@jbrowse/plugin-spreadsheet-view 3.7.0 → 4.0.0

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

@@ -1,25 +0,0 @@
-export declare function parseSTARFusionBuffer(buffer: Uint8Array): {
-    columns: {
-        name: string;
-    }[];
-    rowSet: {
-        rows: {
-            cellData: {
-                [k: string]: string | number;
-            };
-            feature: {
-                mate: {
-                    refName: string | undefined;
-                    start: number;
-                    end: number;
-                    strand: number | undefined;
-                };
-                refName: string | undefined;
-                start: number;
-                end: number;
-                strand: number | undefined;
-                uniqueId: string;
-            };
-        }[];
-    };
-};

package/dist/SpreadsheetView/importAdapters/STARFusionImport.js

@@ -1,35 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseSTARFusionBuffer = parseSTARFusionBuffer;
-const isNumber_1 = require("./isNumber");
-const util_1 = require("./util");
-function parseSTARFusionBreakpointString(str) {
-    const fields = str.split(':');
-    return {
-        refName: fields[0],
-        start: +fields[1],
-        end: +fields[1] + 1,
-        strand: (0, util_1.parseStrand)(fields[2]),
-    };
-}
-function parseSTARFusionBuffer(buffer) {
-    const lines = (0, util_1.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, (0, isNumber_1.isNumber)(cols[i]) ? +cols[i] : cols[i]]));
-                return {
-                    cellData: row,
-                    feature: {
-                        uniqueId: `sf-${rowNumber}`,
-                        ...parseSTARFusionBreakpointString(row.LeftBreakpoint),
-                        mate: parseSTARFusionBreakpointString(row.RightBreakpoint),
-                    },
-                };
-            }),
-        },
-    };
-}

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

@@ -1,20 +0,0 @@
-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/dist/SpreadsheetView/importAdapters/VcfImport.js

@@ -1,66 +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.parseVcfBuffer = parseVcfBuffer;
-const vcf_1 = __importDefault(require("@gmod/vcf"));
-const plugin_variants_1 = require("@jbrowse/plugin-variants");
-const isNumber_1 = require("./isNumber");
-const util_1 = require("./util");
-function parseVcfBuffer(buffer) {
-    const lines = (0, util_1.bufferToLines)(buffer);
-    const header = lines.filter(l => l.startsWith('#')).join('\n');
-    const body = lines.filter(l => !l.startsWith('#'));
-    const vcfParser = new vcf_1.default({ header });
-    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.${key.trim()}`;
-            keys.add(k);
-            const v = val.trim();
-            return [k, (0, isNumber_1.isNumber)(v) ? +v : v];
-        })) || []);
-        rows.push({
-            cellData: {
-                CHROM,
-                POS: +POS,
-                ID,
-                REF,
-                ALT,
-                QUAL: (0, isNumber_1.isNumber)(QUAL) ? +QUAL : QUAL,
-                FILTER,
-                FORMAT,
-                ...ret,
-                ...Object.fromEntries(vcfParser.samples.map((s, idx) => [s, rest[idx]])),
-            },
-            feature: new plugin_variants_1.VcfFeature({
-                parser: vcfParser,
-                variant: vcfParser.parseLine(line),
-                id: `vcf-${i}`,
-            }).toJSON(),
-        });
-        i++;
-    }
-    return {
-        columns: [
-            'CHROM',
-            'POS',
-            'ID',
-            'REF',
-            'ALT',
-            'QUAL',
-            'FILTER',
-            ...keys,
-            'FORMAT',
-            ...vcfParser.samples,
-        ].map(c => ({ name: c })),
-        rowSet: {
-            rows,
-        },
-    };
-}

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

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

package/dist/SpreadsheetView/importAdapters/isNumber.js

@@ -1,14 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isNumber = isNumber;
-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/dist/SpreadsheetView/importAdapters/util.d.ts

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

package/dist/SpreadsheetView/importAdapters/util.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseStrand = parseStrand;
-exports.bufferToLines = bufferToLines;
-function parseStrand(strand) {
-    if (strand === '+') {
-        return 1;
-    }
-    else if (strand === '-') {
-        return -1;
-    }
-    else {
-        return undefined;
-    }
-}
-function bufferToLines(buffer) {
-    return new TextDecoder('utf8')
-        .decode(buffer)
-        .split(/\n|\r\n|\r/)
-        .map(f => f.trim())
-        .filter(f => !!f);
-}

package/dist/SpreadsheetView/index.d.ts

@@ -1,3 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function SpreadsheetViewF(pluginManager: PluginManager): void;
-export type { SpreadsheetViewModel, SpreadsheetViewStateModel, } from './SpreadsheetViewModel';

package/dist/SpreadsheetView/index.js

@@ -1,52 +0,0 @@
-"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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __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 });
-exports.default = SpreadsheetViewF;
-const react_1 = require("react");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const SpreadsheetViewModel_1 = __importDefault(require("./SpreadsheetViewModel"));
-function SpreadsheetViewF(pluginManager) {
-    pluginManager.addViewType(() => {
-        return new pluggableElementTypes_1.ViewType({
-            name: 'SpreadsheetView',
-            displayName: 'Spreadsheet view',
-            stateModel: (0, SpreadsheetViewModel_1.default)(),
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SpreadsheetView')))),
-        });
-    });
-}

package/dist/SpreadsheetView/util.d.ts

@@ -1,7 +0,0 @@
-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/dist/SpreadsheetView/util.js

@@ -1,13 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.locationLinkClick = locationLinkClick;
-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/dist/index.d.ts

@@ -1,8 +0,0 @@
-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;
-    configure(pluginManager: PluginManager): void;
-}
-export { type SpreadsheetViewModel, type SpreadsheetViewStateModel, } from './SpreadsheetView';

package/dist/index.js

@@ -1,33 +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 Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const util_1 = require("@jbrowse/core/util");
-const ViewComfy_1 = __importDefault(require("@mui/icons-material/ViewComfy"));
-const LaunchSpreadsheetView_1 = __importDefault(require("./LaunchSpreadsheetView"));
-const SpreadsheetView_1 = __importDefault(require("./SpreadsheetView"));
-class SpreadsheetViewPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'SpreadsheetViewPlugin';
-    }
-    install(pluginManager) {
-        (0, SpreadsheetView_1.default)(pluginManager);
-        (0, LaunchSpreadsheetView_1.default)(pluginManager);
-    }
-    configure(pluginManager) {
-        const { rootModel } = pluginManager;
-        if ((0, util_1.isAbstractMenuManager)(rootModel)) {
-            rootModel.appendToSubMenu(['Add'], {
-                label: 'Spreadsheet view',
-                icon: ViewComfy_1.default,
-                onClick: (session) => {
-                    session.addView('SpreadsheetView', {});
-                },
-            });
-        }
-    }
-}
-exports.default = SpreadsheetViewPlugin;

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

@@ -1 +0,0 @@
-export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js

@@ -1 +0,0 @@
-export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

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

@@ -1 +0,0 @@
-export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js

@@ -1 +0,0 @@
-export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';