@jbrowse/plugin-gtf 2.18.0 → 3.0.0

package/dist/GtfAdapter/GtfAdapter.js

@@ -25,7 +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);
+            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) {

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.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 Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const GtfAdapter_1 = require("./GtfAdapter");
+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/esm/GtfAdapter/GtfAdapter.js

@@ -20,7 +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);
+            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) {

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.js

@@ -1,36 +1,13 @@
 import Plugin from '@jbrowse/core/Plugin';
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import { getFileName } from '@jbrowse/core/util/tracks';
-import { configSchema as gtfAdapterConfigSchema } from './GtfAdapter';
+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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "2.18.0",
+  "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": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }