@jbrowse/plugin-wiggle 3.0.5 → 3.2.0

package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js

@@ -1,13 +1,13 @@
-import { groupBy } from '@jbrowse/core/util';
+import { forEachWithStopTokenCheck, groupBy } from '@jbrowse/core/util';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 import { YSCALEBAR_LABEL_OFFSET } from '../util';
 export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
     async draw(ctx, props) {
-        const { sources, features } = props;
+        const { stopToken, sources, features } = props;
         const groups = groupBy(features.values(), f => f.get('source'));
         const { drawXY } = await import('../drawXY');
         let feats = [];
-        for (const source of sources) {
+        forEachWithStopTokenCheck(sources, stopToken, source => {
             const features = groups[source.name] || [];
             const { reducedFeatures } = drawXY(ctx, {
                 ...props,
@@ -16,7 +16,7 @@ export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
                 colorCallback: () => source.color || 'blue',
             });
             feats = feats.concat(reducedFeatures);
-        }
+        });
         return { reducedFeatures: feats };
     }
 }

package/esm/WiggleBaseRenderer.d.ts

@@ -17,6 +17,7 @@ export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
     };
     inverted: boolean;
     themeOptions: ThemeOptions;
+    statusCallback?: (arg: string) => void;
 }
 export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
     features: Map<string, Feature>;

package/esm/WiggleBaseRenderer.js

@@ -1,5 +1,5 @@
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import { renderToAbstractCanvas } from '@jbrowse/core/util';
+import { renderToAbstractCanvas, updateStatus } from '@jbrowse/core/util';
 export default class WiggleBaseRenderer extends FeatureRendererType {
     constructor() {
         super(...arguments);
@@ -7,14 +7,14 @@ export default class WiggleBaseRenderer extends FeatureRendererType {
     }
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
-        const { inverted, height, regions, bpPerPx } = renderProps;
+        const { inverted, height, regions, bpPerPx, statusCallback = () => { }, } = renderProps;
         const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
-        const { reducedFeatures, ...rest } = await renderToAbstractCanvas(width, height, renderProps, ctx => this.draw(ctx, {
+        const { reducedFeatures, ...rest } = await updateStatus('Rendering plot', statusCallback, () => renderToAbstractCanvas(width, height, renderProps, ctx => this.draw(ctx, {
             ...renderProps,
             features,
             inverted,
-        }));
+        })));
         const results = await super.render({
             ...renderProps,
             ...rest,

package/esm/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/esm/WiggleRPC/MultiWiggleClusterScoreMatrix.js

@@ -0,0 +1,27 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { clusterData } from './cluster';
+import { getScoreMatrix } from './getScoreMatrix';
+export class MultiWiggleClusterScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiWiggleClusterScoreMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const matrix = await getScoreMatrix({
+            pluginManager: this.pluginManager,
+            args: deserializedArgs,
+        });
+        return 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)}%`);
+            },
+        });
+    }
+}
+function toP(n) {
+    return Number.parseFloat(n.toPrecision(3));
+}

package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.d.ts

@@ -0,0 +1,6 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { GetScoreMatrixArgs } from './types';
+export declare class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: GetScoreMatrixArgs, rpcDriverClassName: string): Promise<Record<string, number[]>>;
+}

package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.js

@@ -0,0 +1,15 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { getScoreMatrix } from './getScoreMatrix';
+export class MultiWiggleGetScoreMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiWiggleGetScoreMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        return getScoreMatrix({
+            args: deserializedArgs,
+            pluginManager: this.pluginManager,
+        });
+    }
+}

package/esm/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/esm/WiggleRPC/cluster.js

@@ -0,0 +1,79 @@
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+export 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);
+}
+export 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);
+}
+export 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) {
+            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/esm/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/esm/WiggleRPC/getScoreMatrix.js

@@ -0,0 +1,32 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { groupBy } from '@jbrowse/core/util';
+import { firstValueFrom, toArray } from 'rxjs';
+export async function getScoreMatrix({ pluginManager, args, }) {
+    const { sources, regions, adapterConfig, sessionId, bpPerPx } = args;
+    const adapter = await 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 firstValueFrom(dataAdapter.getFeatures(r0, args).pipe(toArray()));
+    const groups = 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/esm/WiggleRPC/rpcMethods.d.ts

@@ -1,3 +1,5 @@
 export * from './MultiWiggleGetSources';
 export * from './WiggleGetMultiRegionQuantitativeStats';
 export * from './WiggleGetGlobalQuantitativeStats';
+export * from './MultiWiggleGetScoreMatrix';
+export * from './MultiWiggleClusterScoreMatrix';

package/esm/WiggleRPC/rpcMethods.js

@@ -1,3 +1,5 @@
 export * from './MultiWiggleGetSources';
 export * from './WiggleGetMultiRegionQuantitativeStats';
 export * from './WiggleGetGlobalQuantitativeStats';
+export * from './MultiWiggleGetScoreMatrix';
+export * from './MultiWiggleClusterScoreMatrix';

package/esm/WiggleRPC/type.js

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

package/esm/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/esm/WiggleRPC/types.js

@@ -0,0 +1 @@
+export {};

package/esm/drawDensity.d.ts

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

package/esm/drawDensity.js

@@ -1,10 +1,11 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { featureSpanPx } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { fillRectCtx, getScale } from './util';
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 export 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 = readConfObject(config, 'bicolorPivot');
     const pivotValue = readConfObject(config, 'bicolorPivotValue');
@@ -16,7 +17,7 @@ export function drawDensity(ctx, props) {
     const scale = getScale({
         ...scaleOpts,
         pivotValue: crossing ? pivotValue : undefined,
-        range: crossing ? [negColor, 'white', posColor] : ['white', posColor],
+        range: crossing ? [negColor, '#eee', posColor] : ['#eee', posColor],
     });
     const scale2 = getScale({ ...scaleOpts, range: [0, height] });
     const cb = color === '#f0f'
@@ -28,7 +29,12 @@ export 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) {
+            checkStopToken(stopToken);
+            start = performance.now();
+        }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
             reducedFeatures.push(feature);
@@ -44,6 +50,10 @@ export function drawDensity(ctx, props) {
     if (hasClipping) {
         ctx.fillStyle = clipColor;
         for (const feature of features.values()) {
+            if (performance.now() - start > 400) {
+                checkStopToken(stopToken);
+                start = performance.now();
+            }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
             const w = rightPx - leftPx + fudgeFactor;
             const score = feature.get('score');

package/esm/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/esm/drawLine.js

@@ -1,10 +1,11 @@
 import { readConfObject } from '@jbrowse/core/configuration';
 import { clamp, featureSpanPx } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { getScale } from './util';
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 export 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;
@@ -17,7 +18,12 @@ export 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) {
+            checkStopToken(stopToken);
+            start = performance.now();
+        }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
         if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
             reducedFeatures.push(feature);
@@ -55,12 +61,12 @@ export 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/esm/drawXY.js

@@ -6,17 +6,23 @@ import { fillRectCtx, getOrigin, getScale } from './util';
 function lighten(color, amount) {
     const hslColor = color.toHsl();
     const l = hslColor.l * (1 + amount);
-    return colord({ ...hslColor, l: clamp(l, 0, 100) });
+    return colord({
+        ...hslColor,
+        l: clamp(l, 0, 100),
+    });
 }
 function darken(color, amount) {
     const hslColor = color.toHsl();
     const l = hslColor.l * (1 - amount);
-    return colord({ ...hslColor, l: clamp(l, 0, 100) });
+    return colord({
+        ...hslColor,
+        l: clamp(l, 0, 100),
+    });
 }
 const fudgeFactor = 0.3;
 const clipHeight = 2;
 export 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;
@@ -44,7 +50,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -66,7 +72,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -96,7 +102,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -118,7 +124,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -149,7 +155,7 @@ export function drawXY(ctx, props) {
         start = performance.now();
         for (const feature of features.values()) {
             if (performance.now() - start > 400) {
-                checkStopToken();
+                checkStopToken(stopToken);
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
@@ -167,12 +173,12 @@ export 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/esm/index.js

@@ -16,7 +16,7 @@ import MultiWiggleAddTrackWorkflowF from './MultiWiggleAddTrackWorkflow';
 import MultiXYPlotRendererF from './MultiXYPlotRenderer';
 import QuantitativeTrackF from './QuantitativeTrack';
 import WiggleBaseRenderer from './WiggleBaseRenderer';
-import { MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from './WiggleRPC/rpcMethods';
+import { MultiWiggleClusterScoreMatrix, MultiWiggleGetScoreMatrix, MultiWiggleGetSources, WiggleGetGlobalQuantitativeStats, WiggleGetMultiRegionQuantitativeStats, } from './WiggleRPC/rpcMethods';
 import XYPlotRendererF, { ReactComponent as XYPlotRendererReactComponent, XYPlotRenderer, configSchema as xyPlotRendererConfigSchema, } from './XYPlotRenderer';
 import * as utils from './util';
 export default class WigglePlugin extends Plugin {
@@ -54,6 +54,8 @@ export default class WigglePlugin extends Plugin {
         pm.addRpcMethod(() => new WiggleGetGlobalQuantitativeStats(pm));
         pm.addRpcMethod(() => new WiggleGetMultiRegionQuantitativeStats(pm));
         pm.addRpcMethod(() => new MultiWiggleGetSources(pm));
+        pm.addRpcMethod(() => new MultiWiggleGetScoreMatrix(pm));
+        pm.addRpcMethod(() => new MultiWiggleClusterScoreMatrix(pm));
     }
 }
 export * from './util';

package/esm/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/esm/shared/SharedWiggleMixin.js

@@ -118,7 +118,7 @@ export default function SharedWiggleMixin(configSchema) {
         },
         get rendererTypeNameSimple() {
             var _a;
-            return (_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : getConf(self, 'defaultRendering');
+            return ((_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : getConf(self, 'defaultRendering'));
         },
         get filters() {
             return undefined;
@@ -189,12 +189,12 @@ export default function SharedWiggleMixin(configSchema) {
     })
         .views(self => ({
         get filled() {
-            const { fill, rendererConfig } = self;
-            return fill !== null && fill !== void 0 ? fill : readConfObject(rendererConfig, 'filled');
+            var _a;
+            return ((_a = self.fill) !== null && _a !== void 0 ? _a : readConfObject(self.rendererConfig, 'filled'));
         },
         get summaryScoreModeSetting() {
-            const { summaryScoreMode: mode, rendererConfig } = self;
-            return mode !== null && mode !== void 0 ? mode : readConfObject(rendererConfig, 'summaryScoreMode');
+            var _a;
+            return ((_a = self.summaryScoreMode) !== null && _a !== void 0 ? _a : readConfObject(self.rendererConfig, 'summaryScoreMode'));
         },
         get scaleOpts() {
             return {
@@ -209,8 +209,8 @@ export default function SharedWiggleMixin(configSchema) {
             return self.rendererTypeName === 'XYPlotRenderer';
         },
         get displayCrossHatchesSetting() {
-            const { displayCrossHatches: hatches, rendererConfig } = self;
-            return hatches !== null && hatches !== void 0 ? hatches : readConfObject(rendererConfig, 'displayCrossHatches');
+            var _a;
+            return ((_a = self.displayCrossHatches) !== null && _a !== void 0 ? _a : readConfObject(self.rendererConfig, 'displayCrossHatches'));
         },
         get hasResolution() {
             return self.adapterCapabilities.includes('hasResolution');
@@ -285,7 +285,10 @@ export default function SharedWiggleMixin(configSchema) {
                     onClick: () => {
                         getSession(self).queueDialog(handleClose => [
                             SetMinMaxDialog,
-                            { model: self, handleClose },
+                            {
+                                model: self,
+                                handleClose,
+                            },
                         ]);
                     },
                 },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "3.0.5",
+  "version": "3.2.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,9 +37,9 @@
   },
   "dependencies": {
     "@gmod/bbi": "^6.0.0",
-    "@jbrowse/core": "^3.0.5",
-    "@jbrowse/plugin-data-management": "^3.0.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.5",
+    "@jbrowse/core": "^3.2.0",
+    "@jbrowse/plugin-data-management": "^3.2.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.2.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "@mui/x-charts-vendor": "^7.12.0",
@@ -62,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a03749efe19e51609922272b845a331897346789"
+  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
 }