@jbrowse/plugin-variants 3.2.0 → 3.3.0

package/dist/MultiLinearVariantRenderer/MultiVariantRendering.d.ts

@@ -1,22 +0,0 @@
-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

@@ -1,52 +0,0 @@
-"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/VariantFeatureWidget/VariantConsequencePanel.d.ts

@@ -1,5 +0,0 @@
-export default function VariantConsequencePanel({ data, fields, title, }: {
-    data: string[];
-    fields: string[];
-    title: string;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/VariantFeatureWidget/VariantConsequencePanel.js

@@ -1,15 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = VariantConsequencePanel;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const VariantConsequenceDataGridWrapper_1 = __importDefault(require("./VariantConsequenceDataGridWrapper"));
-function VariantConsequencePanel({ data, fields, title, }) {
-    return data.length ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: title, children: (0, jsx_runtime_1.jsx)(VariantConsequenceDataGridWrapper_1.default, { rows: data.map((elt, id) => ({
-                id,
-                ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
-            })), columns: fields.map(c => ({ field: c })) }) })) : null;
-}

package/dist/VariantRPC/cluster.d.ts

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

package/dist/VariantRPC/cluster.js

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

package/dist/shared/components/LegendBar.d.ts

@@ -1,18 +0,0 @@
-import type { Source } from '../types';
-interface ReducedModel {
-    scrollTop: number;
-    totalHeight: number;
-    rowHeight: number;
-    lineZoneHeight?: number;
-    sources?: Source[];
-    canDisplayLabels: boolean;
-    height: number;
-    samplePloidy?: Record<string, number>;
-    id: string;
-}
-export declare const LegendBar: (props: {
-    model: ReducedModel;
-    orientation?: string;
-    exportSVG?: boolean;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default LegendBar;

package/esm/MultiLinearVariantDisplay/components/Crosshair.d.ts

@@ -1,7 +0,0 @@
-import type { MultiLinearVariantDisplayModel } from '../model';
-declare const Crosshair: ({ mouseX, mouseY, model, }: {
-    mouseX: number;
-    mouseY: number;
-    model: MultiLinearVariantDisplayModel;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default Crosshair;

package/esm/MultiLinearVariantDisplay/components/Crosshair.js

@@ -1,30 +0,0 @@
-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/components/MultiVariantTooltip';
-const useStyles = makeStyles()({
-    rel: {
-        position: 'relative',
-    },
-    cursor: {
-        pointerEvents: 'none',
-        zIndex: 800,
-        position: 'absolute',
-    },
-    color: {
-        width: 10,
-        height: 10,
-    },
-});
-const Crosshair = observer(function ({ mouseX, mouseY, model, }) {
-    const { classes } = useStyles();
-    const { hoveredGenotype, height, scrollTop, rowHeight, sources } = model;
-    const { width } = getContainingView(model);
-    const source = sources === null || sources === void 0 ? void 0 : sources[Math.floor(mouseY / rowHeight)];
-    const y = mouseY - scrollTop;
-    return source ? (_jsxs("div", { className: classes.rel, children: [_jsxs("svg", { className: classes.cursor, width: width, height: height, style: {
-                    top: scrollTop,
-                }, children: [_jsx("line", { x1: 0, x2: width, y1: y, y2: y, stroke: "black" }), _jsx("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })] }), _jsx(MultiVariantTooltip, { source: { ...source, hoveredGenotype } })] })) : null;
-});
-export default Crosshair;

package/esm/MultiLinearVariantMatrixDisplay/components/Crosshair.d.ts

@@ -1,7 +0,0 @@
-import type { MultiLinearVariantMatrixDisplayModel } from '../model';
-declare const Crosshair: ({ mouseX, mouseY, model, }: {
-    mouseX: number;
-    mouseY: number;
-    model: MultiLinearVariantMatrixDisplayModel;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default Crosshair;

package/esm/MultiLinearVariantMatrixDisplay/components/Crosshair.js

@@ -1,23 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } 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/components/MultiVariantTooltip';
-const useStyles = makeStyles()({
-    cursor: {
-        pointerEvents: 'none',
-        zIndex: 800,
-        position: 'relative',
-    },
-});
-const Crosshair = observer(function ({ mouseX, mouseY, model, }) {
-    const { classes } = useStyles();
-    const { hoveredGenotype, lineZoneHeight, totalHeight, rowHeight, sources } = model;
-    const { width } = getContainingView(model);
-    const source = sources === null || sources === void 0 ? void 0 : sources[Math.floor((mouseY - lineZoneHeight) / rowHeight)];
-    const yoff = mouseY - lineZoneHeight;
-    return source ? (_jsxs(_Fragment, { children: [_jsxs("svg", { className: classes.cursor, width: width, height: totalHeight, style: {
-                    top: lineZoneHeight,
-                }, children: [_jsx("line", { x1: 0, x2: width, y1: yoff, y2: yoff, stroke: "black" }), _jsx("line", { x1: mouseX, x2: mouseX, y1: 0, y2: totalHeight, stroke: "black" })] }), _jsx(MultiVariantTooltip, { source: { ...source, hoveredGenotype } })] })) : null;
-});
-export default Crosshair;

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

@@ -1,7 +0,0 @@
-declare const LinearVariantMatrixRendering: (props: {
-    width: number;
-    height: number;
-    displayModel: any;
-    arr: string[];
-}) => import("react/jsx-runtime").JSX.Element;
-export default LinearVariantMatrixRendering;

package/esm/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.js

@@ -1,36 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import { useRef } from 'react';
-import { PrerenderedCanvas } from '@jbrowse/core/ui';
-import { observer } from 'mobx-react';
-const LinearVariantMatrixRendering = observer(function (props) {
-    const { arr, width, height, displayModel } = props;
-    const ref = useRef(null);
-    function getFeatureUnderMouse(eventClientX, eventClientY) {
-        var _a, _b;
-        let offsetX = 0;
-        let offsetY = 0;
-        if (ref.current) {
-            const r = ref.current.getBoundingClientRect();
-            offsetX = eventClientX - r.left;
-            offsetY = eventClientY - r.top;
-        }
-        const dimY = arr.length;
-        const dimX = ((_a = arr[0]) === null || _a === void 0 ? void 0 : _a.length) || 0;
-        return (_b = arr[Math.floor((offsetX / width) * dimY)]) === null || _b === void 0 ? void 0 : _b[Math.floor((offsetY / height) * dimX)];
-    }
-    return (_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,
-        }, children: _jsx(PrerenderedCanvas, { ...props }) }));
-});
-export default LinearVariantMatrixRendering;

package/esm/MultiLinearVariantRenderer/MultiVariantRendering.d.ts

@@ -1,22 +0,0 @@
-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/esm/MultiLinearVariantRenderer/MultiVariantRendering.js

@@ -1,47 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import { useMemo, useRef } from 'react';
-import { PrerenderedCanvas } from '@jbrowse/core/ui';
-import { observer } from 'mobx-react';
-import RBush from 'rbush';
-const MultiVariantRendering = observer(function (props) {
-    const { totalHeight, scrollTop } = props;
-    const { rbush, displayModel } = props;
-    const ref = useRef(null);
-    const rbush2 = useMemo(() => new RBush().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 (_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: _jsx(PrerenderedCanvas, { ...props, style: {
-                position: 'absolute',
-                left: 0,
-                top: scrollTop,
-            } }) }));
-});
-export default MultiVariantRendering;

package/esm/VariantFeatureWidget/VariantConsequencePanel.d.ts

@@ -1,5 +0,0 @@
-export default function VariantConsequencePanel({ data, fields, title, }: {
-    data: string[];
-    fields: string[];
-    title: string;
-}): import("react/jsx-runtime").JSX.Element | null;

package/esm/VariantFeatureWidget/VariantConsequencePanel.js

@@ -1,9 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
-import VariantConsequenceDataGridWrapper from './VariantConsequenceDataGridWrapper';
-export default function VariantConsequencePanel({ data, fields, title, }) {
-    return data.length ? (_jsx(BaseCard, { title: title, children: _jsx(VariantConsequenceDataGridWrapper, { rows: data.map((elt, id) => ({
-                id,
-                ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
-            })), columns: fields.map(c => ({ field: c })) }) })) : null;
-}

package/esm/VariantRPC/cluster.d.ts

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

package/esm/VariantRPC/cluster.js

@@ -1,79 +0,0 @@
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
-export function euclideanDistance(a, b) {
-    const size = Math.min(a.length, b.length);
-    let sum = 0;
-    for (let index = 0; index < size; index++) {
-        sum += (a[index] - b[index]) * (a[index] - b[index]);
-    }
-    return Math.sqrt(sum);
-}
-export function averageDistance(setA, setB, distances) {
-    let distance = 0;
-    for (const a of setA) {
-        for (const b of setB) {
-            distance += distances[a][b];
-        }
-    }
-    return distance / setA.length / setB.length;
-}
-function updateProgress(stepNumber, stepProgress, onProgress) {
-    onProgress(stepNumber / 2 + stepProgress / 2);
-}
-export function clusterData({ data, distance = euclideanDistance, linkage = averageDistance, onProgress, stopToken, }) {
-    const distances = data.map((datum, index) => {
-        if (onProgress) {
-            updateProgress(0, index / (data.length - 1), onProgress);
-        }
-        return data.map(otherDatum => distance(datum, otherDatum));
-    });
-    const clusters = data.map((_datum, index) => ({
-        height: 0,
-        indexes: [Number(index)],
-    }));
-    let clustersGivenK = [];
-    let start = performance.now();
-    for (let iteration = 0; iteration < data.length; iteration++) {
-        if (performance.now() - start > 2000) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
-        if (onProgress) {
-            updateProgress(1, (iteration + 1) / data.length, onProgress);
-        }
-        clustersGivenK.push(clusters.map(cluster => cluster.indexes));
-        if (iteration >= data.length - 1) {
-            break;
-        }
-        let nearestDistance = Infinity;
-        let nearestRow = 0;
-        let nearestCol = 0;
-        for (let row = 0; row < clusters.length; row++) {
-            for (let col = row + 1; col < clusters.length; col++) {
-                const distance = linkage(clusters[row].indexes, clusters[col].indexes, distances);
-                if (distance < nearestDistance) {
-                    nearestDistance = distance;
-                    nearestRow = row;
-                    nearestCol = col;
-                }
-            }
-        }
-        const newCluster = {
-            indexes: [
-                ...clusters[nearestRow].indexes,
-                ...clusters[nearestCol].indexes,
-            ],
-            height: nearestDistance,
-            children: [clusters[nearestRow], clusters[nearestCol]],
-        };
-        clusters.splice(Math.max(nearestRow, nearestCol), 1);
-        clusters.splice(Math.min(nearestRow, nearestCol), 1);
-        clusters.push(newCluster);
-    }
-    clustersGivenK = [[], ...clustersGivenK.reverse()];
-    return {
-        clusters: clusters[0],
-        distances: distances,
-        order: clusters[0].indexes,
-        clustersGivenK: clustersGivenK,
-    };
-}

package/esm/shared/components/LegendBar.d.ts

@@ -1,18 +0,0 @@
-import type { Source } from '../types';
-interface ReducedModel {
-    scrollTop: number;
-    totalHeight: number;
-    rowHeight: number;
-    lineZoneHeight?: number;
-    sources?: Source[];
-    canDisplayLabels: boolean;
-    height: number;
-    samplePloidy?: Record<string, number>;
-    id: string;
-}
-export declare const LegendBar: (props: {
-    model: ReducedModel;
-    orientation?: string;
-    exportSVG?: boolean;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default LegendBar;