@jbrowse/plugin-sequence 2.5.0 → 2.6.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (142) hide show
  1. package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js +0 -1
  2. package/dist/BgzipFastaAdapter/configSchema.js +0 -1
  3. package/dist/BgzipFastaAdapter/index.js +0 -1
  4. package/dist/ChromSizesAdapter/ChromSizesAdapter.js +0 -1
  5. package/dist/ChromSizesAdapter/configSchema.js +0 -1
  6. package/dist/ChromSizesAdapter/index.js +0 -1
  7. package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts +2 -1
  8. package/dist/DivSequenceRenderer/components/DivSequenceRendering.js +0 -1
  9. package/dist/DivSequenceRenderer/configSchema.js +0 -1
  10. package/dist/DivSequenceRenderer/index.js +0 -1
  11. package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js +0 -1
  12. package/dist/IndexedFastaAdapter/configSchema.js +0 -1
  13. package/dist/IndexedFastaAdapter/index.js +0 -1
  14. package/dist/LinearReferenceSequenceDisplay/configSchema.js +0 -1
  15. package/dist/LinearReferenceSequenceDisplay/index.js +0 -1
  16. package/dist/LinearReferenceSequenceDisplay/model.d.ts +60 -53
  17. package/dist/LinearReferenceSequenceDisplay/model.js +0 -1
  18. package/dist/ReferenceSequenceTrack/configSchema.js +0 -1
  19. package/dist/ReferenceSequenceTrack/index.js +0 -1
  20. package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js +0 -1
  21. package/dist/SequenceSearchAdapter/configSchema.js +0 -1
  22. package/dist/SequenceSearchAdapter/index.js +0 -1
  23. package/dist/TwoBitAdapter/TwoBitAdapter.js +2 -2
  24. package/dist/TwoBitAdapter/configSchema.js +0 -1
  25. package/dist/TwoBitAdapter/index.js +0 -1
  26. package/dist/createExtensionPoints.js +0 -1
  27. package/dist/index.js +0 -1
  28. package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js +0 -1
  29. package/esm/BgzipFastaAdapter/configSchema.js +0 -1
  30. package/esm/BgzipFastaAdapter/index.js +0 -1
  31. package/esm/ChromSizesAdapter/ChromSizesAdapter.js +0 -1
  32. package/esm/ChromSizesAdapter/configSchema.js +0 -1
  33. package/esm/ChromSizesAdapter/index.js +0 -1
  34. package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts +2 -1
  35. package/esm/DivSequenceRenderer/components/DivSequenceRendering.js +0 -1
  36. package/esm/DivSequenceRenderer/configSchema.js +0 -1
  37. package/esm/DivSequenceRenderer/index.js +0 -1
  38. package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js +0 -1
  39. package/esm/IndexedFastaAdapter/configSchema.js +0 -1
  40. package/esm/IndexedFastaAdapter/index.js +0 -1
  41. package/esm/LinearReferenceSequenceDisplay/configSchema.js +0 -1
  42. package/esm/LinearReferenceSequenceDisplay/index.js +0 -1
  43. package/esm/LinearReferenceSequenceDisplay/model.d.ts +60 -53
  44. package/esm/LinearReferenceSequenceDisplay/model.js +0 -1
  45. package/esm/ReferenceSequenceTrack/configSchema.js +0 -1
  46. package/esm/ReferenceSequenceTrack/index.js +0 -1
  47. package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js +0 -1
  48. package/esm/SequenceSearchAdapter/configSchema.js +0 -1
  49. package/esm/SequenceSearchAdapter/index.js +0 -1
  50. package/esm/TwoBitAdapter/TwoBitAdapter.js +2 -2
  51. package/esm/TwoBitAdapter/configSchema.js +0 -1
  52. package/esm/TwoBitAdapter/index.js +0 -1
  53. package/esm/createExtensionPoints.js +0 -1
  54. package/esm/index.js +0 -1
  55. package/package.json +3 -4
  56. package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js.map +0 -1
  57. package/dist/BgzipFastaAdapter/configSchema.js.map +0 -1
  58. package/dist/BgzipFastaAdapter/index.js.map +0 -1
  59. package/dist/ChromSizesAdapter/ChromSizesAdapter.js.map +0 -1
  60. package/dist/ChromSizesAdapter/configSchema.js.map +0 -1
  61. package/dist/ChromSizesAdapter/index.js.map +0 -1
  62. package/dist/DivSequenceRenderer/components/DivSequenceRendering.js.map +0 -1
  63. package/dist/DivSequenceRenderer/configSchema.js.map +0 -1
  64. package/dist/DivSequenceRenderer/index.js.map +0 -1
  65. package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map +0 -1
  66. package/dist/IndexedFastaAdapter/configSchema.js.map +0 -1
  67. package/dist/IndexedFastaAdapter/index.js.map +0 -1
  68. package/dist/LinearReferenceSequenceDisplay/configSchema.js.map +0 -1
  69. package/dist/LinearReferenceSequenceDisplay/index.js.map +0 -1
  70. package/dist/LinearReferenceSequenceDisplay/model.js.map +0 -1
  71. package/dist/ReferenceSequenceTrack/configSchema.js.map +0 -1
  72. package/dist/ReferenceSequenceTrack/index.js.map +0 -1
  73. package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js.map +0 -1
  74. package/dist/SequenceSearchAdapter/configSchema.js.map +0 -1
  75. package/dist/SequenceSearchAdapter/index.js.map +0 -1
  76. package/dist/TwoBitAdapter/TwoBitAdapter.js.map +0 -1
  77. package/dist/TwoBitAdapter/configSchema.js.map +0 -1
  78. package/dist/TwoBitAdapter/index.js.map +0 -1
  79. package/dist/createExtensionPoints.js.map +0 -1
  80. package/dist/index.js.map +0 -1
  81. package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js.map +0 -1
  82. package/esm/BgzipFastaAdapter/configSchema.js.map +0 -1
  83. package/esm/BgzipFastaAdapter/index.js.map +0 -1
  84. package/esm/ChromSizesAdapter/ChromSizesAdapter.js.map +0 -1
  85. package/esm/ChromSizesAdapter/configSchema.js.map +0 -1
  86. package/esm/ChromSizesAdapter/index.js.map +0 -1
  87. package/esm/DivSequenceRenderer/components/DivSequenceRendering.js.map +0 -1
  88. package/esm/DivSequenceRenderer/configSchema.js.map +0 -1
  89. package/esm/DivSequenceRenderer/index.js.map +0 -1
  90. package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map +0 -1
  91. package/esm/IndexedFastaAdapter/configSchema.js.map +0 -1
  92. package/esm/IndexedFastaAdapter/index.js.map +0 -1
  93. package/esm/LinearReferenceSequenceDisplay/configSchema.js.map +0 -1
  94. package/esm/LinearReferenceSequenceDisplay/index.js.map +0 -1
  95. package/esm/LinearReferenceSequenceDisplay/model.js.map +0 -1
  96. package/esm/ReferenceSequenceTrack/configSchema.js.map +0 -1
  97. package/esm/ReferenceSequenceTrack/index.js.map +0 -1
  98. package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js.map +0 -1
  99. package/esm/SequenceSearchAdapter/configSchema.js.map +0 -1
  100. package/esm/SequenceSearchAdapter/index.js.map +0 -1
  101. package/esm/TwoBitAdapter/TwoBitAdapter.js.map +0 -1
  102. package/esm/TwoBitAdapter/configSchema.js.map +0 -1
  103. package/esm/TwoBitAdapter/index.js.map +0 -1
  104. package/esm/createExtensionPoints.js.map +0 -1
  105. package/esm/index.js.map +0 -1
  106. package/src/BgzipFastaAdapter/BgzipFastaAdapter.test.ts +0 -40
  107. package/src/BgzipFastaAdapter/BgzipFastaAdapter.ts +0 -19
  108. package/src/BgzipFastaAdapter/__snapshots__/BgzipFastaAdapter.test.ts.snap +0 -15
  109. package/src/BgzipFastaAdapter/configSchema.ts +0 -51
  110. package/src/BgzipFastaAdapter/index.ts +0 -20
  111. package/src/ChromSizesAdapter/ChromSizesAdapter.test.ts +0 -27
  112. package/src/ChromSizesAdapter/ChromSizesAdapter.ts +0 -51
  113. package/src/ChromSizesAdapter/configSchema.ts +0 -25
  114. package/src/ChromSizesAdapter/index.ts +0 -20
  115. package/src/ChromSizesAdapter/test_data/volvox.chrom.sizes +0 -2
  116. package/src/DivSequenceRenderer/components/DivSequenceRendering.test.tsx +0 -161
  117. package/src/DivSequenceRenderer/components/DivSequenceRendering.tsx +0 -308
  118. package/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap +0 -1426
  119. package/src/DivSequenceRenderer/configSchema.ts +0 -23
  120. package/src/DivSequenceRenderer/index.ts +0 -31
  121. package/src/IndexedFastaAdapter/IndexedFastaAdapter.test.ts +0 -53
  122. package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts +0 -113
  123. package/src/IndexedFastaAdapter/__snapshots__/IndexedFastaAdapter.test.ts.snap +0 -15
  124. package/src/IndexedFastaAdapter/configSchema.ts +0 -39
  125. package/src/IndexedFastaAdapter/index.ts +0 -20
  126. package/src/LinearReferenceSequenceDisplay/configSchema.ts +0 -18
  127. package/src/LinearReferenceSequenceDisplay/index.ts +0 -21
  128. package/src/LinearReferenceSequenceDisplay/model.ts +0 -148
  129. package/src/ReferenceSequenceTrack/configSchema.ts +0 -117
  130. package/src/ReferenceSequenceTrack/index.ts +0 -22
  131. package/src/SequenceSearchAdapter/SequenceSearchAdapter.ts +0 -104
  132. package/src/SequenceSearchAdapter/configSchema.ts +0 -51
  133. package/src/SequenceSearchAdapter/index.ts +0 -20
  134. package/src/TwoBitAdapter/TwoBitAdapter.test.ts +0 -55
  135. package/src/TwoBitAdapter/TwoBitAdapter.ts +0 -108
  136. package/src/TwoBitAdapter/__snapshots__/TwoBitAdapter.test.ts.snap +0 -30
  137. package/src/TwoBitAdapter/configSchema.ts +0 -34
  138. package/src/TwoBitAdapter/index.ts +0 -19
  139. package/src/__snapshots__/index.test.ts.snap +0 -5
  140. package/src/createExtensionPoints.ts +0 -122
  141. package/src/index.test.ts +0 -20
  142. package/src/index.ts +0 -28
@@ -20,4 +20,3 @@ class default_1 extends IndexedFastaAdapter_1.default {
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  }
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  }
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  exports.default = default_1;
23
- //# sourceMappingURL=BgzipFastaAdapter.js.map
@@ -46,4 +46,3 @@ const BgzipFastaAdapter = (0, configuration_1.ConfigurationSchema)('BgzipFastaAd
46
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  },
47
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  }, { explicitlyTyped: true });
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  exports.default = BgzipFastaAdapter;
49
- //# sourceMappingURL=configSchema.js.map
@@ -39,4 +39,3 @@ exports.default = (pluginManager) => {
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  getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BgzipFastaAdapter'))).then(r => r.default),
40
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  }));
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  };
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- //# sourceMappingURL=index.js.map
@@ -39,4 +39,3 @@ class default_1 extends BaseAdapter_1.BaseAdapter {
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  freeResources( /* { region } */) { }
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  }
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  exports.default = default_1;
42
- //# sourceMappingURL=ChromSizesAdapter.js.map
@@ -18,4 +18,3 @@ const ChromSizesAdapter = (0, configuration_1.ConfigurationSchema)('ChromSizesAd
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  },
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  }, { explicitlyTyped: true });
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  exports.default = ChromSizesAdapter;
21
- //# sourceMappingURL=configSchema.js.map
@@ -39,4 +39,3 @@ exports.default = (pluginManager) => {
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  getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./ChromSizesAdapter'))).then(r => r.default),
40
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  }));
41
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  };
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- //# sourceMappingURL=index.js.map
@@ -1,3 +1,4 @@
1
+ import React from 'react';
1
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  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
2
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  import { Feature, Region } from '@jbrowse/core/util';
3
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  declare function Sequence(props: {
@@ -12,6 +13,6 @@ declare function Sequence(props: {
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  showForward?: boolean;
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  showReverse?: boolean;
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  showTranslation?: boolean;
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- }): JSX.Element;
16
+ }): React.JSX.Element;
16
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  declare const _default: typeof Sequence;
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  export default _default;
@@ -98,4 +98,3 @@ function Sequence(props) {
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  react_1.default.createElement(SequenceSVG, { ...props })));
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  }
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  exports.default = (0, mobx_react_1.observer)(Sequence);
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- //# sourceMappingURL=DivSequenceRendering.js.map
@@ -16,4 +16,3 @@ const DivSequenceRenderer = (0, configuration_1.ConfigurationSchema)('DivSequenc
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  },
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  }, { explicitlyTyped: true });
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  exports.default = DivSequenceRenderer;
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- //# sourceMappingURL=configSchema.js.map
@@ -28,4 +28,3 @@ exports.default = (pluginManager) => {
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  pluginManager,
29
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  }));
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  };
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- //# sourceMappingURL=index.js.map
@@ -98,4 +98,3 @@ class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
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  freeResources( /* { region } */) { }
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  }
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  exports.default = default_1;
101
- //# sourceMappingURL=IndexedFastaAdapter.js.map
@@ -33,4 +33,3 @@ const IndexedFastaAdapter = (0, configuration_1.ConfigurationSchema)('IndexedFas
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  },
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  }, { explicitlyTyped: true });
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  exports.default = IndexedFastaAdapter;
36
- //# sourceMappingURL=configSchema.js.map
@@ -39,4 +39,3 @@ exports.default = (pluginManager) => {
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  getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./IndexedFastaAdapter'))).then(r => r.default),
40
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  }));
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  };
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- //# sourceMappingURL=index.js.map
@@ -16,4 +16,3 @@ exports.configSchema = (0, configuration_1.ConfigurationSchema)('LinearReference
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  */
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  renderer: configSchema_1.default,
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  }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
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- //# sourceMappingURL=configSchema.js.map
@@ -18,4 +18,3 @@ exports.default = (pluginManager) => {
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  });
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  });
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  };
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- //# sourceMappingURL=index.js.map
@@ -9,10 +9,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  type: import("mobx-state-tree").ISimpleType<string>;
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
11
  } & {
12
- /**
13
- * #getter
14
- */
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  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
13
+ } & {
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+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
15
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
16
+ } & {
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  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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  key: import("mobx-state-tree").ISimpleType<string>;
18
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  region: import("mobx-state-tree").IModelType<{
@@ -62,8 +63,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
62
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  reload(): void;
63
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  beforeDestroy(): void;
64
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
65
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
66
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
67
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  configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
68
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  maxFeatureScreenDensity: {
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  type: string;
@@ -76,9 +75,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
76
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  description: string;
77
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  };
78
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  height: {
79
- /**
80
- * #property
81
- */
82
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  type: string;
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  defaultValue: number;
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  description: string;
@@ -99,6 +95,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
99
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  }, {
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  rendererTypeName: string;
101
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  error: unknown;
98
+ message: string | undefined;
102
99
  } & {
103
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  readonly RenderingComponent: import("react").FC<{
104
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  model: {
@@ -106,8 +103,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  type: string;
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  rpcDriverName: string | undefined;
108
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  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
109
- rendererTypeName: string;
106
+ rendererTypeName: string; /**
107
+ * #property
108
+ */
110
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  error: unknown;
110
+ message: string | undefined;
111
111
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
112
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("mobx-state-tree").ISimpleType<string>;
@@ -115,18 +115,22 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  }, {
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  rendererTypeName: string;
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  error: unknown;
118
+ message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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  onHorizontalScroll?: Function | undefined;
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  blockState?: Record<string, any> | undefined;
121
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  }>;
122
123
  readonly DisplayBlurb: import("react").FC<{
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  model: {
124
- id: string;
125
+ id: string; /**
126
+ * #action
127
+ */
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  type: string;
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  rpcDriverName: string | undefined;
127
130
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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  rendererTypeName: string;
129
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  error: unknown;
133
+ message: string | undefined;
130
134
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("mobx-state-tree").ISimpleType<string>;
@@ -134,8 +138,12 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  }, {
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  rendererTypeName: string;
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  error: unknown;
141
+ message: string | undefined;
137
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
138
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  }> | null;
144
+ /**
145
+ * #method
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+ */
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  readonly adapterConfig: any;
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  readonly parentTrack: any;
141
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  renderProps(): any;
@@ -143,21 +151,51 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
146
- regionCannotBeRendered(): undefined;
154
+ regionCannotBeRendered(): null;
147
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  } & {
156
+ setMessage(arg?: string | undefined): void;
148
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  setError(error?: unknown): void;
149
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  setRpcDriverName(rpcDriverName: string): void;
150
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  reload(): void;
151
160
  } & {
152
- currBpPerPx: number;
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  scrollTop: number;
154
- message: string;
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- featureIdUnderMouse: string | undefined;
156
- contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
162
+ } & {
163
+ readonly height: number;
164
+ } & {
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+ setScrollTop(scrollTop: number): void; /**
166
+ * #property
167
+ */
168
+ setHeight(displayHeight: number): number;
169
+ resizeHeight(distance: number): number;
170
+ } & {
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  featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
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  featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
173
+ currStatsBpPerPx: number;
174
+ } & {
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+ readonly currentBytesRequested: number;
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+ readonly currentFeatureScreenDensity: number;
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+ readonly maxFeatureScreenDensity: any;
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+ readonly featureDensityStatsReady: boolean;
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+ readonly maxAllowableBytes: number;
180
+ } & {
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+ afterAttach(): void;
182
+ } & {
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+ setCurrStatsBpPerPx(n: number): void;
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+ setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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+ getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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+ setFeatureDensityStatsP(arg: any): void;
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+ setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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+ clearFeatureDensityStats(): void;
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+ } & {
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+ readonly regionTooLarge: boolean;
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+ readonly regionTooLargeReason: string;
192
+ } & {
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+ regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
195
+ } & {
196
+ featureIdUnderMouse: string | undefined;
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+ contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
159
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  } & {
160
- readonly height: number;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
162
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
163
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  } & {
@@ -171,49 +209,22 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
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  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
173
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  searchFeatureByID(id: string): [number, number, number, number] | undefined;
174
- readonly currentBytesRequested: number;
175
- readonly currentFeatureScreenDensity: number;
176
- readonly maxFeatureScreenDensity: any;
177
- readonly featureDensityStatsReady: boolean;
178
- readonly maxAllowableBytes: number;
179
212
  } & {
180
- setMessage(message: string): void;
181
- } & {
182
- afterAttach(): void;
183
- getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
184
- setFeatureDensityStatsP(arg: any): void;
185
- setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
186
- clearFeatureDensityStats(): void;
187
- setHeight(displayHeight: number): number;
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- resizeHeight(distance: number): number;
189
- setScrollTop(scrollTop: number): void;
190
- setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
191
213
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
192
- setCurrBpPerPx(n: number): void;
193
214
  deleteBlock(key: string): void;
194
215
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
195
216
  clearFeatureSelection(): void;
196
217
  setFeatureIdUnderMouse(feature?: string | undefined): void;
197
- reload(): void;
198
218
  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
199
- } & {
200
- readonly regionTooLarge: boolean;
201
- readonly regionTooLargeReason: string;
202
219
  } & {
203
220
  reload(): Promise<void>;
204
221
  } & {
205
- afterAttach(): void;
206
- } & {
207
- regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
208
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
209
222
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
210
223
  contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
211
224
  renderProps(): any;
212
225
  } & {
213
- renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
214
- overrideHeight: number;
215
- theme: import("@mui/material").ThemeOptions;
216
- }): Promise<JSX.Element>;
226
+ renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
227
+ afterAttach(): void;
217
228
  } & {
218
229
  /**
219
230
  * #method
@@ -259,10 +270,11 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
259
270
  type: import("mobx-state-tree").ISimpleType<string>;
260
271
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
261
272
  } & {
262
- /**
263
- * #getter
264
- */
265
273
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
274
+ } & {
275
+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
276
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
277
+ } & {
266
278
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
267
279
  key: import("mobx-state-tree").ISimpleType<string>;
268
280
  region: import("mobx-state-tree").IModelType<{
@@ -312,8 +324,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
312
324
  reload(): void;
313
325
  beforeDestroy(): void;
314
326
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
315
- userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
316
- userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
317
327
  configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
318
328
  maxFeatureScreenDensity: {
319
329
  type: string;
@@ -326,9 +336,6 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
326
336
  description: string;
327
337
  };
328
338
  height: {
329
- /**
330
- * #property
331
- */
332
339
  type: string;
333
340
  defaultValue: number;
334
341
  description: string;
@@ -134,4 +134,3 @@ function modelFactory(configSchema) {
134
134
  }));
135
135
  }
136
136
  exports.modelFactory = modelFactory;
137
- //# sourceMappingURL=model.js.map
@@ -103,4 +103,3 @@ function createReferenceSeqTrackConfig(pluginManager) {
103
103
  });
104
104
  }
105
105
  exports.createReferenceSeqTrackConfig = createReferenceSeqTrackConfig;
106
- //# sourceMappingURL=configSchema.js.map
@@ -17,4 +17,3 @@ exports.default = (pluginManager) => {
17
17
  });
18
18
  });
19
19
  };
20
- //# sourceMappingURL=index.js.map
@@ -82,4 +82,3 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
82
82
  freeResources() { }
83
83
  }
84
84
  exports.default = default_1;
85
- //# sourceMappingURL=SequenceSearchAdapter.js.map
@@ -44,4 +44,3 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('SequenceSearchAda
44
44
  },
45
45
  }, { explicitlyTyped: true });
46
46
  exports.default = configSchema;
47
- //# sourceMappingURL=configSchema.js.map
@@ -39,4 +39,3 @@ exports.default = (pluginManager) => {
39
39
  getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SequenceSearchAdapter'))).then(r => r.default),
40
40
  }));
41
41
  };
42
- //# sourceMappingURL=index.js.map
@@ -27,9 +27,10 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
27
27
  }
28
28
  constructor(config, getSubAdapter, pluginManager) {
29
29
  super(config, getSubAdapter, pluginManager);
30
+ const pm = this.pluginManager;
30
31
  this.chromSizesData = this.initChromSizes();
31
32
  this.twobit = new twobit_1.TwoBitFile({
32
- filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), this.pluginManager),
33
+ filehandle: (0, io_1.openLocation)(this.getConf('twoBitLocation'), pm),
33
34
  });
34
35
  }
35
36
  async getRefNames() {
@@ -82,4 +83,3 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
82
83
  freeResources( /* { region } */) { }
83
84
  }
84
85
  exports.default = TwoBitAdapter;
85
- //# sourceMappingURL=TwoBitAdapter.js.map
@@ -26,4 +26,3 @@ const TwoBitAdapter = (0, configuration_1.ConfigurationSchema)('TwoBitAdapter',
26
26
  },
27
27
  }, { explicitlyTyped: true });
28
28
  exports.default = TwoBitAdapter;
29
- //# sourceMappingURL=configSchema.js.map
@@ -39,4 +39,3 @@ exports.default = (pluginManager) => {
39
39
  getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./TwoBitAdapter'))).then(r => r.default),
40
40
  }));
41
41
  };
42
- //# sourceMappingURL=index.js.map
@@ -83,4 +83,3 @@ exports.default = (pluginManager) => {
83
83
  };
84
84
  });
85
85
  };
86
- //# sourceMappingURL=createExtensionPoints.js.map
package/dist/index.js CHANGED
@@ -31,4 +31,3 @@ class SequencePlugin extends Plugin_1.default {
31
31
  }
32
32
  }
33
33
  exports.default = SequencePlugin;
34
- //# sourceMappingURL=index.js.map
@@ -14,4 +14,3 @@ export default class extends IndexedFasta {
14
14
  return { fasta: new BgzipIndexedFasta(fastaOpts) };
15
15
  }
16
16
  }
17
- //# sourceMappingURL=BgzipFastaAdapter.js.map
@@ -44,4 +44,3 @@ const BgzipFastaAdapter = ConfigurationSchema('BgzipFastaAdapter', {
44
44
  },
45
45
  }, { explicitlyTyped: true });
46
46
  export default BgzipFastaAdapter;
47
- //# sourceMappingURL=configSchema.js.map
@@ -11,4 +11,3 @@ export default (pluginManager) => {
11
11
  getAdapterClass: () => import('./BgzipFastaAdapter').then(r => r.default),
12
12
  }));
13
13
  };
14
- //# sourceMappingURL=index.js.map
@@ -36,4 +36,3 @@ export default class extends BaseAdapter {
36
36
  }
37
37
  freeResources( /* { region } */) { }
38
38
  }
39
- //# sourceMappingURL=ChromSizesAdapter.js.map
@@ -16,4 +16,3 @@ const ChromSizesAdapter = ConfigurationSchema('ChromSizesAdapter', {
16
16
  },
17
17
  }, { explicitlyTyped: true });
18
18
  export default ChromSizesAdapter;
19
- //# sourceMappingURL=configSchema.js.map
@@ -11,4 +11,3 @@ export default (pluginManager) => {
11
11
  getAdapterClass: () => import('./ChromSizesAdapter').then(r => r.default),
12
12
  }));
13
13
  };
14
- //# sourceMappingURL=index.js.map
@@ -1,3 +1,4 @@
1
+ import React from 'react';
1
2
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
2
3
  import { Feature, Region } from '@jbrowse/core/util';
3
4
  declare function Sequence(props: {
@@ -12,6 +13,6 @@ declare function Sequence(props: {
12
13
  showForward?: boolean;
13
14
  showReverse?: boolean;
14
15
  showTranslation?: boolean;
15
- }): JSX.Element;
16
+ }): React.JSX.Element;
16
17
  declare const _default: typeof Sequence;
17
18
  export default _default;
@@ -93,4 +93,3 @@ function Sequence(props) {
93
93
  React.createElement(SequenceSVG, { ...props })));
94
94
  }
95
95
  export default observer(Sequence);
96
- //# sourceMappingURL=DivSequenceRendering.js.map
@@ -14,4 +14,3 @@ const DivSequenceRenderer = ConfigurationSchema('DivSequenceRenderer', {
14
14
  },
15
15
  }, { explicitlyTyped: true });
16
16
  export default DivSequenceRenderer;
17
- //# sourceMappingURL=configSchema.js.map
@@ -23,4 +23,3 @@ export default (pluginManager) => {
23
23
  pluginManager,
24
24
  }));
25
25
  };
26
- //# sourceMappingURL=index.js.map
@@ -92,4 +92,3 @@ export default class extends BaseSequenceAdapter {
92
92
  */
93
93
  freeResources( /* { region } */) { }
94
94
  }
95
- //# sourceMappingURL=IndexedFastaAdapter.js.map
@@ -31,4 +31,3 @@ const IndexedFastaAdapter = ConfigurationSchema('IndexedFastaAdapter', {
31
31
  },
32
32
  }, { explicitlyTyped: true });
33
33
  export default IndexedFastaAdapter;
34
- //# sourceMappingURL=configSchema.js.map
@@ -11,4 +11,3 @@ export default (pluginManager) => {
11
11
  getAdapterClass: () => import('./IndexedFastaAdapter').then(r => r.default),
12
12
  }));
13
13
  };
14
- //# sourceMappingURL=index.js.map
@@ -10,4 +10,3 @@ export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay'
10
10
  */
11
11
  renderer: divSequenceRendererConfigSchema,
12
12
  }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
13
- //# sourceMappingURL=configSchema.js.map
@@ -16,4 +16,3 @@ export default (pluginManager) => {
16
16
  });
17
17
  });
18
18
  };
19
- //# sourceMappingURL=index.js.map