@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/shared/components/MultiVariantClusterDialog/ClusterDialogManual.d.ts

@@ -1,7 +0,0 @@
-import type { ReducedModel } from './types';
-declare const ClusterDialogManuals: ({ model, handleClose, children, }: {
-    model: ReducedModel;
-    handleClose: () => void;
-    children: React.ReactNode;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ClusterDialogManuals;

package/dist/shared/components/MultiVariantClusterDialog/ClusterDialogManual.js

@@ -1,145 +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 util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const material_1 = require("@mui/material");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const file_saver_1 = require("file-saver");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-    mgap: {
-        display: 'flex',
-        flexDirection: 'column',
-        gap: theme.spacing(4),
-    },
-}));
-const ClusterDialogManuals = (0, mobx_react_1.observer)(function ({ model, handleClose, children, }) {
-    const { classes } = useStyles();
-    const [paste, setPaste] = (0, react_1.useState)('');
-    const [ret, setRet] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    const [loading, setLoading] = (0, react_1.useState)(false);
-    const [showAdvanced, setShowAdvanced] = (0, util_1.useLocalStorage)('cluster-showAdvanced', false);
-    const [clusterMethod, setClusterMethod] = (0, react_1.useState)('single');
-    (0, react_1.useEffect)(() => {
-        ;
-        (async () => {
-            try {
-                setError(undefined);
-                setRet(undefined);
-                setLoading(true);
-                const view = (0, util_1.getContainingView)(model);
-                if (!view.initialized) {
-                    return;
-                }
-                const { rpcManager } = (0, util_1.getSession)(model);
-                const { sourcesWithoutLayout, minorAlleleFrequencyFilter, lengthCutoffFilter, adapterConfig, } = model;
-                const sessionId = (0, tracks_1.getRpcSessionId)(model);
-                const ret = (await rpcManager.call(sessionId, 'MultiVariantGetGenotypeMatrix', {
-                    regions: view.dynamicBlocks.contentBlocks,
-                    sources: sourcesWithoutLayout,
-                    minorAlleleFrequencyFilter,
-                    lengthCutoffFilter,
-                    sessionId,
-                    adapterConfig,
-                }));
-                setRet(ret);
-            }
-            catch (e) {
-                if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(model)) {
-                    console.error(e);
-                    setError(e);
-                }
-            }
-            finally {
-                setLoading(false);
-            }
-        })();
-    }, [model]);
-    const results = ret
-        ? String.raw `inputMatrix<-matrix(c(${Object.values(ret)
-            .map(val => val.join(','))
-            .join(',\n')}
-),nrow=${Object.values(ret).length},byrow=TRUE)
-rownames(inputMatrix)<-c(${Object.keys(ret)
-            .map(key => `'${key}'`)
-            .join(',')})
-resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
-cat(resultClusters$order,sep='\n')`
-        : undefined;
-    const resultsTsv = ret
-        ? Object.entries(ret)
-            .map(([key, val]) => [key, ...val].join('\t'))
-            .join('\n')
-        : undefined;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [children, (0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 16 }, children: [(0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: {
-                                            display: 'flex',
-                                            gap: '8px',
-                                            flexWrap: 'wrap',
-                                            marginBottom: '16px',
-                                        }, children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, file_saver_1.saveAs)(new Blob([results || ''], {
-                                                        type: 'text/plain;charset=utf-8',
-                                                    }), 'cluster.R');
-                                                }, children: "Download Rscript" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, copy_to_clipboard_1.default)(results || '');
-                                                }, children: "Copy Rscript to clipboard" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, file_saver_1.saveAs)(new Blob([resultsTsv || ''], {
-                                                        type: 'text/plain;charset=utf-8',
-                                                    }), 'genotypes.tsv');
-                                                }, children: "Download TSV" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                        setShowAdvanced(!showAdvanced);
-                                                    }, children: showAdvanced
-                                                        ? 'Hide advanced options'
-                                                        : 'Show advanced options' }) })] }), showAdvanced ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "h6", children: "Advanced options" }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { children: Object.entries({
-                                                    single: 'Single',
-                                                    complete: 'Complete',
-                                                }).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Radio, { checked: clusterMethod === key, onChange: () => {
-                                                            setClusterMethod(key);
-                                                        } }), label: val }, key))) })] })) : null, results ? ((0, jsx_runtime_1.jsx)("div", {})) : loading ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { variant: "h6", message: "Generating genotype matrix" })) : error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : null] }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "subtitle2", gutterBottom: true, style: { marginTop: '16px' }, children: "Clustering Results:" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
-                                            setPaste(event.target.value);
-                                        }, slotProps: {
-                                            input: {
-                                                classes: {
-                                                    input: classes.textAreaFont,
-                                                },
-                                            },
-                                        } })] })] })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                            const { sourcesWithoutLayout } = model;
-                            if (sourcesWithoutLayout) {
-                                try {
-                                    model.setLayout(paste
-                                        .split('\n')
-                                        .map(t => t.trim())
-                                        .filter(f => !!f)
-                                        .map(r => +r)
-                                        .map(idx => {
-                                        const ret = sourcesWithoutLayout[idx - 1];
-                                        if (!ret) {
-                                            throw new Error(`out of bounds at ${idx}`);
-                                        }
-                                        return ret;
-                                    }));
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    (0, util_1.getSession)(model).notifyError(`${e}`, e);
-                                }
-                            }
-                            handleClose();
-                        }, children: "Apply clustering" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-exports.default = ClusterDialogManuals;

package/dist/shared/components/MultiVariantClusterDialog/types.d.ts

@@ -1,10 +0,0 @@
-import type { Source } from '../../types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export interface ReducedModel {
-    sourcesWithoutLayout?: Source[];
-    minorAlleleFrequencyFilter?: number;
-    lengthCutoffFilter: number;
-    adapterConfig: AnyConfigurationModel;
-    setLayout: (arg: Source[]) => void;
-    clearLayout: () => void;
-}

package/dist/shared/components/MultiVariantClusterDialog/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

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

@@ -1,10 +0,0 @@
-import type { Source } from '../types';
-declare const MultiVariantColorLegend: ({ model, labelWidth, }: {
-    model: {
-        canDisplayLabels: boolean;
-        rowHeight: number;
-        sources?: Source[];
-    };
-    labelWidth: number;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default MultiVariantColorLegend;

package/dist/shared/components/MultiVariantColorLegend.js

@@ -1,24 +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 util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const RectBg_1 = __importDefault(require("./RectBg"));
-const MultiVariantColorLegend = (0, mobx_react_1.observer)(function ({ model, labelWidth, }) {
-    const { canDisplayLabels, rowHeight, sources } = model;
-    const svgFontSize = (0, util_1.clamp)(rowHeight, 8, 12);
-    const colorBoxWidth = 15;
-    const hasColors = sources === null || sources === void 0 ? void 0 : sources.some(s => s.color);
-    const legendWidth = labelWidth + (hasColors ? colorBoxWidth + 5 : 0);
-    const theme = (0, material_1.useTheme)();
-    return sources ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [canDisplayLabels ? ((0, jsx_runtime_1.jsx)(RectBg_1.default, { y: 0, x: 0, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null, sources.map((source, idx) => {
-                const { color, name, label } = source;
-                return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [color ? ((0, jsx_runtime_1.jsx)(RectBg_1.default, { y: idx * rowHeight, x: 0, width: colorBoxWidth + 0.5, height: rowHeight + 0.5, color: color })) : null, canDisplayLabels ? ((0, jsx_runtime_1.jsx)("text", { y: idx * rowHeight + svgFontSize, x: color ? colorBoxWidth + 2 : 0, fontSize: svgFontSize, ...(0, util_1.getFillProps)(theme.palette.text.primary), children: label || name })) : null] }, `${label}-${idx}`));
-            })] })) : null;
-});
-exports.default = MultiVariantColorLegend;

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

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

package/dist/shared/components/MultiVariantCrosshairs.js

@@ -1,40 +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 util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const MultiVariantTooltip_1 = __importDefault(require("./MultiVariantTooltip"));
-const useStyles = (0, mui_1.makeStyles)()({
-    rel: {
-        position: 'relative',
-    },
-    cursor: {
-        pointerEvents: 'none',
-        zIndex: 800,
-        position: 'absolute',
-    },
-    color: {
-        width: 10,
-        height: 10,
-    },
-});
-const MultiVariantCrosshairs = (0, mobx_react_1.observer)(function ({ mouseX, mouseY, model, }) {
-    const { classes } = useStyles();
-    const theme = (0, material_1.useTheme)();
-    const { hoveredGenotype, height, scrollTop, sourceMap } = model;
-    const { width } = (0, util_1.getContainingView)(model);
-    const source = hoveredGenotype ? sourceMap === null || sourceMap === void 0 ? void 0 : sourceMap[hoveredGenotype.name] : undefined;
-    const y = mouseY - scrollTop;
-    return ((0, jsx_runtime_1.jsxs)("div", { className: classes.rel, children: [(0, jsx_runtime_1.jsxs)("svg", { className: classes.cursor, width: width, height: height, style: {
-                    top: scrollTop,
-                }, children: [(0, jsx_runtime_1.jsx)("line", { x1: 0, x2: width, y1: y, y2: y, stroke: theme.palette.text.primary }), (0, jsx_runtime_1.jsx)("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: theme.palette.text.primary })] }), source ? ((0, jsx_runtime_1.jsx)(MultiVariantTooltip_1.default, { source: {
-                    ...source,
-                    ...hoveredGenotype,
-                } })) : null] }));
-});
-exports.default = MultiVariantCrosshairs;

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

@@ -1,7 +0,0 @@
-import type { MultiVariantBaseModel } from '../MultiVariantBaseModel';
-export declare const LegendBar: (props: {
-    model: MultiVariantBaseModel;
-    orientation?: string;
-    exportSVG?: boolean;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default LegendBar;

package/dist/shared/components/MultiVariantLegendBar.js

@@ -1,32 +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.LegendBar = void 0;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const mobx_react_1 = require("mobx-react");
-const MultiVariantColorLegend_1 = __importDefault(require("./MultiVariantColorLegend"));
-const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSVG, }) {
-    const { id, scrollTop, height } = model;
-    const clipid = `legend-${id}`;
-    return exportSVG ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: clipid, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: 1000, height: height }) }) }), (0, jsx_runtime_1.jsx)("g", { clipPath: `url(#${clipid})`, children: (0, jsx_runtime_1.jsx)("g", { transform: `translate(0,${-scrollTop})`, children: children }) })] })) : ((0, jsx_runtime_1.jsx)("svg", { style: {
-            position: 'absolute',
-            top: 0,
-            left: 0,
-            zIndex: 100,
-            pointerEvents: 'none',
-            height: model.totalHeight,
-            width: (0, util_1.getContainingView)(model).width,
-        }, children: children }));
-});
-exports.LegendBar = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const { canDisplayLabels, rowHeight, sources } = model;
-    const svgFontSize = (0, util_1.clamp)(rowHeight, 8, 12);
-    return sources ? ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, children: (0, jsx_runtime_1.jsx)(MultiVariantColorLegend_1.default, { model: model, labelWidth: (0, util_1.max)(sources
-                .map(s => (0, util_1.measureText)(s.label, svgFontSize) + 10)
-                .map(width => (canDisplayLabels ? width : 20)), 0) }) })) : null;
-});
-exports.default = exports.LegendBar;

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

@@ -1,10 +0,0 @@
-export default function MultiVariantTooltip({ source, }: {
-    source: {
-        color?: string;
-        hoveredGenotype?: {
-            genotype: string;
-            name: string;
-        };
-        [key: string]: unknown;
-    };
-}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/components/MultiVariantTooltip.js

@@ -1,24 +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 = MultiVariantTooltip;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const BaseTooltip_1 = __importDefault(require("@jbrowse/core/ui/BaseTooltip"));
-const escape_html_1 = __importDefault(require("escape-html"));
-function MultiVariantTooltip({ source, }) {
-    return ((0, jsx_runtime_1.jsxs)(BaseTooltip_1.default, { children: [source.color ? ((0, jsx_runtime_1.jsx)("div", { style: {
-                    width: 10,
-                    height: 10,
-                    backgroundColor: source.color,
-                } })) : null, (0, jsx_runtime_1.jsx)(ui_1.SanitizedHTML, { html: Object.entries(source)
-                    .filter(([key, val]) => key !== 'color' &&
-                    key !== 'HP' &&
-                    key !== 'name' &&
-                    key !== 'id' &&
-                    val !== undefined)
-                    .map(([key, value]) => `${key}:${(0, escape_html_1.default)(`${value}`)}`)
-                    .join('<br/>') })] }));
-}

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

@@ -1,8 +0,0 @@
-declare const RectBg: ({ x, y, width, height, color, }: {
-    x: number;
-    y: number;
-    width: number;
-    height: number;
-    color?: string;
-}) => import("react/jsx-runtime").JSX.Element;
-export default RectBg;

package/dist/shared/components/RectBg.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const RectBg = ({ x, y, width, height, color, }) => {
-    const theme = (0, material_1.useTheme)();
-    return ((0, jsx_runtime_1.jsx)("rect", { pointerEvents: "auto", x: x, y: y, width: width, height: height, ...(0, util_1.getFillProps)(color || (0, material_1.alpha)(theme.palette.background.paper, 0.3)) }));
-};
-exports.default = RectBg;

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

@@ -1,11 +0,0 @@
-import type { Source } from '../types';
-interface ReducedModel {
-    sources?: Source[];
-    setLayout: (s: Source[]) => void;
-    clearLayout: () => void;
-}
-export default function SetColorDialog({ model, handleClose, }: {
-    model: ReducedModel;
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;
-export {};

package/dist/shared/components/SetColorDialog.js

@@ -1,12 +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 = SetColorDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const SourcesGrid_1 = __importDefault(require("./SourcesGrid"));
-const SetColorDialog_1 = __importDefault(require("./ui/SetColorDialog"));
-function SetColorDialog({ model, handleClose, }) {
-    return ((0, jsx_runtime_1.jsx)(SetColorDialog_1.default, { model: model, handleClose: handleClose, title: "Multi-sample variant display - Color/arrangement editor", enableBulkEdit: true, enableRowPalettizer: true, showTipsStorageKey: "multivariant-showTips", SourcesGridComponent: SourcesGrid_1.default }));
-}

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

@@ -1,10 +0,0 @@
-export default function SetColorDialogBulkEditPanel({ onClose, currLayout, }: {
-    currLayout: {
-        name: string;
-        [key: string]: unknown;
-    }[];
-    onClose: (arg?: {
-        name: string;
-        [key: string]: unknown;
-    }[]) => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/components/SetColorDialogBulkEditPanel.js

@@ -1,84 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetColorDialogBulkEditPanel;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-});
-function SetColorDialogBulkEditPanel({ onClose, currLayout, }) {
-    const { classes } = useStyles();
-    const [val, setVal] = (0, react_1.useState)('');
-    const [error, setError] = (0, react_1.useState)();
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Paste CSV or TSV. If a header column is present. First line is a header. If a column called \"name\" is present, it uses that to connect to IDs in the table, otherwise it uses the first column no." }), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, placeholder: 'name,population\nHG00098,GBR\nHG00101,GBR\nHG00459,CHS\n...', maxRows: 10, fullWidth: true, value: val, onChange: event => {
-                            setVal(event.target.value);
-                        }, slotProps: {
-                            input: {
-                                classes: {
-                                    input: classes.textAreaFont,
-                                },
-                            },
-                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            const lines = val
-                                .split('\n')
-                                .map(f => f.trim())
-                                .filter(f => !!f);
-                            const fields = lines[0].split(/[,\t]/gm);
-                            if (fields.includes('name')) {
-                                setError('');
-                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
-                                const newData = Object.fromEntries(lines.slice(1).map(line => {
-                                    const cols = line.split(/[,\t]/gm);
-                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
-                                    return [
-                                        newRecord.name,
-                                        {
-                                            ...newRecord,
-                                            ...oldLayout[newRecord.name],
-                                        },
-                                    ];
-                                }));
-                                onClose(currLayout.map(record => ({
-                                    ...record,
-                                    ...newData[record.name],
-                                })));
-                            }
-                            else {
-                                setError(new Error('No "name" column found on line 1'));
-                            }
-                        }, children: "Update rows" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
-                            const lines = val
-                                .split('\n')
-                                .map(f => f.trim())
-                                .filter(f => !!f);
-                            const fields = lines[0].split(/[,\t]/gm);
-                            if (fields.includes('name')) {
-                                setError('');
-                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
-                                const newData = Object.fromEntries(lines.slice(1).map(line => {
-                                    const cols = line.split(/[,\t]/gm);
-                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
-                                    return [
-                                        newRecord.name,
-                                        {
-                                            ...newRecord,
-                                            ...oldLayout[newRecord.name],
-                                        },
-                                    ];
-                                }));
-                                onClose(currLayout.map(record => ({
-                                    ...newData[record.name],
-                                })));
-                            }
-                            else {
-                                setError(new Error('No "name" column found on line 1'));
-                            }
-                        }, children: "Replace rows" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
-                            onClose();
-                        }, children: "Cancel" })] })] }));
-}

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

@@ -1 +0,0 @@
-export default function SetColorDialogHelpfulTips(): import("react/jsx-runtime").JSX.Element;

package/dist/shared/components/SetColorDialogHelpfulTips.js

@@ -1,7 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetColorDialogHelpfulTips;
-const jsx_runtime_1 = require("react/jsx-runtime");
-function SetColorDialogHelpfulTips() {
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: ["Helpful tips", (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsx)("li", { children: "You can select rows in the table with the checkboxes" }), (0, jsx_runtime_1.jsx)("li", { children: "Multi-select is enabled with shift-click and control-click" }), (0, jsx_runtime_1.jsx)("li", { children: "The \"Move selected items up/down\" can re-arrange subtracks" }), (0, jsx_runtime_1.jsx)("li", { children: "Sorting the data grid itself can also re-arrange subtracks" }), (0, jsx_runtime_1.jsx)("li", { children: "Changes are applied when you hit Submit" }), (0, jsx_runtime_1.jsx)("li", { children: "You can click and drag the dialog box to move it on the screen" }), (0, jsx_runtime_1.jsx)("li", { children: "Columns in the table can be hidden using a vertical '...' menu on the right side of each column" })] })] }));
-}

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

@@ -1,10 +0,0 @@
-export default function SetColorDialogRowPalettizer({ setCurrLayout, currLayout, }: {
-    currLayout: {
-        name: string;
-        [key: string]: unknown;
-    }[];
-    setCurrLayout: (arg: {
-        name: string;
-        [key: string]: unknown;
-    }[]) => void;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/shared/components/SetColorDialogRowPalettizer.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetColorDialogRowPalettizer;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const colors_1 = require("@jbrowse/core/ui/colors");
-const color_1 = require("@jbrowse/core/util/color");
-const material_1 = require("@mui/material");
-function SetColorDialogRowPalettizer({ setCurrLayout, currLayout, }) {
-    if (!currLayout.length || !currLayout[0]) {
-        return null;
-    }
-    const fields = Object.keys(currLayout[0]).filter(f => f !== 'name' &&
-        f !== 'color' &&
-        f !== 'label' &&
-        f !== 'id' &&
-        f !== 'HP');
-    return ((0, jsx_runtime_1.jsxs)("div", { children: ["Create color palette based on...", fields.map(r => ((0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
-                    const map = new Map();
-                    for (const row of currLayout) {
-                        const val = map.get(row[r]);
-                        if (!val) {
-                            map.set(row[r], 1);
-                        }
-                        else {
-                            map.set(row[r], val + 1);
-                        }
-                    }
-                    const ret = Object.fromEntries([...map.entries()]
-                        .sort((a, b) => a[1] - b[1])
-                        .map((r, idx) => [r[0], colors_1.set1[idx] || (0, color_1.randomColor)(r[0])]));
-                    setCurrLayout(currLayout.map(row => ({
-                        ...row,
-                        color: ret[row[r]],
-                    })));
-                }, children: r }, r))), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                    setCurrLayout(currLayout.map(row => ({
-                        ...row,
-                        color: undefined,
-                    })));
-                }, children: "Clear colors" })] }));
-}

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

@@ -1,10 +0,0 @@
-export default function SetMinMaxDialog(props: {
-    model: {
-        minScore: number;
-        maxScore: number;
-        scaleType: string;
-        setMinScore: (arg?: number) => void;
-        setMaxScore: (arg?: number) => void;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/components/SetMinMaxDialog.js

@@ -1,26 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetMinMaxDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-function SetMinMaxDialog(props) {
-    const { model, handleClose } = props;
-    const { minScore, maxScore, scaleType } = model;
-    const [min, setMin] = (0, react_1.useState)(`${minScore !== Number.MIN_VALUE ? minScore : ''}`);
-    const [max, setMax] = (0, react_1.useState)(`${maxScore !== Number.MAX_VALUE ? maxScore : ''}`);
-    const ok = min !== '' && max !== '' && !Number.isNaN(+min) && !Number.isNaN(+max)
-        ? +max > +min
-        : true;
-    const logOk = scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true;
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set min/max score for track", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Enter min/max score: " }), !ok ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: "Max is greater than or equal to min" })) : null, !logOk ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: "Min score should be greater than 0 for log scale" })) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { value: min, onChange: event => {
-                            setMin(event.target.value);
-                        }, placeholder: "Enter min score" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: max, onChange: event => {
-                            setMax(event.target.value);
-                        }, placeholder: "Enter max score" })] }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", style: { marginLeft: 20 }, disabled: !ok, onClick: () => {
-                        model.setMinScore(min !== '' && !Number.isNaN(+min) ? +min : undefined);
-                        model.setMaxScore(max !== '' && !Number.isNaN(+max) ? +max : undefined);
-                        handleClose();
-                    }, children: "Submit" }) })] }));
-}

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

@@ -1,8 +0,0 @@
-import type { Source } from '../types';
-export default function SetRowHeight({ model, handleClose, }: {
-    model: {
-        rowHeight?: Source[];
-        setRowHeight: (arg: number) => void;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/components/SetRowHeightDialog.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetRowHeight;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-function SetRowHeight({ model, handleClose, }) {
-    const [value, setValue] = (0, react_1.useState)(`${model.rowHeight}`);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Set row height", onClose: handleClose, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { value: value, onChange: event => {
-                        setValue(event.target.value);
-                    } }) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: Number.isNaN(+value), variant: "contained", onClick: () => {
-                            model.setRowHeight(+value);
-                            handleClose();
-                        }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-}

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

@@ -1,7 +0,0 @@
-import type { Source } from '../types';
-import type { GridRowId } from '@mui/x-data-grid';
-export default function SourcesDataGrid({ rows, onChange, setSelected, }: {
-    rows: Source[];
-    onChange: (arg: Source[]) => void;
-    setSelected: (arg: GridRowId[]) => void;
-}): import("react/jsx-runtime").JSX.Element;