@jbrowse/plugin-comparative-adapters 2.18.0 → 3.0.1

package/dist/BlastTabularAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
@@ -35,7 +45,7 @@ function BlastTabularAdapterF(pluginManager) {
         displayName: 'Tabular BLAST output adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BlastTabularAdapter'))).then(r => r.default),
     }));

package/dist/ChainAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
@@ -35,7 +45,7 @@ function ChainAdapterF(pluginManager) {
         displayName: 'Liftover chain adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./ChainAdapter'))).then(r => r.default),
     }));

package/dist/ChainAdapter/util.d.ts

@@ -1,5 +1,4 @@
-import type { Buffer } from 'buffer';
-export declare function paf_chain2paf(buffer: Buffer): {
+export declare function paf_chain2paf(buffer: Uint8Array): {
     qname: string;
     qstart: number;
     qend: number;

package/dist/ChainAdapter/util.js

@@ -33,7 +33,7 @@ function paf_chain2paf(buffer) {
     let blockStart = 0;
     const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
-        const n = buffer.indexOf('\n', blockStart);
+        const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
             break;
         }

package/dist/ComparativeAddTrackComponent/ComparativeAddTrackComponent.d.ts

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

package/dist/ComparativeAddTrackComponent/ComparativeAddTrackComponent.js

@@ -0,0 +1,31 @@
+"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 mobx_react_1 = require("mobx-react");
+const ComparativeAddTrackComponent = (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);
+    (0, react_1.useEffect)(() => {
+        model.setMixinData({
+            adapter: {
+                queryAssembly: r0,
+                targetAssembly: r1,
+            },
+        });
+    }, [model, r0, r1]);
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { session: session, label: "Query assembly", helperText: "", selected: r0, onChange: asm => {
+                    setR0(asm);
+                }, TextFieldProps: {
+                    fullWidth: true,
+                } }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { session: session, label: "Target assembly", helperText: "", selected: r1, onChange: asm => {
+                    setR1(asm);
+                }, TextFieldProps: {
+                    fullWidth: true,
+                } })] }));
+});
+exports.default = ComparativeAddTrackComponent;

package/dist/ComparativeAddTrackComponent/index.d.ts

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

package/dist/ComparativeAddTrackComponent/index.js

@@ -0,0 +1,46 @@
+"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 = ComparativeAddTrackComponentF;
+const react_1 = require("react");
+const syntenyTypes_1 = require("../syntenyTypes");
+const ComparativeAddTrackComponent = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ComparativeAddTrackComponent'))));
+function ComparativeAddTrackComponentF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-addTrackComponent', (comp, { model }) => {
+        return syntenyTypes_1.pairwiseTypes.includes(model.trackAdapterType)
+            ? ComparativeAddTrackComponent
+            : comp;
+    });
+}

package/dist/DeltaAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
@@ -35,7 +45,7 @@ function DeltaAdapterF(pluginManager) {
         displayName: 'MUMmer delta adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./DeltaAdapter'))).then(r => r.default),
     }));

package/dist/DeltaAdapter/util.d.ts

@@ -1,5 +1,4 @@
-import type { Buffer } from 'buffer';
-export declare function paf_delta2paf(buffer: Buffer): {
+export declare function paf_delta2paf(buffer: Uint8Array): {
     qname: string;
     qstart: number;
     qend: number;

package/dist/DeltaAdapter/util.js

@@ -20,7 +20,7 @@ function paf_delta2paf(buffer) {
     let i = 0;
     const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
-        const n = buffer.indexOf('\n', blockStart);
+        const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
             break;
         }

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 +1,74 @@
+"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

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

package/dist/MCScanAddTrackComponent/MCScanAddTrackComponent.js

@@ -0,0 +1,39 @@
+"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

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

package/dist/MCScanAddTrackComponent/index.js

@@ -0,0 +1,46 @@
+"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/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
@@ -35,7 +45,7 @@ function MCScanAnchorsAdapterF(pluginManager) {
         displayName: 'MCScan anchors adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MCScanAnchorsAdapter'))).then(r => r.default),
     }));

package/dist/MCScanSimpleAnchorsAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
@@ -35,7 +45,7 @@ function MCScanSimpleAnchorsAdapterF(pluginManager) {
         displayName: 'MCScan anchors.simple adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MCScanSimpleAnchorsAdapter'))).then(r => r.default),
     }));

package/dist/MashMapAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
@@ -35,7 +45,7 @@ function MashMapAdapterF(pluginManager) {
         displayName: 'MashMap adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MashMapAdapter'))).then(r => r.default),
     }));

package/dist/PAFAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
@@ -35,7 +45,7 @@ function PAFAdapterF(pluginManager) {
         displayName: 'PAF adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./PAFAdapter'))).then(r => r.default),
     }));

package/dist/PairwiseIndexedPAFAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
@@ -35,7 +45,7 @@ function PairwiseIndexedPAFAdapterF(pluginManager) {
         displayName: 'Pairwise indexed PAF adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./PairwiseIndexedPAFAdapter'))).then(r => r.default),
     }));