@jbrowse/plugin-linear-genome-view 2.4.1 → 2.5.0

package/dist/BaseLinearDisplay/components/LinearBlocks.d.ts

@@ -1,9 +1,6 @@
-/// <reference types="react" />
 import { BaseLinearDisplayModel } from '../models/BaseLinearDisplayModel';
 declare const useStyles: (params: void, styleOverrides?: {
-    props: {
-        classes?: Record<string, string> | undefined;
-    } & Record<string, unknown>;
+    props: any;
     ownerState?: Record<string, unknown> | undefined;
 } | undefined) => {
     classes: Record<"linearBlocks" | "heightOverflowed", string>;

package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js

@@ -1,32 +1,9 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const react_1 = __importDefault(require("react"));
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -48,40 +25,28 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
 });
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 const LoadingMessage = (0, mobx_react_1.observer)(({ model }) => {
-    // only show the loading message after 300ms to prevent excessive flickering
-    const [shown, setShown] = (0, react_1.useState)(false);
     const { classes } = useStyles();
-    (0, react_1.useEffect)(() => {
-        let killed = false;
-        const timeout = setTimeout(() => {
-            if (!killed) {
-                setShown(true);
-            }
-        }, 300);
-        return () => {
-            clearTimeout(timeout);
-            killed = true;
-        };
-    }, []);
     const { status: blockStatus } = model;
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { message: displayStatus } = (0, mobx_state_tree_1.getParent)(model, 2);
     const status = displayStatus || blockStatus;
-    return (react_1.default.createElement(react_1.default.Fragment, null, shown ? (react_1.default.createElement("div", { className: classes.loading },
-        react_1.default.createElement(ui_1.LoadingEllipses, { message: status }))) : null));
+    return (react_1.default.createElement("div", { className: classes.loading },
+        react_1.default.createElement(ui_1.LoadingEllipses, { message: status })));
 });
 const ServerSideRenderedBlockContent = (0, mobx_react_1.observer)(function ({ model, }) {
     if (model.error) {
         return (react_1.default.createElement(BlockMsg_1.default, { message: `${model.error}`, severity: "error", buttonText: "reload", icon: react_1.default.createElement(Refresh_1.default, null), action: model.reload }));
     }
-    if (model.message) {
+    else if (model.message) {
         // the message can be a fully rendered react component, e.g. the region too large message
         return react_1.default.isValidElement(model.message) ? (model.message) : (react_1.default.createElement(BlockMsg_1.default, { message: `${model.message}`, severity: "info" }));
     }
-    if (!model.filled) {
+    else if (!model.filled) {
         return react_1.default.createElement(LoadingMessage, { model: model });
     }
-    return model.reactElement;
+    else {
+        return model.reactElement;
+    }
 });
 exports.default = ServerSideRenderedBlockContent;
 //# sourceMappingURL=ServerSideRenderedBlockContent.js.map

package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ServerSideRenderedBlockContent.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/components/ServerSideRenderedBlockContent.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,uCAA0C;AAC1C,2CAAqC;AACrC,qDAA2C;AAC3C,yCAAkD;AAElD,QAAQ;AACR,0EAAqD;AAErD,SAAS;AACT,0DAAiC;AAEjC,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE;IACrC,MAAM,EAAE,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,kBAAkB,CAAA;IAClD,OAAO;QACL,OAAO,EAAE;YACP,WAAW,EAAE,OAAO;YACpB,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO;YACjD,eAAe,EAAE,kEAAkE,EAAE,SAAS,EAAE,QAAQ;YACxG,SAAS,EAAE,QAAQ;SACpB;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,8DAA8D;AAC9D,MAAM,cAAc,GAAG,IAAA,qBAAQ,EAAC,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IAC5D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACrC,8DAA8D;IAC9D,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,GAAG,IAAA,2BAAS,EAAM,KAAK,EAAE,CAAC,CAAC,CAAA;IAC3D,MAAM,MAAM,GAAG,aAAa,IAAI,WAAW,CAAA;IAC3C,OAAO,CACL,uCAAK,SAAS,EAAE,OAAO,CAAC,OAAO;QAC7B,8BAAC,oBAAe,IAAC,OAAO,EAAE,MAAM,GAAI,CAChC,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,8BAA8B,GAAG,IAAA,qBAAQ,EAAC,UAAU,EACxD,KAAK,GAIN;IACC,IAAI,KAAK,CAAC,KAAK,EAAE;QACf,OAAO,CACL,8BAAC,kBAAQ,IACP,OAAO,EAAE,GAAG,KAAK,CAAC,KAAK,EAAE,EACzB,QAAQ,EAAC,OAAO,EAChB,UAAU,EAAC,QAAQ,EACnB,IAAI,EAAE,8BAAC,iBAAW,OAAG,EACrB,MAAM,EAAE,KAAK,CAAC,MAAM,GACpB,CACH,CAAA;KACF;SAAM,IAAI,KAAK,CAAC,OAAO,EAAE;QACxB,yFAAyF;QACzF,OAAO,eAAK,CAAC,cAAc,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAC3C,KAAK,CAAC,OAAO,CACd,CAAC,CAAC,CAAC,CACF,8BAAC,kBAAQ,IAAC,OAAO,EAAE,GAAG,KAAK,CAAC,OAAO,EAAE,EAAE,QAAQ,EAAC,MAAM,GAAG,CAC1D,CAAA;KACF;SAAM,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE;QACxB,OAAO,8BAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CAAA;KACxC;SAAM;QACL,OAAO,KAAK,CAAC,YAAY,CAAA;KAC1B;AACH,CAAC,CAAC,CAAA;AAEF,kBAAe,8BAA8B,CAAA"}

package/dist/BaseLinearDisplay/components/TooLargeMessage.d.ts

@@ -1,10 +1,9 @@
-/// <reference types="react" />
-import { Stats } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
 declare function TooLargeMessage({ model, }: {
     model: {
         regionTooLargeReason: string;
-        estimatedRegionStats?: Stats;
-        updateStatsLimit: (s: Stats) => void;
+        featureDensityStats?: FeatureDensityStats;
+        setFeatureDensityStatsLimit: (s?: FeatureDensityStats) => void;
         reload: () => void;
     };
 }): JSX.Element;

package/dist/BaseLinearDisplay/components/TooLargeMessage.js

@@ -4,19 +4,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
+// locals
 const BlockMsg_1 = __importDefault(require("../components/BlockMsg"));
 function TooLargeMessage({ model, }) {
     const { regionTooLargeReason } = model;
     return (react_1.default.createElement(BlockMsg_1.default, { severity: "warning", action: () => {
-            if (!model.estimatedRegionStats) {
-                console.error('No global stats?');
-            }
-            else {
-                model.updateStatsLimit(model.estimatedRegionStats);
-                model.reload();
-            }
-        }, buttonText: "Force load", message: `${regionTooLargeReason ? regionTooLargeReason + '. ' : ''}
-      Zoom in to see features or force load (may be slow).` }));
+            model.setFeatureDensityStatsLimit(model.featureDensityStats);
+            model.reload();
+        }, buttonText: "Force load", message: [
+            regionTooLargeReason,
+            'Zoom in to see features or force load (may be slow)',
+        ]
+            .filter(f => !!f)
+            .join('. ') }));
 }
 exports.default = TooLargeMessage;
 //# sourceMappingURL=TooLargeMessage.js.map

package/dist/BaseLinearDisplay/components/TooLargeMessage.js.map

@@ -1 +1 @@
-{"version":3,"file":"TooLargeMessage.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/components/TooLargeMessage.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,sEAA6C;AAG7C,SAAS,eAAe,CAAC,EACvB,KAAK,GAQN;IACC,MAAM,EAAE,oBAAoB,EAAE,GAAG,KAAK,CAAA;IACtC,OAAO,CACL,8BAAC,kBAAQ,IACP,QAAQ,EAAC,SAAS,EAClB,MAAM,EAAE,GAAG,EAAE;YACX,IAAI,CAAC,KAAK,CAAC,oBAAoB,EAAE;gBAC/B,OAAO,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAA;aAClC;iBAAM;gBACL,KAAK,CAAC,gBAAgB,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBAClD,KAAK,CAAC,MAAM,EAAE,CAAA;aACf;QACH,CAAC,EACD,UAAU,EAAC,YAAY,EACvB,OAAO,EAAE,GAAG,oBAAoB,CAAC,CAAC,CAAC,oBAAoB,GAAG,IAAI,CAAC,CAAC,CAAC,EAAE;2DACd,GACrD,CACH,CAAA;AACH,CAAC;AAED,kBAAe,eAAe,CAAA"}
+{"version":3,"file":"TooLargeMessage.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/components/TooLargeMessage.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AAGzB,SAAS;AACT,sEAA6C;AAE7C,SAAS,eAAe,CAAC,EACvB,KAAK,GAQN;IACC,MAAM,EAAE,oBAAoB,EAAE,GAAG,KAAK,CAAA;IACtC,OAAO,CACL,8BAAC,kBAAQ,IACP,QAAQ,EAAC,SAAS,EAClB,MAAM,EAAE,GAAG,EAAE;YACX,KAAK,CAAC,2BAA2B,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAA;YAC5D,KAAK,CAAC,MAAM,EAAE,CAAA;QAChB,CAAC,EACD,UAAU,EAAC,YAAY,EACvB,OAAO,EAAE;YACP,oBAAoB;YACpB,qDAAqD;SACtD;aACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,IAAI,CAAC,IAAI,CAAC,GACb,CACH,CAAA;AACH,CAAC;AAED,kBAAe,eAAe,CAAA"}

package/dist/BaseLinearDisplay/components/Tooltip.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { BaseLinearDisplayModel } from '../models/BaseLinearDisplayModel';
 type Coord = [number, number];
 declare const Tooltip: ({ model, clientMouseCoord, }: {

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -1,13 +1,13 @@
 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';
 import { Instance } from 'mobx-state-tree';
 import { ExportSvgOptions } from '../../LinearGenomeView';
-import { ThemeOptions } from '@mui/material';
 export interface Layout {
     minX: number;
     minY: number;
@@ -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;
@@ -112,14 +140,15 @@ 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]>;
             type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
-             * #property
-             */
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -136,11 +165,6 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
 } & {
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
-    /**
-     * #getter
-     * returns a string feature ID if the globally-selected object
-     * is probably a feature
-     */
     reload(): void;
 } & {
     currBpPerPx: number;
@@ -148,8 +172,8 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionStatsP: Promise<Stats> | undefined;
-    estimatedRegionStats: Stats | undefined;
+    featureDensityStatsP: Promise<FeatureDensityStats> | undefined;
+    featureDensityStats: FeatureDensityStats | undefined;
 } & {
     readonly height: number;
     /**
@@ -197,7 +221,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     /**
      * #getter
      */
@@ -221,7 +245,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     /**
      * #getter
      */
@@ -231,27 +255,24 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
      * #action
      */
     setMessage(message: string): void;
+} & {
     afterAttach(): void;
     /**
      * #action
      */
-    estimateRegionsStats(regions: Region[], opts: {
-        headers?: Record<string, string>;
-        signal?: AbortSignal;
-        filters?: string[];
-    }): Promise<{}>;
+    getFeatureDensityStats(): Promise<FeatureDensityStats>;
     /**
      * #action
      */
-    setRegionStatsP(p?: Promise<Stats>): void;
+    setFeatureDensityStatsP(arg: any): void;
     /**
      * #action
      */
-    setRegionStats(estimatedRegionStats?: Stats): void;
+    setFeatureDensityStats(featureDensityStats?: FeatureDensityStats): void;
     /**
      * #action
      */
-    clearRegionStats(): void;
+    clearFeatureDensityStats(): void;
     /**
      * #action
      */
@@ -267,7 +288,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    updateStatsLimit(stats: Stats): void;
+    setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
     /**
      * #action
      */
@@ -291,7 +312,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string): void;
     /**
      * #action
      */
@@ -306,7 +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;
     /**
@@ -320,6 +342,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
      * #action
      */
     reload(): Promise<void>;
+} & {
     afterAttach(): void;
 } & {
     /**
@@ -342,13 +365,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     /**
      * #method
      */
-    contextMenuItems(): {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        onClick: () => void;
-    }[];
+    contextMenuItems(): MenuItem[];
     /**
      * #method
      */
@@ -412,7 +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;
@@ -428,9 +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;