@jbrowse/plugin-variants 3.2.0 → 3.4.0

package/dist/shared/drawAlleleCount.js

@@ -1,30 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.getColorAlleleCount = getColorAlleleCount;
 exports.drawColorAlleleCount = drawColorAlleleCount;
 const colord_1 = require("@jbrowse/core/util/colord");
 const constants_1 = require("./constants");
-function getColorAlleleCount(alleles, mostFrequentAlt) {
-    const total = alleles.length;
-    let alt = 0;
-    let uncalled = 0;
-    let alt2 = 0;
-    let ref = 0;
-    for (const allele of alleles) {
-        if (allele === mostFrequentAlt) {
-            alt++;
-        }
-        else if (allele === '0') {
-            ref++;
-        }
-        else if (allele === '.') {
-            uncalled++;
-        }
-        else {
-            alt2++;
-        }
-    }
+function getColorAlleleCount(ref, alt, alt2, uncalled, total, drawReference = true) {
     if (ref === total) {
-        return `#ccc`;
+        return drawReference ? '#ccc' : '';
     }
     else {
         let a1;
@@ -42,7 +24,27 @@ function getColorAlleleCount(alleles, mostFrequentAlt) {
         return (a1 === null || a1 === void 0 ? void 0 : a1.toHex()) || 'black';
     }
 }
-function drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt) {
-    ctx.fillStyle = getColorAlleleCount(alleles, mostFrequentAlt);
-    ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
+function drawColorAlleleCount(c, ctx, x, y, w, h, featureType = '', featureStrand, alpha = 1) {
+    ctx.fillStyle = alpha !== 1 ? (0, colord_1.colord)(c).alpha(alpha).toHex() : c;
+    if (featureType === 'inversion') {
+        if (featureStrand === 1) {
+            ctx.beginPath();
+            ctx.moveTo(x - constants_1.f2, y - constants_1.f2);
+            ctx.lineTo(x - constants_1.f2, y + h + constants_1.f2);
+            ctx.lineTo(x + w + constants_1.f2, y + h / 2);
+            ctx.closePath();
+            ctx.fill();
+        }
+        else {
+            ctx.beginPath();
+            ctx.moveTo(x + w + constants_1.f2, y - constants_1.f2);
+            ctx.lineTo(x + w + constants_1.f2, y + h + constants_1.f2);
+            ctx.lineTo(x - constants_1.f2, y + h / 2);
+            ctx.closePath();
+            ctx.fill();
+        }
+    }
+    else {
+        ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
+    }
 }

package/dist/shared/drawPhased.d.ts

@@ -1 +1 @@
-export declare function drawPhased(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, HP: number, PS?: string): void;
+export declare function drawPhased(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, HP: number, PS?: string, drawReference?: boolean, alpha?: number): string | undefined;

package/dist/shared/drawPhased.js

@@ -2,20 +2,24 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.drawPhased = drawPhased;
 const colors_1 = require("@jbrowse/core/ui/colors");
+const colord_1 = require("@jbrowse/core/util/colord");
 const constants_1 = require("./constants");
 const util_1 = require("./util");
-function getColorPhased(alleles, HP) {
+function getColorPhased(alleles, HP, drawReference = true) {
     const c = +alleles[HP];
-    return c ? colors_1.set1[c - 1] || 'black' : '#ccc';
+    return c ? colors_1.set1[c - 1] || 'black' : drawReference ? '#ccc' : undefined;
 }
-function getColorPhasedWithPhaseSet(alleles, HP, PS) {
+function getColorPhasedWithPhaseSet(alleles, HP, PS, drawReference = true) {
     const c = +alleles[HP];
-    return c ? (0, util_1.colorify)(+PS) || 'black' : '#ccc';
+    return c ? (0, util_1.colorify)(+PS) || 'black' : drawReference ? '#ccc' : undefined;
 }
-function drawPhased(alleles, ctx, x, y, w, h, HP, PS) {
-    ctx.fillStyle =
-        PS !== undefined
-            ? getColorPhasedWithPhaseSet(alleles, HP, PS)
-            : getColorPhased(alleles, HP);
-    ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
+function drawPhased(alleles, ctx, x, y, w, h, HP, PS, drawReference = true, alpha = 1) {
+    const c = PS !== undefined
+        ? getColorPhasedWithPhaseSet(alleles, HP, PS, drawReference)
+        : getColorPhased(alleles, HP, drawReference);
+    if (c) {
+        ctx.fillStyle = alpha !== 1 ? (0, colord_1.colord)(c).alpha(alpha).toHex() : c;
+        ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
+    }
+    return c;
 }

package/dist/shared/minorAlleleFrequencyUtils.d.ts

@@ -1,9 +1,14 @@
 import type { Feature } from '@jbrowse/core/util';
 export declare function findSecondLargestNumber(arr: Iterable<number>): number;
-export declare function calculateAlleleCounts(feat: Feature): Map<any, any>;
-export declare function calculateMinorAlleleFrequency(alleleCounts: Map<string, number>): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number, lengthCutoffFilter?: number): {
+export declare function calculateAlleleCounts(feat: Feature): Record<string, number>;
+export declare function calculateMinorAlleleFrequency(alleleCounts: Record<string, number>): number;
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopToken, }: {
+    features: Iterable<Feature>;
+    minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
+    stopToken?: string;
+}): {
     feature: Feature;
     mostFrequentAlt: string;
-    alleleCounts: Map<string, number>;
+    alleleCounts: Record<string, number>;
 }[];

package/dist/shared/minorAlleleFrequencyUtils.js

@@ -20,24 +20,30 @@ function findSecondLargestNumber(arr) {
     return secondMax;
 }
 function calculateAlleleCounts(feat) {
-    const samp = feat.get('genotypes');
-    const alleleCounts = new Map();
-    for (const val of Object.values(samp)) {
-        const alleles = val.split(/[/|]/);
-        for (const allele of alleles) {
-            alleleCounts.set(allele, (alleleCounts.get(allele) || 0) + 1);
+    var _a;
+    const genotypes = feat.get('genotypes');
+    const alleleCounts = { 0: 0, 1: 0, '.': 0 };
+    const cacheSplit = {};
+    const vals = Object.values(genotypes);
+    const len = vals.length;
+    for (let i = 0; i < len; i++) {
+        const genotype = vals[i];
+        const alleles = cacheSplit[genotype] || (cacheSplit[genotype] = genotype.split(/[/|]/));
+        for (let i = 0, len = alleles.length; i < len; i++) {
+            const a = alleles[i];
+            alleleCounts[a] = ((_a = alleleCounts[a]) !== null && _a !== void 0 ? _a : 0) + 1;
         }
     }
     return alleleCounts;
 }
 function calculateMinorAlleleFrequency(alleleCounts) {
-    return (findSecondLargestNumber(alleleCounts.values()) /
-        ((0, util_1.sum)(alleleCounts.values()) || 1));
+    return (findSecondLargestNumber(Object.values(alleleCounts)) /
+        ((0, util_1.sum)(Object.values(alleleCounts)) || 1));
 }
 function getMostFrequentAlt(alleleCounts) {
     let mostFrequentAlt;
     let max = 0;
-    for (const [alt, altCount] of alleleCounts.entries()) {
+    for (const [alt, altCount] of Object.entries(alleleCounts)) {
         if (alt !== '.' && alt !== '0') {
             if (altCount > max) {
                 mostFrequentAlt = alt;
@@ -47,21 +53,20 @@ function getMostFrequentAlt(alleleCounts) {
     }
     return mostFrequentAlt;
 }
-function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter, lengthCutoffFilter = 10) {
+function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopToken, }) {
     const results = [];
-    for (const feature of feats) {
+    (0, util_1.forEachWithStopTokenCheck)(features, stopToken, feature => {
         if (feature.get('end') - feature.get('start') <= lengthCutoffFilter) {
             const alleleCounts = calculateAlleleCounts(feature);
             if (calculateMinorAlleleFrequency(alleleCounts) >=
                 minorAlleleFrequencyFilter) {
-                const mostFrequentAlt = getMostFrequentAlt(alleleCounts);
                 results.push({
                     feature,
-                    mostFrequentAlt,
+                    mostFrequentAlt: getMostFrequentAlt(alleleCounts),
                     alleleCounts,
                 });
             }
         }
-    }
+    });
     return results;
 }

package/dist/shared/sourcesGridUtils.d.ts

@@ -1,10 +1,11 @@
+import type { GridRowId } from '@mui/x-data-grid';
 export declare function moveUp(arr: {
     name: string;
-}[], sel: string[], by?: number): {
+}[], sel: GridRowId[], by?: number): {
     name: string;
 }[];
 export declare function moveDown(arr: {
     name: string;
-}[], sel: string[], by?: number): {
+}[], sel: GridRowId[], by?: number): {
     name: string;
 }[];

package/esm/LinearVariantDisplay/model.d.ts

@@ -200,7 +200,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.js

@@ -2,8 +2,8 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useRef, useState } from 'react';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import { observer } from 'mobx-react';
-import Crosshair from './Crosshair';
-import LegendBar from '../../shared/components/LegendBar';
+import Crosshair from '../../shared/components/MultiVariantCrosshairs';
+import LegendBar from '../../shared/components/MultiVariantLegendBar';
 const MultiLinearVariantDisplayComponent = observer(function (props) {
     const { model } = props;
     const ref = useRef(null);

package/esm/MultiLinearVariantDisplay/index.js

@@ -7,7 +7,7 @@ export default function MultiLinearVariantDisplayF(pluginManager) {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
             name: 'MultiLinearVariantDisplay',
-            displayName: 'Multi-variant display (regular)',
+            displayName: 'Multi-sample variant display (regular)',
             configSchema,
             stateModel: modelFactory(configSchema),
             trackType: 'VariantTrack',

package/esm/MultiLinearVariantDisplay/model.d.ts

@@ -89,11 +89,13 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    lengthCutoffFilter: import("mobx-state-tree").IType<number | undefined, number, number>;
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
+    referenceDrawingMode: import("mobx-state-tree").IType<string | undefined, string, string>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"MultiLinearVariantDisplay">;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -206,7 +208,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -237,19 +239,28 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
 } & {
     sourcesLoadingStopToken: string | undefined;
+    simplifiedFeaturesStopToken: string | undefined;
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
     sourcesVolatile: import("../shared/types").Source[] | undefined;
     featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
     hasPhased: boolean;
     sampleInfo: undefined | Record<string, import("../shared/types").SampleInfo>;
-    hoveredGenotype: string | undefined;
+    hoveredGenotype: {
+        genotype: string;
+        name: string;
+    } | undefined;
 } & {
+    setJexlFilters(f?: string[]): void;
     setRowHeight(arg: number): void;
-    setHoveredGenotype(arg: string): void;
+    setHoveredGenotype(arg?: {
+        genotype: string;
+        name: string;
+    }): void;
     setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
     setLayout(layout: import("../shared/types").Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
+    setSimplifiedFeaturesLoading(str: string): void;
     setSources(sources: import("../shared/types").Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
@@ -257,7 +268,9 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     setAutoHeight(arg: boolean): void;
     setHasPhased(arg: boolean): void;
     setSampleInfo(arg: Record<string, import("../shared/types").SampleInfo>): void;
+    setReferenceDrawingMode(arg: string): void;
 } & {
+    readonly activeFilters: any;
     readonly preSources: import("../shared/types").Source[] | undefined;
     readonly sourcesWithoutLayout: {
         label: string;
@@ -278,6 +291,17 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         HP?: number;
     }[] | undefined;
 } & {
+    readonly sourceMap: {
+        [k: string]: {
+            label: string;
+            id: string;
+            baseUri?: string;
+            name: string;
+            color?: string;
+            group?: string;
+            HP?: number;
+        };
+    } | undefined;
     readonly rowHeight: number;
     adapterProps(): any;
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
@@ -331,6 +355,18 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         type?: undefined;
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        type: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        icon?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {

package/esm/MultiLinearVariantDisplay/model.js

@@ -7,7 +7,6 @@ export function stateModelFactory(configSchema) {
         type: types.literal('MultiLinearVariantDisplay'),
         rowHeightSetting: types.optional(types.number, 11),
         minorAlleleFrequencyFilter: types.optional(types.number, 0),
-        autoHeight: false,
     }))
         .views(() => ({
         get rendererTypeName() {

package/esm/MultiLinearVariantDisplay/renderSvg.js

@@ -1,7 +1,7 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { getContainingView } from '@jbrowse/core/util';
 import { when } from 'mobx';
-import LegendBar from '../shared/components/LegendBar';
+import LegendBar from '../shared/components/MultiVariantLegendBar';
 export async function renderSvg(self, opts, superRenderSvg) {
     await when(() => !!self.regionCannotBeRenderedText);
     const { offsetPx } = getContainingView(self);

package/esm/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js

@@ -1,6 +1,7 @@
-import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
-import { useState } from 'react';
-import { ResizeHandle } from '@jbrowse/core/ui';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { forwardRef, isValidElement, useState } from 'react';
+import { ResizeHandle, SanitizedHTML } from '@jbrowse/core/ui';
+import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
 import { getContainingView, getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
@@ -35,15 +36,21 @@ const LinesConnectingMatrixToGenomicPosition = observer(function ({ model, expor
     const assembly = assemblyManager.get(assemblyNames[0]);
     const b0 = ((_a = dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.widthPx) || 0;
     const w = b0 / ((featuresVolatile === null || featuresVolatile === void 0 ? void 0 : featuresVolatile.length) || 1);
-    return assembly && featuresVolatile ? (_jsxs(_Fragment, { children: [_jsxs(Wrapper, { exportSVG: exportSVG, model: model, children: [_jsx(AllLines, { model: model, setMouseOverLine: setMouseOverLine }), mouseOverLine ? (_jsx("line", { stroke: "#f00c", strokeWidth: 2, style: {
-                            pointerEvents: 'none',
-                        }, x1: mouseOverLine.idx * w + w / 2, x2: mouseOverLine.c, y1: lineZoneHeight, y2: 0, onMouseLeave: () => {
-                            setMouseOverLine(undefined);
-                        } })) : null] }), !exportSVG ? (_jsx(ResizeHandle, { style: {
+    return assembly && featuresVolatile ? (_jsxs(_Fragment, { children: [_jsxs(Wrapper, { exportSVG: exportSVG, model: model, children: [_jsx(AllLines, { model: model, setMouseOverLine: setMouseOverLine }), mouseOverLine ? (_jsxs(_Fragment, { children: [_jsx("line", { stroke: "#f00c", strokeWidth: 2, style: {
+                                    pointerEvents: 'none',
+                                }, x1: mouseOverLine.idx * w + w / 2, x2: mouseOverLine.c, y1: lineZoneHeight, y2: 0, onMouseLeave: () => {
+                                    setMouseOverLine(undefined);
+                                } }), _jsx(LineTooltip, { contents: mouseOverLine.f.get('name') })] })) : null] }), !exportSVG ? (_jsx(ResizeHandle, { style: {
                     position: 'absolute',
                     top: lineZoneHeight - 4,
                 }, onDrag: n => model.setLineZoneHeight(lineZoneHeight + n), className: classes.resizeHandle })) : null] })) : null;
 });
+const TooltipContents = forwardRef(function TooltipContents2({ message }, ref) {
+    return (_jsx("div", { ref: ref, children: isValidElement(message) ? (message) : message ? (_jsx(SanitizedHTML, { html: String(message) })) : null }));
+});
+const LineTooltip = observer(function ({ contents }) {
+    return contents ? (_jsx(BaseTooltip, { children: _jsx(TooltipContents, { message: contents }) })) : null;
+});
 const AllLines = observer(function ({ model, setMouseOverLine, }) {
     var _a;
     const { assemblyManager } = getSession(model);

package/esm/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js

@@ -2,9 +2,9 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useRef, useState } from 'react';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import { observer } from 'mobx-react';
-import Crosshair from './Crosshair';
 import LinesConnectingMatrixToGenomicPosition from './LinesConnectingMatrixToGenomicPosition';
-import LegendBar from '../../shared/components/LegendBar';
+import Crosshair from '../../shared/components/MultiVariantCrosshairs';
+import LegendBar from '../../shared/components/MultiVariantLegendBar';
 const MultiLinearVariantMatrixDisplayComponent = observer(function (props) {
     const { model } = props;
     const { lineZoneHeight } = model;

package/esm/MultiLinearVariantMatrixDisplay/index.js

@@ -7,7 +7,7 @@ export default function LinearVariantMatrixDisplayF(pluginManager) {
         const configSchema = configSchemaF(pluginManager);
         return new DisplayType({
             name: 'LinearVariantMatrixDisplay',
-            displayName: 'Multi-variant display (matrix)',
+            displayName: 'Multi-sample variant display (matrix)',
             configSchema,
             stateModel: stateModelFactory(configSchema),
             trackType: 'VariantTrack',

package/esm/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -89,6 +89,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    lengthCutoffFilter: import("mobx-state-tree").IType<number | undefined, number, number>;
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
+    referenceDrawingMode: import("mobx-state-tree").IType<string | undefined, string, string>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -205,7 +208,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -236,19 +239,28 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
 } & {
     sourcesLoadingStopToken: string | undefined;
+    simplifiedFeaturesStopToken: string | undefined;
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
     sourcesVolatile: import("../shared/types").Source[] | undefined;
     featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
     hasPhased: boolean;
     sampleInfo: undefined | Record<string, import("../shared/types").SampleInfo>;
-    hoveredGenotype: string | undefined;
+    hoveredGenotype: {
+        genotype: string;
+        name: string;
+    } | undefined;
 } & {
+    setJexlFilters(f?: string[]): void;
     setRowHeight(arg: number): void;
-    setHoveredGenotype(arg: string): void;
+    setHoveredGenotype(arg?: {
+        genotype: string;
+        name: string;
+    }): void;
     setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
     setLayout(layout: import("../shared/types").Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
+    setSimplifiedFeaturesLoading(str: string): void;
     setSources(sources: import("../shared/types").Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
@@ -256,7 +268,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     setAutoHeight(arg: boolean): void;
     setHasPhased(arg: boolean): void;
     setSampleInfo(arg: Record<string, import("../shared/types").SampleInfo>): void;
+    setReferenceDrawingMode(arg: string): void;
 } & {
+    readonly activeFilters: any;
     readonly preSources: import("../shared/types").Source[] | undefined;
     readonly sourcesWithoutLayout: {
         label: string;
@@ -277,6 +291,17 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         HP?: number;
     }[] | undefined;
 } & {
+    readonly sourceMap: {
+        [k: string]: {
+            label: string;
+            id: string;
+            baseUri?: string;
+            name: string;
+            color?: string;
+            group?: string;
+            HP?: number;
+        };
+    } | undefined;
     readonly rowHeight: number;
     adapterProps(): any;
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
@@ -330,6 +355,18 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         type?: undefined;
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        type: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        icon?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {

package/esm/MultiLinearVariantMatrixDisplay/model.js

@@ -38,6 +38,7 @@ export default function stateModelFactory(configSchema) {
                 notReady: superProps.notReady || !self.sources || !self.featuresReady,
                 renderingMode: self.renderingMode,
                 minorAlleleFrequencyFilter: self.minorAlleleFrequencyFilter,
+                lengthCutoffFilter: self.lengthCutoffFilter,
                 height: self.totalHeight,
                 sources: self.sources,
             };

package/esm/MultiLinearVariantMatrixDisplay/renderSvg.js

@@ -2,7 +2,7 @@ import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-run
 import { getContainingView } from '@jbrowse/core/util';
 import { when } from 'mobx';
 import LinesConnectingMatrixToGenomicPosition from './components/LinesConnectingMatrixToGenomicPosition';
-import LegendBar from '../shared/components/LegendBar';
+import LegendBar from '../shared/components/MultiVariantLegendBar';
 export async function renderSvg(model, opts, superRenderSvg) {
     await when(() => !!model.regionCannotBeRenderedText);
     const { offsetPx } = getContainingView(model);

package/esm/MultiLinearVariantMatrixRenderer/{LinearVariantMatrixRenderer.d.ts → MultiLinearVariantMatrixRenderer.d.ts}

@@ -1,33 +1,36 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { SimpleFeature } from '@jbrowse/core/util';
 import type { RenderArgsDeserialized } from './types';
-import type { Feature } from '@jbrowse/core/util';
 export default class LinearVariantMatrixRenderer extends BoxRendererType {
     supportsSVG: boolean;
     render(renderProps: RenderArgsDeserialized): Promise<{
         features: Map<any, any>;
-        simplifiedFeatures: any;
+        simplifiedFeatures: SimpleFeature[];
         height: number;
         width: number;
-        canvasRecordedData: any;
-        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        arr: string[][];
+        canvasRecordedData: Record<string, unknown>;
+        layout: import("@jbrowse/core/util/layouts/BaseLayout").BaseLayout<import("@jbrowse/core/util").Feature>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
-        simplifiedFeatures: any;
+        simplifiedFeatures: SimpleFeature[];
         height: number;
         width: number;
-        reactElement: import("react/jsx-runtime").JSX.Element;
-        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        arr: string[][];
+        imageData: any;
+        layout: import("@jbrowse/core/util/layouts/BaseLayout").BaseLayout<import("@jbrowse/core/util").Feature>;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
-        simplifiedFeatures: any;
+        simplifiedFeatures: SimpleFeature[];
         height: number;
         width: number;
-        imageData: any;
-        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
-        reactElement?: React.ReactElement;
+        arr: string[][];
+        reactElement: React.ReactElement;
+        layout: import("@jbrowse/core/util/layouts/BaseLayout").BaseLayout<import("@jbrowse/core/util").Feature>;
         html?: string;
     }>;
 }

package/esm/MultiLinearVariantMatrixRenderer/{LinearVariantMatrixRenderer.js → MultiLinearVariantMatrixRenderer.js}

@@ -12,7 +12,7 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         const { end, start } = region;
         const width = (end - start) / bpPerPx;
         const { makeImageData } = await import('./makeImageData');
-        const { mafs, ...res } = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData({
+        const { mafs, ...rest } = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData({
             ctx,
             canvasWidth: width,
             canvasHeight: height,
@@ -24,14 +24,14 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         }));
         const results = await super.render({
             ...renderProps,
-            ...res,
+            ...rest,
             features,
             height,
             width,
         });
         return {
             ...results,
-            ...res,
+            ...rest,
             features: new Map(),
             simplifiedFeatures: mafs.map(({ feature }) => new SimpleFeature({
                 id: feature.id(),

package/esm/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.d.ts

@@ -0,0 +1,8 @@
+import type { MultiVariantBaseModel } from '../../shared/MultiVariantBaseModel';
+declare const MultiLinearVariantMatrixRendering: (props: {
+    width: number;
+    height: number;
+    displayModel: MultiVariantBaseModel;
+    arr: string[][];
+}) => import("react/jsx-runtime").JSX.Element;
+export default MultiLinearVariantMatrixRendering;