGED
@@ -22,26 +22,17 @@ var __importStar = (this && this.__importStar) || function (mod) {
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  __setModuleDefault(result, mod);
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  return result;
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  };
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- var __importDefault = (this && this.__importDefault) || function (mod) {
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- return (mod && mod.__esModule) ? mod : { "default": mod };
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- };
28
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  Object.defineProperty(exports, "__esModule", { value: true });
29
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  const react_1 = __importStar(require("react"));
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  const mobx_react_1 = require("mobx-react");
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  const material_1 = require("@mui/material");
29
+ const ui_1 = require("@jbrowse/core/ui");
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  const mui_1 = require("tss-react/mui");
33
- const Close_1 = __importDefault(require("@mui/icons-material/Close"));
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  const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  paper: {
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  padding: theme.spacing(2),
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  margin: theme.spacing(2),
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  },
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- closeButton: {
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- position: 'absolute',
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- right: theme.spacing(1),
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- top: theme.spacing(1),
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- color: theme.palette.grey[500],
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- },
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  field: {
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  margin: theme.spacing(2),
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  },
@@ -91,11 +82,7 @@ function FilterByTagDlg(props) {
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  const [readName, setReadName] = (0, react_1.useState)((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
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  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
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  const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
94
- return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
95
- react_1.default.createElement(material_1.DialogTitle, null,
96
- "Filter options",
97
- react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
98
- react_1.default.createElement(Close_1.default, null))),
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+ return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
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  react_1.default.createElement(material_1.DialogContent, null,
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  react_1.default.createElement(material_1.Typography, null,
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  "Set filter bitmask options. Refer to ",
package/dist/LinearPileupDisplay/components/FilterByTag.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/FilterByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,SAAS,OAAO,CAAC,KAA2C;IAC1D,MAAM,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL;QACE,8BAAC,oBAAS,IACR,IAAI,EAAC,QAAQ,EACb,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAC/C;QACD,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAC/B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,uCAAK,GAAG,EAAE,GAAG;gBACX,yCACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,EAAE;4BACxB,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC7B;6BAAM;4BACL,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC9B;oBACH,CAAC,GACD;gBACF,yCAAO,OAAO,EAAE,GAAG,IAAG,IAAI,CAAS,CAC/B,CACP,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,KAWvB;;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IAC1E,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,QAAQ,KAAI,EAAE,CAAC,CAAA;IAClE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,MAAM,IAAI,GAAG,4DAA4D,CAAA;IAEzE,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa;YACZ,8BAAC,qBAAU;;gBAC4B,8BAAC,eAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,uCAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,8BAAC,qBAAU,yCAA4C;wBACvD,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,8BAAC,qBAAU,6CAAgD;wBAC3D,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,kQAKE;gBACb,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC,EACD,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;wBACV,SAAS,EAAE,CAAC;wBACZ,aAAa,EAAE,sBAAsB;qBACtC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,iBACtD,gBAAgB,GAC5B;gBACF,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,sBAAsB;qBACtC,iBACW,iBAAiB,GAC7B,CACI;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,8BAAiC;gBAC5C,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,0BAA0B;qBAC1C,iBACW,oBAAoB,GAChC,CACI;YACR,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,QACT,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC;4BAChB,WAAW;4BACX,WAAW;4BACX,QAAQ;4BACR,SAAS,EACP,GAAG,KAAK,EAAE;gCACR,CAAC,CAAC;oCACE,GAAG;oCACH,KAAK,EAAE,QAAQ;iCAChB;gCACH,CAAC,CAAC,SAAS;yBAChB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,cAAc,CAAC,CAAA"}
package/dist/LinearPileupDisplay/components/SetFeatureHeight.js CHANGED
@@ -22,35 +22,18 @@ var __importStar = (this && this.__importStar) || function (mod) {
22
22
  __setModuleDefault(result, mod);
23
23
  return result;
24
24
  };
25
- var __importDefault = (this && this.__importDefault) || function (mod) {
26
- return (mod && mod.__esModule) ? mod : { "default": mod };
27
- };
28
25
  Object.defineProperty(exports, "__esModule", { value: true });
29
26
  const react_1 = __importStar(require("react"));
30
27
  const mobx_react_1 = require("mobx-react");
31
28
  const material_1 = require("@mui/material");
32
- const mui_1 = require("tss-react/mui");
33
- const Close_1 = __importDefault(require("@mui/icons-material/Close"));
34
- const useStyles = (0, mui_1.makeStyles)()(theme => ({
35
- closeButton: {
36
- position: 'absolute',
37
- right: theme.spacing(1),
38
- top: theme.spacing(1),
39
- color: theme.palette.grey[500],
40
- },
41
- }));
29
+ const ui_1 = require("@jbrowse/core/ui");
42
30
  function SetFeatureHeightDlg(props) {
43
- const { classes } = useStyles();
44
31
  const { model, handleClose } = props;
45
32
  const { featureHeightSetting, noSpacing: noSpacingSetting } = model;
46
33
  const [height, setHeight] = (0, react_1.useState)(`${featureHeightSetting}`);
47
34
  const [noSpacing, setNoSpacing] = (0, react_1.useState)(noSpacingSetting);
48
35
  const ok = height !== '' && !Number.isNaN(+height);
49
- return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
50
- react_1.default.createElement(material_1.DialogTitle, null,
51
- "Set feature height",
52
- react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: handleClose },
53
- react_1.default.createElement(Close_1.default, null))),
36
+ return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: 'Set feature height' },
54
37
  react_1.default.createElement(material_1.DialogContent, null,
55
38
  react_1.default.createElement(material_1.Typography, null, "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact."),
56
39
  react_1.default.createElement(material_1.TextField, { value: height, helperText: "Feature height", onChange: event => {
package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AAEzC,SAAS,mBAAmB,CAAC,KAQ5B;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,IAAA,gBAAQ,EAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,oBAAoB;QAC5D,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,wKAIE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,GACD;YACF,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,mBAAmB,CAAC,CAAA"}
package/dist/LinearPileupDisplay/components/SetMaxHeight.js CHANGED
@@ -22,39 +22,23 @@ var __importStar = (this && this.__importStar) || function (mod) {
22
22
  __setModuleDefault(result, mod);
23
23
  return result;
24
24
  };
25
- var __importDefault = (this && this.__importDefault) || function (mod) {
26
- return (mod && mod.__esModule) ? mod : { "default": mod };
27
- };
28
25
  Object.defineProperty(exports, "__esModule", { value: true });
29
26
  const react_1 = __importStar(require("react"));
30
27
  const mobx_react_1 = require("mobx-react");
31
28
  const material_1 = require("@mui/material");
29
+ const ui_1 = require("@jbrowse/core/ui");
32
30
  const mui_1 = require("tss-react/mui");
33
- const Close_1 = __importDefault(require("@mui/icons-material/Close"));
34
31
  const useStyles = (0, mui_1.makeStyles)()(theme => ({
35
32
  root: {
36
33
  width: 500,
37
34
  },
38
- closeButton: {
39
- position: 'absolute',
40
- right: theme.spacing(1),
41
- top: theme.spacing(1),
42
- color: theme.palette.grey[500],
43
- },
44
- field: {
45
- margin: theme.spacing(2),
46
- },
47
35
  }));
48
36
  function SetMaxHeightDlg(props) {
49
37
  const { model, handleClose } = props;
50
38
  const { classes } = useStyles();
51
39
  const { maxHeight = '' } = model;
52
40
  const [max, setMax] = (0, react_1.useState)(`${maxHeight}`);
53
- return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
54
- react_1.default.createElement(material_1.DialogTitle, null,
55
- "Filter options",
56
- react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
57
- react_1.default.createElement(Close_1.default, null))),
41
+ return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
58
42
  react_1.default.createElement(material_1.DialogContent, { className: classes.root },
59
43
  react_1.default.createElement(material_1.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
60
44
  react_1.default.createElement(material_1.TextField, { value: max, onChange: event => {
package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,KAMxB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,8BAAC,qBAAU,qHAGE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,EACD,WAAW,EAAC,6BAA6B,GACzC;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,eAAe,CAAC,CAAA"}
package/dist/LinearPileupDisplay/components/SortByTag.js CHANGED
@@ -22,37 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
22
22
  __setModuleDefault(result, mod);
23
23
  return result;
24
24
  };
25
- var __importDefault = (this && this.__importDefault) || function (mod) {
26
- return (mod && mod.__esModule) ? mod : { "default": mod };
27
- };
28
25
  Object.defineProperty(exports, "__esModule", { value: true });
29
26
  const react_1 = __importStar(require("react"));
30
27
  const mobx_react_1 = require("mobx-react");
31
28
  const material_1 = require("@mui/material");
32
- const mui_1 = require("tss-react/mui");
33
- const Close_1 = __importDefault(require("@mui/icons-material/Close"));
34
- const useStyles = (0, mui_1.makeStyles)()(theme => ({
35
- root: {
36
- margin: 0,
37
- padding: theme.spacing(2),
38
- },
39
- closeButton: {
40
- position: 'absolute',
41
- right: theme.spacing(1),
42
- top: theme.spacing(1),
43
- color: theme.palette.grey[500],
44
- },
45
- }));
29
+ const ui_1 = require("@jbrowse/core/ui");
46
30
  function SortByTagDlg(props) {
47
- const { classes } = useStyles();
48
31
  const { model, handleClose } = props;
49
32
  const [tag, setTag] = (0, react_1.useState)('');
50
33
  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
51
- return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
52
- react_1.default.createElement(material_1.DialogTitle, null,
53
- "Sort by tag",
54
- react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
55
- react_1.default.createElement(Close_1.default, null))),
34
+ return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Sort by tag" },
56
35
  react_1.default.createElement(material_1.DialogContent, null,
57
36
  react_1.default.createElement(material_1.Typography, null, "Set the tag to sort by"),
58
37
  react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: HP for haplotype, RG for read group, etc."),
package/dist/LinearPileupDisplay/components/SortByTag.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CASsB;AACtB,uCAA0C;AAE1C,sEAAiD;AAEjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;IACD,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,8BAAC,sBAAW;;YAEV,8BAAC,qBAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,8BAAC,eAAS,OAAG,CACF,CACD;QACd,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,iCAAoC;YAC/C,8BAAC,qBAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,qBAAqB;iBACrC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAClE,YAAY,EAAC,KAAK,iBACN,eAAe,GAC3B;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,YAAY,CAAC,CAAA"}
1
+ {"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AAEzC,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,aAAa;QACpD,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,iCAAoC;YAC/C,8BAAC,qBAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,qBAAqB;iBACrC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAClE,YAAY,EAAC,KAAK,iBACN,eAAe,GAC3B;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,YAAY,CAAC,CAAA"}
package/dist/LinearPileupDisplay/configSchema.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import { Instance } from 'mobx-state-tree';
2
2
  import PluginManager from '@jbrowse/core/PluginManager';
3
- declare function PileupConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4
- export declare type LinearPileupDisplayConfigModel = ReturnType<typeof PileupConfigFactory>;
5
- export declare type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
6
- export default PileupConfigFactory;
3
+ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4
+ export type LinearPileupDisplayConfigModel = ReturnType<typeof configSchemaF>;
5
+ export type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
6
+ export default configSchemaF;
package/dist/LinearPileupDisplay/configSchema.js CHANGED
@@ -7,7 +7,7 @@ const mobx_state_tree_1 = require("mobx-state-tree");
7
7
  * #config LinearPileupDisplay
8
8
  */
9
9
  function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
10
- function PileupConfigFactory(pluginManager) {
10
+ function configSchemaF(pluginManager) {
11
11
  // modify config schema to take in a sub coverage display
12
12
  return (0, configuration_1.ConfigurationSchema)('LinearPileupDisplay', {
13
13
  /**
@@ -56,5 +56,5 @@ function PileupConfigFactory(pluginManager) {
56
56
  explicitlyTyped: true,
57
57
  });
58
58
  }
59
- exports.default = PileupConfigFactory;
59
+ exports.default = configSchemaF;
60
60
  //# sourceMappingURL=configSchema.js.map
package/dist/LinearPileupDisplay/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAiD;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAMD,kBAAe,mBAAmB,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAiD;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAID,kBAAe,aAAa,CAAA"}
package/dist/LinearPileupDisplay/index.d.ts CHANGED
@@ -1,2 +1,5 @@
1
+ import configSchemaFactory from './configSchema';
2
+ import modelFactory from './model';
1
3
  import PluginManager from '@jbrowse/core/PluginManager';
2
4
  export default function register(pluginManager: PluginManager): void;
5
+ export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };
package/dist/LinearPileupDisplay/index.js CHANGED
@@ -3,8 +3,11 @@ 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.linearPileupDisplayConfigSchemaFactory = exports.linearPileupDisplayStateModelFactory = void 0;
6
7
  const configSchema_1 = __importDefault(require("./configSchema"));
8
+ exports.linearPileupDisplayConfigSchemaFactory = configSchema_1.default;
7
9
  const model_1 = __importDefault(require("./model"));
10
+ exports.linearPileupDisplayStateModelFactory = model_1.default;
8
11
  const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
9
12
  const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
10
13
  function register(pluginManager) {
package/dist/LinearPileupDisplay/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAgD;AAChD,oDAAkC;AAClC,kGAAyE;AAEzE,kFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,2BAYC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAgD;AAsBvB,iDAtBlB,sBAAmB,CAsBqC;AArB/D,oDAAkC;AAoBhB,+CApBX,eAAY,CAoBmC;AAnBtD,kGAAyE;AAEzE,kFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,2BAYC"}
package/dist/LinearPileupDisplay/model.d.ts CHANGED
@@ -6,6 +6,7 @@ import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
6
6
  import { LinearPileupDisplayConfigModel } from './configSchema';
7
7
  /**
8
8
  * #stateModel LinearPileupDisplay
9
+ * extends `BaseLinearDisplay`
9
10
  */
10
11
  declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel): import("mobx-state-tree").IModelType<{
11
12
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -29,10 +30,14 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
29
30
  isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
30
31
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
31
32
  }, {
32
- renderInProgress: AbortController | undefined;
33
+ renderInProgress: AbortController | undefined; /**
34
+ * #property
35
+ */
33
36
  filled: boolean;
34
37
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
35
- features: Map<string, Feature> | undefined;
38
+ features: Map<string, Feature> | undefined; /**
39
+ * #property
40
+ */
36
41
  layout: any;
37
42
  status: string;
38
43
  error: unknown;
@@ -43,7 +48,9 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
43
48
  }) => any;
44
49
  renderProps: any;
45
50
  } & {
46
- doReload(): void;
51
+ doReload(): void; /**
52
+ * #property
53
+ */
47
54
  afterAttach(): void;
48
55
  setStatus(message: string): void;
49
56
  setLoading(abortController: AbortController): void;
@@ -104,9 +111,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
104
111
  rendererTypeName: string;
105
112
  error: unknown;
106
113
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
107
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
108
- * #action
109
- */
114
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
110
115
  type: import("mobx-state-tree").ISimpleType<string>;
111
116
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
112
117
  }, {
@@ -221,12 +226,17 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
221
226
  colorTagMap: import("mobx").ObservableMap<string, string>;
222
227
  modificationTagMap: import("mobx").ObservableMap<string, string>;
223
228
  featureUnderMouseVolatile: Feature | undefined;
229
+ currSortBpPerPx: number;
224
230
  ready: boolean;
225
231
  } & {
226
232
  /**
227
233
  * #action
228
234
  */
229
235
  setReady(flag: boolean): void;
236
+ /**
237
+ * #action
238
+ */
239
+ setCurrSortBpPerPx(n: number): void;
230
240
  /**
231
241
  * #action
232
242
  */
@@ -409,12 +419,12 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
409
419
  })[];
410
420
  }, import("mobx-state-tree")._NotCustomized, {
411
421
  type: string;
412
- id: string;
413
422
  height: number;
423
+ id: string;
414
424
  rpcDriverName: string | undefined;
415
425
  userBpPerPxLimit: number | undefined;
416
426
  userByteSizeLimit: number | undefined;
417
427
  } & import("mobx-state-tree")._NotCustomized>;
418
- export declare type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
419
- export declare type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
428
+ export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
429
+ export type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
420
430
  export default stateModelFactory;
package/dist/LinearPileupDisplay/model.js CHANGED
@@ -57,6 +57,7 @@ const rendererTypes = new Map([
57
57
  ]);
58
58
  /**
59
59
  * #stateModel LinearPileupDisplay
60
+ * extends `BaseLinearDisplay`
60
61
  */
61
62
  function stateModelFactory(configSchema) {
62
63
  return mobx_state_tree_1.types
@@ -111,6 +112,9 @@ function stateModelFactory(configSchema) {
111
112
  tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
112
113
  extra: mobx_state_tree_1.types.frozen(),
113
114
  })),
115
+ /**
116
+ * #property
117
+ */
114
118
  filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
115
119
  flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
116
120
  flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
@@ -122,6 +126,7 @@ function stateModelFactory(configSchema) {
122
126
  colorTagMap: mobx_1.observable.map({}),
123
127
  modificationTagMap: mobx_1.observable.map({}),
124
128
  featureUnderMouseVolatile: undefined,
129
+ currSortBpPerPx: 0,
125
130
  ready: false,
126
131
  }))
127
132
  .actions(self => ({
@@ -131,6 +136,12 @@ function stateModelFactory(configSchema) {
131
136
  setReady(flag) {
132
137
  self.ready = flag;
133
138
  },
139
+ /**
140
+ * #action
141
+ */
142
+ setCurrSortBpPerPx(n) {
143
+ self.currSortBpPerPx = n;
144
+ },
134
145
  /**
135
146
  * #action
136
147
  */
@@ -248,7 +259,7 @@ function stateModelFactory(configSchema) {
248
259
  ...self.renderProps(),
249
260
  });
250
261
  self.setReady(true);
251
- self.setCurrBpPerPx(bpPerPx);
262
+ self.setCurrSortBpPerPx(bpPerPx);
252
263
  }
253
264
  else {
254
265
  self.setReady(true);
@@ -260,6 +271,8 @@ function stateModelFactory(configSchema) {
260
271
  }
261
272
  }, { delay: 1000 }));
262
273
  // autorun synchronizes featureUnderMouse with featureIdUnderMouse
274
+ // asynchronously. this is needed due to how we do not serialize all
275
+ // features from the BAM/CRAM over the rpc
263
276
  (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
264
277
  var _a;
265
278
  const session = (0, util_1.getSession)(self);
@@ -479,13 +492,13 @@ function stateModelFactory(configSchema) {
479
492
  */
480
493
  renderProps() {
481
494
  const view = (0, util_1.getContainingView)(self);
482
- const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, currBpPerPx, ready, } = self;
495
+ const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, currSortBpPerPx, ready, } = self;
483
496
  const superProps = superRenderProps();
484
497
  return {
485
498
  ...superProps,
486
499
  notReady: superProps.notReady ||
487
500
  !ready ||
488
- (sortedBy && currBpPerPx !== view.bpPerPx),
501
+ (sortedBy && currSortBpPerPx !== view.bpPerPx),
489
502
  rpcDriverName,
490
503
  displayModel: self,
491
504
  sortedBy,
@@ -604,39 +617,27 @@ function stateModelFactory(configSchema) {
604
617
  subMenu: [
605
618
  {
606
619
  label: 'Normal',
607
- onClick: () => {
608
- self.setColorScheme({ type: 'normal' });
609
- },
620
+ onClick: () => self.setColorScheme({ type: 'normal' }),
610
621
  },
611
622
  {
612
623
  label: 'Mapping quality',
613
- onClick: () => {
614
- self.setColorScheme({ type: 'mappingQuality' });
615
- },
624
+ onClick: () => self.setColorScheme({ type: 'mappingQuality' }),
616
625
  },
617
626
  {
618
627
  label: 'Strand',
619
- onClick: () => {
620
- self.setColorScheme({ type: 'strand' });
621
- },
628
+ onClick: () => self.setColorScheme({ type: 'strand' }),
622
629
  },
623
630
  {
624
631
  label: 'Pair orientation',
625
- onClick: () => {
626
- self.setColorScheme({ type: 'pairOrientation' });
627
- },
632
+ onClick: () => self.setColorScheme({ type: 'pairOrientation' }),
628
633
  },
629
634
  {
630
635
  label: 'Per-base quality',
631
- onClick: () => {
632
- self.setColorScheme({ type: 'perBaseQuality' });
633
- },
636
+ onClick: () => self.setColorScheme({ type: 'perBaseQuality' }),
634
637
  },
635
638
  {
636
639
  label: 'Per-base lettering',
637
- onClick: () => {
638
- self.setColorScheme({ type: 'perBaseLettering' });
639
- },
640
+ onClick: () => self.setColorScheme({ type: 'perBaseLettering' }),
640
641
  },
641
642
  {
642
643
  label: 'Modifications or methylation',
@@ -649,15 +650,11 @@ function stateModelFactory(configSchema) {
649
650
  },
650
651
  {
651
652
  label: 'Insert size',
652
- onClick: () => {
653
- self.setColorScheme({ type: 'insertSize' });
654
- },
653
+ onClick: () => self.setColorScheme({ type: 'insertSize' }),
655
654
  },
656
655
  {
657
656
  label: 'Stranded paired-end',
658
- onClick: () => {
659
- self.setColorScheme({ type: 'reverseTemplate' });
660
- },
657
+ onClick: () => self.setColorScheme({ type: 'reverseTemplate' }),
661
658
  },
662
659
  {
663
660
  label: 'Color by tag...',
@@ -702,9 +699,7 @@ function stateModelFactory(configSchema) {
702
699
  label: 'Fade mismatches by quality',
703
700
  type: 'checkbox',
704
701
  checked: self.mismatchAlphaSetting,
705
- onClick: () => {
706
- self.toggleMismatchAlpha();
707
- },
702
+ onClick: () => self.toggleMismatchAlpha(),
708
703
  },
709
704
  ];
710
705
  },
package/dist/LinearPileupDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  /// <reference types="react" />
2
2
  import { Feature } from '@jbrowse/core/util/simpleFeature';
3
- declare type Coord = [number, number];
3
+ type Coord = [number, number];
4
4
  declare const SNPCoverageTooltip: (props: {
5
5
  model: {
6
6
  featureUnderMouse: Feature;