@jbrowse/plugin-alignments 2.4.2 → 2.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (147) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +0 -1
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts +0 -1
  3. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +0 -1
  4. package/dist/AlignmentsFeatureDetail/index.d.ts +4 -1
  5. package/dist/AlignmentsTrack/configSchemaF.d.ts +74 -0
  6. package/dist/AlignmentsTrack/configSchemaF.js +19 -0
  7. package/dist/AlignmentsTrack/configSchemaF.js.map +1 -0
  8. package/dist/AlignmentsTrack/index.js +2 -15
  9. package/dist/AlignmentsTrack/index.js.map +1 -1
  10. package/dist/BamAdapter/BamAdapter.d.ts +1 -1
  11. package/dist/BamAdapter/BamAdapter.js +2 -2
  12. package/dist/BamAdapter/BamAdapter.js.map +1 -1
  13. package/dist/BamAdapter/configSchema.d.ts +50 -1
  14. package/dist/CramAdapter/CramAdapter.d.ts +1 -1
  15. package/dist/CramAdapter/CramAdapter.js +1 -1
  16. package/dist/CramAdapter/CramAdapter.js.map +1 -1
  17. package/dist/CramAdapter/CramTestAdapters.js +2 -2
  18. package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
  19. package/dist/CramAdapter/configSchema.d.ts +40 -1
  20. package/dist/HtsgetBamAdapter/configSchema.d.ts +26 -1
  21. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +0 -1
  22. package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +39 -1
  23. package/dist/LinearAlignmentsDisplay/models/model.d.ts +8 -4
  24. package/dist/LinearAlignmentsDisplay/models/model.js +7 -3
  25. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
  26. package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +0 -1
  27. package/dist/LinearPileupDisplay/components/ColorByTag.d.ts +0 -1
  28. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +0 -1
  29. package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +0 -1
  30. package/dist/LinearPileupDisplay/components/SetMaxHeight.d.ts +0 -1
  31. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +3 -5
  32. package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
  33. package/dist/LinearPileupDisplay/components/SortByTag.d.ts +0 -1
  34. package/dist/LinearPileupDisplay/configSchema.d.ts +57 -1
  35. package/dist/LinearPileupDisplay/model.d.ts +107 -50
  36. package/dist/LinearPileupDisplay/model.js +21 -24
  37. package/dist/LinearPileupDisplay/model.js.map +1 -1
  38. package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts +0 -1
  39. package/dist/LinearReadArcsDisplay/configSchema.d.ts +62 -1
  40. package/dist/LinearReadArcsDisplay/drawFeats.js +2 -2
  41. package/dist/LinearReadArcsDisplay/drawFeats.js.map +1 -1
  42. package/dist/LinearReadArcsDisplay/model.d.ts +78 -21
  43. package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts +0 -1
  44. package/dist/LinearReadCloudDisplay/configSchema.d.ts +50 -1
  45. package/dist/LinearReadCloudDisplay/drawFeats.d.ts +2 -0
  46. package/dist/LinearReadCloudDisplay/drawFeats.js +4 -4
  47. package/dist/LinearReadCloudDisplay/drawFeats.js.map +1 -1
  48. package/dist/LinearReadCloudDisplay/model.d.ts +65 -18
  49. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +0 -1
  50. package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts +79 -1
  51. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +48 -21
  52. package/dist/LinearSNPCoverageDisplay/models/model.js +1 -1
  53. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  54. package/dist/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  55. package/dist/PileupRenderer/PileupRenderer.js +9 -0
  56. package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
  57. package/dist/PileupRenderer/configSchema.d.ts +87 -1
  58. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +1 -1
  59. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +2 -2
  60. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
  61. package/dist/SNPCoverageAdapter/configSchema.d.ts +10 -1
  62. package/dist/SNPCoverageAdapter/generateCoverageBins.js +50 -46
  63. package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -1
  64. package/dist/SNPCoverageRenderer/configSchema.d.ts +42 -1
  65. package/dist/shared/FilterByTag.d.ts +0 -1
  66. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +0 -1
  67. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts +0 -1
  68. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +0 -1
  69. package/esm/AlignmentsFeatureDetail/index.d.ts +4 -1
  70. package/esm/AlignmentsTrack/configSchemaF.d.ts +74 -0
  71. package/esm/AlignmentsTrack/configSchemaF.js +16 -0
  72. package/esm/AlignmentsTrack/configSchemaF.js.map +1 -0
  73. package/esm/AlignmentsTrack/index.js +3 -16
  74. package/esm/AlignmentsTrack/index.js.map +1 -1
  75. package/esm/BamAdapter/BamAdapter.d.ts +1 -1
  76. package/esm/BamAdapter/BamAdapter.js +2 -2
  77. package/esm/BamAdapter/BamAdapter.js.map +1 -1
  78. package/esm/BamAdapter/configSchema.d.ts +50 -1
  79. package/esm/CramAdapter/CramAdapter.d.ts +1 -1
  80. package/esm/CramAdapter/CramAdapter.js +1 -1
  81. package/esm/CramAdapter/CramAdapter.js.map +1 -1
  82. package/esm/CramAdapter/CramTestAdapters.js +1 -1
  83. package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
  84. package/esm/CramAdapter/configSchema.d.ts +40 -1
  85. package/esm/HtsgetBamAdapter/configSchema.d.ts +26 -1
  86. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +0 -1
  87. package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +39 -1
  88. package/esm/LinearAlignmentsDisplay/models/model.d.ts +8 -4
  89. package/esm/LinearAlignmentsDisplay/models/model.js +7 -3
  90. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
  91. package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +0 -1
  92. package/esm/LinearPileupDisplay/components/ColorByTag.d.ts +0 -1
  93. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +0 -1
  94. package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +0 -1
  95. package/esm/LinearPileupDisplay/components/SetMaxHeight.d.ts +0 -1
  96. package/esm/LinearPileupDisplay/components/SetMaxHeight.js +3 -5
  97. package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
  98. package/esm/LinearPileupDisplay/components/SortByTag.d.ts +0 -1
  99. package/esm/LinearPileupDisplay/configSchema.d.ts +57 -1
  100. package/esm/LinearPileupDisplay/model.d.ts +107 -50
  101. package/esm/LinearPileupDisplay/model.js +21 -24
  102. package/esm/LinearPileupDisplay/model.js.map +1 -1
  103. package/esm/LinearReadArcsDisplay/components/ReactComponent.d.ts +0 -1
  104. package/esm/LinearReadArcsDisplay/configSchema.d.ts +62 -1
  105. package/esm/LinearReadArcsDisplay/drawFeats.js +2 -2
  106. package/esm/LinearReadArcsDisplay/drawFeats.js.map +1 -1
  107. package/esm/LinearReadArcsDisplay/model.d.ts +78 -21
  108. package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts +0 -1
  109. package/esm/LinearReadCloudDisplay/configSchema.d.ts +50 -1
  110. package/esm/LinearReadCloudDisplay/drawFeats.d.ts +2 -0
  111. package/esm/LinearReadCloudDisplay/drawFeats.js +4 -4
  112. package/esm/LinearReadCloudDisplay/drawFeats.js.map +1 -1
  113. package/esm/LinearReadCloudDisplay/model.d.ts +65 -18
  114. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +0 -1
  115. package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts +79 -1
  116. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +48 -21
  117. package/esm/LinearSNPCoverageDisplay/models/model.js +1 -1
  118. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  119. package/esm/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  120. package/esm/PileupRenderer/PileupRenderer.js +9 -0
  121. package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
  122. package/esm/PileupRenderer/configSchema.d.ts +87 -1
  123. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +1 -1
  124. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +2 -2
  125. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
  126. package/esm/SNPCoverageAdapter/configSchema.d.ts +10 -1
  127. package/esm/SNPCoverageAdapter/generateCoverageBins.js +50 -46
  128. package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -1
  129. package/esm/SNPCoverageRenderer/configSchema.d.ts +42 -1
  130. package/esm/shared/FilterByTag.d.ts +0 -1
  131. package/package.json +2 -2
  132. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap +1 -2
  133. package/src/AlignmentsTrack/configSchemaF.ts +22 -0
  134. package/src/AlignmentsTrack/index.ts +3 -24
  135. package/src/BamAdapter/BamAdapter.ts +5 -2
  136. package/src/CramAdapter/CramAdapter.ts +4 -1
  137. package/src/CramAdapter/CramTestAdapters.ts +1 -1
  138. package/src/LinearAlignmentsDisplay/models/model.tsx +11 -3
  139. package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +3 -5
  140. package/src/LinearPileupDisplay/model.ts +38 -36
  141. package/src/LinearReadArcsDisplay/drawFeats.ts +2 -2
  142. package/src/LinearReadCloudDisplay/drawFeats.ts +6 -5
  143. package/src/LinearSNPCoverageDisplay/models/model.ts +1 -1
  144. package/src/PileupRenderer/PileupLayoutSession.ts +1 -1
  145. package/src/PileupRenderer/PileupRenderer.ts +15 -5
  146. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -2
  147. package/src/SNPCoverageAdapter/generateCoverageBins.ts +58 -55
@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  import { IAnyStateTreeNode } from 'mobx-state-tree';
3
2
  declare const _default: (props: {
4
3
  model: IAnyStateTreeNode;
@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  export default function AlignmentFlags(props: {
3
2
  feature: {
4
3
  flags: number;
@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  import { IAnyStateTreeNode } from 'mobx-state-tree';
3
2
  export default function SupplementaryAlignments(props: {
4
3
  tag: string;
@@ -1,5 +1,5 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager';
2
- declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3
3
  export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
4
4
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
5
5
  type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -13,10 +13,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
13
13
  } & {
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  type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
15
15
  }, {
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+ error: unknown;
17
+ } & {
16
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  setFeatureData(featureData: Record<string, unknown>): void;
17
19
  clearFeatureData(): void;
18
20
  setFormattedData(feat: Record<string, unknown>): void;
19
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  setExtra(type?: string | undefined, trackId?: string | undefined): void;
22
+ setError(e: unknown): void;
20
23
  } & {
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24
  afterCreate(): void;
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25
  }, {
@@ -0,0 +1,74 @@
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ export default function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3
+ name: {
4
+ description: string;
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+ type: string;
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+ defaultValue: string;
7
+ };
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+ assemblyNames: {
9
+ description: string;
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+ type: string;
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+ defaultValue: string[];
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+ };
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+ description: {
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+ description: string;
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+ type: string;
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+ defaultValue: string;
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+ };
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+ category: {
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+ description: string;
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+ type: string;
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+ defaultValue: never[];
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+ };
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+ metadata: {
24
+ type: string;
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+ description: string;
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+ defaultValue: {};
27
+ };
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+ adapter: import("mobx-state-tree").IAnyModelType;
29
+ textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
30
+ indexingAttributes: {
31
+ type: string;
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+ description: string;
33
+ defaultValue: string[];
34
+ };
35
+ indexingFeatureTypesToExclude: {
36
+ type: string;
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+ description: string;
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+ defaultValue: string[];
39
+ };
40
+ textSearchAdapter: import("mobx-state-tree").IAnyModelType;
41
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
42
+ displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
43
+ formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
44
+ feature: {
45
+ type: string;
46
+ description: string;
47
+ defaultValue: {};
48
+ contextVariable: string[];
49
+ };
50
+ subfeatures: {
51
+ type: string;
52
+ description: string;
53
+ defaultValue: {};
54
+ contextVariable: string[];
55
+ };
56
+ depth: {
57
+ type: string;
58
+ defaultValue: number;
59
+ description: string;
60
+ };
61
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
62
+ formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
63
+ config: {
64
+ type: string;
65
+ description: string;
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+ defaultValue: {};
67
+ contextVariable: string[];
68
+ };
69
+ hideUris: {
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+ type: string;
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+ defaultValue: boolean;
72
+ };
73
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
74
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
@@ -0,0 +1,19 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ const configuration_1 = require("@jbrowse/core/configuration");
4
+ const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
5
+ /**
6
+ * #config AlignmentsTrack
7
+ * has very little config; most config and state logic is on the display
8
+ */
9
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
10
+ function configSchemaFactory(pluginManager) {
11
+ return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
12
+ /**
13
+ * #baseConfiguration
14
+ */
15
+ baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
16
+ });
17
+ }
18
+ exports.default = configSchemaFactory;
19
+ //# sourceMappingURL=configSchemaF.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"configSchemaF.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/configSchemaF.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,+EAA2E;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAwB,mBAAmB,CAAC,aAA4B;IACtE,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,6CAAqB,EAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AAXD,sCAWC"}
@@ -4,24 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
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  };
5
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  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
7
- const configuration_1 = require("@jbrowse/core/configuration");
8
7
  const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
9
- /**
10
- * #config AlignmentsTrack
11
- * has very little config; most config and state logic is on the display
12
- */
13
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
14
- function configSchemaFactory(pluginManager) {
15
- return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
16
- /**
17
- * #baseConfiguration
18
- */
19
- baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
20
- });
21
- }
8
+ const configSchemaF_1 = __importDefault(require("./configSchemaF"));
22
9
  function register(pm) {
23
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  pm.addTrackType(() => {
24
- const configSchema = configSchemaFactory(pm);
11
+ const configSchema = (0, configSchemaF_1.default)(pm);
25
12
  const track = new TrackType_1.default({
26
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  name: 'AlignmentsTrack',
27
14
  displayName: 'Alignments track',
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,+DAAiE;AACjE,uEAGmD;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,SAAwB,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAhBD,2BAgBC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,uEAAiF;AACjF,oEAA2C;AAE3C,SAAwB,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,IAAA,uBAAa,EAAC,EAAE,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAhBD,2BAgBC"}
@@ -39,7 +39,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
39
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  readName: string;
40
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  };
41
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  }): import("rxjs").Observable<Feature>;
42
- estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats | {
42
+ getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
43
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  bytes: number;
44
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  fetchSizeLimit: any;
45
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  }>;
@@ -161,7 +161,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
161
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  observer.complete();
162
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  }, signal);
163
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  }
164
- async estimateRegionsStats(regions, opts) {
164
+ async getMultiRegionFeatureDensityStats(regions, opts) {
165
165
  const { bam } = await this.configure();
166
166
  // this is a method to avoid calling on htsget adapters
167
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  // @ts-expect-error
@@ -171,7 +171,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
171
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  return { bytes, fetchSizeLimit };
172
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  }
173
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  else {
174
- return super.estimateRegionsStats(regions, opts);
174
+ return super.getMultiRegionFeatureDensityStats(regions, opts);
175
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  }
176
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  }
177
177
  freeResources( /* { region } */) { }
@@ -1 +1 @@
1
- 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@@ -1,2 +1,51 @@
1
- declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ bamLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
13
+ /**
14
+ * #slot index.indexType
15
+ */
16
+ indexType: {
17
+ model: import("mobx-state-tree").ISimpleType<string>;
18
+ type: string;
19
+ defaultValue: string;
20
+ };
21
+ /**
22
+ * #slot index.location
23
+ */
24
+ location: {
25
+ type: string;
26
+ defaultValue: {
27
+ uri: string;
28
+ locationType: string;
29
+ };
30
+ };
31
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
32
+ /**
33
+ * #slot
34
+ */
35
+ fetchSizeLimit: {
36
+ type: string;
37
+ description: string;
38
+ defaultValue: number;
39
+ };
40
+ /**
41
+ * #slot
42
+ * generally refers to the reference genome assembly's sequence adapter
43
+ * currently needs to be manually added
44
+ */
45
+ sequenceAdapter: {
46
+ type: string;
47
+ description: string;
48
+ defaultValue: null;
49
+ };
50
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
51
  export default configSchema;
@@ -45,7 +45,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
45
45
  }): import("rxjs").Observable<Feature>;
46
46
  freeResources(): void;
47
47
  cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
48
- estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
48
+ getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<{
49
49
  bytes: number;
50
50
  fetchSizeLimit: any;
51
51
  }>;
@@ -200,7 +200,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
200
200
  return new CramSlightlyLazyFeature_1.default(record, this);
201
201
  }
202
202
  // we return the configured fetchSizeLimit, and the bytes for the region
203
- async estimateRegionsStats(regions, opts) {
203
+ async getMultiRegionFeatureDensityStats(regions, opts) {
204
204
  const bytes = await this.bytesForRegions(regions, opts);
205
205
  const fetchSizeLimit = this.getConf('fetchSizeLimit');
206
206
  return {
@@ -1 +1 @@
1
- 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@@ -7,7 +7,7 @@ exports.SequenceAdapter = exports.FetchableSmallFasta = exports.parseSmallFasta
7
7
  const rxjs_1 = require("rxjs");
8
8
  const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
9
9
  const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
10
- const configurationSchema_1 = require("@jbrowse/core/configuration/configurationSchema");
10
+ const configuration_1 = require("@jbrowse/core/configuration");
11
11
  // setup for Cram Adapter Testing
12
12
  function parseSmallFasta(text) {
13
13
  return text
@@ -46,7 +46,7 @@ class FetchableSmallFasta {
46
46
  exports.FetchableSmallFasta = FetchableSmallFasta;
47
47
  class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
48
48
  constructor(filehandle) {
49
- super((0, configurationSchema_1.ConfigurationSchema)('empty', {}).create());
49
+ super((0, configuration_1.ConfigurationSchema)('empty', {}).create());
50
50
  this.refNames = [];
51
51
  this.fasta = new FetchableSmallFasta(filehandle);
52
52
  }
@@ -1 +1 @@
1
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@@ -1,2 +1,41 @@
1
- declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot fetchSizeLimit
4
+ */
5
+ fetchSizeLimit: {
6
+ type: string;
7
+ description: string;
8
+ defaultValue: number;
9
+ };
10
+ /**
11
+ * #slot cramLocation
12
+ */
13
+ cramLocation: {
14
+ type: string;
15
+ defaultValue: {
16
+ uri: string;
17
+ locationType: string;
18
+ };
19
+ };
20
+ /**
21
+ * #slot craiLocation
22
+ */
23
+ craiLocation: {
24
+ type: string;
25
+ defaultValue: {
26
+ uri: string;
27
+ locationType: string;
28
+ };
29
+ };
30
+ /**
31
+ * #slot sequenceAdapter
32
+ * generally refers to the reference genome assembly's sequence adapter
33
+ * currently needs to be manually added
34
+ */
35
+ sequenceAdapter: {
36
+ type: string;
37
+ description: string;
38
+ defaultValue: null;
39
+ };
40
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
41
  export default configSchema;
@@ -1,2 +1,27 @@
1
- declare const HtsgetBamAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ htsgetBase: {
6
+ type: string;
7
+ description: string;
8
+ defaultValue: string;
9
+ };
10
+ /**
11
+ * #slot
12
+ */
13
+ htsgetTrackId: {
14
+ type: string;
15
+ description: string;
16
+ defaultValue: string;
17
+ };
18
+ /**
19
+ * #slot
20
+ */
21
+ sequenceAdapter: {
22
+ type: string;
23
+ description: string;
24
+ defaultValue: null;
25
+ };
26
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
27
  export default HtsgetBamAdapter;
@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  import { AlignmentsDisplayModel } from '../models/model';
3
2
  declare function AlignmentsDisplay({ model }: {
4
3
  model: AlignmentsDisplayModel;
@@ -4,4 +4,42 @@ import PluginManager from '@jbrowse/core/PluginManager';
4
4
  * has a "pileup" sub-display, where you can see individual reads and a
5
5
  * quantitative "snpcoverage" sub-display track showing SNP frequencies
6
6
  */
7
- export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
7
+ export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
8
+ /**
9
+ * #slot
10
+ */
11
+ pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
12
+ /**
13
+ * #slot
14
+ */
15
+ snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
16
+ /**
17
+ * #slot
18
+ */
19
+ height: {
20
+ type: string;
21
+ defaultValue: number;
22
+ };
23
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
24
+ maxFeatureScreenDensity: {
25
+ type: string;
26
+ description: string;
27
+ defaultValue: number;
28
+ };
29
+ fetchSizeLimit: {
30
+ type: string;
31
+ defaultValue: number;
32
+ description: string;
33
+ };
34
+ height: {
35
+ type: string;
36
+ defaultValue: number;
37
+ description: string;
38
+ };
39
+ mouseover: {
40
+ type: string;
41
+ description: string;
42
+ defaultValue: string;
43
+ contextVariable: string[];
44
+ };
45
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
@@ -3,6 +3,7 @@ import { Instance, IStateTreeNode } from 'mobx-state-tree';
3
3
  import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
4
4
  import PluginManager from '@jbrowse/core/PluginManager';
5
5
  import { MenuItem } from '@jbrowse/core/ui';
6
+ import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
6
7
  /**
7
8
  * #stateModel LinearAlignmentsDisplay
8
9
  * extends `BaseDisplay`
@@ -16,7 +17,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
16
17
  SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
17
18
  snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
18
19
  type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
19
- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
20
+ configuration: AnyConfigurationSchemaType;
20
21
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
21
22
  userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
22
23
  lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
@@ -66,7 +67,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
66
67
  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
67
68
  readonly DisplayMessageComponent: React.FC<any> | undefined;
68
69
  trackMenuItems(): MenuItem[];
69
- readonly viewMenuActions: MenuItem[];
70
+ readonly viewMenuActions: MenuItem[]; /**
71
+ * #action
72
+ */
70
73
  regionCannotBeRendered(): undefined;
71
74
  } & {
72
75
  setError(error?: unknown): void;
@@ -88,6 +91,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
88
91
  * #getter
89
92
  */
90
93
  readonly height: any;
94
+ readonly featureIdUnderMouse: any;
91
95
  } & {
92
96
  /**
93
97
  * #getter
@@ -125,7 +129,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
125
129
  /**
126
130
  * #action
127
131
  */
128
- updateStatsLimit(stats?: unknown): void;
132
+ setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
129
133
  /**
130
134
  * #action
131
135
  */
@@ -164,7 +168,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
164
168
  SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
165
169
  snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
166
170
  type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
167
- configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
171
+ configuration: AnyConfigurationSchemaType;
168
172
  heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
169
173
  userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
170
174
  lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
@@ -118,6 +118,10 @@ function stateModelFactory(pluginManager, configSchema) {
118
118
  var _a;
119
119
  return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'height');
120
120
  },
121
+ get featureIdUnderMouse() {
122
+ return (self.PileupDisplay.featureIdUnderMouse ||
123
+ self.SNPCoverageDisplay.featureIdUnderMouse);
124
+ },
121
125
  }))
122
126
  .views(self => ({
123
127
  /**
@@ -187,9 +191,9 @@ function stateModelFactory(pluginManager, configSchema) {
187
191
  /**
188
192
  * #action
189
193
  */
190
- updateStatsLimit(stats) {
191
- self.PileupDisplay.updateStatsLimit(stats);
192
- self.SNPCoverageDisplay.updateStatsLimit(stats);
194
+ setFeatureDensityStatsLimit(stats) {
195
+ self.PileupDisplay.setFeatureDensityStatsLimit(stats);
196
+ self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats);
193
197
  },
194
198
  /**
195
199
  * #action
@@ -1 +1 @@
1
- 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@@ -1,4 +1,3 @@
1
- /// <reference types="react" />
2
1
  import { ObservableMap } from 'mobx';
3
2
  declare function ColorByTagDlg(props: {
4
3
  model: {