@jbrowse/plugin-variants 3.0.1 → 3.0.2

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -7,13 +7,16 @@ import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
-    protected configure(): Promise<{
+    protected configurePre2(): Promise<{
+        vcf: TabixIndexedFile;
+        parser: VcfParser;
+    }>;
+    configure(opts?: BaseOptions): Promise<{
         vcf: TabixIndexedFile;
         parser: VcfParser;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(): Promise<string>;
-    getMetadata(): Promise<any>;
+    getHeader(opts?: BaseOptions): Promise<string>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     getSources(): Promise<{
         name: string;

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -11,8 +11,7 @@ const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
 class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configurePre(opts) {
-        const { statusCallback = () => { } } = opts || {};
+    async configurePre(_opts) {
         const vcfGzLocation = this.getConf('vcfGzLocation');
         const location = this.getConf(['index', 'location']);
         const indexType = this.getConf(['index', 'indexType']);
@@ -28,13 +27,14 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 : undefined,
             chunkCacheSize: 50 * 2 ** 20,
         });
-        const header = await (0, util_1.updateStatus)('Downloading index', statusCallback, () => vcf.getHeader());
         return {
             vcf,
-            parser: new vcf_1.default({ header }),
+            parser: new vcf_1.default({
+                header: await vcf.getHeader(),
+            }),
         };
     }
-    async configure() {
+    async configurePre2() {
         if (!this.configured) {
             this.configured = this.configurePre().catch((e) => {
                 this.configured = undefined;
@@ -43,23 +43,23 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
         return this.configured;
     }
+    async configure(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.configurePre2());
+    }
     async getRefNames(opts = {}) {
-        const { vcf } = await this.configure();
+        const { vcf } = await this.configure(opts);
         return vcf.getReferenceSequenceNames(opts);
     }
-    async getHeader() {
-        const { vcf } = await this.configure();
+    async getHeader(opts) {
+        const { vcf } = await this.configure(opts);
         return vcf.getHeader();
     }
-    async getMetadata() {
-        const { parser } = await this.configure();
-        return parser.getMetadata();
-    }
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { refName, start, end } = query;
             const { statusCallback = () => { } } = opts;
-            const { vcf, parser } = await this.configure();
+            const { vcf, parser } = await this.configure(opts);
             await (0, util_1.updateStatus)('Downloading variants', statusCallback, () => vcf.getLines(refName, start, end, {
                 lineCallback: (line, fileOffset) => {
                     observer.next(new VcfFeature_1.default({

package/dist/getMultiVariantFeaturesAutorun.d.ts

@@ -1,4 +1,4 @@
-import type { SampleInfo, Source } from './types';
+import type { SampleInfo, Source } from './shared/types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
 export declare function getMultiVariantFeaturesAutorun(self: {

package/dist/getMultiVariantSourcesAutorun.d.ts

@@ -1,4 +1,4 @@
-import type { Source } from './types';
+import type { Source } from './shared/types';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export declare function getMultiVariantSourcesAutorun(self: {
     configuration: AnyConfigurationModel;

package/dist/shared/MultiVariantBaseModel.d.ts

@@ -1,4 +1,4 @@
-import type { SampleInfo, Source } from '../types';
+import type { SampleInfo, Source } from '../shared/types';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from 'mobx-state-tree';

package/dist/shared/MultiVariantBaseModel.js

@@ -48,10 +48,10 @@ const Splitscreen_1 = __importDefault(require("@mui/icons-material/Splitscreen")
 const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
 const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
 const mobx_state_tree_1 = require("mobx-state-tree");
-const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/SetColorDialog'))));
-const MAFFilterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/MAFFilterDialog'))));
-const ClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/ClusterDialog'))));
-const SetRowHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/SetRowHeightDialog'))));
+const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetColorDialog'))));
+const MAFFilterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/MAFFilterDialog'))));
+const ClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ClusterDialog'))));
+const SetRowHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetRowHeightDialog'))));
 function MultiVariantBaseModelF(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearVariantMatrixDisplay', (0, plugin_linear_genome_view_1.linearBareDisplayStateModelFactory)(configSchema), mobx_state_tree_1.types.model({

package/dist/shared/{SourcesGridHeader.js → components/SourcesGridHeader.js}

@@ -12,20 +12,20 @@ const KeyboardArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardA
 const KeyboardDoubleArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowDown"));
 const KeyboardDoubleArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowUp"));
 const material_1 = require("@mui/material");
-const util_1 = require("./util");
+const sourcesGridUtils_1 = require("../sourcesGridUtils");
 function SourcesGridHeader({ selected, onChange, rows, showTips, }) {
     const [anchorEl, setAnchorEl] = (0, react_1.useState)(null);
     const [widgetColor, setWidgetColor] = (0, react_1.useState)('blue');
     return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !selected.length, onClick: event => {
                     setAnchorEl(event.currentTarget);
                 }, children: "Change color of selected items" }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
-                    onChange((0, util_1.moveUp)([...rows], selected));
+                    onChange((0, sourcesGridUtils_1.moveUp)([...rows], selected));
                 }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardArrowUp_1.default, {}), showTips ? 'Move selected items up' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
-                    onChange((0, util_1.moveDown)([...rows], selected));
+                    onChange((0, sourcesGridUtils_1.moveDown)([...rows], selected));
                 }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardArrowDown_1.default, {}), showTips ? 'Move selected items down' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
-                    onChange((0, util_1.moveUp)([...rows], selected, rows.length));
+                    onChange((0, sourcesGridUtils_1.moveUp)([...rows], selected, rows.length));
                 }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardDoubleArrowUp_1.default, {}), showTips ? 'Move selected items to top' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
-                    onChange((0, util_1.moveDown)([...rows], selected, rows.length));
+                    onChange((0, sourcesGridUtils_1.moveDown)([...rows], selected, rows.length));
                 }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardDoubleArrowDown_1.default, {}), showTips ? 'Move selected items to bottom' : null] }), (0, jsx_runtime_1.jsx)(ColorPicker_1.ColorPopover, { anchorEl: anchorEl, color: widgetColor, onChange: c => {
                     setWidgetColor(c);
                     selected.forEach(id => {

package/dist/shared/constants.d.ts

@@ -0,0 +1,2 @@
+export declare const fudgeFactor = 0.6;
+export declare const f2: number;

package/dist/shared/constants.js

@@ -0,0 +1,5 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.f2 = exports.fudgeFactor = void 0;
+exports.fudgeFactor = 0.6;
+exports.f2 = exports.fudgeFactor / 2;

package/dist/shared/drawAlleleCount.d.ts

@@ -0,0 +1 @@
+export declare function drawColorAlleleCount(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, mostFrequentAlt: string): void;

package/dist/shared/{multiVariantColor.js → drawAlleleCount.js}

@@ -1,19 +1,16 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getColorAlleleCount = getColorAlleleCount;
-exports.getColorPhased = getColorPhased;
-exports.getColorPhasedWithPhaseSet = getColorPhasedWithPhaseSet;
-const colors_1 = require("@jbrowse/core/ui/colors");
+exports.drawColorAlleleCount = drawColorAlleleCount;
 const colord_1 = require("@jbrowse/core/util/colord");
-const util_1 = require("../util");
-function getColorAlleleCount(alleles) {
+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 === '1') {
+        if (allele === mostFrequentAlt) {
             alt++;
         }
         else if (allele === '0') {
@@ -40,11 +37,7 @@ function getColorAlleleCount(alleles) {
         return a1.toHex();
     }
 }
-function getColorPhased(alleles, HP) {
-    const c = +alleles[HP];
-    return c ? colors_1.set1[c - 1] || 'black' : '#ccc';
-}
-function getColorPhasedWithPhaseSet(alleles, HP, PS) {
-    const c = +alleles[HP];
-    return c ? (0, util_1.colorify)(+PS) || 'black' : '#ccc';
+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);
 }

package/dist/shared/drawPhased.d.ts

@@ -0,0 +1 @@
+export declare function drawPhased(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, HP: number, PS?: string): void;

package/dist/shared/drawPhased.js

@@ -0,0 +1,21 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.drawPhased = drawPhased;
+const colors_1 = require("@jbrowse/core/ui/colors");
+const constants_1 = require("./constants");
+const util_1 = require("./util");
+function getColorPhased(alleles, HP) {
+    const c = +alleles[HP];
+    return c ? colors_1.set1[c - 1] || 'black' : '#ccc';
+}
+function getColorPhasedWithPhaseSet(alleles, HP, PS) {
+    const c = +alleles[HP];
+    return c ? (0, util_1.colorify)(+PS) || 'black' : '#ccc';
+}
+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);
+}

package/dist/shared/findSecondLargestNumber.js

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

package/dist/shared/minorAlleleFrequencyUtils.d.ts

@@ -0,0 +1,11 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function findSecondLargestNumber(arr: Iterable<number>): number;
+export declare function calculateAlleleCounts(feat: Feature): {
+    alleleCounts: Map<any, any>;
+    mostFrequentAlt: any;
+};
+export declare function calculateMinorAlleleFrequency(alleleCounts: Map<string, number>): number;
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number): {
+    feature: Feature;
+    mostFrequentAlt: string;
+}[];

package/dist/shared/minorAlleleFrequencyUtils.js

@@ -0,0 +1,62 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.findSecondLargestNumber = findSecondLargestNumber;
+exports.calculateAlleleCounts = calculateAlleleCounts;
+exports.calculateMinorAlleleFrequency = calculateMinorAlleleFrequency;
+exports.getFeaturesThatPassMinorAlleleFrequencyFilter = getFeaturesThatPassMinorAlleleFrequencyFilter;
+const util_1 = require("@jbrowse/core/util");
+function findSecondLargestNumber(arr) {
+    let firstMax = 0;
+    let secondMax = 0;
+    for (const num of arr) {
+        if (num > firstMax) {
+            secondMax = firstMax;
+            firstMax = num;
+        }
+        else if (num > secondMax && num !== firstMax) {
+            secondMax = num;
+        }
+    }
+    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);
+        }
+    }
+    let mostFrequentAlt;
+    let max = 0;
+    for (const [alt, altCount] of alleleCounts.entries()) {
+        if (alt !== '.' && alt !== '0') {
+            if (altCount > max) {
+                mostFrequentAlt = alt;
+                max = altCount;
+            }
+        }
+    }
+    return { alleleCounts, mostFrequentAlt };
+}
+function calculateMinorAlleleFrequency(alleleCounts) {
+    return (findSecondLargestNumber(alleleCounts.values()) /
+        ((0, util_1.sum)(alleleCounts.values()) || 1));
+}
+function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter) {
+    const results = [];
+    for (const feature of feats) {
+        if (feature.get('end') - feature.get('start') <= 10) {
+            const { mostFrequentAlt, alleleCounts } = calculateAlleleCounts(feature);
+            if (calculateMinorAlleleFrequency(alleleCounts) >=
+                minorAlleleFrequencyFilter) {
+                results.push({
+                    feature,
+                    mostFrequentAlt,
+                });
+            }
+        }
+    }
+    return results;
+}

package/dist/shared/sourcesGridUtils.d.ts

@@ -0,0 +1,10 @@
+export declare function moveUp(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];
+export declare function moveDown(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];

package/dist/shared/sourcesGridUtils.js

@@ -0,0 +1,32 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.moveUp = moveUp;
+exports.moveDown = moveDown;
+function moveUp(arr, sel, by = 1) {
+    const idxs = sel
+        .map(l => arr.findIndex(v => v.name === l))
+        .sort((a, b) => a - b);
+    let lastIdx = 0;
+    for (const old of idxs) {
+        const idx = Math.max(lastIdx, old - by);
+        if (idx >= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx + 1;
+    }
+    return arr;
+}
+function moveDown(arr, sel, by = 1) {
+    const idxs = sel
+        .map(l => arr.findIndex(v => v.name === l))
+        .sort((a, b) => b - a);
+    let lastIdx = arr.length - 1;
+    for (const old of idxs) {
+        const idx = Math.min(lastIdx, old + by);
+        if (idx <= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx - 1;
+    }
+    return arr;
+}

package/dist/shared/util.d.ts

@@ -1,10 +1,3 @@
-export declare function moveUp(arr: {
-    name: string;
-}[], sel: string[], by?: number): {
-    name: string;
-}[];
-export declare function moveDown(arr: {
-    name: string;
-}[], sel: string[], by?: number): {
-    name: string;
-}[];
+export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, color?: string): void;
+export declare function randomColor(str: string): string;
+export declare function colorify(n: number): string;

package/dist/shared/util.js

@@ -1,32 +1,29 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.moveUp = moveUp;
-exports.moveDown = moveDown;
-function moveUp(arr, sel, by = 1) {
-    const idxs = sel
-        .map(l => arr.findIndex(v => v.name === l))
-        .sort((a, b) => a - b);
-    let lastIdx = 0;
-    for (const old of idxs) {
-        const idx = Math.max(lastIdx, old - by);
-        if (idx >= lastIdx) {
-            arr.splice(idx, 0, arr.splice(old, 1)[0]);
-        }
-        lastIdx = lastIdx + 1;
+exports.fillRectCtx = fillRectCtx;
+exports.randomColor = randomColor;
+exports.colorify = colorify;
+function fillRectCtx(x, y, width, height, ctx, color) {
+    if (width < 0) {
+        x += width;
+        width = -width;
     }
-    return arr;
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (color) {
+        ctx.fillStyle = color;
+    }
+    ctx.fillRect(x, y, width, height);
 }
-function moveDown(arr, sel, by = 1) {
-    const idxs = sel
-        .map(l => arr.findIndex(v => v.name === l))
-        .sort((a, b) => b - a);
-    let lastIdx = arr.length - 1;
-    for (const old of idxs) {
-        const idx = Math.min(lastIdx, old + by);
-        if (idx <= lastIdx) {
-            arr.splice(idx, 0, arr.splice(old, 1)[0]);
-        }
-        lastIdx = lastIdx - 1;
+function randomColor(str) {
+    let sum = 0;
+    for (let i = 0; i < str.length; i++) {
+        sum += str.charCodeAt(i);
     }
-    return arr;
+    return colorify(sum * 10);
+}
+function colorify(n) {
+    return `hsl(${n % 255}, 50%, 50%)`;
 }

package/dist/util.d.ts

@@ -1,8 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, color?: string): void;
-export declare function getCol(gt: string): "blue" | "teal" | "#ccc" | "#CBC3E3";
-export declare function randomColor(str: string): string;
-export declare function colorify(n: number): string;
-export declare function findSecondLargest(arr: Iterable<number>): number;
-export declare function calculateMinorAlleleFrequency(feat: Feature): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number): Feature[];

package/dist/util.js

@@ -1,86 +1 @@
 "use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fillRectCtx = fillRectCtx;
-exports.getCol = getCol;
-exports.randomColor = randomColor;
-exports.colorify = colorify;
-exports.findSecondLargest = findSecondLargest;
-exports.calculateMinorAlleleFrequency = calculateMinorAlleleFrequency;
-exports.getFeaturesThatPassMinorAlleleFrequencyFilter = getFeaturesThatPassMinorAlleleFrequencyFilter;
-const util_1 = require("@jbrowse/core/util");
-function fillRectCtx(x, y, width, height, ctx, color) {
-    if (width < 0) {
-        x += width;
-        width = -width;
-    }
-    if (height < 0) {
-        y += height;
-        height = -height;
-    }
-    if (color) {
-        ctx.fillStyle = color;
-    }
-    ctx.fillRect(x, y, width, height);
-}
-function getCol(gt) {
-    if (gt === '0|0' || gt === '0/0') {
-        return '#ccc';
-    }
-    else if (gt === '1|0' || gt === '0|1' || gt === '0/1' || gt === '1/0') {
-        return 'teal';
-    }
-    else if (gt === '1|1' || gt === '1/1') {
-        return 'blue';
-    }
-    else {
-        return '#CBC3E3';
-    }
-}
-function randomColor(str) {
-    let sum = 0;
-    for (let i = 0; i < str.length; i++) {
-        sum += str.charCodeAt(i);
-    }
-    return `hsl(${colorify(sum * 10)}, 50%, 50%)`;
-}
-function colorify(n) {
-    return `hsl(${n % 255}, 50%, 50%)`;
-}
-function findSecondLargest(arr) {
-    let firstMax = 0;
-    let secondMax = 0;
-    for (const num of arr) {
-        if (num > firstMax) {
-            secondMax = firstMax;
-            firstMax = num;
-        }
-        else if (num > secondMax && num !== firstMax) {
-            secondMax = num;
-        }
-    }
-    return secondMax;
-}
-function calculateMinorAlleleFrequency(feat) {
-    if (feat.get('end') - feat.get('start') <= 10) {
-        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);
-            }
-        }
-        return (findSecondLargest(alleleCounts.values()) /
-            ((0, util_1.sum)(alleleCounts.values()) || 1));
-    }
-    return -1;
-}
-function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter) {
-    const mafs = [];
-    for (const feat of feats) {
-        if (calculateMinorAlleleFrequency(feat) >= minorAlleleFrequencyFilter) {
-            mafs.push(feat);
-        }
-    }
-    return mafs;
-}

package/esm/MultiLinearVariantDisplay/components/Crosshair.js

@@ -2,7 +2,7 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getContainingView } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import MultiVariantTooltip from '../../shared/MultiVariantTooltip';
+import MultiVariantTooltip from '../../shared/components/MultiVariantTooltip';
 const useStyles = makeStyles()({
     rel: {
         position: 'relative',

package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.js

@@ -3,7 +3,7 @@ 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/LegendBar';
+import LegendBar from '../../shared/components/LegendBar';
 const MultiLinearVariantDisplayComponent = observer(function (props) {
     const { model } = props;
     const ref = useRef(null);

package/esm/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/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/LegendBar';
+import LegendBar from '../shared/components/LegendBar';
 export async function renderSvg(self, opts, superRenderSvg) {
     await when(() => !!self.regionCannotBeRenderedText);
     const { offsetPx } = getContainingView(self);

package/esm/MultiLinearVariantMatrixDisplay/components/Crosshair.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 { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import MultiVariantTooltip from '../../shared/MultiVariantTooltip';
+import MultiVariantTooltip from '../../shared/components/MultiVariantTooltip';
 const useStyles = makeStyles()({
     cursor: {
         pointerEvents: 'none',

package/esm/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js

@@ -4,7 +4,7 @@ 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/LegendBar';
+import LegendBar from '../../shared/components/LegendBar';
 const MultiLinearVariantMatrixDisplayComponent = observer(function (props) {
     const { model } = props;
     const { lineZoneHeight } = model;