@jbrowse/plugin-wiggle 2.4.1 → 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 +93 -58
- 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 +62 -23
- 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 +156 -47
- 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 +93 -58
- 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 +62 -23
- 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 +156 -47
- 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
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@@ -15,9 +15,9 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
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}>;
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getRefNames(opts?: BaseOptions): Promise<string[]>;
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refIdToName(refId: number): Promise<any>;
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getGlobalStats(opts?: BaseOptions): Promise<import("@jbrowse/core/util/stats").
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getGlobalStats(opts?: BaseOptions): Promise<import("@jbrowse/core/util/stats").QuantitativeStats>;
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getFeatures(region: Region, opts?: WiggleOptions): import("rxjs").Observable<Feature>;
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getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
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featureDensity: number;
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}>;
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freeResources(): void;
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@@ -69,15 +69,15 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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}, signal);
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}
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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) {
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return { featureDensity: 0 };
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}
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freeResources() { }
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}
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exports.default = BigWigAdapter;
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BigWigAdapter.capabilities = [
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'hasResolution',
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'hasLocalStats',
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'hasGlobalStats',
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];
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exports.default = BigWigAdapter;
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//# sourceMappingURL=BigWigAdapter.js.map
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@@ -1 +1 @@
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-
{"version":3,"file":"BigWigAdapter.js","sourceRoot":"","sources":["../../src/BigWigAdapter/BigWigAdapter.ts"],"names":[],"mappings":";;AAAA,mCAAkC;AAClC,yEAGgD;AAEhD,8CAAoD;AACpD,6CAA0D;AAC1D,kDAA0D;AAC1D,
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{"version":3,"file":"BigWigAdapter.js","sourceRoot":"","sources":["../../src/BigWigAdapter/BigWigAdapter.ts"],"names":[],"mappings":";;AAAA,mCAAkC;AAClC,yEAGgD;AAEhD,8CAAoD;AACpD,6CAA0D;AAC1D,kDAA0D;AAC1D,oDAGiC;AAMjC,MAAqB,aAAc,SAAQ,oCAAsB;IAUvD,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,MAAM,GAAG,IAAI,YAAM,CAAC;YACxB,UAAU,EAAE,IAAA,iBAAY,EACtB,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,EAC9B,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;QACF,MAAM,MAAM,GAAG,MAAM,IAAA,mBAAY,EAC/B,2BAA2B,EAC3B,cAAc,EACd,GAAG,EAAE,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,CAC7B,CAAA;QACD,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,CAAA;IAC3B,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,KAAa;;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAA,MAAM,CAAC,YAAY,CAAC,KAAK,CAAC,0CAAE,IAAI,CAAA;IACzC,CAAC;IAEM,KAAK,CAAC,cAAc,CAAC,IAAkB;QAC5C,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,OAAO,IAAA,oBAAY,EAAC,MAAM,CAAC,YAA4C,CAAC,CAAA;IAC1E,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAsB,EAAE;QACzD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,MAAM,EACJ,OAAO,GAAG,CAAC,EACX,MAAM,EACN,UAAU,GAAG,CAAC,EACd,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,GAC1B,GAAG,IAAI,CAAA;QACR,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,cAAc,CAAC,yBAAyB,CAAC,CAAA;YACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;YACrC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACzC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBAC1D,GAAG,IAAI;gBACP,YAAY,EAAE,OAAO,GAAG,UAAU;aACnC,CAAC,CAAA;YAEF,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;gBACxB,IAAI,MAAM,EAAE;oBACV,mBAAmB;oBACnB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;iBACrB;gBACD,MAAM,QAAQ,GAAG,GAAG,MAAM,IAAI,MAAM,CAAC,OAAO,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;gBACxE,mBAAmB;gBACnB,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;gBACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;gBACxB,QAAQ,CAAC,IAAI,CAAC;oBACZ,mBAAmB;oBACnB,GAAG,EAAE,CAAC,GAAW,EAAE,EAAE,CAAE,IAAgC,CAAC,GAAG,CAAC;oBAC5D,EAAE,EAAE,GAAG,EAAE,CAAC,QAAQ;oBAClB,mBAAmB;oBACnB,MAAM,EAAE,GAAG,EAAE,CAAC,IAAI;iBACnB,CAAC,CAAA;aACH;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAED,uEAAuE;IACvE,KAAK,CAAC,iCAAiC,CAAC,QAAkB;QACxD,OAAO,EAAE,cAAc,EAAE,CAAC,EAAE,CAAA;IAC9B,CAAC;IAEM,aAAa,KAAU,CAAC;;AA1FjB,0BAAY,GAAG;IAC3B,eAAe;IACf,eAAe;IACf,gBAAgB;CACjB,CAAA;kBARkB,aAAa"}
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declare const BigWigAdapter: import("@jbrowse/core/configuration").
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declare const BigWigAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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/**
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* #slot
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*/
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bigWigLocation: {
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type: string;
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defaultValue: {
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uri: string;
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};
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};
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/**
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* #slot
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*/
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source: {
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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export default BigWigAdapter;
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declare const configSchema: import("@jbrowse/core/configuration").
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declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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color: {
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posColor: {
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
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declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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export default configSchema;
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import PluginManager from '@jbrowse/core/PluginManager';
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export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").
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export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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DensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
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XYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
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LinePlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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height: {
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
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@@ -19,9 +19,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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refName: import("mobx-state-tree").ISimpleType<string>;
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start: import("mobx-state-tree").ISimpleType<number>;
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end: import("mobx-state-tree").ISimpleType<number>;
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reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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* #property
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reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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assemblyName: import("mobx-state-tree").ISimpleType<string>;
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}, {
|
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@@ -41,15 +39,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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message: string | undefined;
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maxHeightReached: boolean;
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ReactComponent: ({ model, }: {
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model: any;
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model: any;
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}) => any;
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renderProps: any;
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} & {
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doReload(): void;
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doReload(): void;
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afterAttach(): void;
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setStatus(message: string): void;
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setLoading(abortController: AbortController): void;
|
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@@ -59,14 +53,41 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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features: Map<string, Feature>;
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layout: any;
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maxHeightReached: boolean;
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renderProps: any;
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renderProps: any; /**
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*/
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} | undefined): void;
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setError(error: unknown): void;
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reload(): void;
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beforeDestroy(): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
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*/
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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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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">>;
|
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} & {
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/**
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@@ -75,7 +96,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
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/**
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configuration:
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configuration: AnyConfigurationSchemaType;
|
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|
/**
|
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*/
|
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@@ -161,13 +182,15 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
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rpcDriverName: string | undefined;
|
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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rendererTypeName: string;
|
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error: unknown;
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error: unknown; /**
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|
|
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|
+
*/
|
|
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
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type: import("mobx-state-tree").ISimpleType<string>;
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type: import("mobx-state-tree").ISimpleType<string>;
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|
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
|
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|
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|
|
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|
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
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|
}, {
|
|
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rendererTypeName: string;
|
|
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|
error: unknown;
|
|
@@ -192,9 +215,12 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
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scrollTop: number;
|
|
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216
|
message: string;
|
|
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217
|
featureIdUnderMouse: string | undefined;
|
|
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|
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|
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|
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|
|
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+
*/
|
|
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|
contextMenuFeature: Feature | undefined;
|
|
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|
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|
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|
|
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|
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featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
|
|
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|
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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";
|
|
@@ -203,67 +229,54 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
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229
|
readonly renderDelay: number;
|
|
204
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|
readonly TooltipComponent: React.FC<any>;
|
|
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|
readonly selectedFeatureId: string | undefined;
|
|
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|
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readonly DisplayMessageComponent: React.FC<any> | undefined;
|
|
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|
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* #action
|
|
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|
-
*/
|
|
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|
+
readonly DisplayMessageComponent: React.FC<any> | undefined;
|
|
209
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|
} & {
|
|
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|
-
readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
|
|
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|
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* #action
|
|
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|
-
*/
|
|
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|
+
readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
|
|
213
235
|
readonly featureUnderMouse: Feature | undefined;
|
|
214
|
-
getFeatureOverlapping(blockKey: string, x: number, y: number):
|
|
215
|
-
* #action
|
|
216
|
-
*/
|
|
236
|
+
getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
|
|
217
237
|
getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
|
|
218
238
|
searchFeatureByID(id: string): [number, number, number, number] | undefined;
|
|
219
239
|
readonly currentBytesRequested: number;
|
|
220
240
|
readonly currentFeatureScreenDensity: number;
|
|
221
241
|
readonly maxFeatureScreenDensity: any;
|
|
222
|
-
/**
|
|
242
|
+
readonly featureDensityStatsReady: boolean; /**
|
|
223
243
|
* #getter
|
|
224
244
|
*/
|
|
225
|
-
readonly estimatedStatsReady: boolean;
|
|
226
245
|
readonly maxAllowableBytes: number;
|
|
227
246
|
} & {
|
|
228
247
|
setMessage(message: string): void;
|
|
248
|
+
} & {
|
|
229
249
|
afterAttach(): void;
|
|
230
|
-
|
|
231
|
-
|
|
232
|
-
|
|
233
|
-
|
|
234
|
-
}): Promise<{}>;
|
|
235
|
-
setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
|
|
236
|
-
setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
|
|
237
|
-
clearRegionStats(): void;
|
|
250
|
+
getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
|
|
251
|
+
setFeatureDensityStatsP(arg: any): void;
|
|
252
|
+
setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
|
|
253
|
+
clearFeatureDensityStats(): void;
|
|
238
254
|
setHeight(displayHeight: number): number;
|
|
239
255
|
resizeHeight(distance: number): number;
|
|
240
256
|
setScrollTop(scrollTop: number): void;
|
|
241
|
-
|
|
257
|
+
setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
|
|
242
258
|
addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
|
|
243
259
|
setCurrBpPerPx(n: number): void;
|
|
244
260
|
deleteBlock(key: string): void;
|
|
245
261
|
selectFeature(feature: Feature): void;
|
|
246
262
|
clearFeatureSelection(): void;
|
|
247
|
-
setFeatureIdUnderMouse(feature
|
|
263
|
+
setFeatureIdUnderMouse(feature?: string | undefined): void;
|
|
248
264
|
reload(): void;
|
|
249
265
|
setContextMenuFeature(feature?: Feature | undefined): void;
|
|
250
266
|
} & {
|
|
251
267
|
readonly regionTooLarge: boolean;
|
|
252
268
|
readonly regionTooLargeReason: string;
|
|
253
269
|
} & {
|
|
254
|
-
reload(): Promise<void>;
|
|
270
|
+
reload(): Promise<void>; /**
|
|
271
|
+
* #method
|
|
272
|
+
*/
|
|
273
|
+
} & {
|
|
255
274
|
afterAttach(): void;
|
|
256
275
|
} & {
|
|
257
276
|
regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
|
|
258
277
|
regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
|
|
259
278
|
trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
260
|
-
contextMenuItems():
|
|
261
|
-
label: string;
|
|
262
|
-
icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
|
|
263
|
-
muiName: string;
|
|
264
|
-
};
|
|
265
|
-
onClick: () => void;
|
|
266
|
-
}[];
|
|
279
|
+
contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
267
280
|
renderProps(): any;
|
|
268
281
|
} & {
|
|
269
282
|
renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
|
|
@@ -281,7 +294,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
281
294
|
/**
|
|
282
295
|
* #action
|
|
283
296
|
*/
|
|
284
|
-
|
|
297
|
+
updateQuantitativeStats(stats: {
|
|
285
298
|
scoreMin: number;
|
|
286
299
|
scoreMax: number;
|
|
287
300
|
}): void;
|
|
@@ -518,9 +531,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
518
531
|
refName: import("mobx-state-tree").ISimpleType<string>;
|
|
519
532
|
start: import("mobx-state-tree").ISimpleType<number>;
|
|
520
533
|
end: import("mobx-state-tree").ISimpleType<number>;
|
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521
|
-
reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
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522
|
-
* #property
|
|
523
|
-
*/
|
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534
|
+
reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
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524
535
|
} & {
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525
536
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assemblyName: import("mobx-state-tree").ISimpleType<string>;
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526
537
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}, {
|
|
@@ -540,15 +551,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
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540
551
|
message: string | undefined;
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541
552
|
maxHeightReached: boolean;
|
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542
553
|
ReactComponent: ({ model, }: {
|
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543
|
-
model: any;
|
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544
|
-
* #property
|
|
545
|
-
*/
|
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554
|
+
model: any;
|
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546
555
|
}) => any;
|
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547
556
|
renderProps: any;
|
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548
557
|
} & {
|
|
549
|
-
doReload(): void;
|
|
550
|
-
* #property
|
|
551
|
-
*/
|
|
558
|
+
doReload(): void;
|
|
552
559
|
afterAttach(): void;
|
|
553
560
|
setStatus(message: string): void;
|
|
554
561
|
setLoading(abortController: AbortController): void;
|
|
@@ -558,17 +565,45 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
558
565
|
features: Map<string, Feature>;
|
|
559
566
|
layout: any;
|
|
560
567
|
maxHeightReached: boolean;
|
|
561
|
-
renderProps: any;
|
|
568
|
+
renderProps: any; /**
|
|
569
|
+
* #action
|
|
570
|
+
*/
|
|
562
571
|
} | undefined): void;
|
|
563
572
|
setError(error: unknown): void;
|
|
564
573
|
reload(): void;
|
|
565
574
|
beforeDestroy(): void;
|
|
566
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
575
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
|
|
576
|
+
* #property
|
|
577
|
+
*/
|
|
567
578
|
userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
568
579
|
userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
580
|
+
configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
581
|
+
maxFeatureScreenDensity: {
|
|
582
|
+
type: string;
|
|
583
|
+
description: string;
|
|
584
|
+
defaultValue: number;
|
|
585
|
+
};
|
|
586
|
+
fetchSizeLimit: {
|
|
587
|
+
type: string;
|
|
588
|
+
defaultValue: number;
|
|
589
|
+
description: string;
|
|
590
|
+
};
|
|
591
|
+
height: {
|
|
592
|
+
type: string;
|
|
593
|
+
defaultValue: number;
|
|
594
|
+
description: string;
|
|
595
|
+
};
|
|
596
|
+
mouseover: {
|
|
597
|
+
type: string;
|
|
598
|
+
description: string;
|
|
599
|
+
defaultValue: string;
|
|
600
|
+
contextVariable: string[];
|
|
601
|
+
};
|
|
602
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
|
|
569
603
|
}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
|
|
570
604
|
type: string;
|
|
571
605
|
id: string;
|
|
606
|
+
configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
|
|
572
607
|
rpcDriverName: string | undefined;
|
|
573
608
|
heightPreConfig: number | undefined;
|
|
574
609
|
userBpPerPxLimit: number | undefined;
|
|
@@ -124,7 +124,7 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
124
124
|
/**
|
|
125
125
|
* #action
|
|
126
126
|
*/
|
|
127
|
-
|
|
127
|
+
updateQuantitativeStats(stats) {
|
|
128
128
|
const { scoreMin, scoreMax } = stats;
|
|
129
129
|
const EPSILON = 0.000001;
|
|
130
130
|
if (!self.stats) {
|
|
@@ -316,8 +316,8 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
316
316
|
* #getter
|
|
317
317
|
*/
|
|
318
318
|
get rendererConfig() {
|
|
319
|
-
const
|
|
320
|
-
const
|
|
319
|
+
const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, rendererTypeName, } = self;
|
|
320
|
+
const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
|
|
321
321
|
return self.rendererType.configSchema.create({
|
|
322
322
|
...configBlob,
|
|
323
323
|
...(scaleType ? { scaleType } : {}),
|
|
@@ -340,15 +340,13 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
340
340
|
* #getter
|
|
341
341
|
*/
|
|
342
342
|
get filled() {
|
|
343
|
-
|
|
344
|
-
return fill !== null && fill !== void 0 ? fill : (0, configuration_1.readConfObject)(conf, 'filled');
|
|
343
|
+
return (0, configuration_1.readConfObject)(self.rendererConfig, 'filled');
|
|
345
344
|
},
|
|
346
345
|
/**
|
|
347
346
|
* #getter
|
|
348
347
|
*/
|
|
349
348
|
get summaryScoreModeSetting() {
|
|
350
|
-
|
|
351
|
-
return summaryScoreMode !== null && summaryScoreMode !== void 0 ? summaryScoreMode : (0, configuration_1.readConfObject)(conf, 'summaryScoreMode');
|
|
349
|
+
return (0, configuration_1.readConfObject)(self.rendererConfig, 'summaryScoreMode');
|
|
352
350
|
},
|
|
353
351
|
/**
|
|
354
352
|
* #getter
|
|
@@ -409,8 +407,7 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
409
407
|
* #getter
|
|
410
408
|
*/
|
|
411
409
|
get displayCrossHatchesSetting() {
|
|
412
|
-
|
|
413
|
-
return hatches !== null && hatches !== void 0 ? hatches : (0, configuration_1.readConfObject)(conf, 'displayCrossHatches');
|
|
410
|
+
return (0, configuration_1.readConfObject)(self.rendererConfig, 'displayCrossHatches');
|
|
414
411
|
},
|
|
415
412
|
};
|
|
416
413
|
})
|
|
@@ -621,24 +618,10 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
621
618
|
*/
|
|
622
619
|
async reload() {
|
|
623
620
|
self.setError();
|
|
624
|
-
|
|
625
|
-
self.setLoading(aborter);
|
|
626
|
-
try {
|
|
627
|
-
const stats = await (0, util_2.getStats)(self, {
|
|
628
|
-
signal: aborter.signal,
|
|
629
|
-
...self.renderProps(),
|
|
630
|
-
});
|
|
631
|
-
if ((0, mobx_state_tree_1.isAlive)(self)) {
|
|
632
|
-
self.updateStats(stats);
|
|
633
|
-
superReload();
|
|
634
|
-
}
|
|
635
|
-
}
|
|
636
|
-
catch (e) {
|
|
637
|
-
self.setError(e);
|
|
638
|
-
}
|
|
621
|
+
superReload();
|
|
639
622
|
},
|
|
640
623
|
afterAttach() {
|
|
641
|
-
(0, util_2.
|
|
624
|
+
(0, util_2.quantitativeStatsAutorun)(self);
|
|
642
625
|
},
|
|
643
626
|
/**
|
|
644
627
|
* #action
|