@jbrowse/plugin-comparative-adapters 3.7.0 → 4.0.0

package/dist/DeltaAdapter/util.js

@@ -1,111 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.paf_delta2paf = paf_delta2paf;
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-function paf_delta2paf(buffer, opts) {
-    const { statusCallback = () => { } } = opts || {};
-    let rname = '';
-    let qname = '';
-    let qs = 0;
-    let qe = 0;
-    let rs = 0;
-    let re = 0;
-    let strand = 0;
-    let NM = 0;
-    let cigar = [];
-    let x = 0;
-    let y = 0;
-    let seen_gt = false;
-    const records = [];
-    const regex = new RegExp(/^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/);
-    (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
-        const m = regex.exec(line);
-        if (m !== null) {
-            rname = m[1];
-            qname = m[2];
-            seen_gt = true;
-            return true;
-        }
-        if (!seen_gt) {
-            return true;
-        }
-        const t = line.split(' ');
-        if (t.length === 7) {
-            const t0 = +t[0];
-            const t1 = +t[1];
-            const t2 = +t[2];
-            const t3 = +t[3];
-            const t4 = +t[4];
-            strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
-            rs = Math.min(t0, t1) - 1;
-            re = Math.max(t1, t0);
-            qs = Math.min(t2, t3) - 1;
-            qe = Math.max(t3, t2);
-            x = y = 0;
-            NM = t4;
-            cigar = [];
-        }
-        else if (t.length === 1) {
-            const d = +t[0];
-            if (d === 0) {
-                let blen = 0;
-                const cigar_str = [];
-                if (re - rs - x !== qe - qs - y) {
-                    throw new Error(`inconsistent alignment on line ${line}`);
-                }
-                cigar.push((re - rs - x) << 4);
-                for (const entry of cigar) {
-                    const rlen = entry >> 4;
-                    blen += rlen;
-                    cigar_str.push(rlen + 'MID'.charAt(entry & 0xf));
-                }
-                records.push({
-                    qname,
-                    qstart: qs,
-                    qend: qe,
-                    tname: rname,
-                    tstart: rs,
-                    tend: re,
-                    strand,
-                    extra: {
-                        numMatches: blen - NM,
-                        blockLen: blen,
-                        mappingQual: 0,
-                        NM,
-                        cg: cigar_str.join(''),
-                    },
-                });
-            }
-            else if (d > 0) {
-                const l = d - 1;
-                x += l + 1;
-                y += l;
-                if (l > 0) {
-                    cigar.push(l << 4);
-                }
-                if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
-                    cigar[cigar.length - 1] += 1 << 4;
-                }
-                else {
-                    cigar.push((1 << 4) | 2);
-                }
-            }
-            else {
-                const l = -d - 1;
-                x += l;
-                y += l + 1;
-                if (l > 0) {
-                    cigar.push(l << 4);
-                }
-                if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
-                    cigar[cigar.length - 1] += 1 << 4;
-                }
-                else {
-                    cigar.push((1 << 4) | 1);
-                }
-            }
-        }
-        return true;
-    }, statusCallback);
-    return records;
-}

package/dist/GuessAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function GuessAdapterF(pluginManager: PluginManager): void;

package/dist/GuessAdapter/index.js

@@ -1,74 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = GuessAdapterF;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const syntenyTypes_1 = require("../syntenyTypes");
-function GuessAdapterF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const fileName = (0, tracks_1.getFileName)(file);
-            const indexName = index && (0, tracks_1.getFileName)(index);
-            if ((0, util_1.testAdapter)(fileName, /\.paf(.gz)?/i, adapterHint, 'PAFAdapter')) {
-                return {
-                    type: 'PAFAdapter',
-                    pafLocation: file,
-                };
-            }
-            else if (adapterHint === 'BlastTabularAdapter') {
-                return {
-                    type: 'BlastTabularAdapter',
-                    blastTableLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.anchors.simple(.gz)?/i, adapterHint, 'MCScanSimpleAnchorsAdapter')) {
-                return {
-                    type: 'MCScanSimpleAnchorsAdapter',
-                    mcscanSimpleAnchorsLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.anchors(.gz)?/i, adapterHint, 'MCScanAnchorsAdapter')) {
-                return {
-                    type: 'MCScanAnchorsAdapter',
-                    mcscanAnchorsLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.delta(.gz)?/i, adapterHint, 'DeltaAdapter')) {
-                return {
-                    type: 'DeltaAdapter',
-                    deltaLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.chain(.gz)?/i, adapterHint, 'ChainAdapter')) {
-                return {
-                    type: 'ChainAdapter',
-                    chainLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.out(.gz)?/i, adapterHint, 'MashMapAdapter')) {
-                return {
-                    type: 'MashMapAdapter',
-                    outLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.pif\.gz/i, adapterHint, 'PairwiseIndexedPAFAdapter')) {
-                return {
-                    type: 'PairwiseIndexedPAFAdapter',
-                    pifGzLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                    },
-                };
-            }
-            else {
-                return adapterGuesser(file, index, adapterHint);
-            }
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-        return (adapterName) => syntenyTypes_1.syntenyTypes.includes(adapterName)
-            ? 'SyntenyTrack'
-            : trackTypeGuesser(adapterName);
-    });
-}

package/dist/MCScanAddTrackComponent/MCScanAddTrackComponent.d.ts

@@ -1,2 +0,0 @@
-declare const MCScanAddTrackComponent: ({ model }: any) => import("react/jsx-runtime").JSX.Element;
-export default MCScanAddTrackComponent;

package/dist/MCScanAddTrackComponent/MCScanAddTrackComponent.js

@@ -1,39 +0,0 @@
-"use strict";
-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 material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const MCScanAddTrackComponent = (0, mobx_react_1.observer)(function ({ model }) {
-    var _a, _b;
-    const session = (0, util_1.getSession)(model);
-    const [r0, setR0] = (0, react_1.useState)((_a = session.assemblies[0]) === null || _a === void 0 ? void 0 : _a.name);
-    const [r1, setR1] = (0, react_1.useState)((_b = session.assemblies[0]) === null || _b === void 0 ? void 0 : _b.name);
-    const [bed1Location, setBed1Location] = (0, react_1.useState)();
-    const [bed2Location, setBed2Location] = (0, react_1.useState)();
-    (0, react_1.useEffect)(() => {
-        model.setMixinData({
-            adapter: {
-                assemblyNamees: [r0, r1],
-                bed1Location,
-                bed2Location,
-            },
-        });
-    }, [model, bed1Location, bed2Location, r0, r1]);
-    return ((0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 20 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "JBrowse requires the two BED files that specify the genomic locations of the genes in the .anchors files" }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { session: session, label: "BED1 assembly", helperText: "", selected: r0, onChange: asm => {
-                    setR0(asm);
-                }, TextFieldProps: {
-                    fullWidth: true,
-                } }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { session: session, label: "BED2 assembly", helperText: "", selected: r1, onChange: asm => {
-                    setR1(asm);
-                }, TextFieldProps: {
-                    fullWidth: true,
-                } }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: "BED1", inline: true, description: "", location: bed1Location, setLocation: loc => {
-                    setBed1Location(loc);
-                } }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: "BED2", inline: true, description: "", location: bed2Location, setLocation: loc => {
-                    setBed2Location(loc);
-                } })] }));
-});
-exports.default = MCScanAddTrackComponent;

package/dist/MCScanAddTrackComponent/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function MCScanAddTrackComponentF(pluginManager: PluginManager): void;

package/dist/MCScanAddTrackComponent/index.js

@@ -1,46 +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;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = MCScanAddTrackComponentF;
-const react_1 = require("react");
-const syntenyTypes_1 = require("../syntenyTypes");
-const MCScanAddTrackComponent = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./MCScanAddTrackComponent'))));
-function MCScanAddTrackComponentF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-addTrackComponent', (comp, { model }) => {
-        return syntenyTypes_1.mcscanTypes.includes(model.trackAdapterType)
-            ? MCScanAddTrackComponent
-            : comp;
-    });
-}

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts

@@ -1,29 +0,0 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature, Region } from '@jbrowse/core/util';
-interface BareFeature {
-    strand: number;
-    refName: string;
-    start: number;
-    end: number;
-    score: number;
-    name: string;
-}
-type Row = [BareFeature, BareFeature, number, number];
-export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
-    private setupP?;
-    static capabilities: string[];
-    setup(opts: BaseOptions): Promise<{
-        assemblyNames: string[];
-        feats: Row[];
-    }>;
-    setupPre(opts: BaseOptions): Promise<{
-        assemblyNames: string[];
-        feats: Row[];
-    }>;
-    hasDataForRefName(): Promise<boolean>;
-    getAssemblyNames(): string[];
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}
-export {};

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -1,98 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_2 = require("../util");
-class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async setup(opts) {
-        if (!this.setupP) {
-            this.setupP = this.setupPre(opts).catch((e) => {
-                this.setupP = undefined;
-                throw e;
-            });
-        }
-        return this.setupP;
-    }
-    async setupPre(opts) {
-        const { statusCallback = () => { } } = opts;
-        const assemblyNames = this.getConf('assemblyNames');
-        const pm = this.pluginManager;
-        const bed1 = (0, io_1.openLocation)(this.getConf('bed1Location'), pm);
-        const bed2 = (0, io_1.openLocation)(this.getConf('bed2Location'), pm);
-        const mcscan = (0, io_1.openLocation)(this.getConf('mcscanAnchorsLocation'), pm);
-        const [bed1text, bed2text, mcscantext] = await (0, util_1.updateStatus)('Downloading data', statusCallback, () => Promise.all([bed1, bed2, mcscan].map(r => (0, util_2.readFile)(r, opts))));
-        const bed1Map = (0, util_2.parseBed)(bed1text);
-        const bed2Map = (0, util_2.parseBed)(bed2text);
-        const feats = mcscantext
-            .split(/\n|\r\n|\r/)
-            .filter(f => !!f && f !== '###')
-            .map((line, index) => {
-            const [name1, name2, score] = line.split('\t');
-            const r1 = bed1Map.get(name1);
-            const r2 = bed2Map.get(name2);
-            if (!r1 || !r2) {
-                throw new Error(`feature not found, ${name1} ${name2} ${r1} ${r2}`);
-            }
-            return [r1, r2, +score, index];
-        });
-        return {
-            assemblyNames,
-            feats,
-        };
-    }
-    async hasDataForRefName() {
-        return true;
-    }
-    getAssemblyNames() {
-        const assemblyNames = this.getConf('assemblyNames');
-        return assemblyNames;
-    }
-    async getRefNames(opts = {}) {
-        var _a;
-        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
-        const { feats } = await this.setup(opts);
-        const idx = this.getAssemblyNames().indexOf(r1);
-        if (idx !== -1) {
-            const set = new Set();
-            for (const feat of feats) {
-                set.add(idx === 0 ? feat[0].refName : feat[1].refName);
-            }
-            return [...set];
-        }
-        console.warn('Unable to do ref renaming on adapter');
-        return [];
-    }
-    getFeatures(region, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { assemblyNames, feats } = await this.setup(opts);
-            const index = assemblyNames.indexOf(region.assemblyName);
-            if (index !== -1) {
-                const flip = index === 0;
-                for (const f of feats) {
-                    const [r1, r2, score, rowNum] = f;
-                    const [f1, f2] = !flip ? [r2, r1] : [r1, r2];
-                    if (f1.refName === region.refName &&
-                        (0, util_1.doesIntersect2)(region.start, region.end, f1.start, f1.end)) {
-                        observer.next(new util_1.SimpleFeature({
-                            ...f1,
-                            uniqueId: `${index}-${rowNum}`,
-                            syntenyId: rowNum,
-                            strand: f1.strand * f2.strand,
-                            assemblyName: assemblyNames[+!flip],
-                            score,
-                            mate: {
-                                ...f2,
-                                assemblyName: assemblyNames[+flip],
-                            },
-                        }));
-                    }
-                }
-            }
-            observer.complete();
-        });
-    }
-}
-MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = MCScanAnchorsAdapter;

package/dist/MCScanAnchorsAdapter/configSchema.d.ts

@@ -1,28 +0,0 @@
-declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    mcscanAnchorsLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    bed1Location: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    bed2Location: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default MCScanAnchorsAdapter;

package/dist/MCScanAnchorsAdapter/configSchema.js

@@ -1,53 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnchorsAdapter', {
-    mcscanAnchorsLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/mcscan.anchors',
-            locationType: 'UriLocation',
-        },
-    },
-    bed1Location: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/file.bed',
-            locationType: 'UriLocation',
-        },
-    },
-    bed2Location: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/file.bed',
-            locationType: 'UriLocation',
-        },
-    },
-    assemblyNames: {
-        type: 'stringArray',
-        defaultValue: [],
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri && snap.bed1 && snap.bed2
-            ? {
-                ...snap,
-                mcscanAnchorsLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                bed1Location: {
-                    uri: snap.bed1,
-                    baseUri: snap.baseUri,
-                },
-                bed2Location: {
-                    uri: snap.bed2,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = MCScanAnchorsAdapter;

package/dist/MCScanAnchorsAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function MCScanAnchorsAdapterF(pluginManager: PluginManager): void;

package/dist/MCScanAnchorsAdapter/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 = MCScanAnchorsAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function MCScanAnchorsAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'MCScanAnchorsAdapter',
-        displayName: 'MCScan anchors adapter',
-        configSchema: configSchema_1.default,
-        adapterMetadata: {
-            category: 'Synteny adapters',
-        },
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MCScanAnchorsAdapter'))).then(r => r.default),
-    }));
-}

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts

@@ -1,37 +0,0 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature } from '@jbrowse/core/util/simpleFeature';
-import type { Region } from '@jbrowse/core/util/types';
-interface BareFeature {
-    refName: string;
-    start: number;
-    end: number;
-    score: number;
-    name: string;
-}
-type Row = [
-    BareFeature,
-    BareFeature,
-    BareFeature,
-    BareFeature,
-    number,
-    number,
-    number
-];
-export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
-    private setupP?;
-    static capabilities: string[];
-    setup(opts: BaseOptions): Promise<{
-        assemblyNames: string[];
-        feats: Row[];
-    }>;
-    setupPre(opts: BaseOptions): Promise<{
-        assemblyNames: string[];
-        feats: Row[];
-    }>;
-    hasDataForRefName(): Promise<boolean>;
-    getAssemblyNames(): string[];
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}
-export {};