@jbrowse/plugin-variants 3.0.1 → 3.0.3

package/dist/MultiLinearVariantDisplay/components/Crosshair.js

@@ -7,7 +7,7 @@ const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-const MultiVariantTooltip_1 = __importDefault(require("../../shared/MultiVariantTooltip"));
+const MultiVariantTooltip_1 = __importDefault(require("../../shared/components/MultiVariantTooltip"));
 const useStyles = (0, mui_1.makeStyles)()({
     rel: {
         position: 'relative',

package/dist/MultiLinearVariantDisplay/components/VariantDisplayComponent.js

@@ -8,7 +8,7 @@ const react_1 = require("react");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_react_1 = require("mobx-react");
 const Crosshair_1 = __importDefault(require("./Crosshair"));
-const LegendBar_1 = __importDefault(require("../../shared/LegendBar"));
+const LegendBar_1 = __importDefault(require("../../shared/components/LegendBar"));
 const MultiLinearVariantDisplayComponent = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const ref = (0, react_1.useRef)(null);

package/dist/MultiLinearVariantDisplay/model.d.ts

@@ -82,7 +82,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
-    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../types").Source[], import("../types").Source[], import("../types").Source[]>, [undefined]>;
+    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../shared/types").Source[], import("../shared/types").Source[], import("../shared/types").Source[]>, [undefined]>;
     configuration: AnyConfigurationSchemaType;
     minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -238,27 +238,27 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     sourcesLoadingStopToken: string | undefined;
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
-    sourcesVolatile: import("../types").Source[] | undefined;
+    sourcesVolatile: import("../shared/types").Source[] | undefined;
     featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
     hasPhased: boolean;
-    sampleInfo: undefined | Record<string, import("../types").SampleInfo>;
+    sampleInfo: undefined | Record<string, import("../shared/types").SampleInfo>;
     hoveredGenotype: string | undefined;
 } & {
     setRowHeight(arg: number): void;
     setHoveredGenotype(arg: string): void;
     setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
-    setLayout(layout: import("../types").Source[]): void;
+    setLayout(layout: import("../shared/types").Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
-    setSources(sources: import("../types").Source[]): void;
+    setSources(sources: import("../shared/types").Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
     setPhasedMode(arg: string): void;
     setAutoHeight(arg: boolean): void;
     setHasPhased(arg: boolean): void;
-    setSampleInfo(arg: Record<string, import("../types").SampleInfo>): void;
+    setSampleInfo(arg: Record<string, import("../shared/types").SampleInfo>): void;
 } & {
-    readonly preSources: import("../types").Source[] | undefined;
+    readonly preSources: import("../shared/types").Source[] | undefined;
     readonly sources: {
         label: string;
         id: string;

package/dist/MultiLinearVariantDisplay/renderSvg.js

@@ -7,7 +7,7 @@ exports.renderSvg = renderSvg;
 const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
-const LegendBar_1 = __importDefault(require("../shared/LegendBar"));
+const LegendBar_1 = __importDefault(require("../shared/components/LegendBar"));
 async function renderSvg(self, opts, superRenderSvg) {
     await (0, mobx_1.when)(() => !!self.regionCannotBeRenderedText);
     const { offsetPx } = (0, util_1.getContainingView)(self);

package/dist/MultiLinearVariantMatrixDisplay/components/Crosshair.js

@@ -7,7 +7,7 @@ const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-const MultiVariantTooltip_1 = __importDefault(require("../../shared/MultiVariantTooltip"));
+const MultiVariantTooltip_1 = __importDefault(require("../../shared/components/MultiVariantTooltip"));
 const useStyles = (0, mui_1.makeStyles)()({
     cursor: {
         pointerEvents: 'none',

package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js

@@ -9,7 +9,7 @@ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view"
 const mobx_react_1 = require("mobx-react");
 const Crosshair_1 = __importDefault(require("./Crosshair"));
 const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./LinesConnectingMatrixToGenomicPosition"));
-const LegendBar_1 = __importDefault(require("../../shared/LegendBar"));
+const LegendBar_1 = __importDefault(require("../../shared/components/LegendBar"));
 const MultiLinearVariantMatrixDisplayComponent = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { lineZoneHeight } = model;

package/dist/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -82,7 +82,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     configuration: AnyConfigurationSchemaType;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
-    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../types").Source[], import("../types").Source[], import("../types").Source[]>, [undefined]>;
+    layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("../shared/types").Source[], import("../shared/types").Source[], import("../shared/types").Source[]>, [undefined]>;
     configuration: AnyConfigurationSchemaType;
     minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -236,27 +236,27 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     sourcesLoadingStopToken: string | undefined;
     featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
-    sourcesVolatile: import("../types").Source[] | undefined;
+    sourcesVolatile: import("../shared/types").Source[] | undefined;
     featuresVolatile: import("@jbrowse/core/util").Feature[] | undefined;
     hasPhased: boolean;
-    sampleInfo: undefined | Record<string, import("../types").SampleInfo>;
+    sampleInfo: undefined | Record<string, import("../shared/types").SampleInfo>;
     hoveredGenotype: string | undefined;
 } & {
     setRowHeight(arg: number): void;
     setHoveredGenotype(arg: string): void;
     setFeatures(f: import("@jbrowse/core/util").Feature[]): void;
-    setLayout(layout: import("../types").Source[]): void;
+    setLayout(layout: import("../shared/types").Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
-    setSources(sources: import("../types").Source[]): void;
+    setSources(sources: import("../shared/types").Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
     setPhasedMode(arg: string): void;
     setAutoHeight(arg: boolean): void;
     setHasPhased(arg: boolean): void;
-    setSampleInfo(arg: Record<string, import("../types").SampleInfo>): void;
+    setSampleInfo(arg: Record<string, import("../shared/types").SampleInfo>): void;
 } & {
-    readonly preSources: import("../types").Source[] | undefined;
+    readonly preSources: import("../shared/types").Source[] | undefined;
     readonly sources: {
         label: string;
         id: string;

package/dist/MultiLinearVariantMatrixDisplay/renderSvg.js

@@ -7,8 +7,8 @@ exports.renderSvg = renderSvg;
 const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
-const LegendBar_1 = __importDefault(require("../shared/LegendBar"));
 const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./components/LinesConnectingMatrixToGenomicPosition"));
+const LegendBar_1 = __importDefault(require("../shared/components/LegendBar"));
 async function renderSvg(model, opts, superRenderSvg) {
     await (0, mobx_1.when)(() => !!model.regionCannotBeRenderedText);
     const { offsetPx } = (0, util_1.getContainingView)(model);

package/dist/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js

@@ -71,12 +71,12 @@ class LinearVariantMatrixRenderer extends BoxRendererType_1.default {
             ...results,
             ...res,
             features: new Map(),
-            simplifiedFeatures: mafs.map((s) => new util_1.SimpleFeature({
-                id: s.id(),
+            simplifiedFeatures: mafs.map(({ feature }) => new util_1.SimpleFeature({
+                id: feature.id(),
                 data: {
-                    start: s.get('start'),
-                    end: s.get('end'),
-                    refName: s.get('refName'),
+                    start: feature.get('start'),
+                    end: feature.get('end'),
+                    refName: feature.get('refName'),
                 },
             })),
             height,

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.d.ts

@@ -4,7 +4,10 @@ export declare function makeImageData({ ctx, canvasWidth, canvasHeight, renderAr
     canvasWidth: number;
     canvasHeight: number;
     renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-}): {
-    mafs: import("@jbrowse/core/util").Feature[];
+}): Promise<{
+    mafs: {
+        feature: import("@jbrowse/core/util").Feature;
+        mostFrequentAlt: string;
+    }[];
     arr: string[][];
-};
+}>;

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -1,97 +1,88 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.makeImageData = makeImageData;
-const multiVariantColor_1 = require("../shared/multiVariantColor");
-const util_1 = require("../util");
-const fudgeFactor = 0.6;
-const f2 = fudgeFactor / 2;
-function drawColorAlleleCount(alleles, ctx, x, y, w, h) {
-    ctx.fillStyle = (0, multiVariantColor_1.getColorAlleleCount)(alleles);
-    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-}
-function drawPhased(alleles, ctx, x, y, w, h, HP, PS) {
-    ctx.fillStyle =
-        PS !== undefined
-            ? (0, multiVariantColor_1.getColorPhasedWithPhaseSet)(alleles, HP, PS)
-            : (0, multiVariantColor_1.getColorPhased)(alleles, HP);
-    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-}
-function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
-    var _a, _b;
+const util_1 = require("@jbrowse/core/util");
+const constants_1 = require("../shared/constants");
+const drawAlleleCount_1 = require("../shared/drawAlleleCount");
+const drawPhased_1 = require("../shared/drawPhased");
+const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
+async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
     const { renderingMode: renderingMode, minorAlleleFrequencyFilter, sources, features, } = renderArgs;
     const { statusCallback = () => { } } = renderArgs;
-    statusCallback('Drawing variant matrix');
     const h = canvasHeight / sources.length;
-    const mafs = (0, util_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(features.values(), minorAlleleFrequencyFilter);
+    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(features.values(), minorAlleleFrequencyFilter);
     const arr = [];
     const m = mafs.length;
     const w = canvasWidth / m;
-    for (let i = 0; i < m; i++) {
-        const arr2 = [];
-        const f = mafs[i];
-        const hasPhaseSet = f.get('format').includes('PS');
-        if (hasPhaseSet) {
-            const samp = f.get('samples');
-            const x = (i / mafs.length) * canvasWidth;
-            const sln = sources.length;
-            for (let j = 0; j < sln; j++) {
-                const y = (j / sln) * canvasHeight;
-                const { name, HP } = sources[j];
-                const s = samp[name];
-                if (s) {
-                    const genotype = (_a = s.GT) === null || _a === void 0 ? void 0 : _a[0];
+    await (0, util_1.updateStatus)('Drawing variant matrix', statusCallback, () => {
+        var _a, _b;
+        for (let i = 0; i < m; i++) {
+            const arr2 = [];
+            const { feature, mostFrequentAlt } = mafs[i];
+            const hasPhaseSet = feature.get('format').includes('PS');
+            if (hasPhaseSet) {
+                const samp = feature.get('samples');
+                const x = (i / mafs.length) * canvasWidth;
+                const sln = sources.length;
+                for (let j = 0; j < sln; j++) {
+                    const y = (j / sln) * canvasHeight;
+                    const { name, HP } = sources[j];
+                    const s = samp[name];
+                    if (s) {
+                        const genotype = (_a = s.GT) === null || _a === void 0 ? void 0 : _a[0];
+                        if (genotype) {
+                            arr2.push(genotype);
+                            const isPhased = genotype.includes('|');
+                            if (renderingMode === 'phased') {
+                                if (isPhased) {
+                                    const PS = (_b = s.PS) === null || _b === void 0 ? void 0 : _b[0];
+                                    const alleles = genotype.split('|');
+                                    (0, drawPhased_1.drawPhased)(alleles, ctx, x, y, w, h, HP, PS);
+                                }
+                                else {
+                                    ctx.fillStyle = 'black';
+                                    ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
+                                }
+                            }
+                            else {
+                                const alleles = genotype.split(/[/|]/);
+                                (0, drawAlleleCount_1.drawColorAlleleCount)(alleles, ctx, x, y, w, h, mostFrequentAlt);
+                            }
+                        }
+                    }
+                }
+            }
+            else {
+                const samp = feature.get('genotypes');
+                const x = (i / mafs.length) * canvasWidth;
+                const sln = sources.length;
+                for (let j = 0; j < sln; j++) {
+                    const y = (j / sln) * canvasHeight;
+                    const { name, HP } = sources[j];
+                    const genotype = samp[name];
                     if (genotype) {
                         arr2.push(genotype);
                         const isPhased = genotype.includes('|');
                         if (renderingMode === 'phased') {
                             if (isPhased) {
-                                const PS = (_b = s.PS) === null || _b === void 0 ? void 0 : _b[0];
                                 const alleles = genotype.split('|');
-                                drawPhased(alleles, ctx, x, y, w, h, HP, PS);
+                                (0, drawPhased_1.drawPhased)(alleles, ctx, x, y, w, h, HP);
                             }
                             else {
                                 ctx.fillStyle = 'black';
-                                ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+                                ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
                             }
                         }
                         else {
                             const alleles = genotype.split(/[/|]/);
-                            drawColorAlleleCount(alleles, ctx, x, y, w, h);
+                            (0, drawAlleleCount_1.drawColorAlleleCount)(alleles, ctx, x, y, w, h, mostFrequentAlt);
                         }
                     }
                 }
             }
+            arr.push(arr2);
         }
-        else {
-            const samp = f.get('genotypes');
-            const x = (i / mafs.length) * canvasWidth;
-            const sln = sources.length;
-            for (let j = 0; j < sln; j++) {
-                const y = (j / sln) * canvasHeight;
-                const { name, HP } = sources[j];
-                const genotype = samp[name];
-                if (genotype) {
-                    arr2.push(genotype);
-                    const isPhased = genotype.includes('|');
-                    if (renderingMode === 'phased') {
-                        if (isPhased) {
-                            const alleles = genotype.split('|');
-                            drawPhased(alleles, ctx, x, y, w, h, HP);
-                        }
-                        else {
-                            ctx.fillStyle = 'black';
-                            ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-                        }
-                    }
-                    else {
-                        const alleles = genotype.split(/[/|]/);
-                        drawColorAlleleCount(alleles, ctx, x, y, w, h);
-                    }
-                }
-            }
-        }
-        arr.push(arr2);
-    }
+    });
     return {
         mafs,
         arr,

package/dist/MultiLinearVariantMatrixRenderer/types.d.ts

@@ -1,4 +1,4 @@
-import type { Source } from '../types';
+import type { Source } from '../shared/types';
 import type { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import type { Feature } from '@jbrowse/core/util';
 export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
@@ -12,4 +12,5 @@ export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsD
     sources: Source[];
     features: Map<string, Feature>;
     renderingMode: string;
+    statusCallback?: (arg: string) => void;
 }

package/dist/MultiLinearVariantRenderer/MultiVariantRendering.d.ts

@@ -1,5 +1,5 @@
 import RBush from 'rbush';
-import type { Source } from '../types';
+import type { Source } from '../shared/types';
 import type { Feature } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
 declare const MultiVariantRendering: (props: {

package/dist/MultiLinearVariantRenderer/components/MultiVariantRendering.d.ts

@@ -0,0 +1,22 @@
+import RBush from 'rbush';
+import type { Source } from '../../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
+declare const MultiVariantRendering: (props: {
+    regions: Region[];
+    features: Map<string, Feature>;
+    bpPerPx: number;
+    width: number;
+    height: number;
+    sources: Source[];
+    scrollTop: number;
+    totalHeight: number;
+    rbush: RBush<{
+        genotype: string;
+    }>;
+    displayModel: any;
+    onMouseLeave?: (event: React.MouseEvent) => void;
+    onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void;
+    onFeatureClick?: (event: React.MouseEvent, arg?: Feature) => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default MultiVariantRendering;

package/dist/MultiLinearVariantRenderer/components/MultiVariantRendering.js

@@ -0,0 +1,52 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const rbush_1 = __importDefault(require("rbush"));
+const MultiVariantRendering = (0, mobx_react_1.observer)(function (props) {
+    const { totalHeight, scrollTop } = props;
+    const { rbush, displayModel } = props;
+    const ref = (0, react_1.useRef)(null);
+    const rbush2 = (0, react_1.useMemo)(() => new rbush_1.default().fromJSON(rbush), [rbush]);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        var _a;
+        let offsetX = 0;
+        let offsetY = 0;
+        if (ref.current) {
+            const r = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - r.left;
+            offsetY = eventClientY - r.top;
+        }
+        const ret = rbush2.search({
+            minX: offsetX,
+            maxX: offsetX + 3,
+            minY: offsetY,
+            maxY: offsetY + 3,
+        });
+        return (_a = ret[0]) === null || _a === void 0 ? void 0 : _a.genotype;
+    }
+    return ((0, jsx_runtime_1.jsx)("div", { ref: ref, onMouseMove: e => {
+            var _a;
+            return (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, getFeatureUnderMouse(e.clientX, e.clientY));
+        }, onMouseLeave: () => {
+            var _a;
+            (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, undefined);
+        }, onMouseOut: () => {
+            var _a;
+            (_a = displayModel.setHoveredGenotype) === null || _a === void 0 ? void 0 : _a.call(displayModel, undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height: totalHeight,
+        }, children: (0, jsx_runtime_1.jsx)(ui_1.PrerenderedCanvas, { ...props, style: {
+                position: 'absolute',
+                left: 0,
+                top: scrollTop,
+            } }) }));
+});
+exports.default = MultiVariantRendering;

package/dist/MultiLinearVariantRenderer/index.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = MultiVariantRendererF;
 const MultiVariantRenderer_1 = __importDefault(require("./MultiVariantRenderer"));
-const MultiVariantRendering_1 = __importDefault(require("./MultiVariantRendering"));
+const MultiVariantRendering_1 = __importDefault(require("./components/MultiVariantRendering"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function MultiVariantRendererF(pluginManager) {
     pluginManager.addRendererType(() => {

package/dist/MultiLinearVariantRenderer/makeImageData.js

@@ -6,24 +6,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.makeImageData = makeImageData;
 const util_1 = require("@jbrowse/core/util");
 const rbush_1 = __importDefault(require("rbush"));
-const multiVariantColor_1 = require("../shared/multiVariantColor");
-const util_2 = require("../util");
-const fudgeFactor = 0.6;
-const f2 = fudgeFactor / 2;
-function drawColorAlleleCount(alleles, ctx, x, y, w, h) {
-    ctx.fillStyle = (0, multiVariantColor_1.getColorAlleleCount)(alleles);
-    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-}
-function drawPhased(alleles, ctx, x, y, w, h, HP) {
-    ctx.fillStyle = (0, multiVariantColor_1.getColorPhased)(alleles, HP);
-    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
-}
+const constants_1 = require("../shared/constants");
+const drawAlleleCount_1 = require("../shared/drawAlleleCount");
+const drawPhased_1 = require("../shared/drawPhased");
+const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
 async function makeImageData(ctx, props) {
     const { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, features, regions, bpPerPx, renderingMode, } = props;
     const region = regions[0];
-    const mafs = (0, util_2.getFeaturesThatPassMinorAlleleFrequencyFilter)(features.values(), minorAlleleFrequencyFilter);
+    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(features.values(), minorAlleleFrequencyFilter);
     const rbush = new rbush_1.default();
-    for (const feature of mafs) {
+    for (const { mostFrequentAlt, feature } of mafs) {
         const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
         const w = Math.max(Math.round(rightPx - leftPx), 2);
         const samp = feature.get('genotypes');
@@ -36,26 +28,26 @@ async function makeImageData(ctx, props) {
             const h = Math.max(rowHeight, 1);
             if (genotype) {
                 rbush.insert({
-                    minX: x - f2,
-                    maxX: x + w + f2,
-                    minY: y - f2,
-                    maxY: y + h + f2,
+                    minX: x - constants_1.f2,
+                    maxX: x + w + constants_1.f2,
+                    minY: y - constants_1.f2,
+                    maxY: y + h + constants_1.f2,
                     genotype,
                 });
                 const isPhased = genotype.includes('|');
                 if (renderingMode === 'phased') {
                     if (isPhased) {
                         const alleles = genotype.split('|');
-                        drawPhased(alleles, ctx, x, y, w, h, HP);
+                        (0, drawPhased_1.drawPhased)(alleles, ctx, x, y, w, h, HP);
                     }
                     else {
                         ctx.fillStyle = 'black';
-                        ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+                        ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
                     }
                 }
                 else {
                     const alleles = genotype.split(/[/|]/);
-                    drawColorAlleleCount(alleles, ctx, x, y, w, h);
+                    (0, drawAlleleCount_1.drawColorAlleleCount)(alleles, ctx, x, y, w, h, mostFrequentAlt);
                 }
             }
             y += rowHeight;

package/dist/MultiLinearVariantRenderer/types.d.ts

@@ -1,4 +1,4 @@
-import type { Source } from '../types';
+import type { Source } from '../shared/types';
 import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import type { Feature } from '@jbrowse/core/util';
 import type { ThemeOptions } from '@mui/material';

package/dist/MultiVariantBaseRenderer.d.ts

@@ -1,15 +1,15 @@
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import type { Source } from './types';
-import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Source } from './shared/types';
+import type { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import type { Feature } from '@jbrowse/core/util';
 import type { ThemeOptions } from '@mui/material';
-export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+export interface RenderArgs extends RenderArgsDeserialized {
     bpPerPx: number;
     height: number;
     highResolutionScaling: number;
     themeOptions: ThemeOptions;
 }
-export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+export interface RenderArgsDeserializedWithFeatures extends RenderArgs {
     features: Map<string, Feature>;
 }
 export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithFeatures {
@@ -17,7 +17,7 @@ export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithF
 }
 export default abstract class MultiVariantBaseRenderer extends FeatureRendererType {
     supportsSVG: boolean;
-    render(renderProps: RenderArgsDeserialized): Promise<{
+    render(renderProps: RenderArgs): Promise<{
         features: Map<string, Feature>;
         height: number;
         width: number;

package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -7,7 +7,7 @@ exports.MultiVariantGetGenotypeMatrix = void 0;
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
 const rxjs_1 = require("rxjs");
-const util_1 = require("../util");
+const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
 class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
     constructor() {
         super(...arguments);
@@ -22,7 +22,7 @@ class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameReg
         const region = regions[0];
         const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeatures(region, deserializedArgs).pipe((0, rxjs_1.toArray)()));
         const genotypeFactor = new Set();
-        const mafs = (0, util_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
+        const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
         for (const feat of feats) {
             const samp = feat.get('genotypes');
             for (const { name } of sources) {
@@ -32,8 +32,8 @@ class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameReg
         }
         const genotypeFactorMap = Object.fromEntries([...genotypeFactor].map((type, idx) => [type, idx]));
         const rows = {};
-        for (const feat of mafs) {
-            const samp = feat.get('genotypes');
+        for (const { feature } of mafs) {
+            const samp = feature.get('genotypes');
             for (const { name } of sources) {
                 if (!rows[name]) {
                     rows[name] = {

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,5 +1,5 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { SampleInfo } from '../types';
+import type { SampleInfo } from '../shared/types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Region } from '@jbrowse/core/util';
 export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -7,7 +7,7 @@ exports.MultiVariantGetSimplifiedFeatures = void 0;
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
 const rxjs_1 = require("rxjs");
-const util_1 = require("../util");
+const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
 class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
     constructor() {
         super(...arguments);
@@ -22,11 +22,11 @@ class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenam
         const feats = await (0, rxjs_1.firstValueFrom)(dataAdapter
             .getFeaturesInMultipleRegions(regions, deserializedArgs)
             .pipe((0, rxjs_1.toArray)()));
-        const features = (0, util_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
+        const features = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)(feats, minorAlleleFrequencyFilter);
         const sampleInfo = {};
         let hasPhased = false;
-        for (const f of features) {
-            const samp = f.get('genotypes');
+        for (const { feature } of features) {
+            const samp = feature.get('genotypes');
             for (const [key, val] of Object.entries(samp)) {
                 const isPhased = val.includes('|');
                 hasPhased || (hasPhased = isPhased);
@@ -39,12 +39,12 @@ class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenam
         return {
             hasPhased,
             sampleInfo,
-            features: features.map(f => ({
-                id: f.id(),
+            features: features.map(({ feature }) => ({
+                id: feature.id(),
                 data: {
-                    start: f.get('start'),
-                    end: f.get('end'),
-                    refName: f.get('refName'),
+                    start: feature.get('start'),
+                    end: feature.get('end'),
+                    refName: feature.get('refName'),
                 },
             })),
         };