@jbrowse/plugin-variants 2.0.0 → 2.1.2

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Files changed (123) hide show
  1. package/dist/ChordVariantDisplay/index.js +9 -9
  2. package/dist/ChordVariantDisplay/index.js.map +1 -1
  3. package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js +23 -25
  4. package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js.map +1 -1
  5. package/dist/LinearVariantDisplay/configSchema.js +3 -3
  6. package/dist/LinearVariantDisplay/configSchema.js.map +1 -1
  7. package/dist/LinearVariantDisplay/index.d.ts +3 -2
  8. package/dist/LinearVariantDisplay/index.js +17 -5
  9. package/dist/LinearVariantDisplay/index.js.map +1 -1
  10. package/dist/LinearVariantDisplay/model.js +24 -72
  11. package/dist/LinearVariantDisplay/model.js.map +1 -1
  12. package/dist/StructuralVariantChordRenderer/ReactComponent.js +57 -103
  13. package/dist/StructuralVariantChordRenderer/ReactComponent.js.map +1 -1
  14. package/dist/StructuralVariantChordRenderer/index.js +7 -7
  15. package/dist/StructuralVariantChordRenderer/index.js.map +1 -1
  16. package/dist/VariantFeatureWidget/AnnotGrid.d.ts +5 -0
  17. package/dist/VariantFeatureWidget/AnnotGrid.js +22 -0
  18. package/dist/VariantFeatureWidget/AnnotGrid.js.map +1 -0
  19. package/dist/VariantFeatureWidget/BreakendOptionDialog.js +23 -40
  20. package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  21. package/dist/VariantFeatureWidget/BreakendPanel.d.ts +7 -0
  22. package/dist/VariantFeatureWidget/BreakendPanel.js +82 -0
  23. package/dist/VariantFeatureWidget/BreakendPanel.js.map +1 -0
  24. package/dist/VariantFeatureWidget/VariantAnnPanel.d.ts +5 -0
  25. package/dist/VariantFeatureWidget/VariantAnnPanel.js +25 -0
  26. package/dist/VariantFeatureWidget/VariantAnnPanel.js.map +1 -0
  27. package/dist/VariantFeatureWidget/VariantCsqPanel.d.ts +5 -0
  28. package/dist/VariantFeatureWidget/VariantCsqPanel.js +25 -0
  29. package/dist/VariantFeatureWidget/VariantCsqPanel.js.map +1 -0
  30. package/dist/VariantFeatureWidget/VariantFeatureWidget.js +23 -184
  31. package/dist/VariantFeatureWidget/VariantFeatureWidget.js.map +1 -1
  32. package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts +2 -0
  33. package/dist/VariantFeatureWidget/VariantSampleGrid.js +83 -0
  34. package/dist/VariantFeatureWidget/VariantSampleGrid.js.map +1 -0
  35. package/dist/VariantFeatureWidget/index.d.ts +2 -0
  36. package/dist/VariantFeatureWidget/index.js +41 -4
  37. package/dist/VariantFeatureWidget/index.js.map +1 -1
  38. package/dist/VariantTrack/index.d.ts +3 -0
  39. package/dist/VariantTrack/index.js +19 -0
  40. package/dist/VariantTrack/index.js.map +1 -0
  41. package/dist/VcfAdapter/VcfAdapter.js +85 -221
  42. package/dist/VcfAdapter/VcfAdapter.js.map +1 -1
  43. package/dist/VcfAdapter/configSchema.js +1 -1
  44. package/dist/VcfAdapter/configSchema.js.map +1 -1
  45. package/dist/VcfAdapter/index.d.ts +3 -1
  46. package/dist/VcfAdapter/index.js +32 -3
  47. package/dist/VcfAdapter/index.js.map +1 -1
  48. package/dist/VcfTabixAdapter/VcfFeature.js +76 -107
  49. package/dist/VcfTabixAdapter/VcfFeature.js.map +1 -1
  50. package/dist/VcfTabixAdapter/VcfTabixAdapter.js +88 -231
  51. package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
  52. package/dist/VcfTabixAdapter/configSchema.js +2 -2
  53. package/dist/VcfTabixAdapter/configSchema.js.map +1 -1
  54. package/dist/VcfTabixAdapter/index.d.ts +3 -0
  55. package/dist/VcfTabixAdapter/index.js +34 -2
  56. package/dist/VcfTabixAdapter/index.js.map +1 -1
  57. package/dist/extensionPoints.d.ts +3 -0
  58. package/dist/extensionPoints.js +51 -0
  59. package/dist/extensionPoints.js.map +1 -0
  60. package/dist/index.js +24 -162
  61. package/dist/index.js.map +1 -1
  62. package/esm/LinearVariantDisplay/index.d.ts +3 -2
  63. package/esm/LinearVariantDisplay/index.js +17 -2
  64. package/esm/LinearVariantDisplay/index.js.map +1 -1
  65. package/esm/VariantFeatureWidget/AnnotGrid.d.ts +5 -0
  66. package/esm/VariantFeatureWidget/AnnotGrid.js +16 -0
  67. package/esm/VariantFeatureWidget/AnnotGrid.js.map +1 -0
  68. package/esm/VariantFeatureWidget/BreakendPanel.d.ts +7 -0
  69. package/esm/VariantFeatureWidget/BreakendPanel.js +53 -0
  70. package/esm/VariantFeatureWidget/BreakendPanel.js.map +1 -0
  71. package/esm/VariantFeatureWidget/VariantAnnPanel.d.ts +5 -0
  72. package/esm/VariantFeatureWidget/VariantAnnPanel.js +19 -0
  73. package/esm/VariantFeatureWidget/VariantAnnPanel.js.map +1 -0
  74. package/esm/VariantFeatureWidget/VariantCsqPanel.d.ts +5 -0
  75. package/esm/VariantFeatureWidget/VariantCsqPanel.js +19 -0
  76. package/esm/VariantFeatureWidget/VariantCsqPanel.js.map +1 -0
  77. package/esm/VariantFeatureWidget/VariantFeatureWidget.js +13 -104
  78. package/esm/VariantFeatureWidget/VariantFeatureWidget.js.map +1 -1
  79. package/esm/VariantFeatureWidget/VariantSampleGrid.d.ts +2 -0
  80. package/esm/VariantFeatureWidget/VariantSampleGrid.js +57 -0
  81. package/esm/VariantFeatureWidget/VariantSampleGrid.js.map +1 -0
  82. package/esm/VariantFeatureWidget/index.d.ts +2 -0
  83. package/esm/VariantFeatureWidget/index.js +11 -0
  84. package/esm/VariantFeatureWidget/index.js.map +1 -1
  85. package/esm/VariantTrack/index.d.ts +3 -0
  86. package/esm/VariantTrack/index.js +14 -0
  87. package/esm/VariantTrack/index.js.map +1 -0
  88. package/esm/VcfAdapter/VcfAdapter.js +9 -7
  89. package/esm/VcfAdapter/VcfAdapter.js.map +1 -1
  90. package/esm/VcfAdapter/index.d.ts +3 -1
  91. package/esm/VcfAdapter/index.js +9 -1
  92. package/esm/VcfAdapter/index.js.map +1 -1
  93. package/esm/VcfTabixAdapter/VcfFeature.js +1 -1
  94. package/esm/VcfTabixAdapter/VcfFeature.js.map +1 -1
  95. package/esm/VcfTabixAdapter/VcfTabixAdapter.js +1 -7
  96. package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
  97. package/esm/VcfTabixAdapter/index.d.ts +3 -0
  98. package/esm/VcfTabixAdapter/index.js +9 -0
  99. package/esm/VcfTabixAdapter/index.js.map +1 -1
  100. package/esm/extensionPoints.d.ts +3 -0
  101. package/esm/extensionPoints.js +49 -0
  102. package/esm/extensionPoints.js.map +1 -0
  103. package/esm/index.js +12 -95
  104. package/esm/index.js.map +1 -1
  105. package/package.json +7 -8
  106. package/src/LinearVariantDisplay/index.ts +19 -2
  107. package/src/VariantFeatureWidget/AnnotGrid.tsx +28 -0
  108. package/src/VariantFeatureWidget/BreakendPanel.tsx +94 -0
  109. package/src/VariantFeatureWidget/VariantAnnPanel.tsx +31 -0
  110. package/src/VariantFeatureWidget/VariantCsqPanel.tsx +31 -0
  111. package/src/VariantFeatureWidget/VariantFeatureWidget.tsx +13 -198
  112. package/src/VariantFeatureWidget/VariantSampleGrid.tsx +105 -0
  113. package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap +6 -0
  114. package/src/VariantFeatureWidget/index.ts +15 -0
  115. package/src/VariantTrack/index.ts +26 -0
  116. package/src/VcfAdapter/VcfAdapter.ts +15 -16
  117. package/src/VcfAdapter/index.ts +14 -1
  118. package/src/VcfTabixAdapter/VcfFeature.ts +1 -1
  119. package/src/VcfTabixAdapter/VcfTabixAdapter.ts +1 -7
  120. package/src/VcfTabixAdapter/index.ts +15 -0
  121. package/src/__snapshots__/index.test.js.snap +4 -4
  122. package/src/extensionPoints.ts +74 -0
  123. package/src/index.ts +12 -155
@@ -3,19 +3,19 @@ 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
- var plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
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- var ChordVariantDisplay_1 = __importDefault(require("./models/ChordVariantDisplay"));
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- var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
9
- exports.default = (function (pluginManager) {
10
- var load = pluginManager.load;
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- var _a = load(ChordVariantDisplay_1.default), stateModel = _a.stateModel, configSchema = _a.configSchema;
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+ const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
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+ const ChordVariantDisplay_1 = __importDefault(require("./models/ChordVariantDisplay"));
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+ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
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+ exports.default = (pluginManager) => {
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+ const { load } = pluginManager;
11
+ const { stateModel, configSchema } = load(ChordVariantDisplay_1.default);
12
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  return new DisplayType_1.default({
13
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  name: 'ChordVariantDisplay',
14
- configSchema: configSchema,
15
- stateModel: stateModel,
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+ configSchema,
15
+ stateModel,
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  trackType: 'VariantTrack',
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  viewType: 'CircularView',
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  ReactComponent: plugin_circular_view_1.BaseChordDisplayComponent,
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  });
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- });
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+ };
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  //# sourceMappingURL=index.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,sEAAyE;AACzE,qFAA8D;AAC9D,gGAAyE;AAEzE,mBAAe,UAAC,aAA4B;IAClC,IAAA,IAAI,GAAK,aAAa,KAAlB,CAAkB;IAExB,IAAA,KAA+B,IAAI,CAAC,6BAAmB,CAAC,EAAtD,UAAU,gBAAA,EAAE,YAAY,kBAA8B,CAAA;IAE9D,OAAO,IAAI,qBAAW,CAAC;QACrB,IAAI,EAAE,qBAAqB;QAC3B,YAAY,cAAA;QACZ,UAAU,YAAA;QACV,SAAS,EAAE,cAAc;QACzB,QAAQ,EAAE,cAAc;QACxB,cAAc,EAAE,gDAAyB;KAC1C,CAAC,CAAA;AACJ,CAAC,EAAA"}
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+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,wEAAyE;AACzE,uFAA8D;AAC9D,kGAAyE;AAEzE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,MAAM,EAAE,IAAI,EAAE,GAAG,aAAa,CAAA;IAE9B,MAAM,EAAE,UAAU,EAAE,YAAY,EAAE,GAAG,IAAI,CAAC,6BAAmB,CAAC,CAAA;IAE9D,OAAO,IAAI,qBAAW,CAAC;QACrB,IAAI,EAAE,qBAAqB;QAC3B,YAAY;QACZ,UAAU;QACV,SAAS,EAAE,cAAc;QACzB,QAAQ,EAAE,cAAc;QACxB,cAAc,EAAE,gDAAyB;KAC1C,CAAC,CAAA;AACJ,CAAC,CAAA"}
@@ -1,40 +1,38 @@
1
1
  "use strict";
2
- var __assign = (this && this.__assign) || function () {
3
- __assign = Object.assign || function(t) {
4
- for (var s, i = 1, n = arguments.length; i < n; i++) {
5
- s = arguments[i];
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- for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
7
- t[p] = s[p];
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- }
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- return t;
10
- };
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- return __assign.apply(this, arguments);
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- };
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2
  Object.defineProperty(exports, "__esModule", { value: true });
14
- var plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
15
- var configuration_1 = require("@jbrowse/core/configuration");
16
- var mobx_state_tree_1 = require("mobx-state-tree");
17
- var util_1 = require("@jbrowse/core/util");
18
- var tracks_1 = require("@jbrowse/core/util/tracks");
19
- var ChordVariantDisplayF = function (pluginManager) {
20
- var configSchema = (0, configuration_1.ConfigurationSchema)('ChordVariantDisplay', {
3
+ const plugin_circular_view_1 = require("@jbrowse/plugin-circular-view");
4
+ const configuration_1 = require("@jbrowse/core/configuration");
5
+ const mobx_state_tree_1 = require("mobx-state-tree");
6
+ const util_1 = require("@jbrowse/core/util");
7
+ const tracks_1 = require("@jbrowse/core/util/tracks");
8
+ const ChordVariantDisplayF = pluginManager => {
9
+ const configSchema = (0, configuration_1.ConfigurationSchema)('ChordVariantDisplay', {
21
10
  renderer: mobx_state_tree_1.types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
22
11
  }, { baseConfiguration: plugin_circular_view_1.baseChordDisplayConfig, explicitlyTyped: true });
23
- var stateModel = mobx_state_tree_1.types
12
+ const stateModel = mobx_state_tree_1.types
24
13
  .compose('ChordVariantDisplay', plugin_circular_view_1.BaseChordDisplayModel, mobx_state_tree_1.types.model({
25
14
  type: mobx_state_tree_1.types.literal('ChordVariantDisplay'),
26
15
  configuration: (0, configuration_1.ConfigurationReference)(configSchema),
27
16
  }))
28
- .views(function (self) { return ({
17
+ .views(self => ({
29
18
  get rendererTypeName() {
30
19
  return self.configuration.renderer.type;
31
20
  },
32
- renderProps: function () {
33
- var view = (0, util_1.getContainingView)(self);
34
- return __assign(__assign({}, (0, tracks_1.getParentRenderProps)(self)), { rpcDriverName: self.rpcDriverName, displayModel: self, bezierRadius: view.radiusPx * self.bezierRadiusRatio, radius: view.radiusPx, blockDefinitions: this.blockDefinitions, config: self.configuration.renderer, onChordClick: self.onChordClick });
21
+ renderProps() {
22
+ const view = (0, util_1.getContainingView)(self);
23
+ return {
24
+ ...(0, tracks_1.getParentRenderProps)(self),
25
+ rpcDriverName: self.rpcDriverName,
26
+ displayModel: self,
27
+ bezierRadius: view.radiusPx * self.bezierRadiusRatio,
28
+ radius: view.radiusPx,
29
+ blockDefinitions: this.blockDefinitions,
30
+ config: self.configuration.renderer,
31
+ onChordClick: self.onChordClick,
32
+ };
35
33
  },
36
- }); });
37
- return { stateModel: stateModel, configSchema: configSchema };
34
+ }));
35
+ return { stateModel, configSchema };
38
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  };
39
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  // http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi
40
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  // render request is for 1.5x the current viewing window
@@ -1 +1 @@
1
- {"version":3,"file":"ChordVariantDisplay.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/ChordVariantDisplay.js"],"names":[],"mappings":";;;;;;;;;;;;;AAAA,sEAGsC;AACtC,6DAGoC;AACpC,mDAAuC;AACvC,2CAAsD;AACtD,oDAAgE;AAEhE,IAAM,oBAAoB,GAAG,UAAA,aAAa;IACxC,IAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,qBAAqB,EACrB;QACE,QAAQ,EAAE,uBAAK,CAAC,QAAQ,CACtB,aAAa,CAAC,yBAAyB,CAAC,UAAU,CAAC,EACnD,EAAE,IAAI,EAAE,gCAAgC,EAAE,CAC3C;KACF,EACD,EAAE,iBAAiB,EAAE,6CAAsB,EAAE,eAAe,EAAE,IAAI,EAAE,CACrE,CAAA;IAED,IAAM,UAAU,GAAG,uBAAK;SACrB,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,UAAA,IAAI,IAAI,OAAA,CAAC;QACd,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED,WAAW;YACT,IAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,6BACK,IAAA,6BAAoB,EAAC,IAAI,CAAC,KAC7B,aAAa,EAAE,IAAI,CAAC,aAAa,EACjC,YAAY,EAAE,IAAI,EAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB,EACpD,MAAM,EAAE,IAAI,CAAC,QAAQ,EACrB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB,EACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ,EACnC,YAAY,EAAE,IAAI,CAAC,YAAY,IAChC;QACH,CAAC;KACF,CAAC,EAlBa,CAkBb,CAAC,CAAA;IAEL,OAAO,EAAE,UAAU,YAAA,EAAE,YAAY,cAAA,EAAE,CAAA;AACrC,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,oBAAoB,CAAA"}
1
+ {"version":3,"file":"ChordVariantDisplay.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/ChordVariantDisplay.js"],"names":[],"mappings":";;AAAA,wEAGsC;AACtC,+DAGoC;AACpC,qDAAuC;AACvC,6CAAsD;AACtD,sDAAgE;AAEhE,MAAM,oBAAoB,GAAG,aAAa,CAAC,EAAE;IAC3C,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,qBAAqB,EACrB;QACE,QAAQ,EAAE,uBAAK,CAAC,QAAQ,CACtB,aAAa,CAAC,yBAAyB,CAAC,UAAU,CAAC,EACnD,EAAE,IAAI,EAAE,gCAAgC,EAAE,CAC3C;KACF,EACD,EAAE,iBAAiB,EAAE,6CAAsB,EAAE,eAAe,EAAE,IAAI,EAAE,CACrE,CAAA;IAED,MAAM,UAAU,GAAG,uBAAK;SACrB,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED,WAAW;YACT,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,IAAA,6BAAoB,EAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBACrB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,IAAI,CAAC,YAAY;aAChC,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;IAEL,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,CAAA;AACrC,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,oBAAoB,CAAA"}
@@ -1,10 +1,10 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.LinearVariantDisplayConfigFactory = void 0;
4
- var configuration_1 = require("@jbrowse/core/configuration");
5
- var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
4
+ const configuration_1 = require("@jbrowse/core/configuration");
5
+ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
6
6
  function LinearVariantDisplayConfigFactory(pluginManager) {
7
- var configSchema = (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager);
7
+ const configSchema = (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager);
8
8
  return (0, configuration_1.ConfigurationSchema)('LinearVariantDisplay', {}, { baseConfiguration: configSchema, explicitlyTyped: true });
9
9
  }
10
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  exports.LinearVariantDisplayConfigFactory = LinearVariantDisplayConfigFactory;
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/configSchema.ts"],"names":[],"mappings":";;;AAAA,6DAAiE;AAGjE,gFAA0F;AAE1F,SAAgB,iCAAiC,CAC/C,aAA4B;IAE5B,IAAM,YAAY,GAAG,IAAA,iEAAqC,EAAC,aAAa,CAAC,CAAA;IAEzE,OAAO,IAAA,mCAAmB,EACxB,sBAAsB,EACtB,EAAE,EACF,EAAE,iBAAiB,EAAE,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA;AACH,CAAC;AAVD,8EAUC"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/configSchema.ts"],"names":[],"mappings":";;;AAAA,+DAAiE;AAGjE,kFAA0F;AAE1F,SAAgB,iCAAiC,CAC/C,aAA4B;IAE5B,MAAM,YAAY,GAAG,IAAA,iEAAqC,EAAC,aAAa,CAAC,CAAA;IAEzE,OAAO,IAAA,mCAAmB,EACxB,sBAAsB,EACtB,EAAE,EACF,EAAE,iBAAiB,EAAE,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA;AACH,CAAC;AAVD,8EAUC"}
@@ -1,2 +1,3 @@
1
- export { LinearVariantDisplayConfigFactory as configSchemaFactory } from './configSchema';
2
- export { default as modelFactory } from './model';
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ declare const _default: (pluginManager: PluginManager) => void;
3
+ export default _default;
@@ -3,9 +3,21 @@ 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.modelFactory = exports.configSchemaFactory = void 0;
7
- var configSchema_1 = require("./configSchema");
8
- Object.defineProperty(exports, "configSchemaFactory", { enumerable: true, get: function () { return configSchema_1.LinearVariantDisplayConfigFactory; } });
9
- var model_1 = require("./model");
10
- Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_1).default; } });
6
+ const configSchema_1 = require("./configSchema");
7
+ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
8
+ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
9
+ const model_1 = __importDefault(require("./model"));
10
+ exports.default = (pluginManager) => {
11
+ pluginManager.addDisplayType(() => {
12
+ const configSchema = (0, configSchema_1.LinearVariantDisplayConfigFactory)(pluginManager);
13
+ return new DisplayType_1.default({
14
+ name: 'LinearVariantDisplay',
15
+ configSchema,
16
+ stateModel: (0, model_1.default)(configSchema),
17
+ trackType: 'VariantTrack',
18
+ viewType: 'LinearGenomeView',
19
+ ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
20
+ });
21
+ });
22
+ };
11
23
  //# sourceMappingURL=index.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAyF;AAAhF,mHAAA,iCAAiC,OAAuB;AACjE,iCAAiD;AAAxC,sHAAA,OAAO,OAAgB"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,iDAAkE;AAClE,kFAA+E;AAC/E,kGAAyE;AACzE,oDAAuC;AAEvC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,gDAAiC,EAAC,aAAa,CAAC,CAAA;QACrE,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
@@ -1,85 +1,37 @@
1
1
  "use strict";
2
- var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
3
- function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
4
- return new (P || (P = Promise))(function (resolve, reject) {
5
- function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
6
- function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
7
- function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
8
- step((generator = generator.apply(thisArg, _arguments || [])).next());
9
- });
10
- };
11
- var __generator = (this && this.__generator) || function (thisArg, body) {
12
- var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
13
- return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
14
- function verb(n) { return function (v) { return step([n, v]); }; }
15
- function step(op) {
16
- if (f) throw new TypeError("Generator is already executing.");
17
- while (_) try {
18
- if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
19
- if (y = 0, t) op = [op[0] & 2, t.value];
20
- switch (op[0]) {
21
- case 0: case 1: t = op; break;
22
- case 4: _.label++; return { value: op[1], done: false };
23
- case 5: _.label++; y = op[1]; op = [0]; continue;
24
- case 7: op = _.ops.pop(); _.trys.pop(); continue;
25
- default:
26
- if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
27
- if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
28
- if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
29
- if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
30
- if (t[2]) _.ops.pop();
31
- _.trys.pop(); continue;
32
- }
33
- op = body.call(thisArg, _);
34
- } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
35
- if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
36
- }
37
- };
38
2
  Object.defineProperty(exports, "__esModule", { value: true });
39
- var configuration_1 = require("@jbrowse/core/configuration");
40
- var tracks_1 = require("@jbrowse/core/util/tracks");
41
- var util_1 = require("@jbrowse/core/util");
42
- var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
43
- var mobx_state_tree_1 = require("mobx-state-tree");
3
+ const configuration_1 = require("@jbrowse/core/configuration");
4
+ const tracks_1 = require("@jbrowse/core/util/tracks");
5
+ const util_1 = require("@jbrowse/core/util");
6
+ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
7
+ const mobx_state_tree_1 = require("mobx-state-tree");
44
8
  function default_1(configSchema) {
45
9
  return mobx_state_tree_1.types
46
10
  .compose('LinearVariantDisplay', (0, plugin_linear_genome_view_1.linearBasicDisplayModelFactory)(configSchema), mobx_state_tree_1.types.model({
47
11
  type: mobx_state_tree_1.types.literal('LinearVariantDisplay'),
48
12
  configuration: (0, configuration_1.ConfigurationReference)(configSchema),
49
13
  }))
50
- .actions(function (self) { return ({
51
- selectFeature: function (feature) {
52
- return __awaiter(this, void 0, void 0, function () {
53
- var session, rpcManager, sessionId, track, adapterConfig, header, featureWidget;
54
- return __generator(this, function (_a) {
55
- switch (_a.label) {
56
- case 0:
57
- session = (0, util_1.getSession)(self);
58
- if (!(0, util_1.isSessionModelWithWidgets)(session)) return [3 /*break*/, 2];
59
- rpcManager = session.rpcManager;
60
- sessionId = (0, tracks_1.getRpcSessionId)(self);
61
- track = (0, util_1.getContainingTrack)(self);
62
- adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
63
- return [4 /*yield*/, rpcManager.call(sessionId, 'CoreGetMetadata', {
64
- adapterConfig: adapterConfig,
65
- })];
66
- case 1:
67
- header = _a.sent();
68
- featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
69
- featureData: feature.toJSON(),
70
- view: (0, util_1.getContainingView)(self),
71
- descriptions: header,
72
- });
73
- session.showWidget(featureWidget);
74
- _a.label = 2;
75
- case 2:
76
- session.setSelection(feature);
77
- return [2 /*return*/];
78
- }
14
+ .actions(self => ({
15
+ async selectFeature(feature) {
16
+ const session = (0, util_1.getSession)(self);
17
+ if ((0, util_1.isSessionModelWithWidgets)(session)) {
18
+ const { rpcManager } = session;
19
+ const sessionId = (0, tracks_1.getRpcSessionId)(self);
20
+ const track = (0, util_1.getContainingTrack)(self);
21
+ const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
22
+ const header = await rpcManager.call(sessionId, 'CoreGetMetadata', {
23
+ adapterConfig,
24
+ });
25
+ const featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
26
+ featureData: feature.toJSON(),
27
+ view: (0, util_1.getContainingView)(self),
28
+ descriptions: header,
79
29
  });
80
- });
30
+ session.showWidget(featureWidget);
31
+ }
32
+ session.setSelection(feature);
81
33
  },
82
- }); });
34
+ }));
83
35
  }
84
36
  exports.default = default_1;
85
37
  //# sourceMappingURL=model.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,6DAA6E;AAC7E,oDAA2D;AAC3D,2CAK2B;AAG3B,gFAAmF;AACnF,mDAAuC;AAGvC,mBAAyB,YAA6C;IACpE,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,UAAA,IAAI,IAAI,OAAA,CAAC;QACV,aAAa,EAAnB,UAAoB,OAAgB;;;;;;4BAC5B,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;iCAC5B,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAlC,wBAAkC;4BAC5B,UAAU,GAAK,OAAO,WAAZ,CAAY;4BACxB,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;4BACjC,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;4BAChC,aAAa,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;4BAChC,qBAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;oCACjE,aAAa,eAAA;iCACd,CAAC,EAAA;;4BAFI,MAAM,GAAG,SAEb;4BACI,aAAa,GAAG,OAAO,CAAC,SAAS,CACrC,sBAAsB,EACtB,gBAAgB,EAChB;gCACE,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;gCAC7B,IAAI,EAAE,IAAA,wBAAiB,EAAC,IAAI,CAAC;gCAC7B,YAAY,EAAE,MAAM;6BACrB,CACF,CAAA;4BACD,OAAO,CAAC,UAAU,CAAC,aAAa,CAAC,CAAA;;;4BAGnC,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;;;;;SAC9B;KACF,CAAC,EAzBe,CAyBf,CAAC,CAAA;AACP,CAAC;AApCD,4BAoCC"}
1
+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAK2B;AAG3B,kFAAmF;AACnF,qDAAuC;AAGvC,mBAAyB,YAA6C;IACpE,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;oBACjE,aAAa;iBACd,CAAC,CAAA;gBACF,MAAM,aAAa,GAAG,OAAO,CAAC,SAAS,CACrC,sBAAsB,EACtB,gBAAgB,EAChB;oBACE,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI,EAAE,IAAA,wBAAiB,EAAC,IAAI,CAAC;oBAC7B,YAAY,EAAE,MAAM;iBACrB,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAAC,aAAa,CAAC,CAAA;aAClC;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AApCD,4BAoCC"}
@@ -22,124 +22,84 @@ var __importStar = (this && this.__importStar) || function (mod) {
22
22
  __setModuleDefault(result, mod);
23
23
  return result;
24
24
  };
25
- var __read = (this && this.__read) || function (o, n) {
26
- var m = typeof Symbol === "function" && o[Symbol.iterator];
27
- if (!m) return o;
28
- var i = m.call(o), r, ar = [], e;
29
- try {
30
- while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
31
- }
32
- catch (error) { e = { error: error }; }
33
- finally {
34
- try {
35
- if (r && !r.done && (m = i["return"])) m.call(i);
36
- }
37
- finally { if (e) throw e.error; }
38
- }
39
- return ar;
40
- };
41
- var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
42
- if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
43
- if (ar || !(i in from)) {
44
- if (!ar) ar = Array.prototype.slice.call(from, 0, i);
45
- ar[i] = from[i];
46
- }
47
- }
48
- return to.concat(ar || Array.prototype.slice.call(from));
49
- };
50
- var __values = (this && this.__values) || function(o) {
51
- var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
52
- if (m) return m.call(o);
53
- if (o && typeof o.length === "number") return {
54
- next: function () {
55
- if (o && i >= o.length) o = void 0;
56
- return { value: o && o[i++], done: !o };
57
- }
58
- };
59
- throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
60
- };
61
25
  var __importDefault = (this && this.__importDefault) || function (mod) {
62
26
  return (mod && mod.__esModule) ? mod : { "default": mod };
63
27
  };
64
28
  Object.defineProperty(exports, "__esModule", { value: true });
65
- var react_1 = __importStar(require("react"));
66
- var mobx_react_1 = require("mobx-react");
67
- var util_1 = require("@jbrowse/core/util");
68
- var configuration_1 = require("@jbrowse/core/configuration");
69
- var mst_1 = require("@jbrowse/core/util/types/mst");
70
- var vcf_1 = require("@gmod/vcf");
71
- var prop_types_1 = __importDefault(require("prop-types"));
29
+ const react_1 = __importStar(require("react"));
30
+ const mobx_react_1 = require("mobx-react");
31
+ const util_1 = require("@jbrowse/core/util");
32
+ const configuration_1 = require("@jbrowse/core/configuration");
33
+ const mst_1 = require("@jbrowse/core/util/types/mst");
34
+ const vcf_1 = require("@gmod/vcf");
35
+ const prop_types_1 = __importDefault(require("prop-types"));
72
36
  function bpToRadians(block, pos) {
73
- var blockStart = block.region.elided ? 0 : block.region.start;
74
- var blockEnd = block.region.elided ? 0 : block.region.end;
75
- var bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
76
- var radians = bpOffset / block.bpPerRadian + block.startRadians;
37
+ const blockStart = block.region.elided ? 0 : block.region.start;
38
+ const blockEnd = block.region.elided ? 0 : block.region.end;
39
+ const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
40
+ const radians = bpOffset / block.bpPerRadian + block.startRadians;
77
41
  return radians;
78
42
  }
79
- var Chord = (0, mobx_react_1.observer)(function Chord(_a) {
80
- var _b;
81
- var _c, _d, _e, _f, _g;
82
- var feature = _a.feature, blocksForRefs = _a.blocksForRefs, radius = _a.radius, config = _a.config, bezierRadius = _a.bezierRadius, selected = _a.selected, onClick = _a.onClick;
43
+ const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
44
+ var _a, _b, _c, _d, _e;
83
45
  // find the blocks that our start and end points belong to
84
- var startBlock = blocksForRefs[feature.get('refName')];
46
+ const startBlock = blocksForRefs[feature.get('refName')];
85
47
  if (!startBlock) {
86
48
  return null;
87
49
  }
88
- var svType;
50
+ let svType;
89
51
  if (feature.get('INFO')) {
90
52
  ;
91
- _b = __read(feature.get('INFO').SVTYPE || [], 1), svType = _b[0];
53
+ [svType] = feature.get('INFO').SVTYPE || [];
92
54
  }
93
55
  else if (feature.get('mate')) {
94
56
  svType = 'mate';
95
57
  }
96
- var endPosition;
97
- var endBlock;
98
- var alt = (_c = feature.get('ALT')) === null || _c === void 0 ? void 0 : _c[0];
99
- var bnd = alt && (0, vcf_1.parseBreakend)(alt);
58
+ let endPosition;
59
+ let endBlock;
60
+ const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
61
+ const bnd = alt && (0, vcf_1.parseBreakend)(alt);
100
62
  if (bnd) {
101
63
  // VCF BND
102
- var matePosition = bnd.MatePosition.split(':');
64
+ const matePosition = bnd.MatePosition.split(':');
103
65
  endPosition = +matePosition[1];
104
66
  endBlock = blocksForRefs[matePosition[0]];
105
67
  }
106
68
  else if (alt === '<TRA>') {
107
69
  // VCF TRA
108
- var chr2 = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.CHR2) === null || _e === void 0 ? void 0 : _e[0];
109
- var end = (_g = (_f = feature.get('INFO')) === null || _f === void 0 ? void 0 : _f.END) === null || _g === void 0 ? void 0 : _g[0];
70
+ const chr2 = (_c = (_b = feature.get('INFO')) === null || _b === void 0 ? void 0 : _b.CHR2) === null || _c === void 0 ? void 0 : _c[0];
71
+ const end = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.END) === null || _e === void 0 ? void 0 : _e[0];
110
72
  endPosition = parseInt(end, 10);
111
73
  endBlock = blocksForRefs[chr2];
112
74
  }
113
75
  else if (svType === 'mate') {
114
76
  // generic simplefeatures arcs
115
- var mate = feature.get('mate');
116
- var chr2 = mate.refName;
77
+ const mate = feature.get('mate');
78
+ const chr2 = mate.refName;
117
79
  endPosition = mate.start;
118
80
  endBlock = blocksForRefs[chr2];
119
81
  }
120
82
  if (endBlock) {
121
- var startPos = feature.get('start');
122
- var startRadians = bpToRadians(startBlock, startPos);
123
- var endRadians = bpToRadians(endBlock, endPosition);
124
- var startXY = (0, util_1.polarToCartesian)(radius, startRadians);
125
- var endXY = (0, util_1.polarToCartesian)(radius, endRadians);
126
- var controlXY = (0, util_1.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
127
- var strokeColor_1 = selected
128
- ? (0, configuration_1.readConfObject)(config, 'strokeColorSelected', { feature: feature })
129
- : (0, configuration_1.readConfObject)(config, 'strokeColor', { feature: feature });
130
- var hoverStrokeColor_1 = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
131
- feature: feature,
83
+ const startPos = feature.get('start');
84
+ const startRadians = bpToRadians(startBlock, startPos);
85
+ const endRadians = bpToRadians(endBlock, endPosition);
86
+ const startXY = (0, util_1.polarToCartesian)(radius, startRadians);
87
+ const endXY = (0, util_1.polarToCartesian)(radius, endRadians);
88
+ const controlXY = (0, util_1.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
89
+ const strokeColor = selected
90
+ ? (0, configuration_1.readConfObject)(config, 'strokeColorSelected', { feature })
91
+ : (0, configuration_1.readConfObject)(config, 'strokeColor', { feature });
92
+ const hoverStrokeColor = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
93
+ feature,
132
94
  });
133
- return (react_1.default.createElement("path", { "data-testid": "chord-".concat(feature.id()), d: __spreadArray(__spreadArray(__spreadArray(__spreadArray(['M'], __read(startXY), false), ['Q'], false), __read(controlXY), false), __read(endXY), false).join(' '), style: { stroke: strokeColor_1 }, onClick: function (evt) {
134
- return onClick(feature, startBlock.region, endBlock.region, evt);
135
- }, onMouseOver: function (evt) {
95
+ return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => onClick(feature, startBlock.region, endBlock.region, evt), onMouseOver: evt => {
136
96
  if (!selected) {
137
- evt.target.style.stroke = hoverStrokeColor_1;
97
+ evt.target.style.stroke = hoverStrokeColor;
138
98
  evt.target.style.strokeWidth = 3;
139
99
  }
140
- }, onMouseOut: function (evt) {
100
+ }, onMouseOut: evt => {
141
101
  if (!selected) {
142
- evt.target.style.stroke = strokeColor_1;
102
+ evt.target.style.stroke = strokeColor;
143
103
  evt.target.style.strokeWidth = 1;
144
104
  }
145
105
  } }));
@@ -147,43 +107,37 @@ var Chord = (0, mobx_react_1.observer)(function Chord(_a) {
147
107
  return null;
148
108
  });
149
109
  function StructuralVariantChords(props) {
150
- var e_1, _a;
151
- var features = props.features, config = props.config, displayModel = props.displayModel, blockDefinitions = props.blockDefinitions, radius = props.radius, bezierRadius = props.bezierRadius, selectedFeatureId = props.displayModel.selectedFeatureId, onChordClick = props.onChordClick;
110
+ const { features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, } = props;
152
111
  // make a map of refName -> blockDefinition
153
- var blocksForRefsMemo = (0, react_1.useMemo)(function () {
154
- var blocksForRefs = {};
155
- blockDefinitions.forEach(function (block) {
156
- var regions = block.region.elided
112
+ const blocksForRefsMemo = (0, react_1.useMemo)(() => {
113
+ const blocksForRefs = {};
114
+ blockDefinitions.forEach(block => {
115
+ const regions = block.region.elided
157
116
  ? block.region.regions
158
117
  : [block.region];
159
- regions.forEach(function (region) {
118
+ regions.forEach(region => {
160
119
  blocksForRefs[region.refName] = block;
161
120
  });
162
121
  });
163
122
  return blocksForRefs;
164
123
  }, [blockDefinitions]);
165
124
  // console.log(blocksForRefs)
166
- var chords = [];
167
- try {
168
- for (var features_1 = __values(features), features_1_1 = features_1.next(); !features_1_1.done; features_1_1 = features_1.next()) {
169
- var _b = __read(features_1_1.value, 2), id = _b[0], feature = _b[1];
170
- var selected = String(selectedFeatureId) === String(feature.id());
171
- chords.push(react_1.default.createElement(Chord, { key: id, feature: feature, config: config, displayModel: displayModel, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
172
- }
173
- }
174
- catch (e_1_1) { e_1 = { error: e_1_1 }; }
175
- finally {
176
- try {
177
- if (features_1_1 && !features_1_1.done && (_a = features_1.return)) _a.call(features_1);
178
- }
179
- finally { if (e_1) throw e_1.error; }
125
+ const chords = [];
126
+ for (const [id, feature] of features) {
127
+ const selected = String(selectedFeatureId) === String(feature.id());
128
+ chords.push(react_1.default.createElement(Chord, { key: id, feature: feature, config: config, displayModel: displayModel, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
180
129
  }
181
- var trackStyleId = "chords-".concat(displayModel.id);
130
+ const trackStyleId = `chords-${displayModel.id}`;
182
131
  return (react_1.default.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
183
132
  react_1.default.createElement("style", {
184
133
  // eslint-disable-next-line react/no-danger
185
134
  dangerouslySetInnerHTML: {
186
- __html: "\n #".concat(trackStyleId, " > path {\n cursor: crosshair;\n fill: none;\n }\n"),
135
+ __html: `
136
+ #${trackStyleId} > path {
137
+ cursor: crosshair;
138
+ fill: none;
139
+ }
140
+ `,
187
141
  } }),
188
142
  chords));
189
143
  }
@@ -1 +1 @@
1
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1
+ 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@@ -3,11 +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
- var CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
7
- var configuration_1 = require("@jbrowse/core/configuration");
8
- var ReactComponent_1 = __importDefault(require("./ReactComponent"));
9
- var ChordRendererConfigF = function (pluginManager) {
10
- var configSchema = (0, configuration_1.ConfigurationSchema)('StructuralVariantChordRenderer', {
6
+ const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
7
+ const configuration_1 = require("@jbrowse/core/configuration");
8
+ const ReactComponent_1 = __importDefault(require("./ReactComponent"));
9
+ const ChordRendererConfigF = pluginManager => {
10
+ const configSchema = (0, configuration_1.ConfigurationSchema)('StructuralVariantChordRenderer', {
11
11
  strokeColor: {
12
12
  type: 'color',
13
13
  description: 'the line color of each arc',
@@ -30,8 +30,8 @@ var ChordRendererConfigF = function (pluginManager) {
30
30
  return new CircularChordRendererType_1.default({
31
31
  name: 'StructuralVariantChordRenderer',
32
32
  ReactComponent: ReactComponent_1.default,
33
- configSchema: configSchema,
34
- pluginManager: pluginManager,
33
+ configSchema,
34
+ pluginManager,
35
35
  });
36
36
  };
37
37
  exports.default = ChordRendererConfigF;
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.js"],"names":[],"mappings":";;;;;AAAA,sIAAuG;AACvG,6DAAiE;AACjE,oEAA6C;AAE7C,IAAM,oBAAoB,GAAG,UAAA,aAAa;IACxC,IAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,gCAAgC,EAChC;QACE,WAAW,EAAE;YACX,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,4BAA4B;YACzC,YAAY,EAAE,sBAAsB;YACpC,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,mBAAmB,EAAE;YACnB,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,iDAAiD;YAC9D,YAAY,EAAE,OAAO;YACrB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,gBAAgB,EAAE;YAChB,IAAI,EAAE,OAAO;YACb,WAAW,EACT,oEAAoE;YACtE,YAAY,EAAE,MAAM;YACpB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;KACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;IACD,OAAO,IAAI,mCAAiB,CAAC;QAC3B,IAAI,EAAE,gCAAgC;QACtC,cAAc,0BAAA;QACd,YAAY,cAAA;QACZ,aAAa,eAAA;KACd,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,kBAAe,oBAAoB,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.js"],"names":[],"mappings":";;;;;AAAA,wIAAuG;AACvG,+DAAiE;AACjE,sEAA6C;AAE7C,MAAM,oBAAoB,GAAG,aAAa,CAAC,EAAE;IAC3C,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,gCAAgC,EAChC;QACE,WAAW,EAAE;YACX,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,4BAA4B;YACzC,YAAY,EAAE,sBAAsB;YACpC,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,mBAAmB,EAAE;YACnB,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,iDAAiD;YAC9D,YAAY,EAAE,OAAO;YACrB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,gBAAgB,EAAE;YAChB,IAAI,EAAE,OAAO;YACb,WAAW,EACT,oEAAoE;YACtE,YAAY,EAAE,MAAM;YACpB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;KACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;IACD,OAAO,IAAI,mCAAiB,CAAC;QAC3B,IAAI,EAAE,gCAAgC;QACtC,cAAc,EAAd,wBAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,kBAAe,oBAAoB,CAAA"}
@@ -0,0 +1,5 @@
1
+ /// <reference types="react" />
2
+ export default function VariantAnnotPanel({ rows, columns, }: {
3
+ rows: any;
4
+ columns: any[];
5
+ }): JSX.Element | null;