@jbrowse/plugin-gtf 2.17.0 → 3.0.0

package/dist/GtfAdapter/GtfAdapter.d.ts

@@ -1,7 +1,8 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import IntervalTree from '@flatten-js/interval-tree';
-import { Feature } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 type StatusCallback = (arg: string) => void;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;

package/dist/GtfAdapter/GtfAdapter.js

@@ -3,13 +3,12 @@ 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 interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const util_1 = require("@jbrowse/core/util");
 const gtf_nostream_1 = require("gtf-nostream");
-// locals
 const util_2 = require("../util");
 class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -26,8 +25,7 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         let i = 0;
         const decoder = new TextDecoder('utf8');
         while (blockStart < buffer.length) {
-            const n = buffer.indexOf('\n', blockStart);
-            // could be a non-newline ended file, so slice to end of file if n===-1
+            const n = buffer.indexOf(10, blockStart);
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
             const line = decoder.decode(b).trim();
             if (line) {
@@ -105,8 +103,8 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = GtfAdapter;

package/dist/GtfAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     gtfLocation: {
         type: string;
         defaultValue: {

package/dist/GtfAdapter/configSchema.js

@@ -1,15 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config GtfAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const GtfAdapter = (0, configuration_1.ConfigurationSchema)('GtfAdapter', {
-    /**
-     * #slot
-     */
     gtfLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.gtf', locationType: 'UriLocation' },

package/dist/GtfAdapter/index.d.ts

@@ -1 +1,2 @@
-export { default as configSchema } from './configSchema';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function GtfAdapterF(pluginManager: PluginManager): void;

package/dist/GtfAdapter/index.js

@@ -1,8 +1,49 @@
 "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.configSchema = void 0;
-var configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+exports.default = GtfAdapterF;
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+const configSchema_1 = __importDefault(require("./configSchema"));
+function GtfAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
+        name: 'GtfAdapter',
+        displayName: 'GTF adapter',
+        configSchema: configSchema_1.default,
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./GtfAdapter'))).then(r => r.default),
+    }));
+}

package/dist/GuessAdapter/index.d.ts

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

package/dist/GuessAdapter/index.js

@@ -0,0 +1,18 @@
+"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");
+function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = (0, tracks_1.getFileName)(file);
+            return (0, util_1.testAdapter)(fileName, /\.gtf(\.gz)?$/i, adapterHint, 'GtfAdapter')
+                ? {
+                    type: 'GtfAdapter',
+                    gtfLocation: file,
+                }
+                : adapterGuesser(file, index, adapterHint);
+        };
+    });
+}

package/dist/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 GtfPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -1,65 +1,19 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const GtfAdapter_1 = require("./GtfAdapter");
-const tracks_1 = require("@jbrowse/core/util/tracks");
+const GtfAdapter_1 = __importDefault(require("./GtfAdapter"));
+const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
 class GtfPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
         this.name = 'GTFPlugin';
     }
     install(pluginManager) {
-        pluginManager.addAdapterType(() => new AdapterType_1.default({
-            name: 'GtfAdapter',
-            displayName: 'GTF adapter',
-            configSchema: GtfAdapter_1.configSchema,
-            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./GtfAdapter/GtfAdapter'))).then(r => r.default),
-        }));
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.gtf(\.gz)?$/i;
-                const adapterName = 'GtfAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                const obj = {
-                    type: adapterName,
-                    gtfLocation: file,
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
+        (0, GtfAdapter_1.default)(pluginManager);
+        (0, GuessAdapter_1.default)(pluginManager);
     }
 }
 exports.default = GtfPlugin;

package/dist/util.js

@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.featureData = featureData;
 function featureData(data) {
     const f = { ...data };
-    f.start -= 1; // convert to interbase
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand]; // convert strand
+    f.start -= 1;
+    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand];
     f.phase = Number(data.frame);
     f.refName = data.seq_name;
     if (data.score === null) {
@@ -26,15 +26,11 @@ function featureData(data) {
     for (const a of Object.keys(data.attributes)) {
         let b = a.toLowerCase();
         if (defaultFields.has(b)) {
-            // add "suffix" to tag name if it already exists
-            // reproduces behavior of NCList
             b += '2';
         }
         if (data.attributes[a]) {
             let attr = data.attributes[a];
             if (Array.isArray(attr) && attr.length === 1) {
-                // gtf uses double quotes for text values in the attributes column,
-                // remove them
                 attr = attr[0].replaceAll(/^"|"$/g, '');
             }
             f[b] = attr;
@@ -42,7 +38,6 @@ function featureData(data) {
     }
     f.refName = f.seq_name;
     f.type = f.featureType;
-    // the SimpleFeature constructor takes care of recursively inflating subfeatures
     if (data.child_features && data.child_features.length > 0) {
         f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
     }

package/esm/GtfAdapter/GtfAdapter.d.ts

@@ -1,7 +1,8 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import IntervalTree from '@flatten-js/interval-tree';
-import { Feature } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 type StatusCallback = (arg: string) => void;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;

package/esm/GtfAdapter/GtfAdapter.js

@@ -1,10 +1,9 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { openLocation } from '@jbrowse/core/util/io';
-import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { parseStringSync } from 'gtf-nostream';
-// locals
 import { featureData } from '../util';
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -21,8 +20,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
         let i = 0;
         const decoder = new TextDecoder('utf8');
         while (blockStart < buffer.length) {
-            const n = buffer.indexOf('\n', blockStart);
-            // could be a non-newline ended file, so slice to end of file if n===-1
+            const n = buffer.indexOf(10, blockStart);
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
             const line = decoder.decode(b).trim();
             if (line) {
@@ -100,7 +98,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/GtfAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     gtfLocation: {
         type: string;
         defaultValue: {

package/esm/GtfAdapter/configSchema.js

@@ -1,13 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config GtfAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const GtfAdapter = ConfigurationSchema('GtfAdapter', {
-    /**
-     * #slot
-     */
     gtfLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.gtf', locationType: 'UriLocation' },

package/esm/GtfAdapter/index.d.ts

@@ -1 +1,2 @@
-export { default as configSchema } from './configSchema';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function GtfAdapterF(pluginManager: PluginManager): void;

package/esm/GtfAdapter/index.js

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

package/esm/GuessAdapter/index.d.ts

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

package/esm/GuessAdapter/index.js

@@ -0,0 +1,15 @@
+import { testAdapter } from '@jbrowse/core/util';
+import { getFileName } from '@jbrowse/core/util/tracks';
+export default function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = getFileName(file);
+            return testAdapter(fileName, /\.gtf(\.gz)?$/i, adapterHint, 'GtfAdapter')
+                ? {
+                    type: 'GtfAdapter',
+                    gtfLocation: file,
+                }
+                : adapterGuesser(file, index, adapterHint);
+        };
+    });
+}

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 GtfPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,36 +1,13 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import Plugin from '@jbrowse/core/Plugin';
-import { configSchema as gtfAdapterConfigSchema } from './GtfAdapter';
-import { getFileName } from '@jbrowse/core/util/tracks';
+import GtfAdapterF from './GtfAdapter';
+import GuessAdapterF from './GuessAdapter';
 export default class GtfPlugin extends Plugin {
     constructor() {
         super(...arguments);
         this.name = 'GTFPlugin';
     }
     install(pluginManager) {
-        pluginManager.addAdapterType(() => new AdapterType({
-            name: 'GtfAdapter',
-            displayName: 'GTF adapter',
-            configSchema: gtfAdapterConfigSchema,
-            getAdapterClass: () => import('./GtfAdapter/GtfAdapter').then(r => r.default),
-        }));
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.gtf(\.gz)?$/i;
-                const adapterName = 'GtfAdapter';
-                const fileName = getFileName(file);
-                const obj = {
-                    type: adapterName,
-                    gtfLocation: file,
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
+        GtfAdapterF(pluginManager);
+        GuessAdapterF(pluginManager);
     }
 }

package/esm/util.js

@@ -1,7 +1,7 @@
 export function featureData(data) {
     const f = { ...data };
-    f.start -= 1; // convert to interbase
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand]; // convert strand
+    f.start -= 1;
+    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand];
     f.phase = Number(data.frame);
     f.refName = data.seq_name;
     if (data.score === null) {
@@ -23,15 +23,11 @@ export function featureData(data) {
     for (const a of Object.keys(data.attributes)) {
         let b = a.toLowerCase();
         if (defaultFields.has(b)) {
-            // add "suffix" to tag name if it already exists
-            // reproduces behavior of NCList
             b += '2';
         }
         if (data.attributes[a]) {
             let attr = data.attributes[a];
             if (Array.isArray(attr) && attr.length === 1) {
-                // gtf uses double quotes for text values in the attributes column,
-                // remove them
                 attr = attr[0].replaceAll(/^"|"$/g, '');
             }
             f[b] = attr;
@@ -39,7 +35,6 @@ export function featureData(data) {
     }
     f.refName = f.seq_name;
     f.type = f.featureType;
-    // the SimpleFeature constructor takes care of recursively inflating subfeatures
     if (data.child_features && data.child_features.length > 0) {
         f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bgzf-filehandle": "^1.4.3",
+    "@gmod/bgzf-filehandle": "^2.0.1",
     "gtf-nostream": "^1.0.0"
   },
   "peerDependencies": {
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }