@jbrowse/plugin-gff3 3.6.5 → 4.0.0

package/esm/Gff3Adapter/Gff3Adapter.d.ts

@@ -1,14 +1,14 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 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 { NoAssemblyRegion } from '@jbrowse/core/util/types';
 type StatusCallback = (arg: string) => void;
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
-    calculatedIntervalTreeMap: Record<string, IntervalTree>;
+    calculatedIntervalTreeMap: Record<string, IntervalTree<Feature>>;
     gffFeatures?: Promise<{
         header: string;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<Feature>>;
     }>;
     private loadDataP;
     private loadData;

package/esm/Gff3Adapter/Gff3Adapter.js

@@ -1,17 +1,14 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { parseStringSync } from 'gff-nostream';
-import { featureData } from '../featureData';
-import { parseGffBuffer } from './gffParser';
+import { parseStringSyncJBrowse } from 'gff-nostream';
+import { parseGffBuffer } from "./gffParser.js";
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.calculatedIntervalTreeMap = {};
-    }
+    calculatedIntervalTreeMap = {};
+    gffFeatures;
     async loadDataP(opts) {
         const { statusCallback = () => { } } = opts || {};
         const buffer = await fetchAndMaybeUnzip(openLocation(this.getConf('gffLocation'), this.pluginManager), opts);
@@ -20,15 +17,16 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
             refName,
             (sc) => {
                 if (!this.calculatedIntervalTreeMap[refName]) {
-                    sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
+                    sc?.('Parsing GFF data');
                     const intervalTree = new IntervalTree();
-                    for (const obj of parseStringSync(lines)
-                        .flat()
-                        .map((f, i) => new SimpleFeature({
-                        data: featureData(f),
-                        id: `${this.id}-${refName}-${i}`,
-                    }))) {
-                        intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+                    const features = parseStringSyncJBrowse(lines);
+                    for (let i = 0, l = features.length; i < l; i++) {
+                        const f = features[i];
+                        const obj = new SimpleFeature({
+                            data: f,
+                            id: `${this.id}-${refName}-${i}`,
+                        });
+                        intervalTree.insert([f.start, f.end], obj);
                     }
                     this.calculatedIntervalTreeMap[refName] = intervalTree;
                 }
@@ -59,14 +57,13 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
     }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
-            var _a;
             try {
                 const { start, end, refName } = query;
                 const { intervalTreeMap } = await this.loadData(opts);
-                for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
+                for (const f of intervalTreeMap[refName]?.(opts.statusCallback).search([
                     start,
                     end,
-                ])) || []) {
+                ]) || []) {
                     observer.next(f);
                 }
                 observer.complete();

package/esm/Gff3Adapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const Gff3Adapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const Gff3Adapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     gffLocation: {
         type: string;
         defaultValue: {
@@ -6,5 +6,5 @@ declare const Gff3Adapter: import("@jbrowse/core/configuration/configurationSche
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default Gff3Adapter;

package/esm/Gff3Adapter/index.js

@@ -1,10 +1,10 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function Gff3AdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'Gff3Adapter',
         displayName: 'GFF3 adapter',
         configSchema,
-        getAdapterClass: () => import('./Gff3Adapter').then(r => r.default),
+        getAdapterClass: () => import("./Gff3Adapter.js").then(r => r.default),
     }));
 }

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -8,15 +8,14 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     private configurePre;
     protected configurePre2(): Promise<{
         gff: TabixIndexedFile;
-        dontRedispatch: string[];
+        dontRedispatchSet: Set<string>;
     }>;
     configure(opts?: BaseOptions): Promise<{
         gff: TabixIndexedFile;
-        dontRedispatch: string[];
+        dontRedispatchSet: Set<string>;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     private getFeaturesHelper;
-    private parseLine;
 }

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -5,9 +5,9 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { parseStringSync } from 'gff-nostream';
-import { featureData } from '../featureData';
+import { parseRecordsJBrowse } from 'gff-nostream';
 export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
+    configured;
     async configurePre(_opts) {
         const gffGzLocation = this.getConf('gffGzLocation');
         const indexType = this.getConf(['index', 'indexType']);
@@ -18,11 +18,10 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
             csiFilehandle: indexType === 'CSI' ? openLocation(loc, this.pluginManager) : undefined,
             tbiFilehandle: indexType !== 'CSI' ? openLocation(loc, this.pluginManager) : undefined,
             chunkCacheSize: 50 * 2 ** 20,
-            renameRefSeqs: (n) => n,
         });
         return {
             gff,
-            dontRedispatch,
+            dontRedispatchSet: new Set(dontRedispatch),
             header: await gff.getHeader(),
         };
     }
@@ -55,26 +54,35 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
         }, opts.stopToken);
     }
     async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
-        var _a, _b;
         const { statusCallback = () => { } } = opts;
         try {
             const lines = [];
-            const { dontRedispatch, gff } = await this.configure(opts);
-            await updateStatus('Downloading features', statusCallback, () => gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
-                lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset));
+            const { dontRedispatchSet, gff } = await this.configure(opts);
+            await updateStatus('Downloading features', statusCallback, () => gff.getLines(query.refName, query.start, query.end, (line, fileOffset, start, end) => {
+                const t1 = line.indexOf('\t');
+                const t2 = line.indexOf('\t', t1 + 1);
+                const t3 = line.indexOf('\t', t2 + 1);
+                const type = line.slice(t2 + 1, t3);
+                lines.push({
+                    line,
+                    lineHash: fileOffset,
+                    start,
+                    end,
+                    hasEscapes: line.includes('%'),
+                    type,
+                });
             }));
             if (allowRedispatch && lines.length) {
                 let minStart = Number.POSITIVE_INFINITY;
                 let maxEnd = Number.NEGATIVE_INFINITY;
-                for (const line of lines) {
-                    const featureType = line.fields[2];
-                    if (!dontRedispatch.includes(featureType)) {
-                        const start = line.start - 1;
+                for (const rec of lines) {
+                    if (!dontRedispatchSet.has(rec.type)) {
+                        const start = rec.start - 1;
                         if (start < minStart) {
                             minStart = start;
                         }
-                        if (line.end > maxEnd) {
-                            maxEnd = line.end;
+                        if (rec.end > maxEnd) {
+                            maxEnd = rec.end;
                         }
                     }
                 }
@@ -83,28 +91,12 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
                     return;
                 }
             }
-            const gff3 = lines
-                .map(lineRecord => {
-                if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
-                    if (!lineRecord.fields[8].includes('_lineHash')) {
-                        lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`;
-                    }
-                }
-                else {
-                    lineRecord.fields[8] = `_lineHash=${lineRecord.lineHash}`;
-                }
-                return lineRecord.fields.join('\t');
-            })
-                .join('\n');
-            for (const featureLocs of parseStringSync(gff3)) {
-                for (const featureLoc of featureLocs) {
-                    const f = new SimpleFeature({
-                        data: featureData(featureLoc),
-                        id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
-                    });
-                    if (doesIntersect2(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
-                        observer.next(f);
-                    }
+            for (const feature of parseRecordsJBrowse(lines)) {
+                if (doesIntersect2(feature.start, feature.end, originalQuery.start, originalQuery.end)) {
+                    observer.next(new SimpleFeature({
+                        data: feature,
+                        id: `${this.id}-offset-${feature._lineHash}`,
+                    }));
                 }
             }
             observer.complete();
@@ -113,13 +105,4 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
             observer.error(e);
         }
     }
-    parseLine(columnNumbers, line, fileOffset) {
-        const fields = line.split('\t');
-        return {
-            start: +fields[columnNumbers.start - 1],
-            end: +fields[columnNumbers.end - 1],
-            lineHash: fileOffset,
-            fields,
-        };
-    }
 }

package/esm/Gff3TabixAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const Gff3TabixAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     gffGzLocation: {
         type: string;
         defaultValue: {
@@ -6,9 +6,9 @@ declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configuratio
             locationType: string;
         };
     };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
@@ -19,10 +19,10 @@ declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configuratio
                 locationType: string;
             };
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     dontRedispatch: {
         type: string;
         defaultValue: string[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default Gff3TabixAdapter;

package/esm/Gff3TabixAdapter/configSchema.js

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 function x() { }
 const Gff3TabixAdapter = ConfigurationSchema('Gff3TabixAdapter', {
     gffGzLocation: {

package/esm/Gff3TabixAdapter/index.js

@@ -1,10 +1,10 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function Gff3TabixAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'Gff3TabixAdapter',
         displayName: 'GFF3 tabix adapter',
         configSchema,
-        getAdapterClass: () => import('./Gff3TabixAdapter').then(r => r.default),
+        getAdapterClass: () => import("./Gff3TabixAdapter.js").then(r => r.default),
     }));
 }

package/esm/featureData.js

@@ -1,3 +1,13 @@
+const DEFAULT_FIELDS = new Set([
+    'start',
+    'end',
+    'seq_id',
+    'score',
+    'type',
+    'source',
+    'phase',
+    'strand',
+]);
 export function featureData(data) {
     const { end, start, child_features, derived_features, attributes, type, source, phase, seq_id, score, strand, } = data;
     let strand2;
@@ -10,21 +20,11 @@ export function featureData(data) {
     else if (strand === '.') {
         strand2 = 0;
     }
-    const defaultFields = new Set([
-        'start',
-        'end',
-        'seq_id',
-        'score',
-        'type',
-        'source',
-        'phase',
-        'strand',
-    ]);
     const dataAttributes = attributes || {};
     const resultAttributes = {};
     for (const a of Object.keys(dataAttributes)) {
         let b = a.toLowerCase();
-        if (defaultFields.has(b)) {
+        if (DEFAULT_FIELDS.has(b)) {
             b += '2';
         }
         if (dataAttributes[a] && a !== '_lineHash') {

package/esm/index.js

@@ -1,12 +1,9 @@
 import Plugin from '@jbrowse/core/Plugin';
-import Gff3AdapterF from './Gff3Adapter';
-import Gff3TabixAdapterF from './Gff3TabixAdapter';
-import GuessGff3F from './GuessGff3';
+import Gff3AdapterF from "./Gff3Adapter/index.js";
+import Gff3TabixAdapterF from "./Gff3TabixAdapter/index.js";
+import GuessGff3F from "./GuessGff3/index.js";
 export default class GFF3Plugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'GFF3Plugin';
-    }
+    name = 'GFF3Plugin';
     install(pluginManager) {
         Gff3TabixAdapterF(pluginManager);
         Gff3AdapterF(pluginManager);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
@@ -15,43 +15,35 @@
     "directory": "plugins/gff3"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/gff3 --passWithNoTests",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bgzf-filehandle": "^4.0.0",
-    "@gmod/tabix": "^3.0.1",
-    "@jbrowse/core": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@mui/material": "^7.0.0",
-    "gff-nostream": "^1.3.3",
-    "mobx": "^6.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0"
+    "@flatten-js/interval-tree": "^2.0.3",
+    "@gmod/tabix": "^3.2.2",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "gff-nostream": "^3.0.2",
+    "mobx": "^6.15.0",
+    "rxjs": "^7.8.2",
+    "@jbrowse/core": "^4.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/gff3 --passWithNoTests",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/Gff3Adapter/Gff3Adapter.d.ts

@@ -1,19 +0,0 @@
-import IntervalTree from '@flatten-js/interval-tree';
-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 { NoAssemblyRegion } from '@jbrowse/core/util/types';
-type StatusCallback = (arg: string) => void;
-export default class Gff3Adapter extends BaseFeatureDataAdapter {
-    calculatedIntervalTreeMap: Record<string, IntervalTree>;
-    gffFeatures?: Promise<{
-        header: string;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
-    }>;
-    private loadDataP;
-    private loadData;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(opts?: BaseOptions): Promise<string>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}
-export {};

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -1,85 +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 interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-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 simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const gff_nostream_1 = require("gff-nostream");
-const featureData_1 = require("../featureData");
-const gffParser_1 = require("./gffParser");
-class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.calculatedIntervalTreeMap = {};
-    }
-    async loadDataP(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('gffLocation'), this.pluginManager), opts);
-        const { header, featureMap } = (0, gffParser_1.parseGffBuffer)(buffer, statusCallback);
-        const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
-            refName,
-            (sc) => {
-                if (!this.calculatedIntervalTreeMap[refName]) {
-                    sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
-                    const intervalTree = new interval_tree_1.default();
-                    for (const obj of (0, gff_nostream_1.parseStringSync)(lines)
-                        .flat()
-                        .map((f, i) => new simpleFeature_1.default({
-                        data: (0, featureData_1.featureData)(f),
-                        id: `${this.id}-${refName}-${i}`,
-                    }))) {
-                        intervalTree.insert([obj.get('start'), obj.get('end')], obj);
-                    }
-                    this.calculatedIntervalTreeMap[refName] = intervalTree;
-                }
-                return this.calculatedIntervalTreeMap[refName];
-            },
-        ]));
-        return {
-            header,
-            intervalTreeMap,
-        };
-    }
-    async loadData(opts) {
-        if (!this.gffFeatures) {
-            this.gffFeatures = this.loadDataP(opts).catch((e) => {
-                this.gffFeatures = undefined;
-                throw e;
-            });
-        }
-        return this.gffFeatures;
-    }
-    async getRefNames(opts = {}) {
-        const { intervalTreeMap } = await this.loadData(opts);
-        return Object.keys(intervalTreeMap);
-    }
-    async getHeader(opts = {}) {
-        const { header } = await this.loadData(opts);
-        return header;
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            var _a;
-            try {
-                const { start, end, refName } = query;
-                const { intervalTreeMap } = await this.loadData(opts);
-                for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
-                    start,
-                    end,
-                ])) || []) {
-                    observer.next(f);
-                }
-                observer.complete();
-            }
-            catch (e) {
-                observer.error(e);
-            }
-        }, opts.stopToken);
-    }
-}
-exports.default = Gff3Adapter;

package/dist/Gff3Adapter/configSchema.d.ts

@@ -1,10 +0,0 @@
-declare const Gff3Adapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    gffLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default Gff3Adapter;

package/dist/Gff3Adapter/configSchema.js

@@ -1,27 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const Gff3Adapter = (0, configuration_1.ConfigurationSchema)('Gff3Adapter', {
-    gffLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.gff',
-            locationType: 'UriLocation',
-        },
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                gffLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = Gff3Adapter;

package/dist/Gff3Adapter/gffParser.d.ts

@@ -1,7 +0,0 @@
-import type { StatusCallback } from '@jbrowse/core/util/parseLineByLine';
-interface GffParseResult {
-    header: string;
-    featureMap: Record<string, string>;
-}
-export declare function parseGffBuffer(buffer: Uint8Array, statusCallback?: StatusCallback): GffParseResult;
-export {};

package/dist/Gff3Adapter/gffParser.js

@@ -1,29 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseGffBuffer = parseGffBuffer;
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-function parseGffBuffer(buffer, statusCallback = () => { }) {
-    const headerLines = [];
-    const featureMap = {};
-    (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
-        if (line.startsWith('#')) {
-            headerLines.push(line);
-        }
-        else if (line.startsWith('>')) {
-            return false;
-        }
-        else {
-            const ret = line.indexOf('\t');
-            const refName = line.slice(0, ret);
-            if (!featureMap[refName]) {
-                featureMap[refName] = '';
-            }
-            featureMap[refName] += `${line}\n`;
-        }
-        return true;
-    }, statusCallback);
-    return {
-        header: headerLines.join('\n'),
-        featureMap,
-    };
-}

package/dist/Gff3Adapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function Gff3AdapterF(pluginManager: PluginManager): void;

package/dist/Gff3Adapter/index.js

@@ -1,49 +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 = Gff3AdapterF;
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const configSchema_1 = __importDefault(require("./configSchema"));
-function Gff3AdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
-        name: 'Gff3Adapter',
-        displayName: 'GFF3 adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3Adapter'))).then(r => r.default),
-    }));
-}

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -1,22 +0,0 @@
-import { TabixIndexedFile } from '@gmod/tabix';
-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';
-export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
-    private configured?;
-    private configurePre;
-    protected configurePre2(): Promise<{
-        gff: TabixIndexedFile;
-        dontRedispatch: string[];
-    }>;
-    configure(opts?: BaseOptions): Promise<{
-        gff: TabixIndexedFile;
-        dontRedispatch: string[];
-    }>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(opts?: BaseOptions): Promise<string>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    private getFeaturesHelper;
-    private parseLine;
-}

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -1,131 +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 tabix_1 = require("@gmod/tabix");
-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 range_1 = require("@jbrowse/core/util/range");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const gff_nostream_1 = require("gff-nostream");
-const featureData_1 = require("../featureData");
-class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configurePre(_opts) {
-        const gffGzLocation = this.getConf('gffGzLocation');
-        const indexType = this.getConf(['index', 'indexType']);
-        const loc = this.getConf(['index', 'location']);
-        const dontRedispatch = this.getConf('dontRedispatch');
-        const gff = new tabix_1.TabixIndexedFile({
-            filehandle: (0, io_1.openLocation)(gffGzLocation, this.pluginManager),
-            csiFilehandle: indexType === 'CSI' ? (0, io_1.openLocation)(loc, this.pluginManager) : undefined,
-            tbiFilehandle: indexType !== 'CSI' ? (0, io_1.openLocation)(loc, this.pluginManager) : undefined,
-            chunkCacheSize: 50 * 2 ** 20,
-            renameRefSeqs: (n) => n,
-        });
-        return {
-            gff,
-            dontRedispatch,
-            header: await gff.getHeader(),
-        };
-    }
-    async configurePre2() {
-        if (!this.configured) {
-            this.configured = this.configurePre().catch((e) => {
-                this.configured = undefined;
-                throw e;
-            });
-        }
-        return this.configured;
-    }
-    async configure(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.configurePre2());
-    }
-    async getRefNames(opts = {}) {
-        const { gff } = await this.configure(opts);
-        return gff.getReferenceSequenceNames(opts);
-    }
-    async getHeader(opts = {}) {
-        const { gff } = await this.configure(opts);
-        return gff.getHeader();
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { gff } = await this.configure(opts);
-            const metadata = await gff.getMetadata();
-            await this.getFeaturesHelper(query, opts, metadata, observer, true);
-        }, opts.stopToken);
-    }
-    async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
-        var _a, _b;
-        const { statusCallback = () => { } } = opts;
-        try {
-            const lines = [];
-            const { dontRedispatch, gff } = await this.configure(opts);
-            await (0, util_1.updateStatus)('Downloading features', statusCallback, () => gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
-                lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset));
-            }));
-            if (allowRedispatch && lines.length) {
-                let minStart = Number.POSITIVE_INFINITY;
-                let maxEnd = Number.NEGATIVE_INFINITY;
-                for (const line of lines) {
-                    const featureType = line.fields[2];
-                    if (!dontRedispatch.includes(featureType)) {
-                        const start = line.start - 1;
-                        if (start < minStart) {
-                            minStart = start;
-                        }
-                        if (line.end > maxEnd) {
-                            maxEnd = line.end;
-                        }
-                    }
-                }
-                if (maxEnd > query.end || minStart < query.start) {
-                    await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
-                    return;
-                }
-            }
-            const gff3 = lines
-                .map(lineRecord => {
-                if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
-                    if (!lineRecord.fields[8].includes('_lineHash')) {
-                        lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`;
-                    }
-                }
-                else {
-                    lineRecord.fields[8] = `_lineHash=${lineRecord.lineHash}`;
-                }
-                return lineRecord.fields.join('\t');
-            })
-                .join('\n');
-            for (const featureLocs of (0, gff_nostream_1.parseStringSync)(gff3)) {
-                for (const featureLoc of featureLocs) {
-                    const f = new simpleFeature_1.default({
-                        data: (0, featureData_1.featureData)(featureLoc),
-                        id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
-                    });
-                    if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
-                        observer.next(f);
-                    }
-                }
-            }
-            observer.complete();
-        }
-        catch (e) {
-            observer.error(e);
-        }
-    }
-    parseLine(columnNumbers, line, fileOffset) {
-        const fields = line.split('\t');
-        return {
-            start: +fields[columnNumbers.start - 1],
-            end: +fields[columnNumbers.end - 1],
-            lineHash: fileOffset,
-            fields,
-        };
-    }
-}
-exports.default = Gff3TabixAdapter;

package/dist/Gff3TabixAdapter/configSchema.d.ts

@@ -1,28 +0,0 @@
-declare const Gff3TabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    gffGzLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
-            type: string;
-            defaultValue: string;
-        };
-        location: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
-            };
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    dontRedispatch: {
-        type: string;
-        defaultValue: string[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default Gff3TabixAdapter;

package/dist/Gff3TabixAdapter/configSchema.js

@@ -1,52 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-const Gff3TabixAdapter = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdapter', {
-    gffGzLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.gff.gz',
-            locationType: 'UriLocation',
-        },
-    },
-    index: (0, configuration_1.ConfigurationSchema)('Gff3TabixIndex', {
-        indexType: {
-            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
-            type: 'stringEnum',
-            defaultValue: 'TBI',
-        },
-        location: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.gff.gz.tbi',
-                locationType: 'UriLocation',
-            },
-        },
-    }),
-    dontRedispatch: {
-        type: 'stringArray',
-        defaultValue: ['chromosome', 'region', 'contig'],
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                gffGzLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                index: {
-                    location: {
-                        uri: `${snap.uri}.tbi`,
-                        baseUri: snap.baseUri,
-                    },
-                },
-            }
-            : snap;
-    },
-});
-exports.default = Gff3TabixAdapter;

package/dist/Gff3TabixAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function Gff3TabixAdapterF(pluginManager: PluginManager): void;

package/dist/Gff3TabixAdapter/index.js

@@ -1,49 +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 = Gff3TabixAdapterF;
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const configSchema_1 = __importDefault(require("./configSchema"));
-function Gff3TabixAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
-        name: 'Gff3TabixAdapter',
-        displayName: 'GFF3 tabix adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3TabixAdapter'))).then(r => r.default),
-    }));
-}

package/dist/GuessGff3/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function GuessGff3F(pluginManager: PluginManager): void;

package/dist/GuessGff3/index.js

@@ -1,33 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = GuessGff3F;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function GuessGff3F(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, /\.gff3?\.b?gz$/i, adapterHint, 'Gff3TabixAdapter')) {
-                return {
-                    type: 'Gff3TabixAdapter',
-                    bamLocation: file,
-                    gffGzLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                    },
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.gff3?$/i, adapterHint, 'Gff3Adapter')) {
-                return {
-                    type: 'Gff3Adapter',
-                    gffLocation: file,
-                };
-            }
-            else {
-                return adapterGuesser(file, index, adapterHint);
-            }
-        };
-    });
-}

package/dist/featureData.d.ts

@@ -1,16 +0,0 @@
-import type { GFF3FeatureLineWithRefs } from 'gff-nostream';
-interface GFF3Feature {
-    start: number;
-    end: number;
-    strand?: number;
-    type: string | null;
-    source: string | null;
-    refName: string;
-    derived_features: unknown[] | null;
-    phase?: number;
-    score?: number;
-    subfeatures: GFF3Feature[] | undefined;
-    [key: string]: unknown;
-}
-export declare function featureData(data: GFF3FeatureLineWithRefs): GFF3Feature;
-export {};

package/dist/featureData.js

@@ -1,55 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.featureData = featureData;
-function featureData(data) {
-    const { end, start, child_features, derived_features, attributes, type, source, phase, seq_id, score, strand, } = data;
-    let strand2;
-    if (strand === '+') {
-        strand2 = 1;
-    }
-    else if (strand === '-') {
-        strand2 = -1;
-    }
-    else if (strand === '.') {
-        strand2 = 0;
-    }
-    const defaultFields = new Set([
-        'start',
-        'end',
-        'seq_id',
-        'score',
-        'type',
-        'source',
-        'phase',
-        'strand',
-    ]);
-    const dataAttributes = attributes || {};
-    const resultAttributes = {};
-    for (const a of Object.keys(dataAttributes)) {
-        let b = a.toLowerCase();
-        if (defaultFields.has(b)) {
-            b += '2';
-        }
-        if (dataAttributes[a] && a !== '_lineHash') {
-            let attr = dataAttributes[a];
-            if (Array.isArray(attr) && attr.length === 1) {
-                ;
-                [attr] = attr;
-            }
-            resultAttributes[b] = attr;
-        }
-    }
-    return {
-        ...resultAttributes,
-        start: start - 1,
-        end: end,
-        strand: strand2,
-        type,
-        source,
-        refName: seq_id,
-        derived_features,
-        phase: phase === null ? undefined : Number(phase),
-        score: score === null ? undefined : score,
-        subfeatures: child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc))),
-    };
-}

package/dist/index.d.ts

@@ -1,6 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class GFF3Plugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}

package/dist/index.js

@@ -1,21 +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 Gff3Adapter_1 = __importDefault(require("./Gff3Adapter"));
-const Gff3TabixAdapter_1 = __importDefault(require("./Gff3TabixAdapter"));
-const GuessGff3_1 = __importDefault(require("./GuessGff3"));
-class GFF3Plugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'GFF3Plugin';
-    }
-    install(pluginManager) {
-        (0, Gff3TabixAdapter_1.default)(pluginManager);
-        (0, Gff3Adapter_1.default)(pluginManager);
-        (0, GuessGff3_1.default)(pluginManager);
-    }
-}
-exports.default = GFF3Plugin;