@jbrowse/plugin-spreadsheet-view 2.6.1

package/esm/SpreadsheetView/components/RowMenu.js.map

@@ -0,0 +1 @@
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package/esm/SpreadsheetView/components/SortIndicator.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { SpreadsheetModel } from '../models/Spreadsheet';
+export default function SortIndicator({ model, columnNumber, }: {
+    model: SpreadsheetModel;
+    columnNumber: number;
+}): React.JSX.Element | null;

package/esm/SpreadsheetView/components/SortIndicator.js

@@ -0,0 +1,22 @@
+import React from 'react';
+import { makeStyles } from 'tss-react/mui';
+// icons
+import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp';
+import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
+const useStyles = makeStyles()({
+    sortIndicator: {
+        position: 'relative',
+        top: '0.2rem',
+        fontSize: '1rem',
+    },
+});
+export default function SortIndicator({ model, columnNumber, }) {
+    const { classes } = useStyles();
+    const sortSpec = model.sortColumns.find(c => c.columnNumber === columnNumber);
+    if (sortSpec) {
+        const { descending } = sortSpec;
+        return descending ? (React.createElement(KeyboardArrowUpIcon, { className: classes.sortIndicator })) : (React.createElement(KeyboardArrowDownIcon, { className: classes.sortIndicator }));
+    }
+    return null;
+}
+//# sourceMappingURL=SortIndicator.js.map

package/esm/SpreadsheetView/components/SortIndicator.js.map

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package/esm/SpreadsheetView/components/Spreadsheet.d.ts

@@ -0,0 +1,11 @@
+import React from 'react';
+import { Instance } from 'mobx-state-tree';
+import SpreadsheetStateModel from '../models/Spreadsheet';
+type SpreadsheetModel = Instance<typeof SpreadsheetStateModel>;
+declare const Spreadsheet: ({ model, height, page, rowsPerPage, }: {
+    model: SpreadsheetModel;
+    height: number;
+    page: number;
+    rowsPerPage: number;
+}) => React.JSX.Element;
+export default Spreadsheet;

package/esm/SpreadsheetView/components/Spreadsheet.js

@@ -0,0 +1,20 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { LoadingEllipses } from '@jbrowse/core/ui';
+import DataTable from './DataTable';
+const useStyles = makeStyles()(theme => ({
+    root: {
+        position: 'relative',
+        marginBottom: theme.spacing(1),
+        background: theme.palette.background.paper,
+        overflow: 'auto',
+    },
+}));
+const Spreadsheet = observer(function ({ model, height, page, rowsPerPage, }) {
+    var _a;
+    const { classes } = useStyles();
+    return (React.createElement("div", { className: classes.root, style: { height } }, ((_a = model === null || model === void 0 ? void 0 : model.rowSet) === null || _a === void 0 ? void 0 : _a.isLoaded) && model.initialized ? (React.createElement(DataTable, { model: model, page: page, rowsPerPage: rowsPerPage })) : (React.createElement(LoadingEllipses, { variant: "h6" }))));
+});
+export default Spreadsheet;
+//# sourceMappingURL=Spreadsheet.js.map

package/esm/SpreadsheetView/components/Spreadsheet.js.map

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package/esm/SpreadsheetView/components/SpreadsheetView.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { SpreadsheetViewModel } from '../models/SpreadsheetView';
+declare const _default: ({ model }: {
+    model: SpreadsheetViewModel;
+}) => React.JSX.Element;
+export default _default;

package/esm/SpreadsheetView/components/SpreadsheetView.js

@@ -0,0 +1,58 @@
+import React, { useState } from 'react';
+import { Grid } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { ResizeHandle } from '@jbrowse/core/ui';
+// locals
+import ImportWizard from './ImportWizard';
+import Spreadsheet from './Spreadsheet';
+import GlobalFilterControls from './GlobalFilterControls';
+import ColumnFilterControls from './ColumnFilterControls';
+import StatusBar from './StatusBar';
+const headerHeight = 52;
+const colFilterHeight = 46;
+const statusBarHeight = 40;
+const useStyles = makeStyles()(theme => ({
+    header: {
+        overflow: 'hidden',
+        whiteSpace: 'nowrap',
+        boxSizing: 'border-box',
+        height: headerHeight,
+        paddingLeft: theme.spacing(1),
+    },
+    contentArea: {
+        overflow: 'auto',
+    },
+    resizeHandle: {
+        height: 3,
+        position: 'absolute',
+        bottom: 0,
+        left: 0,
+        background: theme.palette.action.disabled,
+        boxSizing: 'border-box',
+        borderTop: '1px solid #fafafa',
+    },
+}));
+export default observer(function ({ model }) {
+    const { classes } = useStyles();
+    const { spreadsheet, filterControls, hideFilterControls, hideVerticalResizeHandle, mode, height, } = model;
+    const [page, setPage] = useState(0);
+    const [rowsPerPage, setRowsPerPage] = useState(100);
+    return (React.createElement("div", null,
+        mode !== 'display' || hideFilterControls ? null : (React.createElement(React.Fragment, null,
+            React.createElement(Grid, { container: true, direction: "row", className: classes.header },
+                React.createElement(Grid, { item: true },
+                    React.createElement(GlobalFilterControls, { model: model }))),
+            filterControls.columnFilters.map((f, i) => (React.createElement(ColumnFilterControls, { key: `${f.columnNumber}-${i}`, viewModel: model, filterModel: f, columnNumber: f.columnNumber, height: colFilterHeight }))))),
+        mode === 'import' ? (React.createElement(ImportWizard, { model: model.importWizard })) : (React.createElement("div", { className: classes.contentArea },
+            React.createElement("div", { style: {
+                    position: 'relative',
+                    display: mode === 'display' ? undefined : 'none',
+                } }, spreadsheet ? (React.createElement(Spreadsheet, { page: page, rowsPerPage: rowsPerPage, model: spreadsheet, height: height -
+                    headerHeight -
+                    filterControls.columnFilters.length * colFilterHeight -
+                    statusBarHeight })) : null))),
+        spreadsheet ? (React.createElement(StatusBar, { page: page, setPage: setPage, rowsPerPage: rowsPerPage, setRowsPerPage: setRowsPerPage, mode: mode, spreadsheet: spreadsheet })) : null,
+        hideVerticalResizeHandle ? null : (React.createElement(ResizeHandle, { onDrag: model.resizeHeight, className: classes.resizeHandle }))));
+});
+//# sourceMappingURL=SpreadsheetView.js.map

package/esm/SpreadsheetView/components/SpreadsheetView.js.map

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package/esm/SpreadsheetView/components/StatusBar.d.ts

@@ -0,0 +1,11 @@
+import React from 'react';
+import { SpreadsheetModel } from '../models/Spreadsheet';
+declare const StatusBar: ({ page, rowsPerPage, setPage, setRowsPerPage, spreadsheet, mode, }: {
+    page: number;
+    mode: string;
+    spreadsheet: SpreadsheetModel;
+    rowsPerPage: number;
+    setPage: (arg: number) => void;
+    setRowsPerPage: (arg: number) => void;
+}) => React.JSX.Element;
+export default StatusBar;

package/esm/SpreadsheetView/components/StatusBar.js

@@ -0,0 +1,37 @@
+import React from 'react';
+import { FormGroup, TablePagination } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+// locals
+import RowCountMessage from './RowCountMessage';
+import { observer } from 'mobx-react';
+const statusBarHeight = 40;
+const useStyles = makeStyles()(theme => ({
+    statusBar: {
+        height: statusBarHeight,
+        boxSizing: 'border-box',
+        borderTop: '1px outset #b1b1b1',
+        paddingLeft: theme.spacing(1),
+    },
+    verticallyCenter: {
+        display: 'flex',
+        justifyContent: 'center',
+        flexDirection: 'column',
+    },
+    spacer: {
+        flexGrow: 1,
+    },
+}));
+const StatusBar = observer(function StatusBar({ page, rowsPerPage, setPage, setRowsPerPage, spreadsheet, mode, }) {
+    const { classes } = useStyles();
+    return (React.createElement("div", { className: classes.statusBar, style: { display: mode === 'display' ? undefined : 'none' } }, spreadsheet ? (React.createElement(FormGroup, { row: true },
+        React.createElement("div", { className: classes.verticallyCenter },
+            React.createElement(RowCountMessage, { spreadsheet: spreadsheet })),
+        React.createElement("div", { className: classes.spacer }),
+        React.createElement(TablePagination, { rowsPerPageOptions: [10, 25, 100, 1000], count: spreadsheet.rowSet.count, component: "div", rowsPerPage: rowsPerPage, page: page, onPageChange: (_, newPage) => setPage(newPage), onRowsPerPageChange: event => {
+                setRowsPerPage(+event.target.value);
+                setPage(0);
+            } }),
+        React.createElement("div", { className: classes.spacer }))) : null));
+});
+export default StatusBar;
+//# sourceMappingURL=StatusBar.js.map

package/esm/SpreadsheetView/components/StatusBar.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"StatusBar.js","sourceRoot":"","sources":["../../../src/SpreadsheetView/components/StatusBar.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,SAAS,EAAE,eAAe,EAAE,MAAM,eAAe,CAAA;AAC1D,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,SAAS;AACT,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,MAAM,eAAe,GAAG,EAAE,CAAA;AAE1B,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,SAAS,EAAE;QACT,MAAM,EAAE,eAAe;QACvB,SAAS,EAAE,YAAY;QACvB,SAAS,EAAE,oBAAoB;QAC/B,WAAW,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC9B;IACD,gBAAgB,EAAE;QAChB,OAAO,EAAE,MAAM;QACf,cAAc,EAAE,QAAQ;QACxB,aAAa,EAAE,QAAQ;KACxB;IACD,MAAM,EAAE;QACN,QAAQ,EAAE,CAAC;KACZ;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,SAAS,GAAG,QAAQ,CAAC,SAAS,SAAS,CAAC,EAC5C,IAAI,EACJ,WAAW,EACX,OAAO,EACP,cAAc,EACd,WAAW,EACX,IAAI,GAQL;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BACE,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,OAAO,EAAE,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,EAAE,IAE1D,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,SAAS,IAAC,GAAG;QACZ,6BAAK,SAAS,EAAE,OAAO,CAAC,gBAAgB;YACtC,oBAAC,eAAe,IAAC,WAAW,EAAE,WAAW,GAAI,CACzC;QACN,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM,GAAI;QAClC,oBAAC,eAAe,IACd,kBAAkB,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,GAAG,EAAE,IAAI,CAAC,EACvC,KAAK,EAAE,WAAW,CAAC,MAAM,CAAC,KAAK,EAC/B,SAAS,EAAC,KAAK,EACf,WAAW,EAAE,WAAW,EACxB,IAAI,EAAE,IAAI,EACV,YAAY,EAAE,CAAC,CAAC,EAAE,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,OAAO,CAAC,EAC9C,mBAAmB,EAAE,KAAK,CAAC,EAAE;gBAC3B,cAAc,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACnC,OAAO,CAAC,CAAC,CAAC,CAAA;YACZ,CAAC,GACD;QACF,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM,GAAI,CACxB,CACb,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/esm/SpreadsheetView/components/util.d.ts

@@ -0,0 +1 @@
+export declare function numToColName(num: number): string;

package/esm/SpreadsheetView/components/util.js

@@ -0,0 +1,15 @@
+function letterFor(n) {
+    return String.fromCharCode(n + 65);
+}
+export function numToColName(num) {
+    if (num >= 0) {
+        if (num < 26) {
+            return letterFor(num);
+        }
+        if (num < 27 * 26) {
+            return letterFor(Math.floor(num / 26 - 1)) + letterFor(num % 26);
+        }
+    }
+    throw new RangeError('column number out of range');
+}
+//# sourceMappingURL=util.js.map

package/esm/SpreadsheetView/components/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/SpreadsheetView/components/util.ts"],"names":[],"mappings":"AAAA,SAAS,SAAS,CAAC,CAAS;IAC1B,OAAO,MAAM,CAAC,YAAY,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,GAAW;IACtC,IAAI,GAAG,IAAI,CAAC,EAAE;QACZ,IAAI,GAAG,GAAG,EAAE,EAAE;YACZ,OAAO,SAAS,CAAC,GAAG,CAAC,CAAA;SACtB;QACD,IAAI,GAAG,GAAG,EAAE,GAAG,EAAE,EAAE;YACjB,OAAO,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,GAAG,GAAG,EAAE,CAAC,CAAA;SACjE;KACF;IAED,MAAM,IAAI,UAAU,CAAC,4BAA4B,CAAC,CAAA;AACpD,CAAC"}

package/esm/SpreadsheetView/importAdapters/BedImport.d.ts

@@ -0,0 +1,17 @@
+/// <reference types="node" />
+import { ParseOptions } from './ImportUtils';
+export declare function removeBedHeaders(buffer: Buffer): Buffer;
+export declare function parseBedBuffer(buffer: Buffer, options: ParseOptions): Promise<{
+    rowSet: import("./ImportUtils").RowSet;
+    columnDisplayOrder: number[];
+    hasColumnNames: boolean;
+    columns: import("./ImportUtils").Column[];
+    assemblyName: string | undefined;
+}>;
+export declare function parseBedPEBuffer(buffer: Buffer, options: ParseOptions): Promise<{
+    rowSet: import("./ImportUtils").RowSet;
+    columnDisplayOrder: number[];
+    hasColumnNames: boolean;
+    columns: import("./ImportUtils").Column[];
+    assemblyName: string | undefined;
+}>;

package/esm/SpreadsheetView/importAdapters/BedImport.js

@@ -0,0 +1,141 @@
+import { parseTsvBuffer } from './ImportUtils';
+const browserBytes = 'browser '.split('').map(c => c.charCodeAt(0));
+const trackBytes = 'track '.split('').map(c => c.charCodeAt(0));
+const commentBytes = '#'.split('').map(c => c.charCodeAt(0));
+function bytesAreFoundAt(position, buffer, bytes) {
+    let i = 0;
+    for (; i < bytes.length; i += 1) {
+        if (buffer[position + i] !== bytes[i]) {
+            return false;
+        }
+    }
+    return true;
+}
+export function removeBedHeaders(buffer) {
+    // slice off the first lines of the buffer if it starts with one or more
+    // header lines
+    let i = 0;
+    for (; i < buffer.length; i += 1) {
+        if (bytesAreFoundAt(i, buffer, browserBytes) ||
+            bytesAreFoundAt(i, buffer, trackBytes) ||
+            bytesAreFoundAt(i, buffer, commentBytes)) {
+            // consume up to the next newline
+            do {
+                i += 1;
+            } while (buffer[i] !== 10);
+        }
+        else {
+            // end of headers, return
+            break;
+        }
+    }
+    if (i) {
+        return buffer.slice(i);
+    }
+    return buffer;
+}
+export async function parseBedBuffer(buffer, options) {
+    const b = removeBedHeaders(buffer);
+    const data = await parseTsvBuffer(b);
+    const bedColumns = [
+        { name: 'chrom', dataType: { type: 'LocRef' } },
+        { name: 'chromStart', dataType: { type: 'LocStart' } },
+        { name: 'chromEnd', dataType: { type: 'LocEnd' } },
+        { name: 'name', dataType: { type: 'Text' } },
+        { name: 'score', dataType: { type: 'Number' } },
+        { name: 'strand', dataType: { type: 'Text' } },
+    ];
+    data.columns.forEach((col, colNumber) => {
+        const bedColumn = bedColumns[colNumber];
+        if (bedColumn) {
+            col.name = bedColumn.name;
+            col.dataType = bedColumn.dataType;
+        }
+    });
+    data.hasColumnNames = true;
+    data.assemblyName = options.selectedAssemblyName;
+    data.columnDisplayOrder.push(data.columnDisplayOrder.length);
+    data.columns.unshift({
+        name: 'Location',
+        dataType: { type: 'LocString' },
+        isDerived: true,
+        derivationFunctionText: `jexl:{text:row.cells[0].text+':'+row.cells[1].text+'..'+row.cells[2].text,\n
+    extendedData: {refName: row.cells.ref.text, start: parseInt(row.cells.start.text,10), end: parseInt(row.cells.end.text,10)}}`,
+    });
+    return data;
+}
+export async function parseBedPEBuffer(buffer, options) {
+    const b = removeBedHeaders(buffer);
+    const data = await parseTsvBuffer(b);
+    const bedColumns = [
+        { name: 'chrom1', dataType: { type: 'Text' }, featureField: ['refName'] },
+        { name: 'start1', dataType: { type: 'Number' }, featureField: ['start'] },
+        { name: 'end1', dataType: { type: 'Number' }, featureField: ['end'] },
+        {
+            name: 'chrom2',
+            dataType: { type: 'Text' },
+            featureField: ['mate', 'refName'],
+        },
+        {
+            name: 'start2',
+            dataType: { type: 'Number' },
+            featureField: ['mate', 'start'],
+        },
+        {
+            name: 'end2',
+            dataType: { type: 'Number' },
+            featureField: ['mate', 'end'],
+        },
+        { name: 'name', dataType: { type: 'Text' }, featureField: ['name'] },
+        { name: 'score', dataType: { type: 'Number' }, featureField: ['score'] },
+        { name: 'strand1', dataType: { type: 'Text' }, featureField: ['strand'] },
+        {
+            name: 'strand2',
+            dataType: { type: 'Text' },
+            featureField: ['mate', 'strand'],
+        },
+    ];
+    data.columns.forEach((col, colNumber) => {
+        const bedColumn = bedColumns[colNumber];
+        if (bedColumn) {
+            col.name = bedColumn.name;
+            col.dataType = bedColumn.dataType;
+        }
+    });
+    data.hasColumnNames = true;
+    // decorate each row with a feature object in its extendedData
+    data.rowSet.rows.forEach((row, rowNumber) => {
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const featureData = {};
+        row.cells.forEach(({ text }, columnNumber) => {
+            const bedColumn = bedColumns[columnNumber];
+            const val = bedColumn && bedColumn.dataType.type === 'Number' && text
+                ? parseFloat(text)
+                : text;
+            if (bedColumn) {
+                // a predefined column
+                if (bedColumn.featureField.length === 2) {
+                    if (!featureData[bedColumn.featureField[0]]) {
+                        featureData[bedColumn.featureField[0]] = {};
+                    }
+                    featureData[bedColumn.featureField[0]][bedColumn.featureField[1]] =
+                        val;
+                }
+                else {
+                    featureData[bedColumn.featureField[0]] = val;
+                }
+            }
+            else {
+                // some other column
+                featureData[`column${columnNumber + 1}`] = val;
+            }
+        });
+        featureData.uniqueId = `bedpe-${rowNumber}`;
+        row.extendedData = {
+            feature: featureData,
+        };
+    });
+    data.assemblyName = options.selectedAssemblyName;
+    return data;
+}
+//# sourceMappingURL=BedImport.js.map

package/esm/SpreadsheetView/importAdapters/BedImport.js.map

@@ -0,0 +1 @@
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package/esm/SpreadsheetView/importAdapters/ImportUtils.d.ts

@@ -0,0 +1,42 @@
+/// <reference types="node" />
+export declare function bufferToString(buffer: Buffer): string;
+export interface Row {
+    id: string;
+    extendedData?: any;
+    cells: {
+        text: string;
+        extendedData?: any;
+    }[];
+}
+export interface RowSet {
+    isLoaded: boolean;
+    rows: Row[];
+}
+export interface ParseOptions {
+    hasColumnNameLine?: boolean;
+    columnNameLineNumber?: number;
+    selectedAssemblyName?: string;
+    isValidRefName?: (refName: string, assemblyName?: string) => boolean;
+}
+export interface Column {
+    name: string;
+    dataType: {
+        type: string;
+    };
+    isDerived?: boolean;
+    derivationFunctionText?: string;
+}
+export declare function parseCsvBuffer(buffer: Buffer, options?: ParseOptions): Promise<{
+    rowSet: RowSet;
+    columnDisplayOrder: number[];
+    hasColumnNames: boolean;
+    columns: Column[];
+    assemblyName: string | undefined;
+}>;
+export declare function parseTsvBuffer(buffer: Buffer, options?: ParseOptions): Promise<{
+    rowSet: RowSet;
+    columnDisplayOrder: number[];
+    hasColumnNames: boolean;
+    columns: Column[];
+    assemblyName: string | undefined;
+}>;

package/esm/SpreadsheetView/importAdapters/ImportUtils.js

@@ -0,0 +1,95 @@
+import { parseLocString } from '@jbrowse/core/util';
+export function bufferToString(buffer) {
+    return new TextDecoder('utf8', { fatal: true }).decode(buffer);
+}
+async function parseWith(buffer, options = {}) {
+    const csv = await import('csvtojson').then(module => module.default);
+    return csv({ noheader: true, output: 'csv', ...options }).fromString(bufferToString(buffer));
+}
+function guessColumnType(rowSet, columnNumber, isValidRefName) {
+    const text = rowSet.rows[0].cells[columnNumber].text || '';
+    let guessedType = 'Text';
+    let parsedLoc;
+    try {
+        parsedLoc = parseLocString(text, isValidRefName);
+    }
+    catch (error) {
+        //
+    }
+    if (parsedLoc && parsedLoc.refName && typeof parsedLoc.start === 'number') {
+        guessedType = 'LocString';
+    }
+    else if (/^\d+(\.\d+)?$/.test(text)) {
+        guessedType = 'Number';
+    }
+    // MAYBE TODO: iterate over the rest of the rows to confirm
+    // the type for all the rows
+    return guessedType;
+}
+function dataToSpreadsheetSnapshot(rows, options = {}) {
+    const { hasColumnNameLine = false, columnNameLineNumber = 1, isValidRefName = () => false, selectedAssemblyName, } = options;
+    // rows is an array of row objects and columnNames
+    // is an array of column names (in import order)
+    let maxCols = 0;
+    const rowSet = {
+        isLoaded: true,
+        rows: rows.map((row, rowNumber) => {
+            const id = rowNumber + (hasColumnNameLine ? 0 : 1);
+            if (row.length > maxCols) {
+                maxCols = row.length;
+            }
+            return {
+                id: String(id),
+                cells: row.map((text, columnNumber) => {
+                    return { columnNumber, text };
+                }),
+            };
+        }),
+    };
+    // process the column names row if present
+    const columnNames = {};
+    if (hasColumnNameLine && columnNameLineNumber !== undefined) {
+        const [colNamesRow] = rowSet.rows.splice(columnNameLineNumber - 1, 1);
+        if (colNamesRow) {
+            colNamesRow.cells.forEach((cell, columnNumber) => {
+                columnNames[columnNumber] = cell.text || '';
+            });
+        }
+    }
+    // make our column definitions
+    const columns = [];
+    const columnDisplayOrder = [];
+    for (let columnNumber = 0; columnNumber < maxCols; columnNumber += 1) {
+        columnDisplayOrder.push(columnNumber);
+        const guessedType = guessColumnType(rowSet, columnNumber, isValidRefName);
+        // store extendeddata for LocString column
+        if (guessedType === 'LocString') {
+            for (const row of rowSet.rows) {
+                const cell = row.cells[columnNumber];
+                cell.extendedData = parseLocString(cell.text, isValidRefName);
+            }
+        }
+        columns[columnNumber] = {
+            name: columnNames[columnNumber],
+            dataType: {
+                type: guessedType,
+            },
+        };
+    }
+    return {
+        rowSet,
+        columnDisplayOrder,
+        hasColumnNames: !!hasColumnNameLine,
+        columns,
+        assemblyName: selectedAssemblyName,
+    };
+}
+export async function parseCsvBuffer(buffer, options) {
+    const rows = await parseWith(buffer);
+    return dataToSpreadsheetSnapshot(rows, options);
+}
+export async function parseTsvBuffer(buffer, options) {
+    const rows = await parseWith(buffer, { delimiter: '\t' });
+    return dataToSpreadsheetSnapshot(rows, options);
+}
+//# sourceMappingURL=ImportUtils.js.map

package/esm/SpreadsheetView/importAdapters/ImportUtils.js.map

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package/esm/SpreadsheetView/importAdapters/STARFusionImport.d.ts

@@ -0,0 +1,9 @@
+/// <reference types="node" />
+import { ParseOptions } from './ImportUtils';
+export declare function parseSTARFusionBuffer(buffer: Buffer, options: ParseOptions): Promise<{
+    rowSet: import("./ImportUtils").RowSet;
+    columnDisplayOrder: number[];
+    hasColumnNames: boolean;
+    columns: import("./ImportUtils").Column[];
+    assemblyName: string | undefined;
+}>;

package/esm/SpreadsheetView/importAdapters/STARFusionImport.js

@@ -0,0 +1,69 @@
+import { parseTsvBuffer } from './ImportUtils';
+function parseSTARFusionBreakpointString(str) {
+    const fields = str.split(':');
+    const refName = fields[0];
+    const pos = Number.parseInt(fields[1], 10);
+    const strand = fields[2] === '-' ? -1 : 1;
+    return { refName, pos, strand };
+}
+const numericColumns = {
+    SpanningFragCount: true,
+    FFPM: true,
+    LeftBreakEntropy: true,
+    RightBreakEntropy: true,
+    JunctionReadCount: true,
+};
+export async function parseSTARFusionBuffer(buffer, options) {
+    const data = await parseTsvBuffer(buffer, {
+        hasColumnNameLine: true,
+        columnNameLineNumber: 1,
+        selectedAssemblyName: options.selectedAssemblyName,
+        isValidRefName: () => false,
+    });
+    // remove the # in #FusionName
+    data.columns[0].name = data.columns[0].name.replace('#', '');
+    // set some columns to be numeric
+    data.columns.forEach(col => {
+        if (numericColumns[col.name]) {
+            col.dataType = { type: 'Number' };
+        }
+    });
+    // decorate each row with a feature object in its extendedData
+    data.rowSet.rows.forEach((row, rowNumber) => {
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const featureData = {};
+        row.cells.forEach(({ text }, columnNumber) => {
+            const column = data.columns[columnNumber];
+            if (column.name === 'LeftBreakpoint' && text) {
+                const { refName, pos, strand } = parseSTARFusionBreakpointString(text);
+                featureData.refName = refName;
+                featureData.start = pos;
+                featureData.end = pos;
+                featureData.strand = strand;
+            }
+            else if (column.name === 'RightBreakpoint' && text) {
+                const { refName, pos, strand } = parseSTARFusionBreakpointString(text);
+                featureData.mate = {
+                    refName,
+                    start: pos,
+                    end: pos,
+                    strand,
+                };
+            }
+            else if (text && numericColumns[column.name]) {
+                // some other column, numeric
+                featureData[column.name] = parseFloat(text);
+            }
+            else {
+                // some other column, text
+                featureData[column.name] = text;
+            }
+        });
+        featureData.uniqueId = `sf-${rowNumber + 1}`;
+        row.extendedData = {
+            feature: featureData,
+        };
+    });
+    return data;
+}
+//# sourceMappingURL=STARFusionImport.js.map

package/esm/SpreadsheetView/importAdapters/STARFusionImport.js.map

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