@jbrowse/plugin-spreadsheet-view 2.6.1

package/dist/SpreadsheetView/components/SpreadsheetView.js

@@ -0,0 +1,86 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const ui_1 = require("@jbrowse/core/ui");
+// locals
+const ImportWizard_1 = __importDefault(require("./ImportWizard"));
+const Spreadsheet_1 = __importDefault(require("./Spreadsheet"));
+const GlobalFilterControls_1 = __importDefault(require("./GlobalFilterControls"));
+const ColumnFilterControls_1 = __importDefault(require("./ColumnFilterControls"));
+const StatusBar_1 = __importDefault(require("./StatusBar"));
+const headerHeight = 52;
+const colFilterHeight = 46;
+const statusBarHeight = 40;
+const useStyles = (0, mui_1.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',
+    },
+}));
+exports.default = (0, mobx_react_1.observer)(function ({ model }) {
+    const { classes } = useStyles();
+    const { spreadsheet, filterControls, hideFilterControls, hideVerticalResizeHandle, mode, height, } = model;
+    const [page, setPage] = (0, react_1.useState)(0);
+    const [rowsPerPage, setRowsPerPage] = (0, react_1.useState)(100);
+    return (react_1.default.createElement("div", null,
+        mode !== 'display' || hideFilterControls ? null : (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement(material_1.Grid, { container: true, direction: "row", className: classes.header },
+                react_1.default.createElement(material_1.Grid, { item: true },
+                    react_1.default.createElement(GlobalFilterControls_1.default, { model: model }))),
+            filterControls.columnFilters.map((f, i) => (react_1.default.createElement(ColumnFilterControls_1.default, { key: `${f.columnNumber}-${i}`, viewModel: model, filterModel: f, columnNumber: f.columnNumber, height: colFilterHeight }))))),
+        mode === 'import' ? (react_1.default.createElement(ImportWizard_1.default, { model: model.importWizard })) : (react_1.default.createElement("div", { className: classes.contentArea },
+            react_1.default.createElement("div", { style: {
+                    position: 'relative',
+                    display: mode === 'display' ? undefined : 'none',
+                } }, spreadsheet ? (react_1.default.createElement(Spreadsheet_1.default, { page: page, rowsPerPage: rowsPerPage, model: spreadsheet, height: height -
+                    headerHeight -
+                    filterControls.columnFilters.length * colFilterHeight -
+                    statusBarHeight })) : null))),
+        spreadsheet ? (react_1.default.createElement(StatusBar_1.default, { page: page, setPage: setPage, rowsPerPage: rowsPerPage, setRowsPerPage: setRowsPerPage, mode: mode, spreadsheet: spreadsheet })) : null,
+        hideVerticalResizeHandle ? null : (react_1.default.createElement(ui_1.ResizeHandle, { onDrag: model.resizeHeight, className: classes.resizeHandle }))));
+});
+//# sourceMappingURL=SpreadsheetView.js.map

package/dist/SpreadsheetView/components/SpreadsheetView.js.map

@@ -0,0 +1 @@
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package/dist/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/dist/SpreadsheetView/components/StatusBar.js

@@ -0,0 +1,42 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+// locals
+const RowCountMessage_1 = __importDefault(require("./RowCountMessage"));
+const mobx_react_1 = require("mobx-react");
+const statusBarHeight = 40;
+const useStyles = (0, mui_1.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 = (0, mobx_react_1.observer)(function StatusBar({ page, rowsPerPage, setPage, setRowsPerPage, spreadsheet, mode, }) {
+    const { classes } = useStyles();
+    return (react_1.default.createElement("div", { className: classes.statusBar, style: { display: mode === 'display' ? undefined : 'none' } }, spreadsheet ? (react_1.default.createElement(material_1.FormGroup, { row: true },
+        react_1.default.createElement("div", { className: classes.verticallyCenter },
+            react_1.default.createElement(RowCountMessage_1.default, { spreadsheet: spreadsheet })),
+        react_1.default.createElement("div", { className: classes.spacer }),
+        react_1.default.createElement(material_1.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_1.default.createElement("div", { className: classes.spacer }))) : null));
+});
+exports.default = StatusBar;
+//# sourceMappingURL=StatusBar.js.map

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

@@ -0,0 +1 @@
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package/dist/SpreadsheetView/components/util.d.ts

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

package/dist/SpreadsheetView/components/util.js

@@ -0,0 +1,19 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.numToColName = void 0;
+function letterFor(n) {
+    return String.fromCharCode(n + 65);
+}
+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');
+}
+exports.numToColName = numToColName;
+//# sourceMappingURL=util.js.map

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

@@ -0,0 +1 @@
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package/dist/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/dist/SpreadsheetView/importAdapters/BedImport.js

@@ -0,0 +1,147 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseBedPEBuffer = exports.parseBedBuffer = exports.removeBedHeaders = void 0;
+const ImportUtils_1 = require("./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;
+}
+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;
+}
+exports.removeBedHeaders = removeBedHeaders;
+async function parseBedBuffer(buffer, options) {
+    const b = removeBedHeaders(buffer);
+    const data = await (0, ImportUtils_1.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;
+}
+exports.parseBedBuffer = parseBedBuffer;
+async function parseBedPEBuffer(buffer, options) {
+    const b = removeBedHeaders(buffer);
+    const data = await (0, ImportUtils_1.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;
+}
+exports.parseBedPEBuffer = parseBedPEBuffer;
+//# sourceMappingURL=BedImport.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"BedImport.js","sourceRoot":"","sources":["../../../src/SpreadsheetView/importAdapters/BedImport.ts"],"names":[],"mappings":";;;AAAA,+CAA4D;AAE5D,MAAM,YAAY,GAAG,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;AACnE,MAAM,UAAU,GAAG,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;AAC/D,MAAM,YAAY,GAAG,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;AAE5D,SAAS,eAAe,CAAC,QAAgB,EAAE,MAAc,EAAE,KAAe;IACxE,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QAC/B,IAAI,MAAM,CAAC,QAAQ,GAAG,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,CAAC,EAAE;YACrC,OAAO,KAAK,CAAA;SACb;KACF;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AACD,SAAgB,gBAAgB,CAAC,MAAc;IAC7C,wEAAwE;IACxE,eAAe;IACf,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,OAAO,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QAChC,IACE,eAAe,CAAC,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC;YACxC,eAAe,CAAC,CAAC,EAAE,MAAM,EAAE,UAAU,CAAC;YACtC,eAAe,CAAC,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EACxC;YACA,iCAAiC;YACjC,GAAG;gBACD,CAAC,IAAI,CAAC,CAAA;aACP,QAAQ,MAAM,CAAC,CAAC,CAAC,KAAK,EAAE,EAAC;SAC3B;aAAM;YACL,yBAAyB;YACzB,MAAK;SACN;KACF;IACD,IAAI,CAAC,EAAE;QACL,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;KACvB;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAvBD,4CAuBC;AAEM,KAAK,UAAU,cAAc,CAAC,MAAc,EAAE,OAAqB;IACxE,MAAM,CAAC,GAAG,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAClC,MAAM,IAAI,GAAG,MAAM,IAAA,4BAAc,EAAC,CAAC,CAAC,CAAA;IACpC,MAAM,UAAU,GAAG;QACjB,EAAE,IAAI,EAAE,OAAO,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE;QAC/C,EAAE,IAAI,EAAE,YAAY,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,UAAU,EAAE,EAAE;QACtD,EAAE,IAAI,EAAE,UAAU,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE;QAClD,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE;QAC5C,EAAE,IAAI,EAAE,OAAO,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE;QAC/C,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE;KAC/C,CAAA;IACD,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,SAAS,EAAE,EAAE;QACtC,MAAM,SAAS,GAAG,UAAU,CAAC,SAAS,CAAC,CAAA;QACvC,IAAI,SAAS,EAAE;YACb,GAAG,CAAC,IAAI,GAAG,SAAS,CAAC,IAAI,CAAA;YACzB,GAAG,CAAC,QAAQ,GAAG,SAAS,CAAC,QAAQ,CAAA;SAClC;IACH,CAAC,CAAC,CAAA;IACF,IAAI,CAAC,cAAc,GAAG,IAAI,CAAA;IAC1B,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,oBAAoB,CAAA;IAEhD,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;IAC5D,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC;QACnB,IAAI,EAAE,UAAU;QAChB,QAAQ,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE;QAC/B,SAAS,EAAE,IAAI;QACf,sBAAsB,EAAE;iIACqG;KAC9H,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC;AA9BD,wCA8BC;AAEM,KAAK,UAAU,gBAAgB,CAAC,MAAc,EAAE,OAAqB;IAC1E,MAAM,CAAC,GAAG,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAClC,MAAM,IAAI,GAAG,MAAM,IAAA,4BAAc,EAAC,CAAC,CAAC,CAAA;IAQpC,MAAM,UAAU,GAAgB;QAC9B,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,YAAY,EAAE,CAAC,SAAS,CAAC,EAAE;QACzE,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE,YAAY,EAAE,CAAC,OAAO,CAAC,EAAE;QACzE,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE,YAAY,EAAE,CAAC,KAAK,CAAC,EAAE;QACrE;YACE,IAAI,EAAE,QAAQ;YACd,QAAQ,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;YAC1B,YAAY,EAAE,CAAC,MAAM,EAAE,SAAS,CAAC;SAClC;QACD;YACE,IAAI,EAAE,QAAQ;YACd,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE;YAC5B,YAAY,EAAE,CAAC,MAAM,EAAE,OAAO,CAAC;SAChC;QACD;YACE,IAAI,EAAE,MAAM;YACZ,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE;YAC5B,YAAY,EAAE,CAAC,MAAM,EAAE,KAAK,CAAC;SAC9B;QACD,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,YAAY,EAAE,CAAC,MAAM,CAAC,EAAE;QACpE,EAAE,IAAI,EAAE,OAAO,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE,YAAY,EAAE,CAAC,OAAO,CAAC,EAAE;QACxE,EAAE,IAAI,EAAE,SAAS,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,YAAY,EAAE,CAAC,QAAQ,CAAC,EAAE;QACzE;YACE,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;YAC1B,YAAY,EAAE,CAAC,MAAM,EAAE,QAAQ,CAAC;SACjC;KACF,CAAA;IACD,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,SAAS,EAAE,EAAE;QACtC,MAAM,SAAS,GAAG,UAAU,CAAC,SAAS,CAAC,CAAA;QACvC,IAAI,SAAS,EAAE;YACb,GAAG,CAAC,IAAI,GAAG,SAAS,CAAC,IAAI,CAAA;YACzB,GAAG,CAAC,QAAQ,GAAG,SAAS,CAAC,QAAQ,CAAA;SAClC;IACH,CAAC,CAAC,CAAA;IACF,IAAI,CAAC,cAAc,GAAG,IAAI,CAAA;IAE1B,8DAA8D;IAC9D,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,SAAS,EAAE,EAAE;QAC1C,8DAA8D;QAC9D,MAAM,WAAW,GAAwB,EAAE,CAAA;QAC3C,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,YAAY,EAAE,EAAE;YAC3C,MAAM,SAAS,GAAG,UAAU,CAAC,YAAY,CAAC,CAAA;YAC1C,MAAM,GAAG,GACP,SAAS,IAAI,SAAS,CAAC,QAAQ,CAAC,IAAI,KAAK,QAAQ,IAAI,IAAI;gBACvD,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC;gBAClB,CAAC,CAAC,IAAI,CAAA;YACV,IAAI,SAAS,EAAE;gBACb,sBAAsB;gBACtB,IAAI,SAAS,CAAC,YAAY,CAAC,MAAM,KAAK,CAAC,EAAE;oBACvC,IAAI,CAAC,WAAW,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE;wBAC3C,WAAW,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;qBAC5C;oBACD,WAAW,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC;wBAC/D,GAAG,CAAA;iBACN;qBAAM;oBACL,WAAW,CAAC,SAAS,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAA;iBAC7C;aACF;iBAAM;gBACL,oBAAoB;gBACpB,WAAW,CAAC,SAAS,YAAY,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAA;aAC/C;QACH,CAAC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package/dist/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/dist/SpreadsheetView/importAdapters/ImportUtils.js

@@ -0,0 +1,124 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseTsvBuffer = exports.parseCsvBuffer = exports.bufferToString = void 0;
+const util_1 = require("@jbrowse/core/util");
+function bufferToString(buffer) {
+    return new TextDecoder('utf8', { fatal: true }).decode(buffer);
+}
+exports.bufferToString = bufferToString;
+async function parseWith(buffer, options = {}) {
+    const csv = await Promise.resolve().then(() => __importStar(require('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 = (0, util_1.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 = (0, util_1.parseLocString)(cell.text, isValidRefName);
+            }
+        }
+        columns[columnNumber] = {
+            name: columnNames[columnNumber],
+            dataType: {
+                type: guessedType,
+            },
+        };
+    }
+    return {
+        rowSet,
+        columnDisplayOrder,
+        hasColumnNames: !!hasColumnNameLine,
+        columns,
+        assemblyName: selectedAssemblyName,
+    };
+}
+async function parseCsvBuffer(buffer, options) {
+    const rows = await parseWith(buffer);
+    return dataToSpreadsheetSnapshot(rows, options);
+}
+exports.parseCsvBuffer = parseCsvBuffer;
+async function parseTsvBuffer(buffer, options) {
+    const rows = await parseWith(buffer, { delimiter: '\t' });
+    return dataToSpreadsheetSnapshot(rows, options);
+}
+exports.parseTsvBuffer = parseTsvBuffer;
+//# sourceMappingURL=ImportUtils.js.map

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

@@ -0,0 +1 @@
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package/dist/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/dist/SpreadsheetView/importAdapters/STARFusionImport.js

@@ -0,0 +1,73 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseSTARFusionBuffer = void 0;
+const ImportUtils_1 = require("./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,
+};
+async function parseSTARFusionBuffer(buffer, options) {
+    const data = await (0, ImportUtils_1.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;
+}
+exports.parseSTARFusionBuffer = parseSTARFusionBuffer;
+//# sourceMappingURL=STARFusionImport.js.map

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

@@ -0,0 +1 @@
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package/dist/SpreadsheetView/importAdapters/VcfImport.d.ts

@@ -0,0 +1,13 @@
+/// <reference types="node" />
+import { RowSet, Column, ParseOptions } from './ImportUtils';
+export declare function parseVcfBuffer(buffer: Buffer, options?: ParseOptions): {
+    rowSet: RowSet;
+    columnDisplayOrder: number[];
+    hasColumnNames: boolean;
+    columns: Column[];
+    assemblyName: string | undefined;
+};
+export declare function splitVcfFileHeaderAndBody(wholeFile: string): {
+    header: string;
+    body: string;
+};