jbrowse-plugin-mafviewer 1.0.6 → 1.1.1

package/dist/LinearMafRenderer/util.js.map

@@ -0,0 +1 @@
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package/dist/MafAddTrackWorkflow/AddTrackWorkflow.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+import { AddTrackModel } from '@jbrowse/plugin-data-management';
+export default function MultiMAFWidget({ model }: {
+    model: AddTrackModel;
+}): React.JSX.Element;

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js

@@ -0,0 +1,128 @@
+import React, { useState } from 'react';
+import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
+import { getSession, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { Button, FormControl, FormControlLabel, FormLabel, Paper, Radio, RadioGroup, TextField, } from '@mui/material';
+import { getRoot } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    textbox: {
+        width: '100%',
+    },
+    paper: {
+        margin: theme.spacing(),
+        padding: theme.spacing(),
+    },
+    submit: {
+        marginTop: 25,
+        marginBottom: 100,
+        display: 'block',
+    },
+}));
+export default function MultiMAFWidget({ model }) {
+    const { classes } = useStyles();
+    const [samples, setSamples] = useState('');
+    const [loc, setLoc] = useState();
+    const [indexLoc, setIndexLoc] = useState();
+    const [nhLoc, setNhLoc] = useState();
+    const [error, setError] = useState();
+    const [trackName, setTrackName] = useState('MAF track');
+    const [fileTypeChoice, setFileTypeChoice] = useState('BigMafAdapter');
+    const [indexTypeChoice, setIndexTypeChoice] = useState('TBI');
+    const rootModel = getRoot(model);
+    return (React.createElement(Paper, { className: classes.paper },
+        React.createElement(Paper, null,
+            error ? React.createElement(ErrorMessage, { error: error }) : null,
+            React.createElement(FormControl, null,
+                React.createElement(FormLabel, null, "File type"),
+                React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
+                        setFileTypeChoice(event.target.value);
+                    } }, ['BigMafAdapter', 'MafTabixAdapter', 'BgzipTaffyAdapter'].map(r => (React.createElement(FormControlLabel, { value: r, control: React.createElement(Radio, null), checked: fileTypeChoice === r, label: r }))))),
+            fileTypeChoice === 'BigMafAdapter' ? (React.createElement(FileSelector, { location: loc, name: "Path to bigMaf", rootModel: rootModel, setLocation: arg => {
+                    setLoc(arg);
+                } })) : fileTypeChoice === 'MafTabixAdapter' ? (React.createElement(React.Fragment, null,
+                React.createElement(FormControl, null,
+                    React.createElement(FormLabel, null, "Index type"),
+                    React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
+                            setIndexTypeChoice(event.target.value);
+                        } }, ['TBI', 'CSI'].map(r => (React.createElement(FormControlLabel, { value: r, control: React.createElement(Radio, null), checked: fileTypeChoice === r, label: r }))))),
+                React.createElement(FileSelector, { location: loc, name: "Path to MAF tabix", rootModel: rootModel, setLocation: arg => {
+                        setLoc(arg);
+                    } }),
+                React.createElement(FileSelector, { location: indexLoc, name: "Path to MAF tabix index", rootModel: rootModel, setLocation: arg => {
+                        setIndexLoc(arg);
+                    } }))) : (React.createElement(React.Fragment, null,
+                React.createElement(FileSelector, { location: loc, name: "Path to TAF.gz (Bgzipped TAF)", rootModel: rootModel, setLocation: arg => {
+                        setLoc(arg);
+                    } }),
+                React.createElement(FileSelector, { location: indexLoc, name: "Path to TAF.gz.tai (TAF index)", rootModel: rootModel, setLocation: arg => {
+                        setIndexLoc(arg);
+                    } })))),
+        React.createElement("div", null,
+            React.createElement(FileSelector, { location: nhLoc, name: "Path to newick tree (.nh)", rootModel: rootModel, setLocation: arg => {
+                    setNhLoc(arg);
+                } }),
+            React.createElement(TextField, { multiline: true, rows: 10, value: samples, onChange: event => {
+                    setSamples(event.target.value);
+                }, helperText: "Sample names (optional if .nh supplied, required if not)", placeholder: 'Enter sample names from the MAF file, one per line, or JSON formatted array of samples', variant: "outlined", fullWidth: true })),
+        React.createElement(TextField, { value: trackName, helperText: "Track name", onChange: event => {
+                setTrackName(event.target.value);
+            } }),
+        React.createElement(Button, { variant: "contained", className: classes.submit, onClick: () => {
+                try {
+                    const session = getSession(model);
+                    let sampleNames = [];
+                    try {
+                        sampleNames = JSON.parse(samples);
+                    }
+                    catch (e) {
+                        sampleNames = samples.split(/\n|\r\n|\r/);
+                    }
+                    const trackId = [
+                        `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
+                        session.adminMode ? '' : '-sessionTrack',
+                    ].join('');
+                    if (isSessionWithAddTracks(session)) {
+                        session.addTrackConf({
+                            trackId,
+                            type: 'MafTrack',
+                            name: trackName,
+                            assemblyNames: [model.assembly],
+                            adapter: fileTypeChoice === 'BigMafAdapter'
+                                ? {
+                                    type: fileTypeChoice,
+                                    bigBedLocation: loc,
+                                    samples: sampleNames,
+                                    nhLocation: nhLoc,
+                                }
+                                : fileTypeChoice === 'MafTabixAdapter'
+                                    ? {
+                                        type: fileTypeChoice,
+                                        bedGzLocation: loc,
+                                        nhLocation: nhLoc,
+                                        index: {
+                                            indexType: indexTypeChoice,
+                                            location: indexLoc,
+                                        },
+                                        samples: sampleNames,
+                                    }
+                                    : {
+                                        type: fileTypeChoice,
+                                        tafGzLocation: loc,
+                                        taiLocation: indexLoc,
+                                        nhLocation: nhLoc,
+                                        samples: sampleNames,
+                                    },
+                        });
+                        model.view?.showTrack(trackId);
+                    }
+                    model.clearData();
+                    if (isSessionModelWithWidgets(session)) {
+                        session.hideWidget(model);
+                    }
+                }
+                catch (e) {
+                    setError(e);
+                }
+            } }, "Submit")));
+}
+//# sourceMappingURL=AddTrackWorkflow.js.map

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map

@@ -0,0 +1 @@
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package/dist/MafAddTrackWorkflow/index.d.ts

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

package/dist/MafAddTrackWorkflow/index.js

@@ -0,0 +1,12 @@
+import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes';
+import { types } from 'mobx-state-tree';
+// locals
+import MultiMAFWidget from './AddTrackWorkflow';
+export default function MafAddTrackWorkflowF(pluginManager) {
+    pluginManager.addAddTrackWorkflowType(() => new AddTrackWorkflowType({
+        name: 'MAF track',
+        ReactComponent: MultiMAFWidget,
+        stateModel: types.model({}),
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/MafAddTrackWorkflow/index.js.map

@@ -0,0 +1 @@
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package/dist/MafRPC/index.d.ts

@@ -0,0 +1,16 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<any>;
+}
+export default function MafRPCF(pluginManager: PluginManager): void;

package/dist/MafRPC/index.js

@@ -0,0 +1,19 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+export class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name = 'MafGetSamples';
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
+        // @ts-expect-error
+        return dataAdapter.getSamples(regions, deserializedArgs);
+    }
+}
+export default function MafRPCF(pluginManager) {
+    pluginManager.addRpcMethod(() => {
+        return new MafGetSamples(pluginManager);
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/MafRPC/index.js.map

@@ -0,0 +1 @@
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package/dist/MafTabixAdapter/MafTabixAdapter.d.ts

@@ -0,0 +1,25 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature, Region } from '@jbrowse/core/util';
+export default class MafTabixAdapter extends BaseFeatureDataAdapter {
+    setupP?: Promise<{
+        adapter: BaseFeatureDataAdapter;
+    }>;
+    setup(): Promise<{
+        adapter: BaseFeatureDataAdapter;
+    }>;
+    setupPre(): Promise<{
+        adapter: BaseFeatureDataAdapter;
+    }>;
+    getRefNames(): Promise<string[]>;
+    getHeader(): Promise<unknown>;
+    getFeatures(query: Region): import("rxjs").Observable<Feature>;
+    getSamples(_query: Region): Promise<{
+        samples: {
+            id: string;
+            label: string;
+            color?: string;
+        }[];
+        tree: Record<string, any> | undefined;
+    }>;
+    freeResources(): void;
+}

package/dist/MafTabixAdapter/MafTabixAdapter.js

@@ -0,0 +1,95 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { getSnapshot } from 'mobx-state-tree';
+import { firstValueFrom, toArray } from 'rxjs';
+import parseNewick from '../parseNewick';
+import { normalize } from '../util';
+export default class MafTabixAdapter extends BaseFeatureDataAdapter {
+    setupP;
+    async setup() {
+        const config = this.config;
+        if (!this.getSubAdapter) {
+            throw new Error('no getSubAdapter available');
+        }
+        const adapter = await this.getSubAdapter({
+            ...getSnapshot(config),
+            type: 'BedTabixAdapter',
+        });
+        return {
+            adapter: adapter.dataAdapter,
+        };
+    }
+    async setupPre() {
+        if (!this.setupP) {
+            this.setupP = this.setup().catch((e) => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    async getRefNames() {
+        const { adapter } = await this.setup();
+        return adapter.getRefNames();
+    }
+    async getHeader() {
+        const { adapter } = await this.setup();
+        return adapter.getHeader();
+    }
+    getFeatures(query) {
+        return ObservableCreate(async (observer) => {
+            const { adapter } = await this.setup();
+            const features = await firstValueFrom(adapter.getFeatures(query).pipe(toArray()));
+            for (const feature of features) {
+                const data = feature.get('field5').split(',');
+                const alignments = {};
+                const alns = data.map(elt => elt.split(':')[5]);
+                for (const [j, elt] of data.entries()) {
+                    const ad = elt.split(':');
+                    const idx = ad[0].lastIndexOf('.');
+                    const org = ad[0].slice(0, idx);
+                    const last = ad[0].slice(idx + 1);
+                    if (org) {
+                        alignments[org] = {
+                            chr: last,
+                            start: +ad[1],
+                            srcSize: +ad[2],
+                            strand: ad[3] === '-' ? -1 : 1,
+                            unknown: +ad[4],
+                            data: alns[j],
+                        };
+                    }
+                }
+                observer.next(new SimpleFeature({
+                    id: feature.id(),
+                    data: {
+                        start: feature.get('start'),
+                        end: feature.get('end'),
+                        refName: feature.get('refName'),
+                        name: feature.get('name'),
+                        score: feature.get('score'),
+                        alignments,
+                        seq: alns[0],
+                    },
+                }));
+            }
+            observer.complete();
+        });
+    }
+    async getSamples(_query) {
+        const nhLoc = this.getConf('nhLocation');
+        const nh = nhLoc.uri === '/path/to/my.nh'
+            ? undefined
+            : await openLocation(nhLoc).readFile('utf8');
+        // TODO: we may need to resolve the exact set of rows in the visible region
+        // here
+        return {
+            samples: normalize(this.getConf('samples')),
+            tree: nh ? parseNewick(nh) : undefined,
+        };
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=MafTabixAdapter.js.map

package/dist/MafTabixAdapter/MafTabixAdapter.js.map

@@ -0,0 +1 @@
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package/dist/MafTabixAdapter/configSchema.d.ts

@@ -0,0 +1,50 @@
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    samples: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+    /**
+     * #slot
+     */
+    bedGzLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+            };
+        };
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            type: string;
+            defaultValue: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    nhLocation: {
+        type: string;
+        description: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default configSchema;

package/dist/MafTabixAdapter/configSchema.js

@@ -0,0 +1,56 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config MafTabixAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('MafTabixAdapter', {
+    /**
+     * #slot
+     */
+    samples: {
+        type: 'frozen',
+        description: 'string[] or {id:string,label:string,color?:string}[]',
+        defaultValue: [],
+    },
+    /**
+     * #slot
+     */
+    bedGzLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bed.gz.tbi',
+            locationType: 'UriLocation',
+        },
+    },
+    index: ConfigurationSchema('Index', {
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.bed.gz.tbi',
+            },
+        },
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            type: 'string',
+            defaultValue: 'TBI',
+        },
+    }),
+    /**
+     * #slot
+     */
+    nhLocation: {
+        type: 'fileLocation',
+        description: 'newick tree',
+        defaultValue: {
+            uri: '/path/to/my.nh',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/MafTabixAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/MafTabixAdapter/index.d.ts

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

package/dist/MafTabixAdapter/index.js

@@ -0,0 +1,11 @@
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
+import MafTabixAdapter from './MafTabixAdapter';
+import configSchema from './configSchema';
+export default function MafTabixAdapterF(pluginManager) {
+    return pluginManager.addAdapterType(() => new AdapterType({
+        name: 'MafTabixAdapter',
+        AdapterClass: MafTabixAdapter,
+        configSchema,
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/MafTabixAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,aAA4B;IACnE,OAAO,aAAa,CAAC,cAAc,CACjC,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,iBAAiB;QACvB,YAAY,EAAE,eAAe;QAC7B,YAAY;KACb,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/MafTrack/configSchema.d.ts

@@ -0,0 +1,79 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;

package/dist/MafTrack/configSchema.js

@@ -0,0 +1,15 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+export default function configSchemaF(pluginManager) {
+    return ConfigurationSchema('MafTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: createBaseTrackConfig(pluginManager),
+        /**
+         * #identifier
+         */
+        explicitIdentifier: 'trackId',
+    });
+}
+//# sourceMappingURL=configSchema.js.map

package/dist/MafTrack/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/MafTrack/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAE3E,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,aAA4B;IAChE,OAAO,mBAAmB,CACxB,UAAU,EACV,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;QACvD;;WAEG;QACH,kBAAkB,EAAE,SAAS;KAC9B,CACF,CAAA;AACH,CAAC"}

package/dist/MafTrack/index.d.ts

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

package/dist/MafTrack/index.js

@@ -0,0 +1,14 @@
+import { TrackType, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes';
+import configSchemaF from './configSchema';
+export default function MafTrackF(pluginManager) {
+    return pluginManager.addTrackType(() => {
+        const configSchema = configSchemaF(pluginManager);
+        return new TrackType({
+            name: 'MafTrack',
+            configSchema,
+            displayName: 'MAF track',
+            stateModel: createBaseTrackModel(pluginManager, 'MafTrack', configSchema),
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/MafTrack/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,EACL,SAAS,EACT,oBAAoB,GACrB,MAAM,qCAAqC,CAAA;AAE5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,aAA4B;IAC5D,OAAO,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QACrC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,UAAU;YAChB,YAAY;YACZ,WAAW,EAAE,WAAW;YACxB,UAAU,EAAE,oBAAoB,CAAC,aAAa,EAAE,UAAU,EAAE,YAAY,CAAC;SAC1E,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/index.d.ts

@@ -0,0 +1,8 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class MafViewerPlugin extends Plugin {
+    name: string;
+    version: any;
+    install(pluginManager: PluginManager): void;
+    configure(_pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -0,0 +1,26 @@
+import Plugin from '@jbrowse/core/Plugin';
+import { version } from '../package.json';
+import BgzipTaffyAdapterF from './BgzipTaffyAdapter';
+import BigMafAdapterF from './BigMafAdapter';
+import LinearMafDisplayF from './LinearMafDisplay';
+import LinearMafRendererF from './LinearMafRenderer';
+import MafAddTrackWorkflowF from './MafAddTrackWorkflow';
+import MafRPCF from './MafRPC';
+import MafTabixAdapterF from './MafTabixAdapter';
+import MafTrackF from './MafTrack';
+export default class MafViewerPlugin extends Plugin {
+    name = 'MafViewerPlugin';
+    version = version;
+    install(pluginManager) {
+        BigMafAdapterF(pluginManager);
+        MafTrackF(pluginManager);
+        LinearMafDisplayF(pluginManager);
+        LinearMafRendererF(pluginManager);
+        MafTabixAdapterF(pluginManager);
+        BgzipTaffyAdapterF(pluginManager);
+        MafAddTrackWorkflowF(pluginManager);
+        MafRPCF(pluginManager);
+    }
+    configure(_pluginManager) { }
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,OAAO,MAAM,UAAU,CAAA;AAC9B,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,SAAS,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,MAAM;IACjD,IAAI,GAAG,iBAAiB,CAAA;IACxB,OAAO,GAAG,OAAO,CAAA;IAEjB,OAAO,CAAC,aAA4B;QAClC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,SAAS,CAAC,aAAa,CAAC,CAAA;QACxB,iBAAiB,CAAC,aAAa,CAAC,CAAA;QAChC,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,OAAO,CAAC,aAAa,CAAC,CAAA;IACxB,CAAC;IAED,SAAS,CAAC,cAA6B,IAAG,CAAC;CAC5C"}