@jbrowse/plugin-linear-comparative-view 2.17.0 → 3.0.0

package/dist/LinearSyntenyView/components/ImportForm/Spacer.js

@@ -1,10 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = Spacer;
-const react_1 = __importDefault(require("react"));
-function Spacer() {
-    return react_1.default.createElement("div", { style: { flexGrow: 1 } });
-}

package/dist/LinearSyntenyView/components/ImportForm/TrackSelector.d.ts

@@ -1,10 +0,0 @@
-import React from 'react';
-import { LinearSyntenyViewModel } from '../../model';
-declare const ImportSyntenyTrackSelector: ({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, }: {
-    model: LinearSyntenyViewModel;
-    assembly1: string;
-    assembly2: string;
-    preConfiguredSyntenyTrack: string | undefined;
-    setPreConfiguredSyntenyTrack: (arg: string) => void;
-}) => React.JSX.Element;
-export default ImportSyntenyTrackSelector;

package/dist/LinearSyntenyView/components/ImportForm/TrackSelector.js

@@ -1,59 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const ui_1 = require("@jbrowse/core/ui");
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_react_1 = require("mobx-react");
-const ImportSyntenyTrackSelector = (0, mobx_react_1.observer)(function ({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, }) {
-    var _a;
-    const session = (0, util_1.getSession)(model);
-    const { tracks = [], sessionTracks = [] } = session;
-    const allTracks = [...tracks, ...sessionTracks];
-    const filteredTracks = allTracks.filter(track => {
-        const assemblyNames = (0, configuration_1.readConfObject)(track, 'assemblyNames');
-        return (assemblyNames.includes(assembly1) &&
-            assemblyNames.includes(assembly2) &&
-            track.type.includes('Synteny'));
-    });
-    const resetTrack = ((_a = filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.trackId) || '';
-    const [value, setValue] = (0, react_1.useState)(resetTrack);
-    (0, react_1.useEffect)(() => {
-        // sets track data in a useEffect because the initial load is needed as
-        // well as onChange's to the select box
-        if (value !== preConfiguredSyntenyTrack) {
-            setPreConfiguredSyntenyTrack(value);
-        }
-    }, [value, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack]);
-    return (react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
-        react_1.default.createElement(material_1.Typography, null, "Select a track from the select box below, the track will be shown when you hit \"Launch\"."),
-        filteredTracks.length ? (react_1.default.createElement(material_1.Select, { value: value, onChange: event => {
-                setValue(event.target.value);
-            } }, filteredTracks.map(track => (react_1.default.createElement(material_1.MenuItem, { key: track.trackId, value: track.trackId }, (0, tracks_1.getTrackName)(track, session)))))) : (react_1.default.createElement(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
-});
-exports.default = ImportSyntenyTrackSelector;

package/dist/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.d.ts

@@ -1,14 +0,0 @@
-import React from 'react';
-import { SnapshotIn } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { LinearSyntenyViewModel } from '../../model';
-type Conf = SnapshotIn<AnyConfigurationModel>;
-export default function TrackSelector({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack, }: {
-    model: LinearSyntenyViewModel;
-    assembly1: string;
-    assembly2: string;
-    preConfiguredSyntenyTrack: string | undefined;
-    setUserOpenedSyntenyTrack: (arg: Conf) => void;
-    setPreConfiguredSyntenyTrack: (arg?: string) => void;
-}): React.JSX.Element;
-export {};

package/dist/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.js

@@ -1,52 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = TrackSelector;
-const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const AddCustomTrack_1 = __importDefault(require("./AddCustomTrack"));
-const TrackSelector_1 = __importDefault(require("./TrackSelector"));
-function TrackSelector({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack, }) {
-    const [choice, setChoice] = (0, react_1.useState)('tracklist');
-    (0, react_1.useEffect)(() => {
-        if (choice === 'none') {
-            setPreConfiguredSyntenyTrack(undefined);
-            setUserOpenedSyntenyTrack(undefined);
-        }
-    }, [choice, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack]);
-    return (react_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.FormControl, null,
-            react_1.default.createElement(material_1.RadioGroup, { row: true, value: choice, onChange: event => {
-                    setChoice(event.target.value);
-                }, "aria-labelledby": "group-label" },
-                react_1.default.createElement(material_1.FormControlLabel, { value: "none", control: react_1.default.createElement(material_1.Radio, null), label: "None" }),
-                react_1.default.createElement(material_1.FormControlLabel, { value: "tracklist", control: react_1.default.createElement(material_1.Radio, null), label: "Existing track" }),
-                react_1.default.createElement(material_1.FormControlLabel, { value: "custom", control: react_1.default.createElement(material_1.Radio, null), label: "New track" }))),
-        choice === 'custom' ? (react_1.default.createElement(AddCustomTrack_1.default, { setUserOpenedSyntenyTrack: setUserOpenedSyntenyTrack, assembly2: assembly2, assembly1: assembly1 })) : null,
-        choice === 'tracklist' ? (react_1.default.createElement(TrackSelector_1.default, { key: `${assembly1}-${assembly2}`, model: model, assembly1: assembly1, assembly2: assembly2, preConfiguredSyntenyTrack: preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack: setPreConfiguredSyntenyTrack })) : null));
-}

package/esm/LinearSyntenyView/components/ImportForm/AddCustomTrack.d.ts

@@ -1,10 +0,0 @@
-import React from 'react';
-import { SnapshotIn } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-type Conf = SnapshotIn<AnyConfigurationModel>;
-declare const ImportCustomTrack: ({ assembly1, assembly2, setUserOpenedSyntenyTrack, }: {
-    assembly1: string;
-    assembly2: string;
-    setUserOpenedSyntenyTrack: (arg: Conf) => void;
-}) => React.JSX.Element;
-export default ImportCustomTrack;

package/esm/LinearSyntenyView/components/ImportForm/AddCustomTrack.js

@@ -1,169 +0,0 @@
-import React, { useState, useEffect } from 'react';
-import { FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
-import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
-import { observer } from 'mobx-react';
-import { basename, extName, getName, stripGz } from './util';
-function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, bed1Location, bed2Location, }) {
-    if (radioOption === '.paf') {
-        return {
-            type: 'PAFAdapter',
-            pafLocation: fileLocation,
-            queryAssembly: assembly1,
-            targetAssembly: assembly2,
-        };
-    }
-    else if (radioOption === '.out') {
-        return {
-            type: 'MashMapAdapter',
-            outLocation: fileLocation,
-            queryAssembly: assembly1,
-            targetAssembly: assembly2,
-        };
-    }
-    else if (radioOption === '.delta') {
-        return {
-            type: 'DeltaAdapter',
-            deltaLocation: fileLocation,
-            queryAssembly: assembly1,
-            targetAssembly: assembly2,
-        };
-    }
-    else if (radioOption === '.chain') {
-        return {
-            type: 'ChainAdapter',
-            chainLocation: fileLocation,
-            queryAssembly: assembly1,
-            targetAssembly: assembly2,
-        };
-    }
-    else if (radioOption === '.anchors') {
-        return {
-            type: 'MCScanAnchorsAdapter',
-            mcscanAnchorsLocation: fileLocation,
-            bed1Location,
-            bed2Location,
-            assemblyNames: [assembly1, assembly2],
-        };
-    }
-    else if (radioOption === '.anchors.simple') {
-        return {
-            type: 'MCScanSimpleAnchorsAdapter',
-            mcscanSimpleAnchorsLocation: fileLocation,
-            bed1Location,
-            bed2Location,
-            assemblyNames: [assembly1, assembly2],
-        };
-    }
-    else if (radioOption === '.pif.gz') {
-        return {
-            type: 'PairwiseIndexedPAFAdapter',
-            pifGzLocation: fileLocation,
-            index: { location: indexFileLocation },
-            assemblyNames: [assembly1, assembly2],
-        };
-    }
-    else {
-        throw new Error(`Unknown to detect type ${radioOption} from filename (select radio button to clarify)`);
-    }
-}
-const ImportCustomTrack = observer(function ({ assembly1, assembly2, setUserOpenedSyntenyTrack, }) {
-    const [bed2Location, setBed2Location] = useState();
-    const [bed1Location, setBed1Location] = useState();
-    const [fileLocation, setFileLocation] = useState();
-    const [indexFileLocation, setIndexFileLocation] = useState();
-    const [value, setValue] = useState('');
-    const [error, setError] = useState();
-    const fileName = getName(fileLocation);
-    const radioOption = value || (fileName ? extName(stripGz(fileName)) : '');
-    useEffect(() => {
-        try {
-            if (fileLocation) {
-                const fn = fileName ? basename(fileName) : 'MyTrack';
-                const trackId = `${fn}-${Date.now()}`;
-                setError(undefined);
-                setUserOpenedSyntenyTrack({
-                    trackId,
-                    name: fn,
-                    assemblyNames: [assembly2, assembly1],
-                    type: 'SyntenyTrack',
-                    adapter: getAdapter({
-                        radioOption,
-                        assembly1,
-                        assembly2,
-                        fileLocation,
-                        indexFileLocation,
-                        bed1Location,
-                        bed2Location,
-                    }),
-                });
-            }
-        }
-        catch (e) {
-            console.error(e);
-            setError(e);
-        }
-    }, [
-        fileName,
-        assembly1,
-        assembly2,
-        bed1Location,
-        bed2Location,
-        fileLocation,
-        indexFileLocation,
-        radioOption,
-        setUserOpenedSyntenyTrack,
-    ]);
-    return (React.createElement(Paper, { style: { padding: 12 } },
-        error ? React.createElement(ErrorMessage, { error: error }) : null,
-        React.createElement(Typography, { style: { textAlign: 'center' } }, "Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file to view. These file types can also be gzipped. The first assembly should be the query sequence (e.g. left column of the PAF) and the second assembly should be the target sequence (e.g. right column of the PAF)"),
-        React.createElement(RadioGroup, { value: radioOption, onChange: event => {
-                setValue(event.target.value);
-            } },
-            React.createElement(Grid, { container: true, justifyContent: "center" },
-                React.createElement(Grid, { item: true },
-                    React.createElement(FormControlLabel, { value: ".paf", control: React.createElement(Radio, null), label: ".paf" })),
-                React.createElement(Grid, { item: true },
-                    React.createElement(FormControlLabel, { value: ".out", control: React.createElement(Radio, null), label: ".out" })),
-                React.createElement(Grid, { item: true },
-                    React.createElement(FormControlLabel, { value: ".delta", control: React.createElement(Radio, null), label: ".delta" })),
-                React.createElement(Grid, { item: true },
-                    React.createElement(FormControlLabel, { value: ".chain", control: React.createElement(Radio, null), label: ".chain" })),
-                React.createElement(Grid, { item: true },
-                    React.createElement(FormControlLabel, { value: ".anchors", control: React.createElement(Radio, null), label: ".anchors" })),
-                React.createElement(Grid, { item: true },
-                    React.createElement(FormControlLabel, { value: ".anchors.simple", control: React.createElement(Radio, null), label: ".anchors.simple" })),
-                React.createElement(Grid, { item: true },
-                    React.createElement(FormControlLabel, { value: ".pif.gz", control: React.createElement(Radio, null), label: ".pif.gz" })))),
-        React.createElement(Grid, { container: true, justifyContent: "center" },
-            React.createElement(Grid, { item: true }, value === '.anchors' || value === '.anchors.simple' ? (React.createElement("div", null,
-                React.createElement("div", { style: { margin: 20 } },
-                    "Open the ",
-                    value,
-                    " and .bed files for both genome assemblies from the MCScan (Python version) pipeline",
-                    ' ',
-                    React.createElement("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)" }, "(more info)")),
-                React.createElement("div", { style: { display: 'flex' } },
-                    React.createElement("div", null,
-                        React.createElement(FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => {
-                                setFileLocation(loc);
-                            } })),
-                    React.createElement("div", null,
-                        React.createElement(FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => {
-                                setBed1Location(loc);
-                            } })),
-                    React.createElement("div", null,
-                        React.createElement(FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
-                                setBed2Location(loc);
-                            } }))))) : value === '.pif.gz' ? (React.createElement("div", { style: { display: 'flex' } },
-                React.createElement("div", null,
-                    React.createElement(FileSelector, { name: `${value} location`, description: "", location: fileLocation, setLocation: loc => {
-                            setFileLocation(loc);
-                        } })),
-                React.createElement("div", null,
-                    React.createElement(FileSelector, { name: `${value} index location`, description: "", location: indexFileLocation, setLocation: loc => {
-                            setIndexFileLocation(loc);
-                        } })))) : (React.createElement(FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
-                    setFileLocation(loc);
-                } }))))));
-});
-export default ImportCustomTrack;

package/esm/LinearSyntenyView/components/ImportForm/Spacer.d.ts

@@ -1,2 +0,0 @@
-import React from 'react';
-export default function Spacer(): React.JSX.Element;

package/esm/LinearSyntenyView/components/ImportForm/Spacer.js

@@ -1,4 +0,0 @@
-import React from 'react';
-export default function Spacer() {
-    return React.createElement("div", { style: { flexGrow: 1 } });
-}

package/esm/LinearSyntenyView/components/ImportForm/TrackSelector.d.ts

@@ -1,10 +0,0 @@
-import React from 'react';
-import { LinearSyntenyViewModel } from '../../model';
-declare const ImportSyntenyTrackSelector: ({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, }: {
-    model: LinearSyntenyViewModel;
-    assembly1: string;
-    assembly2: string;
-    preConfiguredSyntenyTrack: string | undefined;
-    setPreConfiguredSyntenyTrack: (arg: string) => void;
-}) => React.JSX.Element;
-export default ImportSyntenyTrackSelector;

package/esm/LinearSyntenyView/components/ImportForm/TrackSelector.js

@@ -1,34 +0,0 @@
-import React, { useState, useEffect } from 'react';
-import { Select, MenuItem, Paper, Typography } from '@mui/material';
-import { getSession } from '@jbrowse/core/util';
-import { getTrackName } from '@jbrowse/core/util/tracks';
-import { ErrorMessage } from '@jbrowse/core/ui';
-import { readConfObject, } from '@jbrowse/core/configuration';
-import { observer } from 'mobx-react';
-const ImportSyntenyTrackSelector = observer(function ({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, }) {
-    var _a;
-    const session = getSession(model);
-    const { tracks = [], sessionTracks = [] } = session;
-    const allTracks = [...tracks, ...sessionTracks];
-    const filteredTracks = allTracks.filter(track => {
-        const assemblyNames = readConfObject(track, 'assemblyNames');
-        return (assemblyNames.includes(assembly1) &&
-            assemblyNames.includes(assembly2) &&
-            track.type.includes('Synteny'));
-    });
-    const resetTrack = ((_a = filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.trackId) || '';
-    const [value, setValue] = useState(resetTrack);
-    useEffect(() => {
-        // sets track data in a useEffect because the initial load is needed as
-        // well as onChange's to the select box
-        if (value !== preConfiguredSyntenyTrack) {
-            setPreConfiguredSyntenyTrack(value);
-        }
-    }, [value, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack]);
-    return (React.createElement(Paper, { style: { padding: 12 } },
-        React.createElement(Typography, null, "Select a track from the select box below, the track will be shown when you hit \"Launch\"."),
-        filteredTracks.length ? (React.createElement(Select, { value: value, onChange: event => {
-                setValue(event.target.value);
-            } }, filteredTracks.map(track => (React.createElement(MenuItem, { key: track.trackId, value: track.trackId }, getTrackName(track, session)))))) : (React.createElement(ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))));
-});
-export default ImportSyntenyTrackSelector;

package/esm/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.d.ts

@@ -1,14 +0,0 @@
-import React from 'react';
-import { SnapshotIn } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { LinearSyntenyViewModel } from '../../model';
-type Conf = SnapshotIn<AnyConfigurationModel>;
-export default function TrackSelector({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack, }: {
-    model: LinearSyntenyViewModel;
-    assembly1: string;
-    assembly2: string;
-    preConfiguredSyntenyTrack: string | undefined;
-    setUserOpenedSyntenyTrack: (arg: Conf) => void;
-    setPreConfiguredSyntenyTrack: (arg?: string) => void;
-}): React.JSX.Element;
-export {};

package/esm/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.js

@@ -1,23 +0,0 @@
-import React, { useState, useEffect } from 'react';
-import { FormControl, FormControlLabel, Radio, RadioGroup } from '@mui/material';
-import ImportCustomTrack from './AddCustomTrack';
-import ImportSyntenyTrackSelector from './TrackSelector';
-export default function TrackSelector({ model, assembly1, assembly2, preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack, }) {
-    const [choice, setChoice] = useState('tracklist');
-    useEffect(() => {
-        if (choice === 'none') {
-            setPreConfiguredSyntenyTrack(undefined);
-            setUserOpenedSyntenyTrack(undefined);
-        }
-    }, [choice, setPreConfiguredSyntenyTrack, setUserOpenedSyntenyTrack]);
-    return (React.createElement("div", null,
-        React.createElement(FormControl, null,
-            React.createElement(RadioGroup, { row: true, value: choice, onChange: event => {
-                    setChoice(event.target.value);
-                }, "aria-labelledby": "group-label" },
-                React.createElement(FormControlLabel, { value: "none", control: React.createElement(Radio, null), label: "None" }),
-                React.createElement(FormControlLabel, { value: "tracklist", control: React.createElement(Radio, null), label: "Existing track" }),
-                React.createElement(FormControlLabel, { value: "custom", control: React.createElement(Radio, null), label: "New track" }))),
-        choice === 'custom' ? (React.createElement(ImportCustomTrack, { setUserOpenedSyntenyTrack: setUserOpenedSyntenyTrack, assembly2: assembly2, assembly1: assembly1 })) : null,
-        choice === 'tracklist' ? (React.createElement(ImportSyntenyTrackSelector, { key: `${assembly1}-${assembly2}`, model: model, assembly1: assembly1, assembly2: assembly2, preConfiguredSyntenyTrack: preConfiguredSyntenyTrack, setPreConfiguredSyntenyTrack: setPreConfiguredSyntenyTrack })) : null));
-}