npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.4.2 → 2.5.0 - Mend

@jbrowse/plugin-linear-genome-view 2.4.2 → 2.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (180) hide show

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts CHANGED Viewed

@@ -2,7 +2,7 @@ import React from 'react';
 import { ThemeOptions } from '@mui/material';
 import { MenuItem } from '@jbrowse/core/ui';
 import { Feature } from '@jbrowse/core/util';
-import { Stats } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { BaseBlock } from '@jbrowse/core/util/blockTypes';
 import { Region } from '@jbrowse/core/util/types';
 import CompositeMap from '@jbrowse/core/util/compositeMap';
@@ -67,7 +67,9 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
             features: Map<string, Feature>;
-            layout: any;
+            layout: any; /**
+             * #getter
+             */
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
@@ -83,6 +85,32 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
      * #property
      */
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     */
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -112,7 +140,10 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
+            rendererTypeName: string; /**
+             * #property
+             * updated via autorun
+             */
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -141,8 +172,8 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionsStatsP: Promise<Stats> | undefined;
-    estimatedRegionsStats: Stats | undefined;
+    featureDensityStatsP: Promise<FeatureDensityStats> | undefined;
+    featureDensityStats: FeatureDensityStats | undefined;
 } & {
     readonly height: number;
     /**
@@ -214,7 +245,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     /**
      * #getter
      */
@@ -229,19 +260,19 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    estimateRegionsStats(): Promise<Stats>;
+    getFeatureDensityStats(): Promise<FeatureDensityStats>;
     /**
      * #action
      */
-    setRegionsStatsP(arg: any): void;
+    setFeatureDensityStatsP(arg: any): void;
     /**
      * #action
      */
-    setRegionsStats(estimatedRegionsStats?: Stats): void;
+    setFeatureDensityStats(featureDensityStats?: FeatureDensityStats): void;
     /**
      * #action
      */
-    clearRegionsStats(): void;
+    clearFeatureDensityStats(): void;
     /**
      * #action
      */
@@ -257,7 +288,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    updateStatsLimit(stats?: Stats): void;
+    setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
     /**
      * #action
      */
@@ -281,7 +312,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
     /**
      * #action
      */
@@ -296,7 +327,8 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
      * region is too large if:
      * - stats are ready
      * - region is greater than 20kb (don't warn when zoomed in less than that)
-     * - and bytes is greater than max allowed bytes or density greater than max density
+     * - and bytes is greater than max allowed bytes or density greater than max
+     *   density
      */
     readonly regionTooLarge: boolean;
     /**
@@ -397,7 +429,9 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         setRendered(props: {
             reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
             features: Map<string, Feature>;
-            layout: any;
+            layout: any; /**
+             * #getter
+             */
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
@@ -413,9 +447,36 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
      * #property
      */
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    /**
+     * #property
+     */
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>>, {
     type: string;
     id: string;
+    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
     rpcDriverName: string | undefined;
     heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js CHANGED Viewed

@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
 import React from 'react';
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
-import { getConf } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { isAbortException, getContainingView, getContainingTrack, getSession, getViewParams, isSelectionContainer, isSessionModelWithWidgets, isFeature, ReactRendering, } from '@jbrowse/core/util';
 import CompositeMap from '@jbrowse/core/util/compositeMap';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
@@ -12,7 +12,8 @@ import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import { Tooltip } from '../components/BaseLinearDisplay';
 import TooLargeMessage from '../components/TooLargeMessage';
 import BlockState, { renderBlockData } from './serverSideRenderedBlock';
-import { getId, getDisplayStr, estimateRegionsStatsPre } from './util';
+import { getId, getDisplayStr, getFeatureDensityStatsPre } from './util';
+import configSchema from './configSchema';
 const minDisplayHeight = 20;
 /**
  * #stateModel BaseLinearDisplay
@@ -38,6 +39,10 @@ function stateModelFactory() {
          * #property
          */
         userByteSizeLimit: types.maybe(types.number),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
     }))
         .volatile(() => ({
         currBpPerPx: 0,
@@ -45,8 +50,8 @@ function stateModelFactory() {
         message: '',
         featureIdUnderMouse: undefined,
         contextMenuFeature: undefined,
-        estimatedRegionsStatsP: undefined,
-        estimatedRegionsStats: undefined,
+        featureDensityStatsP: undefined,
+        featureDensityStats: undefined,
     }))
         .views(self => ({
         get height() {
@@ -165,7 +170,7 @@ function stateModelFactory() {
          */
         get currentBytesRequested() {
             var _a;
-            return ((_a = self.estimatedRegionsStats) === null || _a === void 0 ? void 0 : _a.bytes) || 0;
+            return ((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.bytes) || 0;
         },
         /**
          * #getter
@@ -173,7 +178,7 @@ function stateModelFactory() {
         get currentFeatureScreenDensity() {
             var _a;
             const view = getContainingView(self);
-            return (((_a = self.estimatedRegionsStats) === null || _a === void 0 ? void 0 : _a.featureDensity) || 0) * view.bpPerPx;
+            return (((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.featureDensity) || 0) * view.bpPerPx;
         },
         /**
          * #getter
@@ -184,8 +189,8 @@ function stateModelFactory() {
         /**
          * #getter
          */
-        get estimatedStatsReady() {
-            return !!self.estimatedRegionsStats || !!self.userBpPerPxLimit;
+        get featureDensityStatsReady() {
+            return !!self.featureDensityStats || !!self.userBpPerPxLimit;
         },
         /**
          * #getter
@@ -193,7 +198,7 @@ function stateModelFactory() {
         get maxAllowableBytes() {
             var _a;
             return (self.userByteSizeLimit ||
-                ((_a = self.estimatedRegionsStats) === null || _a === void 0 ? void 0 : _a.fetchSizeLimit) ||
+                ((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.fetchSizeLimit) ||
                 getConf(self, 'fetchSizeLimit'));
         },
     }))
@@ -231,33 +236,33 @@ function stateModelFactory() {
         /**
          * #action
          */
-        async estimateRegionsStats() {
-            if (!self.estimatedRegionsStatsP) {
-                self.estimatedRegionsStatsP = estimateRegionsStatsPre(self).catch(e => {
-                    this.setRegionsStatsP(undefined);
+        async getFeatureDensityStats() {
+            if (!self.featureDensityStatsP) {
+                self.featureDensityStatsP = getFeatureDensityStatsPre(self).catch(e => {
+                    this.setFeatureDensityStatsP(undefined);
                     throw e;
                 });
             }
-            return self.estimatedRegionsStatsP;
+            return self.featureDensityStatsP;
         },
         /**
          * #action
          */
-        setRegionsStatsP(arg) {
-            self.estimatedRegionsStatsP = arg;
+        setFeatureDensityStatsP(arg) {
+            self.featureDensityStatsP = arg;
         },
         /**
          * #action
          */
-        setRegionsStats(estimatedRegionsStats) {
-            self.estimatedRegionsStats = estimatedRegionsStats;
+        setFeatureDensityStats(featureDensityStats) {
+            self.featureDensityStats = featureDensityStats;
         },
         /**
          * #action
          */
-        clearRegionsStats() {
-            self.estimatedRegionsStatsP = undefined;
-            self.estimatedRegionsStats = undefined;
+        clearFeatureDensityStats() {
+            self.featureDensityStatsP = undefined;
+            self.featureDensityStats = undefined;
         },
         /**
          * #action
@@ -284,7 +289,7 @@ function stateModelFactory() {
         /**
          * #action
          */
-        updateStatsLimit(stats) {
+        setFeatureDensityStatsLimit(stats) {
             const view = getContainingView(self);
             if (stats === null || stats === void 0 ? void 0 : stats.bytes) {
                 self.userByteSizeLimit = stats.bytes;
@@ -335,8 +340,7 @@ function stateModelFactory() {
          * #action
          */
         clearFeatureSelection() {
-            const session = getSession(self);
-            session.clearSelection();
+            getSession(self).clearSelection();
         },
         /**
          * #action
@@ -364,11 +368,13 @@ function stateModelFactory() {
          * region is too large if:
          * - stats are ready
          * - region is greater than 20kb (don't warn when zoomed in less than that)
-         * - and bytes is greater than max allowed bytes or density greater than max density
+         * - and bytes is greater than max allowed bytes or density greater than max
+         *   density
          */
         get regionTooLarge() {
             const view = getContainingView(self);
-            if (!self.estimatedStatsReady || view.dynamicBlocks.totalBp < 20000) {
+            if (!self.featureDensityStatsReady ||
+                view.dynamicBlocks.totalBp < 20000) {
                 return false;
             }
             return (self.currentBytesRequested > self.maxAllowableBytes ||
@@ -404,9 +410,9 @@ function stateModelFactory() {
                     return;
                 }
                 try {
-                    const estimatedRegionsStats = await self.estimateRegionsStats();
+                    const featureDensityStats = await self.getFeatureDensityStats();
                     if (isAlive(self)) {
-                        self.setRegionsStats(estimatedRegionsStats);
+                        self.setFeatureDensityStats(featureDensityStats);
                         superReload();
                     }
                 }
@@ -421,7 +427,7 @@ function stateModelFactory() {
         afterAttach() {
             // this autorun performs stats estimation
             //
-            // the chain of events calls estimateRegionsStats against the data
+            // the chain of events calls getFeatureDensityStats against the data
             // adapter which by default uses featureDensity, but can also respond
             // with a byte size estimate and fetch size limit (data adapter can
             // define what is too much data)
@@ -437,7 +443,7 @@ function stateModelFactory() {
                     }
                     // don't re-estimate featureDensity even if zoom level changes,
                     // jbrowse1-style assume it's sort of representative
-                    if (((_a = self.estimatedRegionsStats) === null || _a === void 0 ? void 0 : _a.featureDensity) !== undefined) {
+                    if (((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.featureDensity) !== undefined) {
                         self.setCurrBpPerPx(view.bpPerPx);
                         return;
                     }
@@ -445,11 +451,11 @@ function stateModelFactory() {
                     if (view.bpPerPx === self.currBpPerPx) {
                         return;
                     }
-                    self.clearRegionsStats();
+                    self.clearFeatureDensityStats();
                     self.setCurrBpPerPx(view.bpPerPx);
-                    const estimatedRegionsStats = await self.estimateRegionsStats();
+                    const featureDensityStats = await self.getFeatureDensityStats();
                     if (isAlive(self)) {
-                        self.setRegionsStats(estimatedRegionsStats);
+                        self.setFeatureDensityStats(featureDensityStats);
                     }
                 }
                 catch (e) {
@@ -512,7 +518,7 @@ function stateModelFactory() {
             const view = getContainingView(self);
             return {
                 ...getParentRenderProps(self),
-                notReady: self.currBpPerPx !== view.bpPerPx || !self.estimatedRegionsStats,
+                notReady: self.currBpPerPx !== view.bpPerPx || !self.featureDensityStatsReady,
                 rpcDriverName: self.rpcDriverName,
                 displayModel: self,
                 onFeatureClick(_, featureId) {

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/BaseLinearDisplay/models/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,36 @@
-declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 export default baseLinearDisplayConfigSchema;

package/esm/BaseLinearDisplay/models/configSchema.js CHANGED Viewed

@@ -31,6 +31,15 @@ const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
         defaultValue: 100,
         description: 'default height for the track',
     },
+    /**
+     * #slot
+     */
+    mouseover: {
+        type: 'string',
+        description: 'text to display when the cursor hovers over a feature',
+        defaultValue: `jexl:get(feature,'name')`,
+        contextVariable: ['feature'],
+    },
 }, {
     /**
      * #identifier

package/esm/BaseLinearDisplay/models/configSchema.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;;GAKG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,6BAA6B,GAAG,mBAAmB,CACvD,mBAAmB,EACnB;IACE;;OAEG;IACH,uBAAuB,EAAE;QACvB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,qGAAqG;QACvG,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,OAAS;QACvB,WAAW,EACT,4FAA4F;KAC/F;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,GAAG;QACjB,WAAW,EAAE,8BAA8B;KAC5C;CACF,EACD;IACE;;OAEG;IACH,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AAED,eAAe,6BAA6B,CAAA"}
1	+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;;GAKG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,6BAA6B,GAAG,mBAAmB,CACvD,mBAAmB,EACnB;IACE;;OAEG;IACH,uBAAuB,EAAE;QACvB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,qGAAqG;QACvG,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,OAAS;QACvB,WAAW,EACT,4FAA4F;KAC/F;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,GAAG;QACjB,WAAW,EAAE,8BAA8B;KAC5C;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,uDAAuD;QACpE,YAAY,EAAE,0BAA0B;QAExC,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;CACF,EACD;IACE;;OAEG;IACH,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AAED,eAAe,6BAA6B,CAAA"}

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js CHANGED Viewed

@@ -37,12 +37,16 @@ const blockState = types
         },
         afterAttach() {
             const display = getContainingDisplay(self);
-            makeAbortableReaction(self, renderBlockData, renderBlockEffect, // reaction doesn't expect async here
-            {
-                name: `${display.id}/${assembleLocString(self.region)} rendering`,
-                delay: display.renderDelay,
-                fireImmediately: true,
-            }, this.setLoading, this.setRendered, this.setError);
+            setTimeout(() => {
+                if (isAlive(self)) {
+                    makeAbortableReaction(self, renderBlockData, renderBlockEffect, // reaction doesn't expect async here
+                    {
+                        name: `${display.id}/${assembleLocString(self.region)} rendering`,
+                        delay: display.renderDelay,
+                        fireImmediately: true,
+                    }, this.setLoading, this.setRendered, this.setError);
+                }
+            }, display.renderDelay);
         },
         setStatus(message) {
             self.status = message;

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"serverSideRenderedBlock.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/serverSideRenderedBlock.ts"],"names":[],"mappings":"AAEA,OAAO,EACL,KAAK,EACL,SAAS,EACT,OAAO,EACP,IAAI,EAEJ,WAAW,GACZ,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EACL,iBAAiB,EACjB,UAAU,EACV,oBAAoB,EACpB,iBAAiB,EACjB,aAAa,EACb,qBAAqB,GAEtB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAA;AACrD,OAAO,EAEL,gBAAgB,GACjB,MAAM,0BAA0B,CAAA;AAEjC,OAAO,EACL,qBAAqB,EACrB,eAAe,GAChB,MAAM,2BAA2B,CAAA;AAElC,SAAS;AACT,OAAO,8BAA8B,MAAM,8CAA8C,CAAA;AAEzF,oEAAoE;AACpE,MAAM,UAAU,GAAG,KAAK;KACrB,KAAK,CAAC,YAAY,EAAE;IACnB,GAAG,EAAE,KAAK,CAAC,MAAM;IACjB,MAAM,EAAE,MAAM;IACd,UAAU,EAAE,CAAC;IACb,0BAA0B,EAAE,KAAK;IACjC,2BAA2B,EAAE,KAAK;CACnC,CAAC;IACF,yFAAyF;KACxF,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;IACf,gBAAgB,EAAE,SAAwC;IAC1D,MAAM,EAAE,KAAK;IACb,YAAY,EAAE,SAA2C;IACzD,QAAQ,EAAE,SAA6C;IACvD,MAAM,EAAE,SAAgB;IACxB,MAAM,EAAE,EAAE;IACV,KAAK,EAAE,SAAoB;IAC3B,OAAO,EAAE,SAA+B;IACxC,gBAAgB,EAAE,KAAK;IACvB,cAAc,EAAE,8BAA8B;IAC9C,WAAW,EAAE,SAAgB;CAC9B,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE;IACd,IAAI,gBAA6C,CAAA;IACjD,OAAO;QACL,QAAQ;YACN,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;QACvC,CAAC;QACD,WAAW;YACT,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAA;YAC1C,UAAU,CAAC,GAAG,EAAE;gBACd,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE;oBACjB,qBAAqB,CACnB,IAAW,EACX,eAAe,EACf,iBAAiB,EAAE,qCAAqC;oBACxD;wBACE,IAAI,EAAE,GAAG,OAAO,CAAC,EAAE,IAAI,iBAAiB,CACtC,IAAI,CAAC,MAAM,CACZ,YAAY;wBACb,KAAK,EAAE,OAAO,CAAC,WAAW;wBAC1B,eAAe,EAAE,IAAI;qBACtB,EACD,IAAI,CAAC,UAAU,EACf,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,QAAQ,CACd,CAAA;iBACF;YACH,CAAC,EAAE,OAAO,CAAC,WAAW,CAAC,CAAA;QACzB,CAAC;QACD,SAAS,CAAC,OAAe;YACvB,IAAI,CAAC,MAAM,GAAG,OAAO,CAAA;QACvB,CAAC;QACD,UAAU,CAAC,eAAgC;YACzC,IACE,gBAAgB,KAAK,SAAS;gBAC9B,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAChC;gBACA,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,eAAe,CAAA;QACpC,CAAC;QACD,UAAU,CAAC,WAAmB;YAC5B,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,WAAW,CAAA;YAC1B,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,SAAS,CAAA;QAC9B,CAAC;QACD,WAAW,CACT,KAQa;YAEb,IAAI,CAAC,KAAK,EAAE;gBACV,OAAM;aACP;YACD,MAAM,EACJ,YAAY,EACZ,QAAQ,EACR,MAAM,EACN,gBAAgB,EAChB,WAAW,GACZ,GAAG,KAAK,CAAA;YACT,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;YAClB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;YAChC,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YACxB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;YACpB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;YACxC,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;YAC9B,gBAAgB,GAAG,SAAS,CAAA;QAC9B,CAAC;QACD,QAAQ,CAAC,KAAc;YACrB,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;YACpB,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,uCAAuC;YACvC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;YAClB,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,SAAS,CAAA;YAC5B,IAAI,gBAAgB,CAAC,KAAc,CAAC,EAAE;gBACpC,IAAI,CAAC,MAAM,EAAE,CAAA;aACd;QACH,CAAC;QACD,MAAM;YACJ,IAAI,CAAC,gBAAgB,GAAG,SAAS,CAAA;YACjC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,cAAc,GAAG,8BAA8B,CAAA;YACpD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,SAAS,CAAM,IAAI,EAAE,CAAC,CAAC,CAAC,MAAM,EAAE,CAAA;QAClC,CAAC;QACD,aAAa;YACX,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAA;YAC1C,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YACvC,MAAM,EAAE,YAAY,EAAE,GAAG,OAAO,CAAA;YAChC,MAAM,EAAE,UAAU,EAAE,GAAG,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;YAClD,iEAAiE;YACjE,IAAI,UAAU,EAAE;gBACd,YAAY;qBACT,qBAAqB,CACpB,UAAU,EACV,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CACvC;qBACA,KAAK,CAAC,CAAC,CAAQ,EAAE,EAAE;oBAClB,kEAAkE;oBAClE,OAAO,CAAC,IAAI,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;gBACjD,CAAC,CAAC,CAAA;aACL;QACH,CAAC;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAEJ,eAAe,UAAU,CAAA;AAIzB,2EAA2E;AAC3E,mDAAmD;AACnD,MAAM,UAAU,eAAe,CAC7B,IAAgB,EAChB,UAAiC;IAEjC,IAAI;QACF,MAAM,OAAO,GAAG,UAAU,IAAK,oBAAoB,CAAC,IAAI,CAAS,CAAA;QACjE,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,OAAO,CAAC,CAAA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package/esm/BaseLinearDisplay/models/util.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
-import { Stats } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 export interface RenderProps {
     rendererType: any;
@@ -19,4 +20,7 @@ export interface ErrorProps {
 }
 export declare function getDisplayStr(totalBytes: number): string;
 export declare function getId(id: string, index: number): string;
-export declare function estimateRegionsStatsPre(self: IAnyStateTreeNode): Promise<Stats>;
+export declare function getFeatureDensityStatsPre(self: IAnyStateTreeNode & {
+    adapterConfig?: AnyConfigurationModel;
+    setMessage: (arg: string) => void;
+}): Promise<FeatureDensityStats>;

package/esm/BaseLinearDisplay/models/util.js CHANGED Viewed

@@ -19,7 +19,7 @@ export function getId(id, index) {
     const isJest = typeof jest === 'undefined';
     return `clip-${isJest ? id : 'jest'}-${index}`;
 }
-export async function estimateRegionsStatsPre(self) {
+export async function getFeatureDensityStatsPre(self) {
     const view = getContainingView(self);
     const regions = view.staticBlocks.contentBlocks;
     const { rpcManager } = getSession(self);
@@ -30,7 +30,7 @@ export async function estimateRegionsStatsPre(self) {
         return {};
     }
     const sessionId = getRpcSessionId(self);
-    return rpcManager.call(sessionId, 'CoreEstimateRegionStats', {
+    return rpcManager.call(sessionId, 'CoreGetFeatureDensityStats', {
         sessionId,
         regions,
         adapterConfig,

package/esm/BaseLinearDisplay/models/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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