@jbrowse/plugin-wiggle 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.
- package/dist/BigWigAdapter/BigWigAdapter.d.ts +2 -2
- package/dist/BigWigAdapter/BigWigAdapter.js +2 -2
- package/dist/BigWigAdapter/BigWigAdapter.js.map +1 -1
- package/dist/BigWigAdapter/configSchema.d.ts +20 -1
- package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts +0 -1
- package/dist/DensityRenderer/configSchema.d.ts +33 -1
- package/dist/LinePlotRenderer/configSchema.d.ts +44 -1
- package/dist/LinearWiggleDisplay/components/SetColorDialog.d.ts +0 -1
- package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +0 -1
- package/dist/LinearWiggleDisplay/models/configSchema.d.ts +98 -1
- package/dist/LinearWiggleDisplay/models/model.d.ts +82 -35
- package/dist/LinearWiggleDisplay/models/model.js +8 -25
- package/dist/LinearWiggleDisplay/models/model.js.map +1 -1
- package/dist/MultiDensityRenderer/configSchema.d.ts +33 -1
- package/dist/MultiLineRenderer/configSchema.d.ts +51 -1
- package/dist/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts +0 -1
- package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +0 -1
- package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js +36 -37
- package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js.map +1 -1
- package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +0 -1
- package/dist/MultiLinearWiggleDisplay/models/configSchema.d.ts +107 -1
- package/dist/MultiLinearWiggleDisplay/models/model.d.ts +58 -11
- package/dist/MultiLinearWiggleDisplay/models/model.js +3 -19
- package/dist/MultiLinearWiggleDisplay/models/model.js.map +1 -1
- package/dist/MultiQuantitativeTrack/configSchema.d.ts +73 -1
- package/dist/MultiRowLineRenderer/configSchema.d.ts +51 -1
- package/dist/MultiRowXYPlotRenderer/configSchema.d.ts +68 -1
- package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +1 -1
- package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js +2 -2
- package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js.map +1 -1
- package/dist/MultiWiggleAdapter/configSchema.d.ts +18 -1
- package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts +0 -1
- package/dist/MultiWiggleRendering.d.ts +0 -1
- package/dist/MultiXYPlotRenderer/configSchema.d.ts +65 -1
- package/dist/QuantitativeTrack/configSchema.d.ts +73 -1
- package/dist/WiggleRPC/MultiWiggleGetSources.d.ts +21 -0
- package/dist/WiggleRPC/MultiWiggleGetSources.js +51 -0
- package/dist/WiggleRPC/MultiWiggleGetSources.js.map +1 -0
- package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts +14 -0
- package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +37 -0
- package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js.map +1 -0
- package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +20 -0
- package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +54 -0
- package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js.map +1 -0
- package/dist/WiggleRPC/rpcMethods.d.ts +3 -47
- package/dist/WiggleRPC/rpcMethods.js +16 -117
- package/dist/WiggleRPC/rpcMethods.js.map +1 -1
- package/dist/WiggleRendering.d.ts +0 -1
- package/dist/XYPlotRenderer/configSchema.d.ts +65 -1
- package/dist/configSchema.d.ts +51 -1
- package/dist/index.d.ts +148 -23
- package/dist/index.js +2 -2
- package/dist/index.js.map +1 -1
- package/dist/shared/SetMinMaxDialog.d.ts +0 -1
- package/dist/shared/YScaleBar.d.ts +0 -1
- package/dist/util.d.ts +9 -6
- package/dist/util.js +13 -12
- package/dist/util.js.map +1 -1
- package/esm/BigWigAdapter/BigWigAdapter.d.ts +2 -2
- package/esm/BigWigAdapter/BigWigAdapter.js +4 -3
- package/esm/BigWigAdapter/BigWigAdapter.js.map +1 -1
- package/esm/BigWigAdapter/configSchema.d.ts +20 -1
- package/esm/CreateMultiWiggleExtension/ConfirmDialog.d.ts +0 -1
- package/esm/DensityRenderer/configSchema.d.ts +33 -1
- package/esm/LinePlotRenderer/configSchema.d.ts +44 -1
- package/esm/LinearWiggleDisplay/components/SetColorDialog.d.ts +0 -1
- package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +0 -1
- package/esm/LinearWiggleDisplay/models/configSchema.d.ts +98 -1
- package/esm/LinearWiggleDisplay/models/model.d.ts +82 -35
- package/esm/LinearWiggleDisplay/models/model.js +10 -27
- package/esm/LinearWiggleDisplay/models/model.js.map +1 -1
- package/esm/MultiDensityRenderer/configSchema.d.ts +33 -1
- package/esm/MultiLineRenderer/configSchema.d.ts +51 -1
- package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts +0 -1
- package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +0 -1
- package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js +36 -37
- package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js.map +1 -1
- package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +0 -1
- package/esm/MultiLinearWiggleDisplay/models/configSchema.d.ts +107 -1
- package/esm/MultiLinearWiggleDisplay/models/model.d.ts +58 -11
- package/esm/MultiLinearWiggleDisplay/models/model.js +4 -20
- package/esm/MultiLinearWiggleDisplay/models/model.js.map +1 -1
- package/esm/MultiQuantitativeTrack/configSchema.d.ts +73 -1
- package/esm/MultiRowLineRenderer/configSchema.d.ts +51 -1
- package/esm/MultiRowXYPlotRenderer/configSchema.d.ts +68 -1
- package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +1 -1
- package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js +3 -2
- package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js.map +1 -1
- package/esm/MultiWiggleAdapter/configSchema.d.ts +18 -1
- package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts +0 -1
- package/esm/MultiWiggleRendering.d.ts +0 -1
- package/esm/MultiXYPlotRenderer/configSchema.d.ts +65 -1
- package/esm/QuantitativeTrack/configSchema.d.ts +73 -1
- package/esm/WiggleRPC/MultiWiggleGetSources.d.ts +21 -0
- package/esm/WiggleRPC/MultiWiggleGetSources.js +44 -0
- package/esm/WiggleRPC/MultiWiggleGetSources.js.map +1 -0
- package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts +14 -0
- package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +30 -0
- package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js.map +1 -0
- package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +20 -0
- package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +47 -0
- package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js.map +1 -0
- package/esm/WiggleRPC/rpcMethods.d.ts +3 -47
- package/esm/WiggleRPC/rpcMethods.js +3 -111
- package/esm/WiggleRPC/rpcMethods.js.map +1 -1
- package/esm/WiggleRendering.d.ts +0 -1
- package/esm/XYPlotRenderer/configSchema.d.ts +65 -1
- package/esm/configSchema.d.ts +51 -1
- package/esm/index.d.ts +148 -23
- package/esm/index.js +3 -3
- package/esm/index.js.map +1 -1
- package/esm/shared/SetMinMaxDialog.d.ts +0 -1
- package/esm/shared/YScaleBar.d.ts +0 -1
- package/esm/util.d.ts +9 -6
- package/esm/util.js +10 -9
- package/esm/util.js.map +1 -1
- package/package.json +3 -3
- package/src/BigWigAdapter/BigWigAdapter.test.ts +8 -3
- package/src/BigWigAdapter/BigWigAdapter.ts +6 -3
- package/src/LinearWiggleDisplay/models/model.tsx +11 -29
- package/src/MultiLinearWiggleDisplay/components/SetColorDialog.tsx +53 -50
- package/src/MultiLinearWiggleDisplay/models/model.tsx +4 -20
- package/src/MultiWiggleAdapter/MultiWiggleAdapter.ts +1 -1
- package/src/WiggleRPC/MultiWiggleGetSources.ts +68 -0
- package/src/WiggleRPC/WiggleGetGlobalQuantitativeStats.ts +44 -0
- package/src/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.ts +73 -0
- package/src/WiggleRPC/rpcMethods.ts +3 -170
- package/src/index.ts +4 -4
- package/src/util.ts +24 -17
package/esm/index.d.ts
CHANGED
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@@ -108,7 +108,33 @@ export default class WigglePlugin extends Plugin {
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
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userBpPerPxLimit: number | undefined;
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userByteSizeLimit: number | undefined;
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configuration:
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configuration: {
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[x: string]: any;
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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setSubschema(slotName: string, data: unknown): any;
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} & import("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;
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defaultValue: number;
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};
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fetchSizeLimit: {
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type: string;
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defaultValue: number;
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description: string;
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};
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height: {
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type: string;
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defaultValue: number;
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description: string;
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};
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mouseover: {
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type: string;
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description: string;
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defaultValue: string;
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contextVariable: string[];
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">> & import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
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selectedRendering: string;
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resolution: number;
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fill: boolean | undefined;
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@@ -186,8 +212,8 @@ export default class WigglePlugin extends Plugin {
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message: string;
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featureIdUnderMouse: string | undefined;
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contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
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featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
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featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
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} & {
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readonly height: number;
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readonly blockType: "dynamicBlocks" | "staticBlocks";
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@@ -206,26 +232,26 @@ export default class WigglePlugin extends Plugin {
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readonly currentBytesRequested: number;
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readonly currentFeatureScreenDensity: number;
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readonly maxFeatureScreenDensity: any;
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readonly
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readonly featureDensityStatsReady: boolean;
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readonly maxAllowableBytes: number;
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} & {
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setMessage(message: string): void;
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} & {
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afterAttach(): void;
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getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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setFeatureDensityStatsP(arg: any): void;
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setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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clearFeatureDensityStats(): void;
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setHeight(displayHeight: number): number;
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resizeHeight(distance: number): number;
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setScrollTop(scrollTop: number): void;
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setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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setCurrBpPerPx(n: number): void;
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deleteBlock(key: string): void;
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selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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clearFeatureSelection(): void;
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setFeatureIdUnderMouse(feature
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setFeatureIdUnderMouse(feature?: string | undefined): void;
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reload(): void;
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setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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} & {
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} | undefined;
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statsFetchInProgress: AbortController | undefined;
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} & {
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updateQuantitativeStats(stats: {
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scoreMin: number;
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scoreMax: number;
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}): void;
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@@ -400,9 +426,32 @@ export default class WigglePlugin extends Plugin {
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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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;
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defaultValue: number;
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};
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fetchSizeLimit: {
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type: string;
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defaultValue: number;
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description: string;
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};
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height: {
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type: string;
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defaultValue: number;
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description: string;
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};
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mouseover: {
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description: string;
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defaultValue: string;
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contextVariable: string[];
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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} & {
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type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
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configuration: import("
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configuration: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
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selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
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fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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message: string;
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featureIdUnderMouse: string | undefined;
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featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
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featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
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} & {
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readonly featureDensityStatsReady: boolean;
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} & {
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setMessage(message: string): void;
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afterAttach(): void;
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getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
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setFeatureDensityStatsP(arg: any): void;
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setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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clearFeatureDensityStats(): void;
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setHeight(displayHeight: number): number;
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resizeHeight(distance: number): number;
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setScrollTop(scrollTop: number): void;
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setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
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addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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setCurrBpPerPx(n: number): void;
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deleteBlock(key: string): void;
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selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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clearFeatureSelection(): void;
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setFeatureIdUnderMouse(feature
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setFeatureIdUnderMouse(feature?: string | undefined): void;
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reload(): void;
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setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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} & {
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} | undefined;
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statsFetchInProgress: AbortController | undefined;
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} & {
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updateQuantitativeStats(stats: {
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scoreMax: number;
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}): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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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;
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defaultValue: number;
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|
+
};
|
|
751
|
+
fetchSizeLimit: {
|
|
752
|
+
type: string;
|
|
753
|
+
defaultValue: number;
|
|
754
|
+
description: string;
|
|
755
|
+
};
|
|
756
|
+
height: {
|
|
757
|
+
type: string;
|
|
758
|
+
defaultValue: number;
|
|
759
|
+
description: string;
|
|
760
|
+
};
|
|
761
|
+
mouseover: {
|
|
762
|
+
type: string;
|
|
763
|
+
description: string;
|
|
764
|
+
defaultValue: string;
|
|
765
|
+
contextVariable: string[];
|
|
766
|
+
};
|
|
767
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
|
|
696
768
|
}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
|
|
697
769
|
type: string;
|
|
698
770
|
id: string;
|
|
771
|
+
configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
|
|
699
772
|
rpcDriverName: string | undefined;
|
|
700
773
|
heightPreConfig: number | undefined;
|
|
701
774
|
userBpPerPxLimit: number | undefined;
|
|
@@ -716,7 +789,59 @@ export default class WigglePlugin extends Plugin {
|
|
|
716
789
|
XYPlotRenderer: typeof XYPlotRenderer;
|
|
717
790
|
WiggleBaseRenderer: typeof WiggleBaseRenderer;
|
|
718
791
|
linearWiggleDisplayModelFactory: typeof linearWiggleDisplayModelFactory;
|
|
719
|
-
xyPlotRendererConfigSchema: import("@jbrowse/core/configuration").
|
|
792
|
+
xyPlotRendererConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
793
|
+
filled: {
|
|
794
|
+
type: string;
|
|
795
|
+
defaultValue: boolean;
|
|
796
|
+
};
|
|
797
|
+
displayCrossHatches: {
|
|
798
|
+
type: string;
|
|
799
|
+
description: string;
|
|
800
|
+
defaultValue: boolean;
|
|
801
|
+
};
|
|
802
|
+
summaryScoreMode: {
|
|
803
|
+
type: string;
|
|
804
|
+
model: import("mobx-state-tree").ISimpleType<string>;
|
|
805
|
+
description: string;
|
|
806
|
+
defaultValue: string;
|
|
807
|
+
};
|
|
808
|
+
minSize: {
|
|
809
|
+
type: string;
|
|
810
|
+
defaultValue: number;
|
|
811
|
+
};
|
|
812
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
813
|
+
color: {
|
|
814
|
+
type: string;
|
|
815
|
+
description: string;
|
|
816
|
+
defaultValue: string;
|
|
817
|
+
};
|
|
818
|
+
posColor: {
|
|
819
|
+
type: string;
|
|
820
|
+
description: string;
|
|
821
|
+
defaultValue: string;
|
|
822
|
+
};
|
|
823
|
+
negColor: {
|
|
824
|
+
type: string;
|
|
825
|
+
description: string;
|
|
826
|
+
defaultValue: string;
|
|
827
|
+
};
|
|
828
|
+
clipColor: {
|
|
829
|
+
type: string;
|
|
830
|
+
description: string;
|
|
831
|
+
defaultValue: string;
|
|
832
|
+
};
|
|
833
|
+
bicolorPivot: {
|
|
834
|
+
type: string;
|
|
835
|
+
model: import("mobx-state-tree").ISimpleType<string>;
|
|
836
|
+
description: string;
|
|
837
|
+
defaultValue: string;
|
|
838
|
+
};
|
|
839
|
+
bicolorPivotValue: {
|
|
840
|
+
type: string;
|
|
841
|
+
defaultValue: number;
|
|
842
|
+
description: string;
|
|
843
|
+
};
|
|
844
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
|
|
720
845
|
utils: typeof utils;
|
|
721
846
|
};
|
|
722
847
|
}
|
package/esm/index.js
CHANGED
|
@@ -19,7 +19,7 @@ import MultiRowLineRendererF from './MultiRowLineRenderer';
|
|
|
19
19
|
import CreateMultiWiggleExtensionF from './CreateMultiWiggleExtension';
|
|
20
20
|
import MultiWiggleAddTrackWidgetF from './MultiWiggleAddTrackWidget';
|
|
21
21
|
import * as utils from './util';
|
|
22
|
-
import {
|
|
22
|
+
import { WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, MultiWiggleGetSources, } from './WiggleRPC/rpcMethods';
|
|
23
23
|
import { ReactComponent as LinearWiggleDisplayReactComponent, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
|
|
24
24
|
import { ReactComponent as XYPlotRendererReactComponent, configSchema as xyPlotRendererConfigSchema, XYPlotRenderer, } from './XYPlotRenderer';
|
|
25
25
|
export default class WigglePlugin extends Plugin {
|
|
@@ -79,8 +79,8 @@ export default class WigglePlugin extends Plugin {
|
|
|
79
79
|
return trackTypeGuesser(adapterName);
|
|
80
80
|
};
|
|
81
81
|
});
|
|
82
|
-
pm.addRpcMethod(() => new
|
|
83
|
-
pm.addRpcMethod(() => new
|
|
82
|
+
pm.addRpcMethod(() => new WiggleGetGlobalQuantitativeStats(pm));
|
|
83
|
+
pm.addRpcMethod(() => new WiggleGetMultiRegionQuantitativeStats(pm));
|
|
84
84
|
pm.addRpcMethod(() => new MultiWiggleGetSources(pm));
|
|
85
85
|
}
|
|
86
86
|
}
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAGL,WAAW,GACZ,MAAM,2BAA2B,CAAA;AAElC,SAAS;AACT,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AAErD,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,mBAAmB,MAAM,sBAAsB,CAAA;AACtD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAC9C,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,yBAAyB,MAAM,4BAA4B,CAAA;AAClE,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,2BAA2B,MAAM,8BAA8B,CAAA;AACtE,OAAO,0BAA0B,MAAM,6BAA6B,CAAA;AAEpE,OAAO,KAAK,KAAK,MAAM,QAAQ,CAAA;AAE/B,OAAO,EACL,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAGL,WAAW,GACZ,MAAM,2BAA2B,CAAA;AAElC,SAAS;AACT,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AAErD,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,mBAAmB,MAAM,sBAAsB,CAAA;AACtD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAC9C,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,yBAAyB,MAAM,4BAA4B,CAAA;AAClE,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,2BAA2B,MAAM,8BAA8B,CAAA;AACtE,OAAO,0BAA0B,MAAM,6BAA6B,CAAA;AAEpE,OAAO,KAAK,KAAK,MAAM,QAAQ,CAAA;AAE/B,OAAO,EACL,gCAAgC,EAChC,qCAAqC,EACrC,qBAAqB,GACtB,MAAM,wBAAwB,CAAA;AAE/B,OAAO,EACL,cAAc,IAAI,iCAAiC,EACnD,YAAY,IAAI,+BAA+B,GAChD,MAAM,uBAAuB,CAAA;AAE9B,OAAO,EACL,cAAc,IAAI,4BAA4B,EAC9C,YAAY,IAAI,0BAA0B,EAC1C,cAAc,GACf,MAAM,kBAAkB,CAAA;AAEzB,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,MAAM;IAAhD;;QACE,SAAI,GAAG,cAAc,CAAA;QA2DrB,YAAO,GAAG;YACR,iCAAiC;YACjC,4BAA4B;YAC5B,cAAc;YACd,kBAAkB;YAClB,+BAA+B;YAC/B,0BAA0B;YAC1B,KAAK;SACN,CAAA;IACH,CAAC;IAlEC,OAAO,CAAC,EAAiB;QACvB,mBAAmB,CAAC,EAAE,CAAC,CAAA;QACvB,cAAc,CAAC,EAAE,CAAC,CAAA;QAClB,kBAAkB,CAAC,EAAE,CAAC,CAAA;QACtB,uBAAuB,CAAC,EAAE,CAAC,CAAA;QAC3B,oBAAoB,CAAC,EAAE,CAAC,CAAA;QACxB,yBAAyB,CAAC,EAAE,CAAC,CAAA;QAC7B,iBAAiB,CAAC,EAAE,CAAC,CAAA;QACrB,eAAe,CAAC,EAAE,CAAC,CAAA;QACnB,gBAAgB,CAAC,EAAE,CAAC,CAAA;QACpB,oBAAoB,CAAC,EAAE,CAAC,CAAA;QACxB,uBAAuB,CAAC,EAAE,CAAC,CAAA;QAC3B,qBAAqB,CAAC,EAAE,CAAC,CAAA;QACzB,kBAAkB,CAAC,EAAE,CAAC,CAAA;QACtB,qBAAqB,CAAC,EAAE,CAAC,CAAA;QACzB,0BAA0B,CAAC,EAAE,CAAC,CAAA;QAC9B,2BAA2B,CAAC,EAAE,CAAC,CAAA;QAE/B,EAAE,CAAC,mBAAmB,CACpB,8BAA8B,EAC9B,CAAC,EAAkB,EAAE,EAAE;YACrB,OAAO,CAAC,IAAkB,EAAE,KAAoB,EAAE,IAAa,EAAE,EAAE;gBACjE,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,cAAc,EAAE,IAAI;iBACrB,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,IAAI,KAAK,WAAW,EAAE;oBAC/B,OAAO,GAAG,CAAA;iBACX;gBAED,OAAO,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;YAC9B,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,EAAE,CAAC,mBAAmB,CACpB,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,eAAe,EAAE;oBACnC,OAAO,mBAAmB,CAAA;iBAC3B;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,gCAAgC,CAAC,EAAE,CAAC,CAAC,CAAA;QAC/D,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,qCAAqC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpE,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,qBAAqB,CAAC,EAAE,CAAC,CAAC,CAAA;IACtD,CAAC;CAWF;AAED,cAAc,QAAQ,CAAA;AAEtB,OAAO,EAAE,OAAO,IAAI,eAAe,EAAE,MAAM,mBAAmB,CAAA;AAC9D,OAAO,EACL,OAAO,EACP,cAAc,IAAI,iCAAiC,EACnD,YAAY,IAAI,+BAA+B,GAChD,MAAM,uBAAuB,CAAA;AAG9B,OAAO,EAAE,OAAO,IAAI,kBAAkB,EAAE,MAAM,sBAAsB,CAAA"}
|
package/esm/util.d.ts
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import { QuantitativeStats } from '@jbrowse/core/util/stats';
|
|
2
2
|
import { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
3
3
|
export declare const YSCALEBAR_LABEL_OFFSET = 5;
|
|
4
4
|
export interface ScaleOpts {
|
|
@@ -50,22 +50,25 @@ export declare function getNiceDomain({ scaleType, domain, bounds, }: {
|
|
|
50
50
|
export declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
|
|
51
51
|
[key: string]: T[];
|
|
52
52
|
};
|
|
53
|
-
export declare function
|
|
53
|
+
export declare function getQuantitativeStats(self: {
|
|
54
54
|
adapterConfig: AnyConfigurationModel;
|
|
55
|
+
configuration: AnyConfigurationModel;
|
|
55
56
|
autoscaleType: string;
|
|
56
57
|
setMessage: (str: string) => void;
|
|
57
58
|
}, opts: {
|
|
58
59
|
headers?: Record<string, string>;
|
|
59
60
|
signal?: AbortSignal;
|
|
60
61
|
filters?: string[];
|
|
61
|
-
}): Promise<
|
|
62
|
-
export declare function
|
|
63
|
-
|
|
62
|
+
}): Promise<QuantitativeStats>;
|
|
63
|
+
export declare function quantitativeStatsAutorun(self: {
|
|
64
|
+
featureDensityStatsReady: boolean;
|
|
64
65
|
regionTooLarge: boolean;
|
|
66
|
+
error: unknown;
|
|
65
67
|
setLoading: (aborter: AbortController) => void;
|
|
66
68
|
setError: (error: unknown) => void;
|
|
67
|
-
|
|
69
|
+
updateQuantitativeStats: (stats: QuantitativeStats, statsRegion: string) => void;
|
|
68
70
|
renderProps: () => Record<string, unknown>;
|
|
71
|
+
configuration: AnyConfigurationModel;
|
|
69
72
|
adapterConfig: AnyConfigurationModel;
|
|
70
73
|
autoscaleType: string;
|
|
71
74
|
setMessage: (str: string) => void;
|
package/esm/util.js
CHANGED
|
@@ -135,7 +135,7 @@ export function groupBy(array, predicate) {
|
|
|
135
135
|
}
|
|
136
136
|
return result;
|
|
137
137
|
}
|
|
138
|
-
export async function
|
|
138
|
+
export async function getQuantitativeStats(self, opts) {
|
|
139
139
|
const { rpcManager } = getSession(self);
|
|
140
140
|
const nd = getConf(self, 'numStdDev') || 3;
|
|
141
141
|
const { adapterConfig, autoscaleType } = self;
|
|
@@ -151,7 +151,7 @@ export async function getStats(self, opts) {
|
|
|
151
151
|
...opts,
|
|
152
152
|
};
|
|
153
153
|
if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
|
|
154
|
-
const results = (await rpcManager.call(sessionId, '
|
|
154
|
+
const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params));
|
|
155
155
|
const { scoreMin, scoreMean, scoreStdDev } = results;
|
|
156
156
|
// globalsd uses heuristic to avoid unnecessary scoreMin<0
|
|
157
157
|
// if the scoreMin is never less than 0
|
|
@@ -166,7 +166,7 @@ export async function getStats(self, opts) {
|
|
|
166
166
|
}
|
|
167
167
|
if (autoscaleType === 'local' || autoscaleType === 'localsd') {
|
|
168
168
|
const { dynamicBlocks, bpPerPx } = getContainingView(self);
|
|
169
|
-
const results = (await rpcManager.call(sessionId, '
|
|
169
|
+
const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionQuantitativeStats', {
|
|
170
170
|
...params,
|
|
171
171
|
regions: dynamicBlocks.contentBlocks.map(region => {
|
|
172
172
|
const { start, end } = region;
|
|
@@ -191,28 +191,29 @@ export async function getStats(self, opts) {
|
|
|
191
191
|
: results;
|
|
192
192
|
}
|
|
193
193
|
if (autoscaleType === 'zscale') {
|
|
194
|
-
return rpcManager.call(sessionId, '
|
|
194
|
+
return rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params);
|
|
195
195
|
}
|
|
196
196
|
throw new Error(`invalid autoscaleType '${autoscaleType}'`);
|
|
197
197
|
}
|
|
198
|
-
export function
|
|
198
|
+
export function quantitativeStatsAutorun(self) {
|
|
199
199
|
addDisposer(self, autorun(async () => {
|
|
200
200
|
try {
|
|
201
201
|
const aborter = new AbortController();
|
|
202
202
|
const view = getContainingView(self);
|
|
203
203
|
self.setLoading(aborter);
|
|
204
204
|
if (!view.initialized ||
|
|
205
|
-
!self.
|
|
206
|
-
self.regionTooLarge
|
|
205
|
+
!self.featureDensityStatsReady ||
|
|
206
|
+
self.regionTooLarge ||
|
|
207
|
+
self.error) {
|
|
207
208
|
return;
|
|
208
209
|
}
|
|
209
210
|
const statsRegion = JSON.stringify(view.dynamicBlocks);
|
|
210
|
-
const wiggleStats = await
|
|
211
|
+
const wiggleStats = await getQuantitativeStats(self, {
|
|
211
212
|
signal: aborter.signal,
|
|
212
213
|
...self.renderProps(),
|
|
213
214
|
});
|
|
214
215
|
if (isAlive(self)) {
|
|
215
|
-
self.
|
|
216
|
+
self.updateQuantitativeStats(wiggleStats, statsRegion);
|
|
216
217
|
}
|
|
217
218
|
}
|
|
218
219
|
catch (e) {
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,QAAQ,EAAE,aAAa,EAAE,MAAM,UAAU,CAAA;AAC/D,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EACL,gBAAgB,EAChB,UAAU,EACV,iBAAiB,GAClB,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAGtD,OAAO,EAAyB,OAAO,EAAE,MAAM,6BAA6B,CAAA;AAI5E,MAAM,CAAC,MAAM,sBAAsB,GAAG,CAAC,CAAA;AAgBvC;;;;;;;;;;GAUG;AACH,MAAM,UAAU,QAAQ,CAAC,EACvB,MAAM,GAAG,EAAE,EACX,KAAK,GAAG,EAAE,EACV,SAAS,EACT,UAAU,EACV,QAAQ,GACE;IACV,IAAI,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,MAAM,CAAA;IACzB,IAAI,GAAG,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS,EAAE;QAC1C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;KAClC;IACD,IAAI,SAAS,KAAK,QAAQ,EAAE;QAC1B,KAAK,GAAG,WAAW,EAAE,CAAA;KACtB;SAAM,IAAI,SAAS,KAAK,KAAK,EAAE;QAC9B,KAAK,GAAG,QAAQ,EAAE,CAAA;QAClB,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KACd;SAAM,IAAI,SAAS,KAAK,UAAU,EAAE;QACnC,KAAK,GAAG,aAAa,EAAE,CAAA;KACxB;SAAM;QACL,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;KACvC;IACD,KAAK,CAAC,MAAM,CAAC,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,UAAU,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IAC5E,KAAK,CAAC,IAAI,EAAE,CAAA;IAEZ,MAAM,CAAC,QAAQ,EAAE,QAAQ,CAAC,GAAG,KAAK,CAAA;IAClC,IAAI,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;QACpD,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;KACjC;IACD,KAAK,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;IACvD,OAAO,KAAK,CAAA;AACd,CAAC;AACD;;;;GAIG;AACH,MAAM,UAAU,SAAS,CAAC,SAAiB,CAAC,oBAAoB;IAC9D,eAAe;IACf,4BAA4B;IAC5B,kCAAkC;IAClC,MAAM;IACN,4BAA4B;IAC5B,eAAe;IACf,MAAM;IACN,wBAAwB;IACxB,IAAI;IACJ,iCAAiC;IACjC,gCAAgC;IAChC,IAAI;IACJ,IAAI,SAAS,KAAK,KAAK,EAAE;QACvB,OAAO,CAAC,CAAA;KACT;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,aAAa,CAAC,EAC5B,SAAS,EACT,MAAM,EACN,MAAM,GAKP;IACC,MAAM,CAAC,QAAQ,EAAE,QAAQ,CAAC,GAAG,MAAM,CAAA;IACnC,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,MAAM,CAAA;IAEvB,IAAI,SAAS,KAAK,QAAQ,EAAE;QAC1B,IAAI,GAAG,GAAG,CAAC,EAAE;YACX,GAAG,GAAG,CAAC,CAAA;SACR;QACD,IAAI,GAAG,GAAG,CAAC,EAAE;YACX,GAAG,GAAG,CAAC,CAAA;SACR;KACF;IACD,IAAI,SAAS,KAAK,KAAK,EAAE;QACvB,mDAAmD;QACnD,qEAAqE;QACrE,0DAA0D;QAC1D,uDAAuD;QACvD,IAAI,GAAG,KAAK,CAAC,IAAI,GAAG,GAAG,CAAC,EAAE;YACxB,GAAG,GAAG,CAAC,CAAA;SACR;KACF;IACD,IAAI,GAAG,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS,EAAE;QAC1C,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAA;KAC7D;IACD,IAAI,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,MAAM,CAAC,SAAS,EAAE;QAC3D,GAAG,GAAG,QAAQ,CAAA;KACf;IACD,IAAI,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,MAAM,CAAC,SAAS,EAAE;QAC3D,GAAG,GAAG,QAAQ,CAAA;KACf;IACD,MAAM,YAAY,GAAG,CAAC,IAAY,EAAE,EAAE;QACpC,IAAI,IAAI,KAAK,QAAQ,EAAE;YACrB,OAAO,WAAW,EAAE,CAAA;SACrB;QACD,IAAI,IAAI,KAAK,KAAK,EAAE;YAClB,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;YACxB,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACb,OAAO,KAAK,CAAA;SACb;QACD,IAAI,IAAI,KAAK,UAAU,EAAE;YACvB,OAAO,aAAa,EAAE,CAAA;SACvB;QACD,MAAM,IAAI,KAAK,CAAC,uBAAuB,IAAI,EAAE,CAAC,CAAA;IAChD,CAAC,CAAA;IACD,MAAM,KAAK,GAAG,YAAY,CAAC,SAAS,CAAC,CAAA;IAErC,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IACxB,KAAK,CAAC,IAAI,EAAE,CAAA;IACZ,OAAO,KAAK,CAAC,MAAM,EAAsB,CAAA;AAC3C,CAAC;AAED,MAAM,UAAU,OAAO,CAAI,KAAU,EAAE,SAA2B;;IAChE,MAAM,MAAM,GAAG,EAA4B,CAAA;IAC3C,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE;QACzB,MAAM,KAAK,GAAG,CAAC,MAAM,MAAC,SAAS,CAAC,KAAK,CAAC,MAAvB,MAAM,OAAuB,EAAE,EAAC,CAAA;QAC/C,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;KAClB;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,QAAQ,EAAE,aAAa,EAAE,MAAM,UAAU,CAAA;AAC/D,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EACL,gBAAgB,EAChB,UAAU,EACV,iBAAiB,GAClB,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAGtD,OAAO,EAAyB,OAAO,EAAE,MAAM,6BAA6B,CAAA;AAI5E,MAAM,CAAC,MAAM,sBAAsB,GAAG,CAAC,CAAA;AAgBvC;;;;;;;;;;GAUG;AACH,MAAM,UAAU,QAAQ,CAAC,EACvB,MAAM,GAAG,EAAE,EACX,KAAK,GAAG,EAAE,EACV,SAAS,EACT,UAAU,EACV,QAAQ,GACE;IACV,IAAI,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,MAAM,CAAA;IACzB,IAAI,GAAG,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS,EAAE;QAC1C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;KAClC;IACD,IAAI,SAAS,KAAK,QAAQ,EAAE;QAC1B,KAAK,GAAG,WAAW,EAAE,CAAA;KACtB;SAAM,IAAI,SAAS,KAAK,KAAK,EAAE;QAC9B,KAAK,GAAG,QAAQ,EAAE,CAAA;QAClB,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;KACd;SAAM,IAAI,SAAS,KAAK,UAAU,EAAE;QACnC,KAAK,GAAG,aAAa,EAAE,CAAA;KACxB;SAAM;QACL,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;KACvC;IACD,KAAK,CAAC,MAAM,CAAC,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,UAAU,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IAC5E,KAAK,CAAC,IAAI,EAAE,CAAA;IAEZ,MAAM,CAAC,QAAQ,EAAE,QAAQ,CAAC,GAAG,KAAK,CAAA;IAClC,IAAI,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,SAAS,EAAE;QACpD,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;KACjC;IACD,KAAK,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;IACvD,OAAO,KAAK,CAAA;AACd,CAAC;AACD;;;;GAIG;AACH,MAAM,UAAU,SAAS,CAAC,SAAiB,CAAC,oBAAoB;IAC9D,eAAe;IACf,4BAA4B;IAC5B,kCAAkC;IAClC,MAAM;IACN,4BAA4B;IAC5B,eAAe;IACf,MAAM;IACN,wBAAwB;IACxB,IAAI;IACJ,iCAAiC;IACjC,gCAAgC;IAChC,IAAI;IACJ,IAAI,SAAS,KAAK,KAAK,EAAE;QACvB,OAAO,CAAC,CAAA;KACT;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,aAAa,CAAC,EAC5B,SAAS,EACT,MAAM,EACN,MAAM,GAKP;IACC,MAAM,CAAC,QAAQ,EAAE,QAAQ,CAAC,GAAG,MAAM,CAAA;IACnC,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,MAAM,CAAA;IAEvB,IAAI,SAAS,KAAK,QAAQ,EAAE;QAC1B,IAAI,GAAG,GAAG,CAAC,EAAE;YACX,GAAG,GAAG,CAAC,CAAA;SACR;QACD,IAAI,GAAG,GAAG,CAAC,EAAE;YACX,GAAG,GAAG,CAAC,CAAA;SACR;KACF;IACD,IAAI,SAAS,KAAK,KAAK,EAAE;QACvB,mDAAmD;QACnD,qEAAqE;QACrE,0DAA0D;QAC1D,uDAAuD;QACvD,IAAI,GAAG,KAAK,CAAC,IAAI,GAAG,GAAG,CAAC,EAAE;YACxB,GAAG,GAAG,CAAC,CAAA;SACR;KACF;IACD,IAAI,GAAG,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS,EAAE;QAC1C,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAA;KAC7D;IACD,IAAI,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,MAAM,CAAC,SAAS,EAAE;QAC3D,GAAG,GAAG,QAAQ,CAAA;KACf;IACD,IAAI,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,MAAM,CAAC,SAAS,EAAE;QAC3D,GAAG,GAAG,QAAQ,CAAA;KACf;IACD,MAAM,YAAY,GAAG,CAAC,IAAY,EAAE,EAAE;QACpC,IAAI,IAAI,KAAK,QAAQ,EAAE;YACrB,OAAO,WAAW,EAAE,CAAA;SACrB;QACD,IAAI,IAAI,KAAK,KAAK,EAAE;YAClB,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;YACxB,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACb,OAAO,KAAK,CAAA;SACb;QACD,IAAI,IAAI,KAAK,UAAU,EAAE;YACvB,OAAO,aAAa,EAAE,CAAA;SACvB;QACD,MAAM,IAAI,KAAK,CAAC,uBAAuB,IAAI,EAAE,CAAC,CAAA;IAChD,CAAC,CAAA;IACD,MAAM,KAAK,GAAG,YAAY,CAAC,SAAS,CAAC,CAAA;IAErC,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IACxB,KAAK,CAAC,IAAI,EAAE,CAAA;IACZ,OAAO,KAAK,CAAC,MAAM,EAAsB,CAAA;AAC3C,CAAC;AAED,MAAM,UAAU,OAAO,CAAI,KAAU,EAAE,SAA2B;;IAChE,MAAM,MAAM,GAAG,EAA4B,CAAA;IAC3C,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE;QACzB,MAAM,KAAK,GAAG,CAAC,MAAM,MAAC,SAAS,CAAC,KAAK,CAAC,MAAvB,MAAM,OAAuB,EAAE,EAAC,CAAA;QAC/C,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;KAClB;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,IAKC,EACD,IAIC;IAED,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,EAAE,WAAW,CAAC,IAAI,CAAC,CAAA;IAC1C,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC7C,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,MAAM,GAAG;QACb,SAAS;QACT,aAAa;QACb,cAAc,EAAE,CAAC,OAAe,EAAE,EAAE;YAClC,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE;gBACjB,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAA;aACzB;QACH,CAAC;QACD,GAAG,IAAI;KACR,CAAA;IAED,IAAI,aAAa,KAAK,QAAQ,IAAI,aAAa,KAAK,UAAU,EAAE;QAC9D,MAAM,OAAO,GAAsB,CAAC,MAAM,UAAU,CAAC,IAAI,CACvD,SAAS,EACT,kCAAkC,EAClC,MAAM,CACP,CAAsB,CAAA;QACvB,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;QACpD,0DAA0D;QAC1D,uCAAuC;QACvC,iDAAiD;QACjD,OAAO,aAAa,KAAK,UAAU;YACjC,CAAC,CAAC;gBACE,GAAG,OAAO;gBACV,QAAQ,EAAE,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,GAAG,EAAE,GAAG,WAAW;gBAC1D,QAAQ,EAAE,SAAS,GAAG,EAAE,GAAG,WAAW;aACvC;YACH,CAAC,CAAC,OAAO,CAAA;KACZ;IACD,IAAI,aAAa,KAAK,OAAO,IAAI,aAAa,KAAK,SAAS,EAAE;QAC5D,MAAM,EAAE,aAAa,EAAE,OAAO,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;QACjE,MAAM,OAAO,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CACpC,SAAS,EACT,uCAAuC,EACvC;YACE,GAAG,MAAM;YACT,OAAO,EAAE,aAAa,CAAC,aAAa,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBAChD,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;gBAC7B,OAAO;oBACL,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC;oBACrC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC;oBACxB,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;iBACpB,CAAA;YACH,CAAC,CAAC;YACF,OAAO;SACR,CACF,CAAsB,CAAA;QACvB,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;QAEpD,gEAAgE;QAChE,iEAAiE;QACjE,gBAAgB;QAChB,OAAO,aAAa,KAAK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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-wiggle",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.5.0",
|
|
4
4
|
"description": "JBrowse 2 wiggle adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -55,7 +55,7 @@
|
|
|
55
55
|
"@jbrowse/plugin-data-management": "^2.0.0",
|
|
56
56
|
"@jbrowse/plugin-linear-genome-view": "^2.0.0",
|
|
57
57
|
"@mui/material": "^5.0.0",
|
|
58
|
-
"@mui/x-data-grid": "^
|
|
58
|
+
"@mui/x-data-grid": "^6.0.1",
|
|
59
59
|
"mobx": "^6.0.0",
|
|
60
60
|
"mobx-react": "^7.0.0",
|
|
61
61
|
"mobx-state-tree": "^5.0.0",
|
|
@@ -69,5 +69,5 @@
|
|
|
69
69
|
"distModule": "esm/index.js",
|
|
70
70
|
"srcModule": "src/index.ts",
|
|
71
71
|
"module": "esm/index.js",
|
|
72
|
-
"gitHead": "
|
|
72
|
+
"gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
|
|
73
73
|
}
|
|
@@ -36,7 +36,7 @@ describe('adapter can fetch features from volvox.bw', () => {
|
|
|
36
36
|
})
|
|
37
37
|
it('get region stats', async () => {
|
|
38
38
|
expect(
|
|
39
|
-
await adapter.
|
|
39
|
+
await adapter.getRegionQuantitativeStats({
|
|
40
40
|
refName: 'ctgA',
|
|
41
41
|
start: 10000,
|
|
42
42
|
end: 40000,
|
|
@@ -47,14 +47,19 @@ describe('adapter can fetch features from volvox.bw', () => {
|
|
|
47
47
|
|
|
48
48
|
it('get local stats', async () => {
|
|
49
49
|
expect(
|
|
50
|
-
await adapter.
|
|
50
|
+
await adapter.getMultiRegionQuantitativeStats([
|
|
51
51
|
{
|
|
52
52
|
refName: 'ctgA',
|
|
53
53
|
start: 10000,
|
|
54
54
|
end: 39999,
|
|
55
55
|
assemblyName: 'volvox',
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},
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{
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{
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refName: 'ctgB',
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start: 0,
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end: 99,
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assemblyName: 'volvox',
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},
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]),
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).toMatchSnapshot()
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})
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@@ -7,7 +7,10 @@ import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
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7
7
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import { openLocation } from '@jbrowse/core/util/io'
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8
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import { updateStatus, Feature } from '@jbrowse/core/util'
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import { ObservableCreate } from '@jbrowse/core/util/rxjs'
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-
import {
|
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+
import {
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+
rectifyStats,
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UnrectifiedQuantitativeStats,
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+
} from '@jbrowse/core/util/stats'
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14
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12
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interface WiggleOptions extends BaseOptions {
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resolution?: number
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@@ -61,7 +64,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
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public async getGlobalStats(opts?: BaseOptions) {
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const { header } = await this.setup(opts)
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-
return rectifyStats(header.totalSummary as
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+
return rectifyStats(header.totalSummary as UnrectifiedQuantitativeStats)
|
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}
|
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66
69
|
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public getFeatures(region: Region, opts: WiggleOptions = {}) {
|
|
@@ -103,7 +106,7 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
|
|
|
103
106
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}
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105
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// always render bigwig instead of calculating a feature density for it
|
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-
async
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|
+
async getMultiRegionFeatureDensityStats(_regions: Region[]) {
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110
|
return { featureDensity: 0 }
|
|
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111
|
}
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112
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@@ -17,15 +17,14 @@ import {
|
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17
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LinearGenomeViewModel,
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18
18
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} from '@jbrowse/plugin-linear-genome-view'
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import { when } from 'mobx'
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-
import {
|
|
20
|
+
import { types, Instance } from 'mobx-state-tree'
|
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21
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import PluginManager from '@jbrowse/core/PluginManager'
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|
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23
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import { axisPropsFromTickScale } from 'react-d3-axis-mod'
|
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import {
|
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25
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getNiceDomain,
|
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26
26
|
getScale,
|
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27
|
-
|
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28
|
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statsAutorun,
|
|
27
|
+
quantitativeStatsAutorun,
|
|
29
28
|
YSCALEBAR_LABEL_OFFSET,
|
|
30
29
|
} from '../../util'
|
|
31
30
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|
@@ -134,7 +133,7 @@ function stateModelFactory(
|
|
|
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/**
|
|
135
134
|
* #action
|
|
136
135
|
*/
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|
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|
-
|
|
136
|
+
updateQuantitativeStats(stats: { scoreMin: number; scoreMax: number }) {
|
|
138
137
|
const { scoreMin, scoreMax } = stats
|
|
139
138
|
const EPSILON = 0.000001
|
|
140
139
|
if (!self.stats) {
|
|
@@ -343,9 +342,6 @@ function stateModelFactory(
|
|
|
343
342
|
* #getter
|
|
344
343
|
*/
|
|
345
344
|
get rendererConfig() {
|
|
346
|
-
const configBlob =
|
|
347
|
-
getConf(self, ['renderers', self.rendererTypeName]) || {}
|
|
348
|
-
|
|
349
345
|
const {
|
|
350
346
|
color,
|
|
351
347
|
displayCrossHatches,
|
|
@@ -355,8 +351,9 @@ function stateModelFactory(
|
|
|
355
351
|
posColor,
|
|
356
352
|
summaryScoreMode,
|
|
357
353
|
scaleType,
|
|
354
|
+
rendererTypeName,
|
|
358
355
|
} = self
|
|
359
|
-
|
|
356
|
+
const configBlob = getConf(self, ['renderers', rendererTypeName]) || {}
|
|
360
357
|
return self.rendererType.configSchema.create(
|
|
361
358
|
{
|
|
362
359
|
...configBlob,
|
|
@@ -382,15 +379,13 @@ function stateModelFactory(
|
|
|
382
379
|
* #getter
|
|
383
380
|
*/
|
|
384
381
|
get filled() {
|
|
385
|
-
|
|
386
|
-
return fill ?? readConfObject(conf, 'filled')
|
|
382
|
+
return readConfObject(self.rendererConfig, 'filled')
|
|
387
383
|
},
|
|
388
384
|
/**
|
|
389
385
|
* #getter
|
|
390
386
|
*/
|
|
391
387
|
get summaryScoreModeSetting() {
|
|
392
|
-
|
|
393
|
-
return summaryScoreMode ?? readConfObject(conf, 'summaryScoreMode')
|
|
388
|
+
return readConfObject(self.rendererConfig, 'summaryScoreMode')
|
|
394
389
|
},
|
|
395
390
|
/**
|
|
396
391
|
* #getter
|
|
@@ -460,8 +455,7 @@ function stateModelFactory(
|
|
|
460
455
|
* #getter
|
|
461
456
|
*/
|
|
462
457
|
get displayCrossHatchesSetting() {
|
|
463
|
-
|
|
464
|
-
return hatches ?? readConfObject(conf, 'displayCrossHatches')
|
|
458
|
+
return readConfObject(self.rendererConfig, 'displayCrossHatches')
|
|
465
459
|
},
|
|
466
460
|
}
|
|
467
461
|
})
|
|
@@ -682,23 +676,11 @@ function stateModelFactory(
|
|
|
682
676
|
*/
|
|
683
677
|
async reload() {
|
|
684
678
|
self.setError()
|
|
685
|
-
|
|
686
|
-
self.setLoading(aborter)
|
|
687
|
-
try {
|
|
688
|
-
const stats = await getStats(self, {
|
|
689
|
-
signal: aborter.signal,
|
|
690
|
-
...self.renderProps(),
|
|
691
|
-
})
|
|
692
|
-
if (isAlive(self)) {
|
|
693
|
-
self.updateStats(stats)
|
|
694
|
-
superReload()
|
|
695
|
-
}
|
|
696
|
-
} catch (e) {
|
|
697
|
-
self.setError(e)
|
|
698
|
-
}
|
|
679
|
+
superReload()
|
|
699
680
|
},
|
|
681
|
+
|
|
700
682
|
afterAttach() {
|
|
701
|
-
|
|
683
|
+
quantitativeStatsAutorun(self)
|
|
702
684
|
},
|
|
703
685
|
/**
|
|
704
686
|
* #action
|