@jbrowse/plugin-variants 4.1.1 → 4.1.4

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 (57) hide show
  1. package/esm/ChordVariantDisplay/models/configSchema.d.ts +2 -2
  2. package/esm/LDDisplay/SharedLDConfigSchema.d.ts +3 -3
  3. package/esm/LDDisplay/components/LDDisplayComponent.js +3 -1
  4. package/esm/LDDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts +0 -9
  5. package/esm/LDDisplay/components/LinesConnectingMatrixToGenomicPosition.js +3 -29
  6. package/esm/LDDisplay/components/VariantLabels.d.ts +5 -0
  7. package/esm/LDDisplay/components/VariantLabels.js +27 -0
  8. package/esm/LDDisplay/components/Wrapper.d.ts +8 -0
  9. package/esm/LDDisplay/components/Wrapper.js +16 -0
  10. package/esm/LDDisplay/configSchema1.d.ts +6 -6
  11. package/esm/LDDisplay/configSchema2.d.ts +6 -6
  12. package/esm/LDDisplay/renderSvg.js +3 -1
  13. package/esm/LDRenderer/LDRenderer.js +3 -3
  14. package/esm/LDRenderer/configSchema.d.ts +2 -2
  15. package/esm/LDRenderer/makeImageData.d.ts +2 -2
  16. package/esm/LDRenderer/makeImageData.js +4 -5
  17. package/esm/LDTrack/configSchema.d.ts +8 -8
  18. package/esm/LinearVariantDisplay/configSchema.d.ts +3 -3
  19. package/esm/LinearVariantDisplay/model.d.ts +18 -8
  20. package/esm/MultiLinearVariantDisplay/configSchema.d.ts +6 -6
  21. package/esm/MultiLinearVariantDisplay/model.d.ts +72 -18
  22. package/esm/MultiLinearVariantMatrixDisplay/configSchema.d.ts +5 -5
  23. package/esm/MultiLinearVariantMatrixDisplay/model.d.ts +76 -20
  24. package/esm/MultiLinearVariantMatrixRenderer/configSchema.d.ts +1 -1
  25. package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js +8 -11
  26. package/esm/MultiLinearVariantRenderer/configSchema.d.ts +1 -1
  27. package/esm/MultiLinearVariantRenderer/makeImageData.js +8 -11
  28. package/esm/PlinkLDAdapter/configSchema.d.ts +2 -2
  29. package/esm/PlinkLDAdapter/configSchemaTabix.d.ts +4 -4
  30. package/esm/SplitVcfTabixAdapter/configSchema.d.ts +2 -2
  31. package/esm/StructuralVariantChordRenderer/configSchema.d.ts +2 -2
  32. package/esm/VariantFeatureWidget/configSchema.d.ts +1 -1
  33. package/esm/VariantFeatureWidget/stateModelFactory.d.ts +2 -2
  34. package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js +4 -1
  35. package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js +3 -3
  36. package/esm/VariantRPC/executeClusterGenotypeMatrix.js +6 -3
  37. package/esm/VariantRPC/getGenotypeMatrix.d.ts +2 -3
  38. package/esm/VariantRPC/getGenotypeMatrix.js +4 -5
  39. package/esm/VariantRPC/getLDMatrix.d.ts +2 -3
  40. package/esm/VariantRPC/getLDMatrix.js +5 -6
  41. package/esm/VariantRPC/getPhasedGenotypeMatrix.d.ts +2 -3
  42. package/esm/VariantRPC/getPhasedGenotypeMatrix.js +4 -5
  43. package/esm/VariantTrack/configSchema.d.ts +8 -8
  44. package/esm/VcfAdapter/configSchema.d.ts +2 -2
  45. package/esm/VcfTabixAdapter/configSchema.d.ts +4 -4
  46. package/esm/shared/MultiVariantBaseModel.d.ts +76 -20
  47. package/esm/shared/MultiVariantBaseModel.js +53 -3
  48. package/esm/shared/SharedVariantConfigSchema.d.ts +3 -3
  49. package/esm/shared/components/RectBg.js +3 -1
  50. package/esm/shared/components/TreeSidebar.js +38 -5
  51. package/esm/shared/components/types.d.ts +2 -0
  52. package/esm/shared/constants.d.ts +1 -0
  53. package/esm/shared/constants.js +1 -0
  54. package/esm/shared/makeSidebarSvg.js +3 -2
  55. package/esm/shared/minorAlleleFrequencyUtils.d.ts +2 -2
  56. package/esm/shared/minorAlleleFrequencyUtils.js +2 -2
  57. package/package.json +8 -8
package/esm/MultiLinearVariantDisplay/model.d.ts CHANGED
@@ -35,6 +35,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
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  reactElement?: React.ReactElement;
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  isRenderingPending?: boolean;
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+ displayHeight?: number;
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  };
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -53,10 +54,11 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  beforeDestroy(): void;
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  } & {
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  readonly statusMessage: any;
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+ readonly displayHeight: number | undefined;
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  } & {
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  afterAttach(): void;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  maxFeatureScreenDensity: {
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  type: string;
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  description: string;
@@ -83,7 +85,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  description: string;
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  defaultValue: never[];
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  };
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- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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  showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
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  showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
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  } & {
@@ -104,6 +106,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  clusterTree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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  treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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  lineZoneHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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+ subtreeFilter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
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  } & {
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  type: import("@jbrowse/mobx-state-tree").ISimpleType<"MultiLinearVariantDisplay">;
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  }, {
@@ -394,6 +397,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
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  reactElement?: React.ReactElement;
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  isRenderingPending?: boolean;
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+ displayHeight?: number;
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  };
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -412,6 +416,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  beforeDestroy(): void;
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  } & {
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  readonly statusMessage: any;
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+ readonly displayHeight: number | undefined;
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  } & {
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  afterAttach(): void;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -438,6 +443,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
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  reactElement?: React.ReactElement;
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  isRenderingPending?: boolean;
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+ displayHeight?: number;
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  };
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -456,6 +462,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  beforeDestroy(): void;
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  } & {
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  readonly statusMessage: any;
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+ readonly displayHeight: number | undefined;
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  } & {
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  afterAttach(): void;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -469,7 +476,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  [x: string]: any;
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  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
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- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  maxFeatureScreenDensity: {
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  type: string;
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  description: string;
@@ -496,7 +503,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  description: string;
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  defaultValue: never[];
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  };
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- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
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  showLegend: boolean | undefined;
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  showTooltips: boolean | undefined;
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  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -786,6 +793,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
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  reactElement?: React.ReactElement;
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  isRenderingPending?: boolean;
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+ displayHeight?: number;
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  };
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -804,10 +812,11 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  beforeDestroy(): void;
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  } & {
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  readonly statusMessage: any;
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+ readonly displayHeight: number | undefined;
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  } & {
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  afterAttach(): void;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  maxFeatureScreenDensity: {
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  type: string;
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  description: string;
@@ -834,7 +843,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  description: string;
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  defaultValue: never[];
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  };
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- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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  showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
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  showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
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  }, {
@@ -1144,6 +1153,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  setMafFilter(arg: number): void;
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  setShowSidebarLabels(arg: boolean): void;
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  setShowTree(arg: boolean): void;
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+ setSubtreeFilter(names?: string[]): void;
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  setPhasedMode(arg: string): void;
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  setAutoHeight(auto: boolean): void;
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  setHasPhased(arg: boolean): void;
@@ -1189,6 +1199,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  disabled: boolean;
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  onClick: () => void;
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  helpText?: undefined;
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+ } | {
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+ label: string;
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+ onClick: () => void;
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+ type?: undefined;
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+ checked?: undefined;
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+ disabled?: undefined;
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+ helpText?: undefined;
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  } | {
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  label: string;
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  helpText: string;
@@ -1308,6 +1325,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
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  reactElement?: React.ReactElement;
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  isRenderingPending?: boolean;
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+ displayHeight?: number;
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  };
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -1326,6 +1344,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  beforeDestroy(): void;
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  } & {
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  readonly statusMessage: any;
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+ readonly displayHeight: number | undefined;
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  } & {
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  afterAttach(): void;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1352,6 +1371,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
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  reactElement?: React.ReactElement;
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  isRenderingPending?: boolean;
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+ displayHeight?: number;
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  };
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -1370,6 +1390,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  beforeDestroy(): void;
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  } & {
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  readonly statusMessage: any;
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+ readonly displayHeight: number | undefined;
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  } & {
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  afterAttach(): void;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -1383,7 +1404,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  [x: string]: any;
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  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
1385
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
1386
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
1407
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  maxFeatureScreenDensity: {
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  type: string;
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  description: string;
@@ -1410,7 +1431,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
1410
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  description: string;
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  defaultValue: never[];
1412
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  };
1413
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">> & AnyConfigurationSchemaType> & {
1434
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">> & AnyConfigurationSchemaType> & {
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  setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
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  [x: string]: any;
1416
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  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
@@ -1429,6 +1450,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  clusterTree: string | undefined;
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  treeAreaWidth: number;
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  lineZoneHeight: number;
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+ subtreeFilter: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").ISimpleType<string>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>>) | undefined;
1432
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  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
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  rendererTypeName: string;
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  error: unknown;
@@ -1717,6 +1739,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
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  reactElement?: React.ReactElement;
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  isRenderingPending?: boolean;
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+ displayHeight?: number;
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  };
1721
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -1735,6 +1758,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  beforeDestroy(): void;
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  } & {
1737
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  readonly statusMessage: any;
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+ readonly displayHeight: number | undefined;
1738
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  } & {
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  afterAttach(): void;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1761,6 +1785,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
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  reactElement?: React.ReactElement;
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  isRenderingPending?: boolean;
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+ displayHeight?: number;
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  };
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -1779,6 +1804,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  beforeDestroy(): void;
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  } & {
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  readonly statusMessage: any;
1807
+ readonly displayHeight: number | undefined;
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  } & {
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  afterAttach(): void;
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -1792,7 +1818,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
1792
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  [x: string]: any;
1793
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  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
1794
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  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
1795
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
1821
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  maxFeatureScreenDensity: {
1797
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  type: string;
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  description: string;
@@ -1819,7 +1845,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
1819
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  description: string;
1820
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  defaultValue: never[];
1821
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  };
1822
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
1848
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
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  showLegend: boolean | undefined;
1824
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  showTooltips: boolean | undefined;
1825
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  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -2109,6 +2135,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  statusMessage?: string;
2110
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  reactElement?: React.ReactElement;
2111
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  isRenderingPending?: boolean;
2138
+ displayHeight?: number;
2112
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  };
2113
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  }) => import("react/jsx-runtime").JSX.Element;
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  renderProps: any;
@@ -2127,10 +2154,11 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2127
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  beforeDestroy(): void;
2128
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  } & {
2129
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  readonly statusMessage: any;
2157
+ readonly displayHeight: number | undefined;
2130
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  } & {
2131
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  afterAttach(): void;
2132
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  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
2133
- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
2161
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2134
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  maxFeatureScreenDensity: {
2135
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  type: string;
2136
2164
  description: string;
@@ -2157,7 +2185,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2157
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  description: string;
2158
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  defaultValue: never[];
2159
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  };
2160
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
2188
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
2161
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  showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
2162
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  showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
2163
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  }, {
@@ -2467,6 +2495,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2467
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  setMafFilter(arg: number): void;
2468
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  setShowSidebarLabels(arg: boolean): void;
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  setShowTree(arg: boolean): void;
2498
+ setSubtreeFilter(names?: string[]): void;
2470
2499
  setPhasedMode(arg: string): void;
2471
2500
  setAutoHeight(auto: boolean): void;
2472
2501
  setHasPhased(arg: boolean): void;
@@ -2512,6 +2541,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2512
2541
  disabled: boolean;
2513
2542
  onClick: () => void;
2514
2543
  helpText?: undefined;
2544
+ } | {
2545
+ label: string;
2546
+ onClick: () => void;
2547
+ type?: undefined;
2548
+ checked?: undefined;
2549
+ disabled?: undefined;
2550
+ helpText?: undefined;
2515
2551
  } | {
2516
2552
  label: string;
2517
2553
  helpText: string;
@@ -2631,6 +2667,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2631
2667
  statusMessage?: string;
2632
2668
  reactElement?: React.ReactElement;
2633
2669
  isRenderingPending?: boolean;
2670
+ displayHeight?: number;
2634
2671
  };
2635
2672
  }) => import("react/jsx-runtime").JSX.Element;
2636
2673
  renderProps: any;
@@ -2649,10 +2686,11 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2649
2686
  beforeDestroy(): void;
2650
2687
  } & {
2651
2688
  readonly statusMessage: any;
2689
+ readonly displayHeight: number | undefined;
2652
2690
  } & {
2653
2691
  afterAttach(): void;
2654
2692
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
2655
- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
2693
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2656
2694
  maxFeatureScreenDensity: {
2657
2695
  type: string;
2658
2696
  description: string;
@@ -2679,7 +2717,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2679
2717
  description: string;
2680
2718
  defaultValue: never[];
2681
2719
  };
2682
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
2720
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
2683
2721
  showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
2684
2722
  showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
2685
2723
  } & {
@@ -2700,6 +2738,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2700
2738
  clusterTree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
2701
2739
  treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
2702
2740
  lineZoneHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
2741
+ subtreeFilter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
2703
2742
  }, {
2704
2743
  rendererTypeName: string;
2705
2744
  error: unknown;
@@ -2988,6 +3027,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
2988
3027
  statusMessage?: string;
2989
3028
  reactElement?: React.ReactElement;
2990
3029
  isRenderingPending?: boolean;
3030
+ displayHeight?: number;
2991
3031
  };
2992
3032
  }) => import("react/jsx-runtime").JSX.Element;
2993
3033
  renderProps: any;
@@ -3006,6 +3046,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3006
3046
  beforeDestroy(): void;
3007
3047
  } & {
3008
3048
  readonly statusMessage: any;
3049
+ readonly displayHeight: number | undefined;
3009
3050
  } & {
3010
3051
  afterAttach(): void;
3011
3052
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -3032,6 +3073,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3032
3073
  statusMessage?: string;
3033
3074
  reactElement?: React.ReactElement;
3034
3075
  isRenderingPending?: boolean;
3076
+ displayHeight?: number;
3035
3077
  };
3036
3078
  }) => import("react/jsx-runtime").JSX.Element;
3037
3079
  renderProps: any;
@@ -3050,6 +3092,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3050
3092
  beforeDestroy(): void;
3051
3093
  } & {
3052
3094
  readonly statusMessage: any;
3095
+ readonly displayHeight: number | undefined;
3053
3096
  } & {
3054
3097
  afterAttach(): void;
3055
3098
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -3063,7 +3106,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3063
3106
  [x: string]: any;
3064
3107
  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
3065
3108
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
3066
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
3109
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3067
3110
  maxFeatureScreenDensity: {
3068
3111
  type: string;
3069
3112
  description: string;
@@ -3090,7 +3133,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3090
3133
  description: string;
3091
3134
  defaultValue: never[];
3092
3135
  };
3093
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
3136
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
3094
3137
  showLegend: boolean | undefined;
3095
3138
  showTooltips: boolean | undefined;
3096
3139
  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -3380,6 +3423,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3380
3423
  statusMessage?: string;
3381
3424
  reactElement?: React.ReactElement;
3382
3425
  isRenderingPending?: boolean;
3426
+ displayHeight?: number;
3383
3427
  };
3384
3428
  }) => import("react/jsx-runtime").JSX.Element;
3385
3429
  renderProps: any;
@@ -3398,10 +3442,11 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3398
3442
  beforeDestroy(): void;
3399
3443
  } & {
3400
3444
  readonly statusMessage: any;
3445
+ readonly displayHeight: number | undefined;
3401
3446
  } & {
3402
3447
  afterAttach(): void;
3403
3448
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
3404
- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
3449
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3405
3450
  maxFeatureScreenDensity: {
3406
3451
  type: string;
3407
3452
  description: string;
@@ -3428,7 +3473,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3428
3473
  description: string;
3429
3474
  defaultValue: never[];
3430
3475
  };
3431
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
3476
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
3432
3477
  showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
3433
3478
  showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
3434
3479
  }, {
@@ -3738,6 +3783,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3738
3783
  setMafFilter(arg: number): void;
3739
3784
  setShowSidebarLabels(arg: boolean): void;
3740
3785
  setShowTree(arg: boolean): void;
3786
+ setSubtreeFilter(names?: string[]): void;
3741
3787
  setPhasedMode(arg: string): void;
3742
3788
  setAutoHeight(auto: boolean): void;
3743
3789
  setHasPhased(arg: boolean): void;
@@ -3783,6 +3829,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3783
3829
  disabled: boolean;
3784
3830
  onClick: () => void;
3785
3831
  helpText?: undefined;
3832
+ } | {
3833
+ label: string;
3834
+ onClick: () => void;
3835
+ type?: undefined;
3836
+ checked?: undefined;
3837
+ disabled?: undefined;
3838
+ helpText?: undefined;
3786
3839
  } | {
3787
3840
  label: string;
3788
3841
  helpText: string;
@@ -3911,6 +3964,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
3911
3964
  clusterTree: string | undefined;
3912
3965
  treeAreaWidth: number;
3913
3966
  lineZoneHeight: number;
3967
+ subtreeFilter: string[] | undefined;
3914
3968
  } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized>;
3915
3969
  export type MultiLinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;
3916
3970
  export type MultiLinearVariantDisplayModel = Instance<MultiLinearVariantDisplayStateModel>;
package/esm/MultiLinearVariantMatrixDisplay/configSchema.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import type PluginManager from '@jbrowse/core/PluginManager';
2
- export default function configSchemaF(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
3
- renderer: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
2
+ export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3
+ renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
4
4
  height: {
5
5
  type: string;
6
6
  defaultValue: number;
@@ -30,9 +30,9 @@ export default function configSchemaF(pluginManager: PluginManager): import("nod
30
30
  type: string;
31
31
  defaultValue: string;
32
32
  };
33
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
33
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
34
34
  renderer: import("@jbrowse/mobx-state-tree").IAnyModelType;
35
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
35
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
36
36
  maxFeatureScreenDensity: {
37
37
  type: string;
38
38
  description: string;
@@ -59,4 +59,4 @@ export default function configSchemaF(pluginManager: PluginManager): import("nod
59
59
  description: string;
60
60
  defaultValue: never[];
61
61
  };
62
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
62
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;