@jbrowse/plugin-comparative-adapters 2.18.0 → 3.0.0

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),
     }));

package/dist/index.js

@@ -4,10 +4,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const tracks_1 = require("@jbrowse/core/util/tracks");
 const BlastTabularAdapter_1 = __importDefault(require("./BlastTabularAdapter"));
 const ChainAdapter_1 = __importDefault(require("./ChainAdapter"));
+const ComparativeAddTrackComponent_1 = __importDefault(require("./ComparativeAddTrackComponent"));
 const DeltaAdapter_1 = __importDefault(require("./DeltaAdapter"));
+const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
+const MCScanAddTrackComponent_1 = __importDefault(require("./MCScanAddTrackComponent"));
 const MCScanAnchorsAdapter_1 = __importDefault(require("./MCScanAnchorsAdapter"));
 const MCScanSimpleAnchorsAdapter_1 = __importDefault(require("./MCScanSimpleAnchorsAdapter"));
 const MashMapAdapter_1 = __importDefault(require("./MashMapAdapter"));
@@ -27,25 +29,9 @@ class ComparativeAdaptersPlugin extends Plugin_1.default {
         (0, MCScanSimpleAnchorsAdapter_1.default)(pluginManager);
         (0, MashMapAdapter_1.default)(pluginManager);
         (0, BlastTabularAdapter_1.default)(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.paf/i;
-                const adapterName = 'PAFAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        pafLocation: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-            return (adapterName) => adapterName === 'PAFAdapter'
-                ? 'SyntenyTrack'
-                : trackTypeGuesser(adapterName);
-        });
+        (0, ComparativeAddTrackComponent_1.default)(pluginManager);
+        (0, MCScanAddTrackComponent_1.default)(pluginManager);
+        (0, GuessAdapter_1.default)(pluginManager);
     }
 }
 exports.default = ComparativeAdaptersPlugin;

package/dist/syntenyTypes.d.ts

@@ -0,0 +1,3 @@
+export declare const syntenyTypes: string[];
+export declare const pairwiseTypes: string[];
+export declare const mcscanTypes: string[];

package/dist/syntenyTypes.js

@@ -0,0 +1,25 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.mcscanTypes = exports.pairwiseTypes = exports.syntenyTypes = void 0;
+exports.syntenyTypes = [
+    'PAFAdapter',
+    'ChainAdapter',
+    'DeltaAdapter',
+    'BlastTabularAdapter',
+    'MashMapAdapter',
+    'MCScanAnchorsAdapter',
+    'MCScanSimpleAnchorsAdapter',
+    'PairwiseIndexedPAFAdapter',
+];
+exports.pairwiseTypes = [
+    'PAFAdapter',
+    'ChainAdapter',
+    'DeltaAdapter',
+    'MashMapAdapter',
+    'BlastTabularAdapter',
+    'PairwiseIndexedPAFAdapter',
+];
+exports.mcscanTypes = [
+    'MCScanAnchorsAdapter',
+    'MCScanSimpleAnchorsAdapter',
+];

package/dist/util.d.ts

@@ -1,7 +1,6 @@
 import type { PAFRecord } from './PAFAdapter/util';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Buffer } from 'buffer';
-import type { GenericFilehandle } from 'generic-filehandle';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export declare function parseBed(text: string): Map<string | undefined, {
     refName: string | undefined;
     start: number;
@@ -12,7 +11,7 @@ export declare function parseBed(text: string): Map<string | undefined, {
 }>;
 export declare function readFile(file: GenericFilehandle, opts?: BaseOptions): Promise<string>;
 export declare function zip(a: number[], b: number[]): [number, number][];
-export declare function parseLineByLine<T>(buffer: Buffer, cb: (line: string) => T | undefined): T[];
+export declare function parseLineByLine<T>(buffer: Uint8Array, cb: (line: string) => T | undefined): T[];
 export declare function parsePAFLine(line: string): PAFRecord;
 export declare function flipCigar(cigar: string[]): (string | undefined)[];
 export declare function swapIndelCigar(cigar: string): string;

package/dist/util.js

@@ -28,9 +28,7 @@ function parseBed(text) {
     }));
 }
 async function readFile(file, opts) {
-    const buf = await (0, util_1.fetchAndMaybeUnzip)(file, opts);
-    const decoder = new TextDecoder('utf8');
-    return decoder.decode(buf);
+    return (0, util_1.fetchAndMaybeUnzipText)(file, opts);
 }
 function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
@@ -40,7 +38,7 @@ function parseLineByLine(buffer, cb) {
     const entries = [];
     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/esm/BlastTabularAdapter/index.js

@@ -6,7 +6,7 @@ export default function BlastTabularAdapterF(pluginManager) {
         displayName: 'Tabular BLAST output adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./BlastTabularAdapter').then(r => r.default),
     }));

package/esm/ChainAdapter/index.js

@@ -6,7 +6,7 @@ export default function ChainAdapterF(pluginManager) {
         displayName: 'Liftover chain adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./ChainAdapter').then(r => r.default),
     }));

package/esm/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/esm/ChainAdapter/util.js

@@ -30,7 +30,7 @@ export 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/esm/ComparativeAddTrackComponent/ComparativeAddTrackComponent.d.ts

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

package/esm/ComparativeAddTrackComponent/ComparativeAddTrackComponent.js

@@ -0,0 +1,29 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { AssemblySelector } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+const ComparativeAddTrackComponent = observer(function ({ model }) {
+    var _a, _b;
+    const session = getSession(model);
+    const [r0, setR0] = useState((_a = session.assemblies[0]) === null || _a === void 0 ? void 0 : _a.name);
+    const [r1, setR1] = useState((_b = session.assemblies[0]) === null || _b === void 0 ? void 0 : _b.name);
+    useEffect(() => {
+        model.setMixinData({
+            adapter: {
+                queryAssembly: r0,
+                targetAssembly: r1,
+            },
+        });
+    }, [model, r0, r1]);
+    return (_jsxs(_Fragment, { children: [_jsx(AssemblySelector, { session: session, label: "Query assembly", helperText: "", selected: r0, onChange: asm => {
+                    setR0(asm);
+                }, TextFieldProps: {
+                    fullWidth: true,
+                } }), _jsx(AssemblySelector, { session: session, label: "Target assembly", helperText: "", selected: r1, onChange: asm => {
+                    setR1(asm);
+                }, TextFieldProps: {
+                    fullWidth: true,
+                } })] }));
+});
+export default ComparativeAddTrackComponent;

package/esm/ComparativeAddTrackComponent/index.d.ts

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

package/esm/ComparativeAddTrackComponent/index.js

@@ -0,0 +1,10 @@
+import { lazy } from 'react';
+import { pairwiseTypes } from '../syntenyTypes';
+const ComparativeAddTrackComponent = lazy(() => import('./ComparativeAddTrackComponent'));
+export default function ComparativeAddTrackComponentF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-addTrackComponent', (comp, { model }) => {
+        return pairwiseTypes.includes(model.trackAdapterType)
+            ? ComparativeAddTrackComponent
+            : comp;
+    });
+}

package/esm/DeltaAdapter/index.js

@@ -6,7 +6,7 @@ export default function DeltaAdapterF(pluginManager) {
         displayName: 'MUMmer delta adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./DeltaAdapter').then(r => r.default),
     }));

package/esm/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/esm/DeltaAdapter/util.js

@@ -17,7 +17,7 @@ export 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/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 +1,71 @@
+import { testAdapter } from '@jbrowse/core/util';
+import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
+import { syntenyTypes } from '../syntenyTypes';
+export default function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = getFileName(file);
+            const indexName = index && getFileName(index);
+            if (testAdapter(fileName, /\.paf(.gz)?/i, adapterHint, 'PAFAdapter')) {
+                return {
+                    type: 'PAFAdapter',
+                    pafLocation: file,
+                };
+            }
+            else if (adapterHint === 'BlastTabularAdapter') {
+                return {
+                    type: 'BlastTabularAdapter',
+                    blastTableLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.anchors.simple(.gz)?/i, adapterHint, 'MCScanSimpleAnchorsAdapter')) {
+                return {
+                    type: 'MCScanSimpleAnchorsAdapter',
+                    mcscanSimpleAnchorsLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.anchors(.gz)?/i, adapterHint, 'MCScanAnchorsAdapter')) {
+                return {
+                    type: 'MCScanAnchorsAdapter',
+                    mcscanAnchorsLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.delta(.gz)?/i, adapterHint, 'DeltaAdapter')) {
+                return {
+                    type: 'DeltaAdapter',
+                    deltaLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.chain(.gz)?/i, adapterHint, 'ChainAdapter')) {
+                return {
+                    type: 'ChainAdapter',
+                    chainLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.out(.gz)?/i, adapterHint, 'MashMapAdapter')) {
+                return {
+                    type: 'MashMapAdapter',
+                    outLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.pif\.gz/i, adapterHint, 'PairwiseIndexedPAFAdapter')) {
+                return {
+                    type: 'PairwiseIndexedPAFAdapter',
+                    pifGzLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.tbi'),
+                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else {
+                return adapterGuesser(file, index, adapterHint);
+            }
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => syntenyTypes.includes(adapterName)
+            ? 'SyntenyTrack'
+            : trackTypeGuesser(adapterName);
+    });
+}

package/esm/MCScanAddTrackComponent/MCScanAddTrackComponent.d.ts

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

package/esm/MCScanAddTrackComponent/MCScanAddTrackComponent.js

@@ -0,0 +1,37 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { AssemblySelector, FileSelector } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
+import { Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+const MCScanAddTrackComponent = observer(function ({ model }) {
+    var _a, _b;
+    const session = getSession(model);
+    const [r0, setR0] = useState((_a = session.assemblies[0]) === null || _a === void 0 ? void 0 : _a.name);
+    const [r1, setR1] = useState((_b = session.assemblies[0]) === null || _b === void 0 ? void 0 : _b.name);
+    const [bed1Location, setBed1Location] = useState();
+    const [bed2Location, setBed2Location] = useState();
+    useEffect(() => {
+        model.setMixinData({
+            adapter: {
+                assemblyNamees: [r0, r1],
+                bed1Location,
+                bed2Location,
+            },
+        });
+    }, [model, bed1Location, bed2Location, r0, r1]);
+    return (_jsxs("div", { style: { marginTop: 20 }, children: [_jsx(Typography, { children: "JBrowse requires the two BED files that specify the genomic locations of the genes in the .anchors files" }), _jsx(AssemblySelector, { session: session, label: "BED1 assembly", helperText: "", selected: r0, onChange: asm => {
+                    setR0(asm);
+                }, TextFieldProps: {
+                    fullWidth: true,
+                } }), _jsx(AssemblySelector, { session: session, label: "BED2 assembly", helperText: "", selected: r1, onChange: asm => {
+                    setR1(asm);
+                }, TextFieldProps: {
+                    fullWidth: true,
+                } }), _jsx(FileSelector, { name: "BED1", inline: true, description: "", location: bed1Location, setLocation: loc => {
+                    setBed1Location(loc);
+                } }), _jsx(FileSelector, { name: "BED2", inline: true, description: "", location: bed2Location, setLocation: loc => {
+                    setBed2Location(loc);
+                } })] }));
+});
+export default MCScanAddTrackComponent;

package/esm/MCScanAddTrackComponent/index.d.ts

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

package/esm/MCScanAddTrackComponent/index.js

@@ -0,0 +1,10 @@
+import { lazy } from 'react';
+import { mcscanTypes } from '../syntenyTypes';
+const MCScanAddTrackComponent = lazy(() => import('./MCScanAddTrackComponent'));
+export default function MCScanAddTrackComponentF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-addTrackComponent', (comp, { model }) => {
+        return mcscanTypes.includes(model.trackAdapterType)
+            ? MCScanAddTrackComponent
+            : comp;
+    });
+}

package/esm/MCScanAnchorsAdapter/index.js

@@ -6,7 +6,7 @@ export default function MCScanAnchorsAdapterF(pluginManager) {
         displayName: 'MCScan anchors adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./MCScanAnchorsAdapter').then(r => r.default),
     }));

package/esm/MCScanSimpleAnchorsAdapter/index.js

@@ -6,7 +6,7 @@ export default function MCScanSimpleAnchorsAdapterF(pluginManager) {
         displayName: 'MCScan anchors.simple adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./MCScanSimpleAnchorsAdapter').then(r => r.default),
     }));

package/esm/MashMapAdapter/index.js

@@ -6,7 +6,7 @@ export default function MashMapAdapterF(pluginManager) {
         displayName: 'MashMap adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./MashMapAdapter').then(r => r.default),
     }));

package/esm/PAFAdapter/index.js

@@ -6,7 +6,7 @@ export default function PAFAdapterF(pluginManager) {
         displayName: 'PAF adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./PAFAdapter').then(r => r.default),
     }));

package/esm/PairwiseIndexedPAFAdapter/index.js

@@ -6,7 +6,7 @@ export default function PairwiseIndexedPAFAdapterF(pluginManager) {
         displayName: 'Pairwise indexed PAF adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./PairwiseIndexedPAFAdapter').then(r => r.default),
     }));

package/esm/index.js

@@ -1,8 +1,10 @@
 import Plugin from '@jbrowse/core/Plugin';
-import { getFileName } from '@jbrowse/core/util/tracks';
 import BlastTabularAdapter from './BlastTabularAdapter';
 import ChainAdapterF from './ChainAdapter';
+import ComparativeAddTrackComponentF from './ComparativeAddTrackComponent';
 import DeltaAdapterF from './DeltaAdapter';
+import GuessAdapterF from './GuessAdapter';
+import MCScanAddTrackComponentF from './MCScanAddTrackComponent';
 import MCScanAnchorsAdapterF from './MCScanAnchorsAdapter';
 import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter';
 import MashMapAdapterF from './MashMapAdapter';
@@ -22,24 +24,8 @@ export default class ComparativeAdaptersPlugin extends Plugin {
         MCScanSimpleAnchorsAdapterF(pluginManager);
         MashMapAdapterF(pluginManager);
         BlastTabularAdapter(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.paf/i;
-                const adapterName = 'PAFAdapter';
-                const fileName = getFileName(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        pafLocation: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-            return (adapterName) => adapterName === 'PAFAdapter'
-                ? 'SyntenyTrack'
-                : trackTypeGuesser(adapterName);
-        });
+        ComparativeAddTrackComponentF(pluginManager);
+        MCScanAddTrackComponentF(pluginManager);
+        GuessAdapterF(pluginManager);
     }
 }

package/esm/syntenyTypes.d.ts

@@ -0,0 +1,3 @@
+export declare const syntenyTypes: string[];
+export declare const pairwiseTypes: string[];
+export declare const mcscanTypes: string[];

package/esm/syntenyTypes.js

@@ -0,0 +1,22 @@
+export const syntenyTypes = [
+    'PAFAdapter',
+    'ChainAdapter',
+    'DeltaAdapter',
+    'BlastTabularAdapter',
+    'MashMapAdapter',
+    'MCScanAnchorsAdapter',
+    'MCScanSimpleAnchorsAdapter',
+    'PairwiseIndexedPAFAdapter',
+];
+export const pairwiseTypes = [
+    'PAFAdapter',
+    'ChainAdapter',
+    'DeltaAdapter',
+    'MashMapAdapter',
+    'BlastTabularAdapter',
+    'PairwiseIndexedPAFAdapter',
+];
+export const mcscanTypes = [
+    'MCScanAnchorsAdapter',
+    'MCScanSimpleAnchorsAdapter',
+];

package/esm/util.d.ts

@@ -1,7 +1,6 @@
 import type { PAFRecord } from './PAFAdapter/util';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Buffer } from 'buffer';
-import type { GenericFilehandle } from 'generic-filehandle';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export declare function parseBed(text: string): Map<string | undefined, {
     refName: string | undefined;
     start: number;
@@ -12,7 +11,7 @@ export declare function parseBed(text: string): Map<string | undefined, {
 }>;
 export declare function readFile(file: GenericFilehandle, opts?: BaseOptions): Promise<string>;
 export declare function zip(a: number[], b: number[]): [number, number][];
-export declare function parseLineByLine<T>(buffer: Buffer, cb: (line: string) => T | undefined): T[];
+export declare function parseLineByLine<T>(buffer: Uint8Array, cb: (line: string) => T | undefined): T[];
 export declare function parsePAFLine(line: string): PAFRecord;
 export declare function flipCigar(cigar: string[]): (string | undefined)[];
 export declare function swapIndelCigar(cigar: string): string;

package/esm/util.js

@@ -1,4 +1,4 @@
-import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 export function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
@@ -19,9 +19,7 @@ export function parseBed(text) {
     }));
 }
 export async function readFile(file, opts) {
-    const buf = await fetchAndMaybeUnzip(file, opts);
-    const decoder = new TextDecoder('utf8');
-    return decoder.decode(buf);
+    return fetchAndMaybeUnzipText(file, opts);
 }
 export function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
@@ -31,7 +29,7 @@ export function parseLineByLine(buffer, cb) {
     const entries = [];
     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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.18.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -36,9 +36,9 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/tabix": "^1.5.6",
-    "generic-filehandle": "^3.0.0"
+    "@gmod/bgzf-filehandle": "^2.0.1",
+    "@gmod/tabix": "^2.0.0",
+    "generic-filehandle2": "^1.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }