@jbrowse/plugin-spreadsheet-view 2.16.1 → 2.18.0

package/esm/SpreadsheetView/importAdapters/STARFusionImport.js

@@ -1,67 +1,32 @@
-import { parseTsvBuffer } from './ImportUtils';
+import { isNumber } from './isNumber';
+import { bufferToLines, parseStrand } from './util';
 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 };
+    return {
+        refName: fields[0],
+        start: +fields[1],
+        end: +fields[1] + 1,
+        strand: parseStrand(fields[2]),
+    };
 }
-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) => {
-        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,
+export function parseSTARFusionBuffer(buffer) {
+    const lines = bufferToLines(buffer);
+    const columns = lines[0].slice(1).split('\t');
+    return {
+        columns: columns.map(c => ({ name: c })),
+        rowSet: {
+            rows: lines.slice(1).map((line, rowNumber) => {
+                const cols = line.split('\t');
+                const row = Object.fromEntries(columns.map((h, i) => [h, isNumber(cols[i]) ? +cols[i] : cols[i]]));
+                return {
+                    cellData: row,
+                    feature: {
+                        uniqueId: `sf-${rowNumber}`,
+                        ...parseSTARFusionBreakpointString(row.LeftBreakpoint),
+                        mate: parseSTARFusionBreakpointString(row.RightBreakpoint),
+                    },
                 };
-            }
-            else if (text && numericColumns[column.name]) {
-                // some other column, numeric
-                featureData[column.name] = Number.parseFloat(text);
-            }
-            else {
-                // some other column, text
-                featureData[column.name] = text;
-            }
-        });
-        featureData.uniqueId = `sf-${rowNumber + 1}`;
-        row.extendedData = {
-            feature: featureData,
-        };
-    });
-    return data;
+            }),
+        },
+    };
 }

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

@@ -1,13 +1,20 @@
-import { RowSet, Column, ParseOptions } from './ImportUtils';
-import type { Buffer } from 'buffer';
-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;
+export declare function parseVcfBuffer(buffer: Uint8Array): {
+    columns: {
+        name: string;
+    }[];
+    rowSet: {
+        rows: {
+            cellData: {
+                CHROM: string | undefined;
+                POS: number;
+                ID: string | undefined;
+                REF: string | undefined;
+                ALT: string | undefined;
+                QUAL: string | number | undefined;
+                FILTER: string | undefined;
+                FORMAT: string | undefined;
+            };
+            feature: any;
+        }[];
+    };
 };

package/esm/SpreadsheetView/importAdapters/VcfImport.js

@@ -1,104 +1,60 @@
 import VCF from '@gmod/vcf';
 import { VcfFeature } from '@jbrowse/plugin-variants';
-import { bufferToString, } from './ImportUtils';
-const vcfCoreColumns = [
-    { name: 'CHROM', type: 'Text' }, // 0
-    { name: 'POS', type: 'Number' }, // 1
-    { name: 'ID', type: 'Text' }, // 2
-    { name: 'REF', type: 'Text' }, // 3
-    { name: 'ALT', type: 'Text' }, // 4
-    { name: 'QUAL', type: 'Number' }, // 5
-    { name: 'FILTER', type: 'Text' }, // 6
-    { name: 'INFO', type: 'Text' }, // 7
-    { name: 'FORMAT', type: 'Text' }, // 8
-];
-function vcfRecordToRow(vcfParser, line, lineNumber) {
-    const vcfVariant = vcfParser.parseLine(line);
-    const vcfFeature = new VcfFeature({
-        variant: vcfVariant,
-        parser: vcfParser,
-        id: `vcf-${lineNumber}`,
-    });
-    const data = line.split('\t').map(d => (d === '.' ? '' : d));
-    // no format column, add blank
-    if (data.length === 8) {
-        data.push('');
-    }
-    const row = {
-        id: String(lineNumber + 1),
-        extendedData: { vcfFeature: vcfFeature.toJSON() },
-        cells: data.map((text, columnNumber) => {
-            return {
-                columnNumber,
-                text,
-            };
-        }),
-    };
-    return row;
-}
-export function parseVcfBuffer(buffer, options = {}) {
-    const { selectedAssemblyName } = options;
-    let { header, body } = splitVcfFileHeaderAndBody(bufferToString(buffer));
-    const rows = [];
+import { isNumber } from './isNumber';
+import { bufferToLines } from './util';
+export function parseVcfBuffer(buffer) {
+    const lines = bufferToLines(buffer);
+    const header = lines.filter(l => l.startsWith('#')).join('\n');
+    const body = lines.filter(l => !l.startsWith('#'));
     const vcfParser = new VCF({ header });
-    header = ''; // garbage collect
-    body.split(/\n|\r\n|\r/).forEach((line, lineNumber) => {
-        if (/\S/.test(line)) {
-            rows.push(vcfRecordToRow(vcfParser, line, lineNumber));
-        }
-    });
-    body = ''; // garbage collect
-    const rowSet = {
-        isLoaded: true,
-        rows,
-    };
-    const columnDisplayOrder = [];
-    const columns = [];
-    for (let i = 0; i < vcfCoreColumns.length; i += 1) {
-        columnDisplayOrder.push(i);
-        columns[i] = {
-            name: vcfCoreColumns[i].name,
-            dataType: { type: vcfCoreColumns[i].type },
-        };
-    }
-    for (let i = 0; i < vcfParser.samples.length; i += 1) {
-        const oi = vcfCoreColumns.length + i;
-        columnDisplayOrder.push(oi);
-        columns[oi] = {
-            name: vcfParser.samples[i],
-            dataType: { type: 'Text' },
-        };
-    }
-    columnDisplayOrder.push(columnDisplayOrder.length);
-    columns.unshift({
-        name: 'Location',
-        dataType: { type: 'LocString' },
-        isDerived: true,
-        derivationFunctionText: `jexl:{text:row.extendedData.vcfFeature.refName+':'\n
-    +row.extendedData.vcfFeature.start+'..'+row.extendedData.vcfFeature.end, extendedData:\n
-    {refName:row.extendedData.vcfFeature.refName,start:row.extendedData.vcfFeature.start,end:row.extendedData.vcfFeature.end}}`,
-    });
-    return {
-        rowSet,
-        columnDisplayOrder,
-        hasColumnNames: true,
-        columns,
-        assemblyName: selectedAssemblyName,
-    };
-}
-export function splitVcfFileHeaderAndBody(wholeFile) {
-    // split into header and the rest of the file
-    let headerEndIndex = 0;
-    let prevChar;
-    for (; headerEndIndex < wholeFile.length; headerEndIndex += 1) {
-        const c = wholeFile[headerEndIndex];
-        if (prevChar === '\n' && c !== '#') {
-            break;
-        }
-        prevChar = c;
+    const keys = new Set();
+    const rows = [];
+    let i = 0;
+    for (const line of body) {
+        const [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, ...rest] = line.split('\t');
+        const ret = Object.fromEntries((INFO === null || INFO === void 0 ? void 0 : INFO.split(';').map(f => f.trim()).map(e => {
+            const [key, val = 'true'] = e.split('=');
+            const k = `INFO.${key.trim()}`;
+            keys.add(k);
+            const v = val.trim();
+            return [k, isNumber(v) ? +v : v];
+        })) || []);
+        rows.push({
+            cellData: {
+                CHROM,
+                POS: +POS,
+                ID,
+                REF,
+                ALT,
+                QUAL: isNumber(QUAL) ? +QUAL : QUAL,
+                FILTER,
+                FORMAT,
+                ...ret,
+                ...Object.fromEntries(vcfParser.samples.map((s, idx) => [s, rest[idx]])),
+            },
+            feature: new VcfFeature({
+                parser: vcfParser,
+                variant: vcfParser.parseLine(line),
+                id: `vcf-${i}`,
+            }).toJSON(),
+        });
+        i++;
     }
     return {
-        header: wholeFile.slice(0, Math.max(0, headerEndIndex)),
-        body: wholeFile.slice(headerEndIndex),
+        columns: [
+            'CHROM',
+            'POS',
+            'ID',
+            'REF',
+            'ALT',
+            'QUAL',
+            'FILTER',
+            ...keys,
+            'FORMAT',
+            ...vcfParser.samples,
+        ].map(c => ({ name: c })),
+        rowSet: {
+            rows,
+        },
     };
 }

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

@@ -0,0 +1 @@
+export declare function isNumber(num: unknown): num is number;

package/esm/SpreadsheetView/importAdapters/isNumber.js

@@ -0,0 +1,11 @@
+export function isNumber(num) {
+    if (typeof num === 'number') {
+        return num - num === 0;
+    }
+    else if (typeof num === 'string' && num.trim() !== '') {
+        return Number.isFinite(+num);
+    }
+    else {
+        return false;
+    }
+}

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

@@ -0,0 +1,2 @@
+export declare function parseStrand(strand?: string): 1 | -1 | undefined;
+export declare function bufferToLines(buffer: Uint8Array): string[];

package/esm/SpreadsheetView/importAdapters/util.js

@@ -0,0 +1,18 @@
+export function parseStrand(strand) {
+    if (strand === '+') {
+        return 1;
+    }
+    else if (strand === '-') {
+        return -1;
+    }
+    else {
+        return undefined;
+    }
+}
+export function bufferToLines(buffer) {
+    return new TextDecoder('utf8')
+        .decode(buffer)
+        .split(/\n|\r\n|\r/)
+        .map(f => f.trim())
+        .filter(f => !!f);
+}

package/esm/SpreadsheetView/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SpreadsheetViewF(pluginManager: PluginManager): void;
-export { type SpreadsheetViewModel, type SpreadsheetViewStateModel, } from './models/SpreadsheetView';
+export type { SpreadsheetViewModel, SpreadsheetViewStateModel, } from './SpreadsheetViewModel';

package/esm/SpreadsheetView/index.js

@@ -1,12 +1,12 @@
 import { lazy } from 'react';
 import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import stateModel from './models/SpreadsheetView';
+import stateModelFactory from './SpreadsheetViewModel';
 export default function SpreadsheetViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new ViewType({
             name: 'SpreadsheetView',
             displayName: 'Spreadsheet view',
-            stateModel,
+            stateModel: stateModelFactory(),
             ReactComponent: lazy(() => import('./components/SpreadsheetView')),
         });
     });

package/esm/SpreadsheetView/util.d.ts

@@ -0,0 +1,7 @@
+import type { AbstractSessionModel } from '@jbrowse/core/util';
+export declare function locationLinkClick({ assemblyName, session, locString, spreadsheetViewId, }: {
+    assemblyName: string;
+    session: AbstractSessionModel;
+    locString: string;
+    spreadsheetViewId: string;
+}): Promise<void>;

package/esm/SpreadsheetView/util.js

@@ -0,0 +1,10 @@
+export function locationLinkClick({ assemblyName, session, locString, spreadsheetViewId, }) {
+    const newViewId = `${spreadsheetViewId}_${assemblyName}`;
+    let view = session.views.find(v => v.id === newViewId);
+    if (!view) {
+        view = session.addView('LinearGenomeView', {
+            id: newViewId,
+        });
+    }
+    return view.navToLocString(locString, assemblyName);
+}

package/esm/index.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
 import Plugin from '@jbrowse/core/Plugin';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class SpreadsheetViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,10 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { isAbstractMenuManager } from '@jbrowse/core/util';
-// icons
 import ViewComfyIcon from '@mui/icons-material/ViewComfy';
-// locals
-import SpreadsheetViewF from './SpreadsheetView';
 import LaunchSpreadsheetViewF from './LaunchSpreadsheetView';
+import SpreadsheetViewF from './SpreadsheetView';
 export default class SpreadsheetViewPlugin extends Plugin {
     constructor() {
         super(...arguments);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-spreadsheet-view",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 spreadsheet view",
   "keywords": [
     "jbrowse",
@@ -37,15 +37,15 @@
   },
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/vcf": "^5.0.9",
-    "@jbrowse/plugin-variants": "^2.16.1",
-    "@mui/icons-material": "^6.0.0",
-    "csvtojson": "^2.0.10"
+    "@gmod/vcf": "^6.0.0",
+    "@jbrowse/plugin-variants": "^2.18.0",
+    "@mui/icons-material": "^6.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
     "@mui/material": "^6.0.0",
+    "@mui/x-data-grid": "^7.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -60,5 +60,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }

package/dist/SpreadsheetView/components/CellData.d.ts

@@ -1,9 +0,0 @@
-import { Instance } from 'mobx-state-tree';
-import type SpreadsheetStateModel from '../models/Spreadsheet';
-type SpreadsheetModel = Instance<typeof SpreadsheetStateModel>;
-declare const CellData: ({ cell, spreadsheetModel, columnNumber, }: {
-    cell: any;
-    spreadsheetModel: SpreadsheetModel;
-    columnNumber: number;
-}) => any;
-export default CellData;

package/dist/SpreadsheetView/components/CellData.js

@@ -1,14 +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 react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
-const CellData = (0, mobx_react_1.observer)(function ({ cell, spreadsheetModel, columnNumber, }) {
-    const column = spreadsheetModel.columns[columnNumber];
-    return column &&
-        'dataType' in column &&
-        column.dataType.DataCellReactComponent ? (react_1.default.createElement(column.dataType.DataCellReactComponent, { cell: cell, dataType: column.dataType, columnNumber: columnNumber, spreadsheet: spreadsheetModel })) : (cell.text);
-});
-exports.default = CellData;

package/dist/SpreadsheetView/components/ColumnFilterControls.d.ts

@@ -1,3 +0,0 @@
-import React from 'react';
-declare const ColumnFilterControls: ({ viewModel, filterModel, columnNumber, height, }: any) => React.JSX.Element;
-export default ColumnFilterControls;

package/dist/SpreadsheetView/components/ColumnFilterControls.js

@@ -1,58 +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 react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mui_1 = require("tss-react/mui");
-// icons
-const FilterList_1 = __importDefault(require("@mui/icons-material/FilterList"));
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    columnName: {
-        verticalAlign: 'middle',
-        paddingRight: '0.3em',
-    },
-    columnFilter: {
-        overflow: 'hidden',
-        whiteSpace: 'nowrap',
-        boxSizing: 'border-box',
-        width: '100%',
-        position: 'relative',
-    },
-    filterIcon: {
-        position: 'relative',
-        top: '12px',
-    },
-    filterIconBg: {
-        background: theme.palette.tertiary.main,
-        color: 'white',
-        padding: theme.spacing(1.5),
-    },
-}));
-function FilterOperations({ filterModel }) {
-    if (filterModel) {
-        return react_1.default.createElement(filterModel.ReactComponent, { filterModel: filterModel });
-    }
-    return null;
-}
-const ColumnFilterControls = (0, mobx_react_1.observer)(function ({ viewModel, filterModel, columnNumber, height, }) {
-    const { classes } = useStyles();
-    const columnDefinition = viewModel.spreadsheet.columns[columnNumber];
-    if (!columnDefinition) {
-        throw new Error('no column definition! filters are probably out of date');
-    }
-    return (react_1.default.createElement(material_1.Grid, { container: true, direction: "row", className: classes.columnFilter, style: { height } },
-        react_1.default.createElement(material_1.Grid, { item: true, className: classes.filterIconBg },
-            react_1.default.createElement(FilterList_1.default, { className: classes.filterIcon })),
-        react_1.default.createElement(material_1.Grid, { item: true },
-            react_1.default.createElement(material_1.IconButton, { onClick: () => (0, mobx_state_tree_1.getParent)(filterModel, 2).removeColumnFilter(filterModel), title: "remove filter" },
-                react_1.default.createElement(Close_1.default, null)),
-            react_1.default.createElement(material_1.Typography, { className: classes.columnName, component: "span" }, columnDefinition.name),
-            ' ',
-            react_1.default.createElement(FilterOperations, { filterModel: filterModel }))));
-});
-exports.default = ColumnFilterControls;

package/dist/SpreadsheetView/components/ColumnMenu.d.ts

@@ -1,16 +0,0 @@
-import React from 'react';
-import { SpreadsheetModel } from '../models/Spreadsheet';
-import { SpreadsheetViewModel } from '../models/SpreadsheetView';
-declare const ColumnMenu: ({ viewModel, spreadsheetModel, currentColumnMenu, setColumnMenu, }: {
-    spreadsheetModel: SpreadsheetModel;
-    viewModel: SpreadsheetViewModel;
-    currentColumnMenu?: {
-        colNumber: number;
-        anchorEl: HTMLElement;
-    };
-    setColumnMenu: (arg?: {
-        anchorEl: HTMLElement;
-        colNumber: number;
-    }) => void;
-}) => React.JSX.Element;
-export default ColumnMenu;