@jbrowse/plugin-wiggle 3.1.0 → 3.2.0

package/dist/WiggleRPC/MultiWiggleClusterScoreMatrix.d.ts

@@ -0,0 +1,14 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { GetScoreMatrixArgs } from './types';
+export declare class MultiWiggleClusterScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: GetScoreMatrixArgs, rpcDriverClassName: string): Promise<{
+        clusters: {
+            height: number;
+            indexes: number[];
+        } | undefined;
+        distances: number[][];
+        order: number[];
+        clustersGivenK: number[][][];
+    }>;
+}

package/dist/WiggleRPC/MultiWiggleClusterScoreMatrix.js

@@ -0,0 +1,34 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MultiWiggleClusterScoreMatrix = void 0;
+const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
+const cluster_1 = require("./cluster");
+const getScoreMatrix_1 = require("./getScoreMatrix");
+class MultiWiggleClusterScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiWiggleClusterScoreMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const matrix = await (0, getScoreMatrix_1.getScoreMatrix)({
+            pluginManager: this.pluginManager,
+            args: deserializedArgs,
+        });
+        return (0, cluster_1.clusterData)({
+            data: Object.values(matrix),
+            stopToken: deserializedArgs.stopToken,
+            onProgress: a => {
+                var _a;
+                (_a = deserializedArgs.statusCallback) === null || _a === void 0 ? void 0 : _a.call(deserializedArgs, `${toP(a * 100)}%`);
+            },
+        });
+    }
+}
+exports.MultiWiggleClusterScoreMatrix = MultiWiggleClusterScoreMatrix;
+function toP(n) {
+    return Number.parseFloat(n.toPrecision(3));
+}

package/dist/WiggleRPC/MultiWiggleGetScoreMatrix.d.ts

@@ -1,17 +1,6 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { type Region } from '@jbrowse/core/util';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { GetScoreMatrixArgs } from './types';
 export declare class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: {
-        adapterConfig: AnyConfigurationModel;
-        stopToken?: string;
-        sessionId: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        bpPerPx: number;
-    }, rpcDriverClassName: string): Promise<Record<string, {
-        name: string;
-        scores: string[];
-    }>>;
+    execute(args: GetScoreMatrixArgs, rpcDriverClassName: string): Promise<Record<string, number[]>>;
 }

package/dist/WiggleRPC/MultiWiggleGetScoreMatrix.js

@@ -4,51 +4,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultiWiggleGetScoreMatrix = void 0;
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
-const util_1 = require("@jbrowse/core/util");
-const rxjs_1 = require("rxjs");
+const getScoreMatrix_1 = require("./getScoreMatrix");
 class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
     constructor() {
         super(...arguments);
         this.name = 'MultiWiggleGetScoreMatrix';
     }
     async execute(args, rpcDriverClassName) {
-        var _a, _b;
-        const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { sources, regions, adapterConfig, sessionId, bpPerPx } = deserializedArgs;
-        const adapter = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
-        const dataAdapter = adapter.dataAdapter;
-        const resolution = 2;
-        const bpScale = bpPerPx / resolution;
-        const r0 = regions[0];
-        const r0len = r0.end - r0.start;
-        const w = Math.floor(r0len / bpScale);
-        const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeatures(r0, deserializedArgs).pipe((0, rxjs_1.toArray)()));
-        const groups = (0, util_1.groupBy)(feats, f => f.get('source'));
-        const rows = {};
-        for (const source of sources) {
-            const { name } = source;
-            const features = groups[name] || [];
-            for (const feat of features) {
-                if (!rows[name]) {
-                    rows[name] = {
-                        name,
-                        scores: new Array(w),
-                    };
-                }
-                const fstart = feat.get('start');
-                const fend = feat.get('end');
-                const score = feat.get('score');
-                for (let i = fstart; i < fend; i += bpScale) {
-                    if (i > r0.start && i < r0.end) {
-                        (_a = rows[name].scores)[_b = Math.floor((i - r0.start) / bpScale)] || (_a[_b] = score);
-                    }
-                }
-            }
-        }
-        return rows;
+        return (0, getScoreMatrix_1.getScoreMatrix)({
+            args: deserializedArgs,
+            pluginManager: this.pluginManager,
+        });
     }
 }
 exports.MultiWiggleGetScoreMatrix = MultiWiggleGetScoreMatrix;

package/dist/WiggleRPC/cluster.d.ts

@@ -0,0 +1,17 @@
+export declare function euclideanDistance(a: number[], b: number[]): number;
+export declare function averageDistance(setA: number[], setB: number[], distances: number[][]): number;
+export declare function clusterData({ data, distance, linkage, onProgress, stopToken, }: {
+    data: number[][];
+    distance?: (a: number[], b: number[]) => number;
+    linkage?: (a: number[], b: number[], distances: number[][]) => number;
+    onProgress?: (a: number) => void;
+    stopToken?: string;
+}): {
+    clusters: {
+        height: number;
+        indexes: number[];
+    } | undefined;
+    distances: number[][];
+    order: number[];
+    clustersGivenK: number[][][];
+};

package/dist/WiggleRPC/cluster.js

@@ -0,0 +1,84 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.euclideanDistance = euclideanDistance;
+exports.averageDistance = averageDistance;
+exports.clusterData = clusterData;
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+function euclideanDistance(a, b) {
+    const size = Math.min(a.length, b.length);
+    let sum = 0;
+    for (let index = 0; index < size; index++) {
+        sum += (a[index] - b[index]) * (a[index] - b[index]);
+    }
+    return Math.sqrt(sum);
+}
+function averageDistance(setA, setB, distances) {
+    let distance = 0;
+    for (const a of setA) {
+        for (const b of setB) {
+            distance += distances[a][b];
+        }
+    }
+    return distance / setA.length / setB.length;
+}
+function updateProgress(stepNumber, stepProgress, onProgress) {
+    onProgress(stepNumber / 2 + stepProgress / 2);
+}
+function clusterData({ data, distance = euclideanDistance, linkage = averageDistance, onProgress, stopToken, }) {
+    const distances = data.map((datum, index) => {
+        if (onProgress) {
+            updateProgress(0, index / (data.length - 1), onProgress);
+        }
+        return data.map(otherDatum => distance(datum, otherDatum));
+    });
+    const clusters = data.map((_datum, index) => ({
+        height: 0,
+        indexes: [Number(index)],
+    }));
+    let clustersGivenK = [];
+    let start = performance.now();
+    for (let iteration = 0; iteration < data.length; iteration++) {
+        if (performance.now() - start > 2000) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+            start = performance.now();
+        }
+        if (onProgress) {
+            updateProgress(1, (iteration + 1) / data.length, onProgress);
+        }
+        clustersGivenK.push(clusters.map(cluster => cluster.indexes));
+        if (iteration >= data.length - 1) {
+            break;
+        }
+        let nearestDistance = Infinity;
+        let nearestRow = 0;
+        let nearestCol = 0;
+        for (let row = 0; row < clusters.length; row++) {
+            for (let col = row + 1; col < clusters.length; col++) {
+                const distance = linkage(clusters[row].indexes, clusters[col].indexes, distances);
+                if (distance < nearestDistance) {
+                    nearestDistance = distance;
+                    nearestRow = row;
+                    nearestCol = col;
+                }
+            }
+        }
+        const newCluster = {
+            indexes: [
+                ...clusters[nearestRow].indexes,
+                ...clusters[nearestCol].indexes,
+            ],
+            height: nearestDistance,
+            children: [clusters[nearestRow], clusters[nearestCol]],
+        };
+        clusters.splice(Math.max(nearestRow, nearestCol), 1);
+        clusters.splice(Math.min(nearestRow, nearestCol), 1);
+        clusters.push(newCluster);
+    }
+    clustersGivenK = [[], ...clustersGivenK.reverse()];
+    return {
+        clusters: clusters[0],
+        distances: distances,
+        order: clusters[0].indexes,
+        clustersGivenK: clustersGivenK,
+    };
+}

package/dist/WiggleRPC/getScoreMatrix.d.ts

@@ -0,0 +1,6 @@
+import type { GetScoreMatrixArgs } from './types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function getScoreMatrix({ pluginManager, args, }: {
+    args: GetScoreMatrixArgs;
+    pluginManager: PluginManager;
+}): Promise<Record<string, number[]>>;

package/dist/WiggleRPC/getScoreMatrix.js

@@ -0,0 +1,35 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getScoreMatrix = getScoreMatrix;
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const util_1 = require("@jbrowse/core/util");
+const rxjs_1 = require("rxjs");
+async function getScoreMatrix({ pluginManager, args, }) {
+    const { sources, regions, adapterConfig, sessionId, bpPerPx } = args;
+    const adapter = await (0, dataAdapterCache_1.getAdapter)(pluginManager, sessionId, adapterConfig);
+    const dataAdapter = adapter.dataAdapter;
+    const r0 = regions[0];
+    const r0len = r0.end - r0.start;
+    const w = Math.floor(r0len / bpPerPx);
+    const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeatures(r0, args).pipe((0, rxjs_1.toArray)()));
+    const groups = (0, util_1.groupBy)(feats, f => f.get('source'));
+    const rows = {};
+    for (const source of sources) {
+        const { name } = source;
+        const features = groups[name] || [];
+        const arr = new Array(w).fill(0);
+        for (const feat of features) {
+            const fstart = feat.get('start');
+            const fend = feat.get('end');
+            const score = feat.get('score');
+            for (let i = fstart; i < fend; i += bpPerPx) {
+                const x = Math.floor((i - r0.start) / bpPerPx);
+                if (x >= 0 && x < w) {
+                    arr[x] || (arr[x] = score);
+                }
+            }
+        }
+        rows[name] = arr;
+    }
+    return rows;
+}

package/dist/WiggleRPC/rpcMethods.d.ts

@@ -2,3 +2,4 @@ export * from './MultiWiggleGetSources';
 export * from './WiggleGetMultiRegionQuantitativeStats';
 export * from './WiggleGetGlobalQuantitativeStats';
 export * from './MultiWiggleGetScoreMatrix';
+export * from './MultiWiggleClusterScoreMatrix';

package/dist/WiggleRPC/rpcMethods.js

@@ -18,3 +18,4 @@ __exportStar(require("./MultiWiggleGetSources"), exports);
 __exportStar(require("./WiggleGetMultiRegionQuantitativeStats"), exports);
 __exportStar(require("./WiggleGetGlobalQuantitativeStats"), exports);
 __exportStar(require("./MultiWiggleGetScoreMatrix"), exports);
+__exportStar(require("./MultiWiggleClusterScoreMatrix"), exports);

package/dist/WiggleRPC/type.js

@@ -0,0 +1 @@
+"use strict";

package/dist/WiggleRPC/types.d.ts

@@ -0,0 +1,13 @@
+import type { Source } from '../util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export interface GetScoreMatrixArgs {
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    sources: Source[];
+    statusCallback?: (arg: string) => void;
+}

package/dist/WiggleRPC/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/drawDensity.d.ts

@@ -12,6 +12,7 @@ export declare function drawDensity(ctx: CanvasRenderingContext2D, props: {
     };
     displayCrossHatches: boolean;
     config: AnyConfigurationModel;
+    stopToken?: string;
 }): {
     reducedFeatures: Feature[];
 };

package/dist/drawDensity.js

@@ -3,11 +3,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.drawDensity = drawDensity;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
 const util_2 = require("./util");
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 function drawDensity(ctx, props) {
-    const { features, regions, bpPerPx, scaleOpts, height, config } = props;
+    const { stopToken, features, regions, bpPerPx, scaleOpts, height, config } = props;
     const region = regions[0];
     const pivot = (0, configuration_1.readConfObject)(config, 'bicolorPivot');
     const pivotValue = (0, configuration_1.readConfObject)(config, 'bicolorPivotValue');
@@ -19,7 +20,7 @@ function drawDensity(ctx, props) {
     const scale = (0, util_2.getScale)({
         ...scaleOpts,
         pivotValue: crossing ? pivotValue : undefined,
-        range: crossing ? [negColor, 'white', posColor] : ['white', posColor],
+        range: crossing ? [negColor, '#eee', posColor] : ['#eee', posColor],
     });
     const scale2 = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
     const cb = color === '#f0f'
@@ -31,7 +32,12 @@ function drawDensity(ctx, props) {
     let prevLeftPx = Number.NEGATIVE_INFINITY;
     let hasClipping = false;
     const reducedFeatures = [];
+    let start = performance.now();
     for (const feature of features.values()) {
+        if (performance.now() - start > 400) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+            start = performance.now();
+        }
         const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
         if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
             reducedFeatures.push(feature);
@@ -47,6 +53,10 @@ function drawDensity(ctx, props) {
     if (hasClipping) {
         ctx.fillStyle = clipColor;
         for (const feature of features.values()) {
+            if (performance.now() - start > 400) {
+                (0, stopToken_1.checkStopToken)(stopToken);
+                start = performance.now();
+            }
             const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
             const w = rightPx - leftPx + fudgeFactor;
             const score = feature.get('score');

package/dist/drawLine.d.ts

@@ -14,6 +14,7 @@ export declare function drawLine(ctx: CanvasRenderingContext2D, props: {
     colorCallback: (f: Feature, score: number) => string;
     config: AnyConfigurationModel;
     offset?: number;
+    stopToken?: string;
 }): {
     reducedFeatures: Feature[];
 };

package/dist/drawLine.js

@@ -3,11 +3,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.drawLine = drawLine;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
 const util_2 = require("./util");
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 function drawLine(ctx, props) {
-    const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, } = props;
+    const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, stopToken, } = props;
     const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
     const height = unadjustedHeight - offset * 2;
@@ -20,7 +21,12 @@ function drawLine(ctx, props) {
     let lastVal;
     let prevLeftPx = Number.NEGATIVE_INFINITY;
     const reducedFeatures = [];
+    let start = performance.now();
     for (const feature of features.values()) {
+        if (performance.now() - start > 400) {
+            (0, stopToken_1.checkStopToken)(stopToken);
+            start = performance.now();
+        }
         const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
         if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
             reducedFeatures.push(feature);
@@ -58,12 +64,12 @@ function drawLine(ctx, props) {
     if (displayCrossHatches) {
         ctx.lineWidth = 1;
         ctx.strokeStyle = 'rgba(200,200,200,0.5)';
-        values.forEach(tick => {
+        for (const tick of values) {
             ctx.beginPath();
             ctx.moveTo(0, Math.round(toY(tick)));
             ctx.lineTo(width, Math.round(toY(tick)));
             ctx.stroke();
-        });
+        }
     }
     return { reducedFeatures };
 }

package/dist/drawXY.js

@@ -25,7 +25,7 @@ function darken(color, amount) {
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 function drawXY(ctx, props) {
-    const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, inverted, } = props;
+    const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, inverted, stopToken, } = props;
     const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
     const height = unadjustedHeight - offset * 2;
@@ -53,7 +53,7 @@ function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                (0, stopToken_1.checkStopToken)();
+                (0, stopToken_1.checkStopToken)(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
@@ -75,7 +75,7 @@ function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                (0, stopToken_1.checkStopToken)();
+                (0, stopToken_1.checkStopToken)(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
@@ -105,7 +105,7 @@ function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                (0, stopToken_1.checkStopToken)();
+                (0, stopToken_1.checkStopToken)(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
@@ -127,7 +127,7 @@ function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                (0, stopToken_1.checkStopToken)();
+                (0, stopToken_1.checkStopToken)(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
@@ -158,7 +158,7 @@ function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                (0, stopToken_1.checkStopToken)();
+                (0, stopToken_1.checkStopToken)(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
@@ -176,12 +176,12 @@ function drawXY(ctx, props) {
     if (displayCrossHatches) {
         ctx.lineWidth = 1;
         ctx.strokeStyle = 'rgba(200,200,200,0.5)';
-        ticks.values.forEach(tick => {
+        for (const tick of ticks.values) {
             ctx.beginPath();
             ctx.moveTo(0, Math.round(toY(tick)));
             ctx.lineTo(width, Math.round(toY(tick)));
             ctx.stroke();
-        });
+        }
     }
     return { reducedFeatures };
 }

package/dist/index.js

@@ -97,6 +97,7 @@ class WigglePlugin extends Plugin_1.default {
         pm.addRpcMethod(() => new rpcMethods_1.WiggleGetMultiRegionQuantitativeStats(pm));
         pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleGetSources(pm));
         pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleGetScoreMatrix(pm));
+        pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleClusterScoreMatrix(pm));
     }
 }
 exports.default = WigglePlugin;

package/dist/shared/SharedWiggleMixin.d.ts

@@ -252,11 +252,11 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
     setCrossHatches(cross: boolean): void;
 } & {
     readonly adapterTypeName: any;
-    readonly rendererTypeNameSimple: any;
+    readonly rendererTypeNameSimple: string;
     readonly filters: undefined;
-    readonly scaleType: any;
-    readonly maxScore: any;
-    readonly minScore: any;
+    readonly scaleType: string;
+    readonly maxScore: number;
+    readonly minScore: number;
 } & {
     readonly adapterCapabilities: string[];
     readonly rendererConfig: {
@@ -270,7 +270,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
-    readonly autoscaleType: any;
+    readonly autoscaleType: string;
 } & {
     readonly domain: number[] | undefined;
 } & {
@@ -283,9 +283,9 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             scoreMin: number;
             scoreMax: number;
         } | undefined;
-        autoscaleType: any;
-        scaleType: any;
-        inverted: any;
+        autoscaleType: string;
+        scaleType: string;
+        inverted: boolean;
     };
     readonly canHaveFill: boolean;
     readonly displayCrossHatchesSetting: boolean;

package/dist/shared/SharedWiggleMixin.js

@@ -154,7 +154,7 @@ function SharedWiggleMixin(configSchema) {
         },
         get rendererTypeNameSimple() {
             var _a;
-            return (_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'defaultRendering');
+            return ((_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'defaultRendering'));
         },
         get filters() {
             return undefined;
@@ -225,12 +225,12 @@ function SharedWiggleMixin(configSchema) {
     })
         .views(self => ({
         get filled() {
-            const { fill, rendererConfig } = self;
-            return fill !== null && fill !== void 0 ? fill : (0, configuration_1.readConfObject)(rendererConfig, 'filled');
+            var _a;
+            return ((_a = self.fill) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(self.rendererConfig, 'filled'));
         },
         get summaryScoreModeSetting() {
-            const { summaryScoreMode: mode, rendererConfig } = self;
-            return mode !== null && mode !== void 0 ? mode : (0, configuration_1.readConfObject)(rendererConfig, 'summaryScoreMode');
+            var _a;
+            return ((_a = self.summaryScoreMode) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(self.rendererConfig, 'summaryScoreMode'));
         },
         get scaleOpts() {
             return {
@@ -245,8 +245,8 @@ function SharedWiggleMixin(configSchema) {
             return self.rendererTypeName === 'XYPlotRenderer';
         },
         get displayCrossHatchesSetting() {
-            const { displayCrossHatches: hatches, rendererConfig } = self;
-            return hatches !== null && hatches !== void 0 ? hatches : (0, configuration_1.readConfObject)(rendererConfig, 'displayCrossHatches');
+            var _a;
+            return ((_a = self.displayCrossHatches) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(self.rendererConfig, 'displayCrossHatches'));
         },
         get hasResolution() {
             return self.adapterCapabilities.includes('hasResolution');
@@ -321,7 +321,10 @@ function SharedWiggleMixin(configSchema) {
                     onClick: () => {
                         (0, util_1.getSession)(self).queueDialog(handleClose => [
                             SetMinMaxDialog,
-                            { model: self, handleClose },
+                            {
+                                model: self,
+                                handleClose,
+                            },
                         ]);
                     },
                 },

package/esm/BigWigAdapter/BigWigAdapter.js

@@ -40,7 +40,7 @@ class BigWigAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(region, opts = {}) {
         const { refName, start, end } = region;
-        const { bpPerPx = 0, stopToken, resolution = 1, statusCallback = () => { }, } = opts;
+        const { bpPerPx = 0, resolution = 1, stopToken, statusCallback = () => { }, } = opts;
         return ObservableCreate(async (observer) => {
             const source = this.getConf('source');
             const resolutionMultiplier = this.getConf('resolutionMultiplier');

package/esm/LinearWiggleDisplay/model.d.ts

@@ -258,11 +258,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     setCrossHatches(cross: boolean): void;
 } & {
     readonly adapterTypeName: any;
-    readonly rendererTypeNameSimple: any;
+    readonly rendererTypeNameSimple: string;
     readonly filters: undefined;
-    readonly scaleType: any;
-    readonly maxScore: any;
-    readonly minScore: any;
+    readonly scaleType: string;
+    readonly maxScore: number;
+    readonly minScore: number;
 } & {
     readonly adapterCapabilities: string[];
     readonly rendererConfig: {
@@ -276,7 +276,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
-    readonly autoscaleType: any;
+    readonly autoscaleType: string;
 } & {
     readonly domain: number[] | undefined;
 } & {
@@ -289,9 +289,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             scoreMin: number;
             scoreMax: number;
         } | undefined;
-        autoscaleType: any;
-        scaleType: any;
-        inverted: any;
+        autoscaleType: string;
+        scaleType: string;
+        inverted: boolean;
     };
     readonly canHaveFill: boolean;
     readonly displayCrossHatchesSetting: boolean;
@@ -328,7 +328,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly rendererTypeName: string;
     readonly quantitativeStatsRelevantToCurrentZoom: boolean;
     readonly graphType: boolean;
-    readonly inverted: any;
+    readonly inverted: boolean;
 } & {
     adapterProps(): any;
     readonly ticks: {
@@ -374,7 +374,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     } | {
         label: string;
         type: string;
-        checked: any;
+        checked: boolean;
         onClick: () => void;
         icon?: undefined;
         subMenu?: undefined;