@jbrowse/plugin-alignments 2.1.4 → 2.1.6

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Files changed (38) hide show
  1. package/dist/AlignmentsFeatureDetail/index.d.ts +7 -0
  2. package/dist/CramAdapter/CramTestAdapters.js +1 -1
  3. package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
  4. package/dist/LinearAlignmentsDisplay/models/model.d.ts +1 -1
  5. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +2 -2
  6. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -1
  7. package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +1 -5
  8. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  9. package/dist/LinearPileupDisplay/model.d.ts +8 -4
  10. package/dist/LinearPileupDisplay/model.js +7 -8
  11. package/dist/LinearPileupDisplay/model.js.map +1 -1
  12. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +15 -7
  13. package/dist/LinearSNPCoverageDisplay/models/model.js +10 -16
  14. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  15. package/dist/SNPCoverageRenderer/configSchema.js.map +1 -1
  16. package/esm/AlignmentsFeatureDetail/index.d.ts +7 -0
  17. package/esm/CramAdapter/CramTestAdapters.js +1 -1
  18. package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
  19. package/esm/LinearAlignmentsDisplay/models/model.d.ts +1 -1
  20. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +1 -1
  21. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -1
  22. package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +1 -5
  23. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  24. package/esm/LinearPileupDisplay/model.d.ts +8 -4
  25. package/esm/LinearPileupDisplay/model.js +8 -9
  26. package/esm/LinearPileupDisplay/model.js.map +1 -1
  27. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +15 -7
  28. package/esm/LinearSNPCoverageDisplay/models/model.js +10 -16
  29. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  30. package/esm/SNPCoverageRenderer/configSchema.js.map +1 -1
  31. package/package.json +2 -2
  32. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +51 -12
  33. package/src/CramAdapter/CramTestAdapters.ts +1 -1
  34. package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx +1 -1
  35. package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +1 -5
  36. package/src/LinearPileupDisplay/model.ts +11 -12
  37. package/src/LinearSNPCoverageDisplay/models/model.ts +18 -20
  38. /package/src/SNPCoverageRenderer/{configSchema.js → configSchema.ts} +0 -0
package/dist/AlignmentsFeatureDetail/index.d.ts CHANGED
@@ -8,12 +8,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
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  view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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  track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
11
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  } & {
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  type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
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  }, {
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  setFeatureData(featureData: Record<string, unknown>): void;
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  clearFeatureData(): void;
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  setFormattedData(feat: Record<string, unknown>): void;
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+ setExtra(type?: string | undefined, trackId?: string | undefined): void;
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  } & {
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  afterCreate(): void;
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  }, {
@@ -26,11 +29,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
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  view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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  track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
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  id: string;
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  type: "BaseFeatureWidget";
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  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
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  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
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+ trackId: string | undefined;
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+ trackType: string | undefined;
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  formattedFields: any;
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  finalizedFeatureData: any;
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  } & import("mobx-state-tree")._NotCustomized>;
package/dist/CramAdapter/CramTestAdapters.js CHANGED
@@ -14,7 +14,7 @@ function parseSmallFasta(text) {
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  .split('>')
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  .filter(t => /\S/.test(t))
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  .map(entryText => {
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- const [defLine, ...seqLines] = entryText.split('\n');
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+ const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/);
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  const [id, ...descriptionLines] = defLine.split(' ');
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  const description = descriptionLines.join(' ');
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  const sequence = seqLines.join('').replace(/\s/g, '');
package/dist/CramAdapter/CramTestAdapters.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":";;;;;;AACA,+BAAiC;AACjC,qFAA4D;AAC5D,yEAAgF;AAChF,yFAAqF;AAErF,iCAAiC;AACjC,SAAgB,eAAe,CAAC,IAAY;IAC1C,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;QAC5D,MAAM,CAAC,EAAE,EAAE,GAAG,gBAAgB,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QACpD,MAAM,WAAW,GAAG,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACrD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAA;IACtC,CAAC,CAAC,CAAA;AACN,CAAC;AAXD,0CAWC;AAID,MAAa,mBAAmB;IAG9B,YAAY,UAAsB;QAChC,IAAI,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;YAC9C,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACpC,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9B,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,EAAU,EAAE,KAAa,EAAE,GAAW;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,MAAM,KAAK,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACtB,MAAM,MAAM,GAAG,GAAG,GAAG,KAAK,GAAG,CAAC,CAAA;QAC9B,IAAI,CAAC,KAAK,EAAE;YACV,MAAM,IAAI,KAAK,CAAC,uBAAuB,EAAE,SAAS,CAAC,CAAA;SACpD;QACD,OAAO,KAAK,CAAC,QAAQ,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,EAAE,MAAM,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,eAAe;QACnB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,OAAO,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;IACpC,CAAC;CACF;AAxBD,kDAwBC;AAED,MAAa,eAAgB,SAAQ,oCAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,IAAA,yCAAmB,EAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAA;QAHlD,aAAQ,GAAa,EAAE,CAAA;QAIrB,IAAI,CAAC,KAAK,GAAG,IAAI,mBAAmB,CAAC,UAAU,CAAC,CAAA;IAClD,CAAC;IAED,KAAK,CAAC,WAAW;QACf,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,WAAW,CAAC,EACV,OAAO,EACP,KAAK,EACL,GAAG,GAKJ;QACC,OAAO,IAAI,iBAAU,CAAC,QAAQ,CAAC,EAAE;YAC/B,IAAI,CAAC,KAAK;iBACP,eAAe,EAAE;iBACjB,IAAI,CAAC,QAAQ,CAAC,EAAE;gBACf,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YAC1B,CAAC,CAAC;iBACD,IAAI,CAAC,GAAG,EAAE,CACT,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,KAAK,EAAE,GAAG,CAAC,CAC7D;iBACA,IAAI,CAAC,GAAG,CAAC,EAAE;gBACV,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,QAAQ,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,GAAG,EAAE;oBACtC,GAAG,EAAE,GAAG;oBACR,KAAK;oBACL,GAAG;iBACJ,CAAC,CACH,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;YACrB,CAAC,CAAC,CAAA;YACJ,OAAO,EAAE,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,CAAA;QAClC,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAhDD,0CAgDC"}
package/dist/LinearAlignmentsDisplay/models/model.d.ts CHANGED
@@ -61,7 +61,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
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  readonly adapterConfig: any;
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  readonly parentTrack: any;
63
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  renderProps(): any;
64
- readonly rendererType: any;
64
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
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  readonly DisplayMessageComponent: React.FC<any> | undefined;
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  trackMenuItems(): MenuItem[];
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  readonly viewMenuActions: MenuItem[];
package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js CHANGED
@@ -5,12 +5,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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5
  Object.defineProperty(exports, "__esModule", { value: true });
6
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  const react_1 = __importDefault(require("react"));
7
7
  const mobx_react_1 = require("mobx-react");
8
- const Typography_1 = __importDefault(require("@mui/material/Typography"));
8
+ const material_1 = require("@mui/material");
9
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  function LinearPileupDisplayBlurb(props) {
10
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  const { model } = props;
11
11
  const { sortedBy } = model;
12
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  return sortedBy ? (react_1.default.createElement("div", { "data-testid": `blurb-${model.sortedBy}`, style: { backgroundColor: 'white' } },
13
- react_1.default.createElement(Typography_1.default, { color: "secondary", variant: "caption" }, model.sortedBy
13
+ react_1.default.createElement(material_1.Typography, { color: "secondary", variant: "caption" }, model.sortedBy
14
14
  ? `Sorted by ${sortedBy.type.toLowerCase()} at ${sortedBy.refName}:${sortedBy.pos}`
15
15
  : null))) : null;
16
16
  }
package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"LinearPileupDisplayBlurb.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,4CAA0C;AAY1C,SAAS,wBAAwB,CAAC,KAAoC;IACpE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,sDACe,SAAS,KAAK,CAAC,QAAQ,EAAE,EACtC,KAAK,EAAE,EAAE,eAAe,EAAE,OAAO,EAAE;QAEnC,8BAAC,qBAAU,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,SAAS,IAC5C,KAAK,CAAC,QAAQ;YACb,CAAC,CAAC,aAAa,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,QAAQ,CAAC,OAAO,IAC7D,QAAQ,CAAC,GACX,EAAE;YACJ,CAAC,CAAC,IAAI,CACG,CACT,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,wBAAwB,CAAC,CAAA"}
package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts CHANGED
@@ -1,14 +1,10 @@
1
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  /// <reference types="react" />
2
2
  declare function SetFeatureHeightDlg(props: {
3
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  model: {
4
- minScore: number;
5
- maxScore: number;
6
- setMinScore: Function;
7
- setMaxScore: Function;
8
4
  setFeatureHeight: Function;
9
5
  setNoSpacing: Function;
10
6
  featureHeightSetting: number;
11
- noSpacing: boolean;
7
+ noSpacing?: boolean;
12
8
  };
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9
  handleClose: () => void;
14
10
  }): JSX.Element;
package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAWsB;AACtB,uCAA0C;AAC1C,sEAAiD;AAEjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,mBAAmB,CAAC,KAY5B;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,IAAA,gBAAQ,EAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,8BAAC,sBAAW;;YAEV,8BAAC,qBAAU,IAAC,SAAS,EAAE,OAAO,CAAC,WAAW,EAAE,OAAO,EAAE,WAAW;gBAC9D,8BAAC,eAAS,OAAG,CACF,CACD;QACd,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,wKAIE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,GACD;YACF,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,mBAAmB,CAAC,CAAA"}
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+ {"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAWsB;AACtB,uCAA0C;AAC1C,sEAAiD;AAEjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,mBAAmB,CAAC,KAQ5B;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,IAAA,gBAAQ,EAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,8BAAC,sBAAW;;YAEV,8BAAC,qBAAU,IAAC,SAAS,EAAE,OAAO,CAAC,WAAW,EAAE,OAAO,EAAE,WAAW;gBAC9D,8BAAC,eAAS,OAAG,CACF,CACD;QACd,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,wKAIE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,GACD;YACF,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,mBAAmB,CAAC,CAAA"}
package/dist/LinearPileupDisplay/model.d.ts CHANGED
@@ -131,7 +131,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
131
131
  readonly adapterConfig: any;
132
132
  readonly parentTrack: any;
133
133
  renderProps(): any;
134
- readonly rendererType: any;
134
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
135
135
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
136
136
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
137
137
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -198,7 +198,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
198
198
  afterAttach(): void;
199
199
  } & {
200
200
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
201
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
201
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
202
202
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
203
203
  contextMenuItems(): {
204
204
  label: string;
@@ -251,7 +251,11 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
251
251
  reload(): void;
252
252
  } & {
253
253
  readonly maxHeight: any;
254
- readonly rendererConfig: any;
254
+ readonly rendererConfig: {
255
+ [x: string]: any;
256
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
257
+ setSubschema(slotName: string, data: unknown): any;
258
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
255
259
  readonly featureHeightSetting: any;
256
260
  readonly mismatchAlphaSetting: any;
257
261
  readonly featureUnderMouse: Feature | undefined;
@@ -320,9 +324,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
320
324
  subMenu?: undefined;
321
325
  })[];
322
326
  }, import("mobx-state-tree")._NotCustomized, {
323
- type: string;
324
327
  height: number;
325
328
  id: string;
329
+ type: string;
326
330
  rpcDriverName: string | undefined;
327
331
  userBpPerPxLimit: number | undefined;
328
332
  userByteSizeLimit: number | undefined;
package/dist/LinearPileupDisplay/model.js CHANGED
@@ -153,18 +153,16 @@ const stateModelFactory = (configSchema) => mobx_state_tree_1.types
153
153
  const { rpcManager } = (0, util_1.getSession)(self);
154
154
  const view = (0, util_1.getContainingView)(self);
155
155
  const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
156
- const { staticBlocks, bpPerPx } = view;
157
- if (!self.estimatedStatsReady) {
158
- return;
159
- }
160
- if (self.regionTooLarge) {
156
+ if (!view.initialized ||
157
+ !self.estimatedStatsReady ||
158
+ self.regionTooLarge) {
161
159
  return;
162
160
  }
161
+ const { staticBlocks, bpPerPx } = view;
163
162
  // continually generate the vc pairing, set and rerender if any
164
163
  // new values seen
165
164
  if (colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) {
166
- const uniqueTagSet = await (0, shared_1.getUniqueTagValues)(self, colorBy, staticBlocks);
167
- self.updateColorTagMap(uniqueTagSet);
165
+ self.updateColorTagMap(await (0, shared_1.getUniqueTagValues)(self, colorBy, staticBlocks));
168
166
  }
169
167
  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
170
168
  const adapter = (0, configuration_1.getConf)(parentTrack, ['adapter']);
@@ -173,6 +171,7 @@ const stateModelFactory = (configSchema) => mobx_state_tree_1.types
173
171
  if (sortedBy) {
174
172
  const { pos, refName, assemblyName } = sortedBy;
175
173
  // render just the sorted region first
174
+ // @ts-ignore
176
175
  await self.rendererType.renderInClient(rpcManager, {
177
176
  assemblyName,
178
177
  regions: [
@@ -314,7 +313,7 @@ const stateModelFactory = (configSchema) => mobx_state_tree_1.types
314
313
  noSpacing: self.noSpacing,
315
314
  maxHeight: this.maxHeight,
316
315
  mismatchAlpha: self.mismatchAlpha,
317
- }, (0, mobx_state_tree_1.getEnv)(self));
316
+ }, (0, util_1.getEnv)(self));
318
317
  },
319
318
  get featureHeightSetting() {
320
319
  return (self.featureHeight || (0, configuration_1.readConfObject)(this.rendererConfig, 'height'));
package/dist/LinearPileupDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
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1
+ 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package/dist/LinearSNPCoverageDisplay/models/model.d.ts CHANGED
@@ -135,7 +135,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
135
135
  readonly adapterConfig: any;
136
136
  readonly parentTrack: any;
137
137
  renderProps(): any;
138
- readonly rendererType: any;
138
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
139
139
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
140
140
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
141
141
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -202,7 +202,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
202
202
  afterAttach(): void;
203
203
  } & {
204
204
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
205
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
205
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
206
206
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
207
207
  contextMenuItems(): {
208
208
  label: string;
@@ -229,9 +229,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
229
229
  scoreMin: number;
230
230
  scoreMax: number;
231
231
  }): void;
232
- setColor(color: string): void;
233
- setPosColor(color: string): void;
234
- setNegColor(color: string): void;
232
+ setColor(color?: string | undefined): void;
233
+ setPosColor(color?: string | undefined): void;
234
+ setNegColor(color?: string | undefined): void;
235
235
  setLoading(aborter: AbortController): void;
236
236
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
237
237
  setResolution(res: number): void;
@@ -255,7 +255,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
255
255
  readonly maxScore: any;
256
256
  readonly minScore: any;
257
257
  } & {
258
- readonly rendererConfig: any;
258
+ readonly rendererConfig: {
259
+ [x: string]: any;
260
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
261
+ setSubschema(slotName: string, data: unknown): any;
262
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
259
263
  } & {
260
264
  readonly filled: any;
261
265
  readonly summaryScoreModeSetting: any;
@@ -331,7 +335,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
331
335
  }): void;
332
336
  updateModificationColorMap(uniqueModifications: string[]): void;
333
337
  } & {
334
- readonly rendererConfig: any;
338
+ readonly rendererConfig: {
339
+ [x: string]: any;
340
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
341
+ setSubschema(slotName: string, data: unknown): any;
342
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
335
343
  readonly drawArcsSetting: any;
336
344
  readonly drawInterbaseCountsSetting: any;
337
345
  readonly drawIndicatorsSetting: any;
package/dist/LinearSNPCoverageDisplay/models/model.js CHANGED
@@ -115,16 +115,16 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
115
115
  (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
116
116
  try {
117
117
  const { colorBy } = self;
118
- const { staticBlocks } = (0, util_1.getContainingView)(self);
119
- if (!self.estimatedStatsReady) {
120
- return;
121
- }
122
- if (self.regionTooLarge) {
118
+ const view = (0, util_1.getContainingView)(self);
119
+ if (!view.initialized ||
120
+ !self.estimatedStatsReady ||
121
+ self.regionTooLarge) {
123
122
  return;
124
123
  }
124
+ const { staticBlocks } = view;
125
125
  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
126
- const vals = await (0, shared_1.getUniqueModificationValues)(self, (0, configuration_1.getConf)(self.parentTrack, 'adapter'), colorBy, staticBlocks);
127
- self.updateModificationColorMap(vals);
126
+ const adapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
127
+ self.updateModificationColorMap(await (0, shared_1.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks));
128
128
  }
129
129
  }
130
130
  catch (error) {
@@ -163,25 +163,19 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
163
163
  label: 'Draw insertion/clipping indicators',
164
164
  type: 'checkbox',
165
165
  checked: self.drawIndicatorsSetting,
166
- onClick: () => {
167
- self.toggleDrawIndicators();
168
- },
166
+ onClick: () => self.toggleDrawIndicators(),
169
167
  },
170
168
  {
171
169
  label: 'Draw insertion/clipping counts',
172
170
  type: 'checkbox',
173
171
  checked: self.drawInterbaseCountsSetting,
174
- onClick: () => {
175
- self.toggleDrawInterbaseCounts();
176
- },
172
+ onClick: () => self.toggleDrawInterbaseCounts(),
177
173
  },
178
174
  {
179
175
  label: 'Draw arcs',
180
176
  type: 'checkbox',
181
177
  checked: self.drawArcsSetting,
182
- onClick: () => {
183
- self.toggleDrawArcs();
184
- },
178
+ onClick: () => self.toggleDrawArcs(),
185
179
  },
186
180
  ];
187
181
  },
package/dist/LinearSNPCoverageDisplay/models/model.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/SNPCoverageRenderer/configSchema.js.map CHANGED
@@ -1 +1 @@
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package/esm/AlignmentsFeatureDetail/index.d.ts CHANGED
@@ -8,12 +8,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
8
8
  unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
9
9
  view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
10
10
  track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
11
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
12
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
13
  } & {
12
14
  type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
13
15
  }, {
14
16
  setFeatureData(featureData: Record<string, unknown>): void;
15
17
  clearFeatureData(): void;
16
18
  setFormattedData(feat: Record<string, unknown>): void;
19
+ setExtra(type?: string | undefined, trackId?: string | undefined): void;
17
20
  } & {
18
21
  afterCreate(): void;
19
22
  }, {
@@ -26,11 +29,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
26
29
  unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
27
30
  view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
28
31
  track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
32
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
33
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
29
34
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
30
35
  id: string;
31
36
  type: "BaseFeatureWidget";
32
37
  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
33
38
  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
39
+ trackId: string | undefined;
40
+ trackType: string | undefined;
34
41
  formattedFields: any;
35
42
  finalizedFeatureData: any;
36
43
  } & import("mobx-state-tree")._NotCustomized>;
package/esm/CramAdapter/CramTestAdapters.js CHANGED
@@ -8,7 +8,7 @@ export function parseSmallFasta(text) {
8
8
  .split('>')
9
9
  .filter(t => /\S/.test(t))
10
10
  .map(entryText => {
11
- const [defLine, ...seqLines] = entryText.split('\n');
11
+ const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/);
12
12
  const [id, ...descriptionLines] = defLine.split(' ');
13
13
  const description = descriptionLines.join(' ');
14
14
  const sequence = seqLines.join('').replace(/\s/g, '');
package/esm/CramAdapter/CramTestAdapters.js.map CHANGED
@@ -1 +1 @@
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package/esm/LinearAlignmentsDisplay/models/model.d.ts CHANGED
@@ -61,7 +61,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
61
61
  readonly adapterConfig: any;
62
62
  readonly parentTrack: any;
63
63
  renderProps(): any;
64
- readonly rendererType: any;
64
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
65
65
  readonly DisplayMessageComponent: React.FC<any> | undefined;
66
66
  trackMenuItems(): MenuItem[];
67
67
  readonly viewMenuActions: MenuItem[];
package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import React from 'react';
2
2
  import { observer } from 'mobx-react';
3
- import Typography from '@mui/material/Typography';
3
+ import { Typography } from '@mui/material';
4
4
  function LinearPileupDisplayBlurb(props) {
5
5
  const { model } = props;
6
6
  const { sortedBy } = model;
package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"LinearPileupDisplayBlurb.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAY1C,SAAS,wBAAwB,CAAC,KAAoC;IACpE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,4CACe,SAAS,KAAK,CAAC,QAAQ,EAAE,EACtC,KAAK,EAAE,EAAE,eAAe,EAAE,OAAO,EAAE;QAEnC,oBAAC,UAAU,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,SAAS,IAC5C,KAAK,CAAC,QAAQ;YACb,CAAC,CAAC,aAAa,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,QAAQ,CAAC,OAAO,IAC7D,QAAQ,CAAC,GACX,EAAE;YACJ,CAAC,CAAC,IAAI,CACG,CACT,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AACD,eAAe,QAAQ,CAAC,wBAAwB,CAAC,CAAA"}
package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts CHANGED
@@ -1,14 +1,10 @@
1
1
  /// <reference types="react" />
2
2
  declare function SetFeatureHeightDlg(props: {
3
3
  model: {
4
- minScore: number;
5
- maxScore: number;
6
- setMinScore: Function;
7
- setMaxScore: Function;
8
4
  setFeatureHeight: Function;
9
5
  setNoSpacing: Function;
10
6
  featureHeightSetting: number;
11
- noSpacing: boolean;
7
+ noSpacing?: boolean;
12
8
  };
13
9
  handleClose: () => void;
14
10
  }): JSX.Element;
package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,mBAAmB,CAAC,KAY5B;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAEV,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,WAAW,EAAE,OAAO,EAAE,WAAW;gBAC9D,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa;YACZ,oBAAC,UAAU,wKAIE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,GACD;YACF,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,mBAAmB,CAAC,CAAA"}
1
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package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -131,7 +131,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
131
131
  readonly adapterConfig: any;
132
132
  readonly parentTrack: any;
133
133
  renderProps(): any;
134
- readonly rendererType: any;
134
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
135
135
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
136
136
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
137
137
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -198,7 +198,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
198
198
  afterAttach(): void;
199
199
  } & {
200
200
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
201
- regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
201
+ regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
202
202
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
203
203
  contextMenuItems(): {
204
204
  label: string;
@@ -251,7 +251,11 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
251
251
  reload(): void;
252
252
  } & {
253
253
  readonly maxHeight: any;
254
- readonly rendererConfig: any;
254
+ readonly rendererConfig: {
255
+ [x: string]: any;
256
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
257
+ setSubschema(slotName: string, data: unknown): any;
258
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
255
259
  readonly featureHeightSetting: any;
256
260
  readonly mismatchAlphaSetting: any;
257
261
  readonly featureUnderMouse: Feature | undefined;
@@ -320,9 +324,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
320
324
  subMenu?: undefined;
321
325
  })[];
322
326
  }, import("mobx-state-tree")._NotCustomized, {
323
- type: string;
324
327
  height: number;
325
328
  id: string;
329
+ type: string;
326
330
  rpcDriverName: string | undefined;
327
331
  userBpPerPxLimit: number | undefined;
328
332
  userByteSizeLimit: number | undefined;