@jbrowse/plugin-comparative-adapters 2.17.0 → 3.0.0

package/esm/ChainAdapter/util.js

@@ -1,27 +1,3 @@
-/* adapted from chain2paf by Andrea Guarracino, license reproduced below
- *
- * MIT License
- *
- * Copyright (c) 2021 Andrea Guarracino
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- */
 function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, cigar, numMatches) {
     return {
         qname,
@@ -54,33 +30,19 @@ 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;
         }
         const b = buffer.subarray(blockStart, n);
         const l = decoder.decode(b).trim();
         blockStart = n + 1;
-        const l_tab = l.replaceAll(' ', '\t'); // There are CHAIN files with space-separated fields
+        const l_tab = l.replaceAll(' ', '\t');
         const l_vec = l_tab.split('\t');
         if (l_vec[0] === 'chain') {
-            // Emit previous PAF row, if available
             if (cigar) {
                 records.push(generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches));
             }
-            // Save query/target information
-            // score -- chain score
-            // tName -- chromosome (reference sequence)
-            // tSize -- chromosome size (reference sequence)
-            // tStrand -- strand (reference sequence)
-            // tStart -- alignment start position (reference sequence)
-            // tEnd -- alignment end position (reference sequence)
-            // qName -- chromosome (query sequence)
-            // qSize -- chromosome size (query sequence)
-            // qStrand -- strand (query sequence)
-            // qStart -- alignment start position (query sequence)
-            // qEnd -- alignment end position (query sequence)
-            // id -- chain ID
             t_name = l_vec[2];
             t_start = +l_vec[5];
             t_end = +l_vec[6];
@@ -94,18 +56,10 @@ export function paf_chain2paf(buffer) {
                 q_start = +q_size - q_end;
                 q_end = +q_size - tmp;
             }
-            // Initialize PAF fields
             num_matches = 0;
             cigar = '';
         }
         else {
-            // size -- the size of the ungapped alignment
-            //
-            // dt -- the difference between the end of this block and the beginning
-            //    of the next block (reference sequence)
-            //
-            // dq -- the difference between the end of this block and the beginning
-            //    of the next block (query sequence)
             const size_ungapped_alignment = +l_vec[0] || 0;
             const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0;
             const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
@@ -121,7 +75,6 @@ export function paf_chain2paf(buffer) {
             }
         }
     }
-    // Emit last PAF row, if available
     if (cigar) {
         generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
     }

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/DeltaAdapter.d.ts

@@ -1,5 +1,5 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class DeltaAdapter extends PAFAdapter {
     setupPre(opts?: BaseOptions): Promise<{
         qname: string;

package/esm/DeltaAdapter/DeltaAdapter.js

@@ -1,8 +1,7 @@
-import { openLocation } from '@jbrowse/core/util/io';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
-// locals
-import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
 import { paf_delta2paf } from './util';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
 export default class DeltaAdapter extends PAFAdapter {
     async setupPre(opts) {
         const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager);

package/esm/DeltaAdapter/configSchema.d.ts

@@ -1,33 +1,19 @@
 declare const DeltaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     deltaLocation: {
         type: string;
         defaultValue: {

package/esm/DeltaAdapter/configSchema.js

@@ -1,39 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config DeltaAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const DeltaAdapter = ConfigurationSchema('DeltaAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     deltaLocation: {
         type: 'fileLocation',
         defaultValue: {

package/esm/DeltaAdapter/index.d.ts

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

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

@@ -1,30 +1,3 @@
-/* paf2delta from paftools.js in the minimap2 repository, license reproduced below
- *
- * The MIT License
- *
- * Copyright (c) 2018-     Dana-Farber Cancer Institute
- *               2017-2018 Broad Institute, Inc.
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject to
- * the following conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- */
 export function paf_delta2paf(buffer) {
     let rname = '';
     let qname = '';
@@ -44,7 +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;
         }
@@ -122,7 +95,7 @@ export function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 2);
-                    } // deletion
+                    }
                 }
                 else {
                     const l = -d - 1;
@@ -136,7 +109,7 @@ export function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 1);
-                    } // insertion
+                    }
                 }
             }
         }

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/MCScanAnchorsAdapter.d.ts

@@ -1,5 +1,6 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 interface BareFeature {
     strand: number;
     refName: string;
@@ -24,11 +25,6 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }
 export {};

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -1,8 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, doesIntersect2 } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { doesIntersect2, SimpleFeature, } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { readFile, parseBed } from '../util';
+import { parseBed, readFile } from '../util';
 class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
@@ -40,9 +40,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         };
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures so is not
-        // really that important, and has to be true or else getFeatures is never
-        // called (BaseFeatureDataAdapter filters it out)
         return true;
     }
     getAssemblyNames() {
@@ -51,7 +48,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     }
     async getRefNames(opts = {}) {
         var _a;
-        // @ts-expect-error
         const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
         const { feats } = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -68,8 +64,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { assemblyNames, feats } = await this.setup(opts);
-            // The index of the assembly name in the region list corresponds to
-            // the adapter in the subadapters list
             const index = assemblyNames.indexOf(region.assemblyName);
             if (index !== -1) {
                 const flip = index === 0;
@@ -82,8 +76,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
                             ...f1,
                             uniqueId: `${index}-${rowNum}`,
                             syntenyId: rowNum,
-                            // note: strand would be -1 if the two features are on opposite
-                            // strands, indicating inverted alignment
                             strand: f1.strand * f2.strand,
                             assemblyName: assemblyNames[+!flip],
                             score,
@@ -98,12 +90,7 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default MCScanAnchorsAdapter;

package/esm/MCScanAnchorsAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     mcscanAnchorsLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed1Location: {
         type: string;
         defaultValue: {
@@ -19,9 +13,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed2Location: {
         type: string;
         defaultValue: {
@@ -29,9 +20,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/esm/MCScanAnchorsAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config MCScanAnchorsAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
-    /**
-     * #slot
-     */
     mcscanAnchorsLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -14,9 +8,6 @@ const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed1Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -24,9 +15,6 @@ const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed2Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -34,9 +22,6 @@ const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],

package/esm/MCScanAnchorsAdapter/index.d.ts

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

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/MCScanSimpleAnchorsAdapter.d.ts

@@ -1,6 +1,7 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 interface BareFeature {
     refName: string;
     start: number;
@@ -32,11 +33,6 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }
 export {};