@jbrowse/plugin-linear-comparative-view 3.7.0 → 4.0.0

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

@@ -1,81 +0,0 @@
-"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 material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const getAdapter_1 = require("./getAdapter");
-const selectors_1 = require("./selectors");
-const util_1 = require("./util");
-const ImportSyntenyOpenCustomTrack = (0, mobx_react_1.observer)(function ({ model, assembly1, assembly2, selectedRow, }) {
-    const [swap, setSwap] = (0, react_1.useState)(false);
-    const [bed2Location, setBed2Location] = (0, react_1.useState)();
-    const [bed1Location, setBed1Location] = (0, react_1.useState)();
-    const [fileLocation, setFileLocation] = (0, react_1.useState)();
-    const [indexFileLocation, setIndexFileLocation] = (0, react_1.useState)();
-    const [value, setValue] = (0, react_1.useState)('');
-    const [error, setError] = (0, react_1.useState)();
-    const fileName = (0, util_1.getName)(fileLocation);
-    const radioOption = value || (fileName ? (0, util_1.extName)((0, util_1.stripGz)(fileName)) : '');
-    (0, react_1.useEffect)(() => {
-        try {
-            if (fileLocation) {
-                const fn = fileName ? (0, util_1.basename)(fileName) : 'MyTrack';
-                const trackId = `${fn}-${Date.now()}-sessionTrack`;
-                setError(undefined);
-                model.setImportFormSyntenyTrack(selectedRow, {
-                    type: 'userOpened',
-                    value: {
-                        trackId,
-                        name: fn,
-                        assemblyNames: [assembly2, assembly1],
-                        type: 'SyntenyTrack',
-                        adapter: (0, getAdapter_1.getAdapter)({
-                            radioOption,
-                            assembly1: swap ? assembly2 : assembly1,
-                            assembly2: swap ? assembly1 : assembly2,
-                            fileLocation,
-                            indexFileLocation,
-                            bed1Location,
-                            bed2Location,
-                        }),
-                    },
-                });
-            }
-        }
-        catch (e) {
-            console.error(e);
-            setError(e);
-        }
-    }, [
-        swap,
-        model,
-        selectedRow,
-        fileName,
-        assembly1,
-        assembly2,
-        bed1Location,
-        bed2Location,
-        fileLocation,
-        indexFileLocation,
-        radioOption,
-    ]);
-    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)(material_1.Typography, { style: { textAlign: 'center' }, children: "Add a .paf (minimap2), .delta (Mummer), .chain (UCSC liftover), .anchors or .anchors.simple (MCScan), or .pif.gz (jbrowse CLI make-pif) file to view. These file types can also be gzipped." }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { value: radioOption, onChange: event => {
-                    setValue(event.target.value);
-                }, children: (0, jsx_runtime_1.jsx)(material_1.Grid, { container: true, justifyContent: "center", children: [
-                        '.paf',
-                        '.delta',
-                        '.out',
-                        '.chain',
-                        '.anchors',
-                        '.anchors.simple',
-                        '.pif.gz',
-                    ].map(extension => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: extension, control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: extension }, extension))) }) }), (0, jsx_runtime_1.jsx)(material_1.Grid, { container: true, justifyContent: "center", children: radioOption === '.paf' ||
-                    radioOption === '.out' ||
-                    radioOption === '.delta' ||
-                    radioOption === '.chain' ? ((0, jsx_runtime_1.jsx)(selectors_1.StandardFormatSelector, { assembly1: assembly1, assembly2: assembly2, swap: swap, setSwap: setSwap, fileLocation: fileLocation, setFileLocation: setFileLocation, radioOption: radioOption })) : radioOption === '.pif.gz' ? ((0, jsx_runtime_1.jsx)(selectors_1.PifGzSelector, { assembly1: assembly1, assembly2: assembly2, swap: swap, setSwap: setSwap, fileLocation: fileLocation, setFileLocation: setFileLocation, indexFileLocation: indexFileLocation, setIndexFileLocation: setIndexFileLocation, radioOption: radioOption })) : value === '.anchors' || value === '.anchors.simple' ? ((0, jsx_runtime_1.jsx)(selectors_1.AnchorsSelector, { assembly1: assembly1, assembly2: assembly2, swap: swap, setSwap: setSwap, fileLocation: fileLocation, setFileLocation: setFileLocation, bed1Location: bed1Location, setBed1Location: setBed1Location, bed2Location: bed2Location, setBed2Location: setBed2Location, radioOption: value })) : ((0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
-                        setFileLocation(loc);
-                    } })) })] }));
-});
-exports.default = ImportSyntenyOpenCustomTrack;

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

@@ -1,8 +0,0 @@
-import type { LinearSyntenyViewModel } from '../../model';
-declare const ImportSyntenyTrackSelector: ({ model, selectedRow, assembly1, assembly2, }: {
-    model: LinearSyntenyViewModel;
-    selectedRow: number;
-    assembly1: string;
-    assembly2: string;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ImportSyntenyTrackSelector;

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

@@ -1,39 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const ImportSyntenyTrackSelector = (0, mobx_react_1.observer)(function ({ model, selectedRow, assembly1, assembly2, }) {
-    var _a;
-    const session = (0, util_1.getSession)(model);
-    const { importFormSyntenyTrackSelections } = 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 r = importFormSyntenyTrackSelections[selectedRow];
-    const value = (r === null || r === void 0 ? void 0 : r.type) === 'preConfigured' ? r.value : undefined;
-    (0, react_1.useEffect)(() => {
-        model.setImportFormSyntenyTrack(selectedRow, {
-            type: 'preConfigured',
-            value: resetTrack,
-        });
-    }, [assembly2, assembly1, resetTrack, selectedRow, model]);
-    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Select a track from the select box below, the track will be shown when you hit \"Launch\"." }), value && filteredTracks.map(r => r.trackId).includes(value) ? ((0, jsx_runtime_1.jsx)(material_1.Select, { value: value, onChange: event => {
-                    model.setImportFormSyntenyTrack(selectedRow, {
-                        type: 'preConfigured',
-                        value: event.target.value,
-                    });
-                }, children: filteredTracks.map(track => ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: track.trackId, children: (0, tracks_1.getTrackName)(track, session) }, track.trackId))) })) : ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: `No synteny tracks found for ${assembly1},${assembly2}` }))] }));
-});
-exports.default = ImportSyntenyTrackSelector;

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

@@ -1,7 +0,0 @@
-import type { LinearSyntenyViewModel } from '../../model';
-export default function ImportSyntenyTrackSelectorArea({ model, assembly1, assembly2, selectedRow, }: {
-    model: LinearSyntenyViewModel;
-    assembly1: string;
-    assembly2: string;
-    selectedRow: number;
-}): import("react/jsx-runtime").JSX.Element;

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

@@ -1,22 +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 = ImportSyntenyTrackSelectorArea;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const material_1 = require("@mui/material");
-const ImportSyntenyOpenCustomTrack_1 = __importDefault(require("./ImportSyntenyOpenCustomTrack"));
-const ImportSyntenyPreConfigured_1 = __importDefault(require("./ImportSyntenyPreConfigured"));
-function ImportSyntenyTrackSelectorArea({ model, assembly1, assembly2, selectedRow, }) {
-    const [choice, setChoice] = (0, react_1.useState)('tracklist');
-    (0, react_1.useEffect)(() => {
-        if (choice === 'none') {
-            model.setImportFormSyntenyTrack(selectedRow, { type: 'none' });
-        }
-    }, [choice, model, selectedRow]);
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.FormControl, { children: (0, jsx_runtime_1.jsxs)(material_1.RadioGroup, { row: true, value: choice, "aria-labelledby": "group-label", onChange: event => {
-                        setChoice(event.target.value);
-                    }, children: [(0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: "none", control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: "None" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: "tracklist", control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: "Existing track" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { value: "custom", control: (0, jsx_runtime_1.jsx)(material_1.Radio, {}), label: "New track" })] }) }), choice === 'custom' ? ((0, jsx_runtime_1.jsx)(ImportSyntenyOpenCustomTrack_1.default, { model: model, selectedRow: selectedRow, assembly2: assembly2, assembly1: assembly1 })) : null, choice === 'tracklist' ? ((0, jsx_runtime_1.jsx)(ImportSyntenyPreConfigured_1.default, { model: model, selectedRow: selectedRow, assembly1: assembly1, assembly2: assembly2 })) : null] }));
-}

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

@@ -1,11 +0,0 @@
-import type { LinearSyntenyViewModel } from '../../model';
-declare const LeftPanel: ({ model, selectedAssemblyNames, setSelectedAssemblyNames, selectedRow, setSelectedRow, defaultAssemblyName, onLaunch, }: {
-    model: LinearSyntenyViewModel;
-    selectedAssemblyNames: string[];
-    setSelectedAssemblyNames: (names: string[]) => void;
-    selectedRow: number;
-    setSelectedRow: (row: number) => void;
-    defaultAssemblyName: string;
-    onLaunch: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default LeftPanel;

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

@@ -1,58 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const ArrowForwardIos_1 = __importDefault(require("@mui/icons-material/ArrowForwardIos"));
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    mb: {
-        marginBottom: 10,
-    },
-    button: {
-        margin: theme.spacing(2),
-    },
-    rel: {
-        position: 'relative',
-    },
-    synbutton: {
-        position: 'absolute',
-        top: 30,
-    },
-    bg: {
-        background: theme.palette.divider,
-    },
-}));
-const AssemblyRows = (0, mobx_react_1.observer)(function ({ selectedRow, selectedAssemblyNames, setSelectedRow, setSelectedAssemblyNames, model, }) {
-    const { classes, cx } = useStyles();
-    const session = (0, util_1.getSession)(model);
-    return selectedAssemblyNames.map((assemblyName, idx) => ((0, jsx_runtime_1.jsxs)("div", { className: classes.rel, children: [(0, jsx_runtime_1.jsxs)("span", { children: ["Row ", idx + 1, ": "] }), (0, jsx_runtime_1.jsx)(material_1.IconButton, { disabled: selectedAssemblyNames.length <= 2, onClick: () => {
-                    model.importFormRemoveRow(idx);
-                    setSelectedAssemblyNames(selectedAssemblyNames
-                        .map((asm, idx2) => (idx2 === idx ? undefined : asm))
-                        .filter(util_1.notEmpty));
-                    if (selectedRow >= selectedAssemblyNames.length - 2) {
-                        setSelectedRow(0);
-                    }
-                }, children: (0, jsx_runtime_1.jsx)(Close_1.default, {}) }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "", selected: assemblyName, onChange: newAssembly => {
-                    setSelectedAssemblyNames(selectedAssemblyNames.map((asm, idx2) => idx2 === idx ? newAssembly : asm));
-                }, session: session }), idx !== selectedAssemblyNames.length - 1 ? ((0, jsx_runtime_1.jsx)(material_1.IconButton, { "data-testid": "synbutton", className: cx(classes.synbutton, idx === selectedRow ? classes.bg : undefined), onClick: () => {
-                    setSelectedRow(idx);
-                }, children: (0, jsx_runtime_1.jsx)(ArrowForwardIos_1.default, {}) })) : null] }, `${assemblyName}-${idx}`)));
-});
-const LeftPanel = (0, mobx_react_1.observer)(function ({ model, selectedAssemblyNames, setSelectedAssemblyNames, selectedRow, setSelectedRow, defaultAssemblyName, onLaunch, }) {
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", { className: classes.mb, children: "Select assemblies for linear synteny view" }), (0, jsx_runtime_1.jsx)(AssemblyRows, { model: model, selectedAssemblyNames: selectedAssemblyNames, setSelectedAssemblyNames: setSelectedAssemblyNames, selectedRow: selectedRow, setSelectedRow: setSelectedRow }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { className: classes.button, variant: "contained", color: "secondary", onClick: () => {
-                            setSelectedAssemblyNames([
-                                ...selectedAssemblyNames,
-                                defaultAssemblyName,
-                            ]);
-                        }, children: "Add row" }), (0, jsx_runtime_1.jsx)(material_1.Button, { className: classes.button, onClick: onLaunch, variant: "contained", color: "primary", children: "Launch" })] })] }));
-});
-exports.default = LeftPanel;

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

@@ -1,5 +0,0 @@
-import type { LinearSyntenyViewModel } from '../../model';
-declare const LinearSyntenyViewImportForm: ({ model, }: {
-    model: LinearSyntenyViewModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default LinearSyntenyViewImportForm;

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

@@ -1,60 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-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 mui_1 = require("tss-react/mui");
-const ImportSyntenyTrackSelectorArea_1 = __importDefault(require("./ImportSyntenyTrackSelectorArea"));
-const LeftPanel_1 = __importDefault(require("./LeftPanel"));
-const doSubmit_1 = require("./doSubmit");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    importFormContainer: {
-        padding: theme.spacing(4),
-    },
-    flex: {
-        display: 'flex',
-        gap: 90,
-    },
-    rightPanel: {
-        flexGrow: 11,
-    },
-    leftPanel: {
-        flexGrow: 4,
-        flexShrink: 0,
-    },
-}));
-const LinearSyntenyViewImportForm = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    const session = (0, util_1.getSession)(model);
-    const { assemblyNames } = session;
-    const defaultAssemblyName = assemblyNames[0] || '';
-    const [selectedRow, setSelectedRow] = (0, react_1.useState)(0);
-    const [selectedAssemblyNames, setSelectedAssemblyNames] = (0, react_1.useState)([
-        defaultAssemblyName,
-        defaultAssemblyName,
-    ]);
-    const [error, setError] = (0, react_1.useState)();
-    const handleLaunch = async () => {
-        try {
-            setError(undefined);
-            await (0, doSubmit_1.doSubmit)({
-                selectedAssemblyNames,
-                model,
-            });
-        }
-        catch (e) {
-            console.error(e);
-            setError(e);
-        }
-    };
-    return ((0, jsx_runtime_1.jsxs)(material_1.Container, { className: classes.importFormContainer, children: [error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsxs)("div", { className: classes.flex, children: [(0, jsx_runtime_1.jsx)("div", { className: classes.leftPanel, children: (0, jsx_runtime_1.jsx)(LeftPanel_1.default, { model: model, selectedAssemblyNames: selectedAssemblyNames, setSelectedAssemblyNames: setSelectedAssemblyNames, selectedRow: selectedRow, setSelectedRow: setSelectedRow, defaultAssemblyName: defaultAssemblyName, onLaunch: () => {
-                                handleLaunch();
-                            } }) }), (0, jsx_runtime_1.jsxs)("div", { className: classes.rightPanel, children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Synteny dataset to display between row ", selectedRow + 1, " and", ' ', selectedRow + 2] }), (0, jsx_runtime_1.jsx)(ImportSyntenyTrackSelectorArea_1.default, { model: model, selectedRow: selectedRow, assembly1: selectedAssemblyNames[selectedRow], assembly2: selectedAssemblyNames[selectedRow + 1] })] })] })] }));
-});
-exports.default = LinearSyntenyViewImportForm;

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

@@ -1,5 +0,0 @@
-import type { LinearSyntenyViewModel } from '../../model';
-export declare function doSubmit({ selectedAssemblyNames, model, }: {
-    selectedAssemblyNames: string[];
-    model: LinearSyntenyViewModel;
-}): Promise<void>;

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

@@ -1,43 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.doSubmit = doSubmit;
-const util_1 = require("@jbrowse/core/util");
-const mobx_1 = require("mobx");
-async function doSubmit({ selectedAssemblyNames, model, }) {
-    const session = (0, util_1.getSession)(model);
-    const { assemblyManager } = session;
-    const { importFormSyntenyTrackSelections } = model;
-    model.setViews(await Promise.all(selectedAssemblyNames.map(async (assemblyName) => {
-        const asm = await assemblyManager.waitForAssembly(assemblyName);
-        if (!asm) {
-            throw new Error(`Assembly "${assemblyName}" failed to load`);
-        }
-        return {
-            type: 'LinearGenomeView',
-            bpPerPx: 1,
-            offsetPx: 0,
-            hideHeader: true,
-            displayedRegions: asm.regions,
-        };
-    })));
-    for (const view of model.views) {
-        view.setWidth(model.width);
-        view.showAllRegions();
-    }
-    if (!(0, util_1.isSessionWithAddTracks)(session)) {
-        session.notify("Can't add tracks", 'warning');
-    }
-    else {
-        (0, mobx_1.toJS)(importFormSyntenyTrackSelections).map((f, idx) => {
-            var _a;
-            if (f.type === 'userOpened') {
-                session.addTrackConf(f.value);
-                model.toggleTrack((_a = f.value) === null || _a === void 0 ? void 0 : _a.trackId, idx);
-            }
-            else if (f.type === 'preConfigured') {
-                model.showTrack(f.value, idx);
-            }
-        });
-    }
-    model.clearImportFormSyntenyTracks();
-}

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

@@ -1,117 +0,0 @@
-import type { FileLocation } from '@jbrowse/core/util';
-export declare function getAdapter({ radioOption, assembly1, assembly2, fileLocation, indexFileLocation, bed1Location, bed2Location, }: {
-    radioOption: string;
-    assembly1: string;
-    assembly2: string;
-    fileLocation?: FileLocation;
-    indexFileLocation?: FileLocation;
-    bed1Location?: FileLocation;
-    bed2Location?: FileLocation;
-}): {
-    type: string;
-    pafLocation: FileLocation | undefined;
-    queryAssembly: string;
-    targetAssembly: string;
-    outLocation?: undefined;
-    deltaLocation?: undefined;
-    chainLocation?: undefined;
-    mcscanAnchorsLocation?: undefined;
-    bed1Location?: undefined;
-    bed2Location?: undefined;
-    assemblyNames?: undefined;
-    mcscanSimpleAnchorsLocation?: undefined;
-    pifGzLocation?: undefined;
-    index?: undefined;
-} | {
-    type: string;
-    outLocation: FileLocation | undefined;
-    queryAssembly: string;
-    targetAssembly: string;
-    pafLocation?: undefined;
-    deltaLocation?: undefined;
-    chainLocation?: undefined;
-    mcscanAnchorsLocation?: undefined;
-    bed1Location?: undefined;
-    bed2Location?: undefined;
-    assemblyNames?: undefined;
-    mcscanSimpleAnchorsLocation?: undefined;
-    pifGzLocation?: undefined;
-    index?: undefined;
-} | {
-    type: string;
-    deltaLocation: FileLocation | undefined;
-    queryAssembly: string;
-    targetAssembly: string;
-    pafLocation?: undefined;
-    outLocation?: undefined;
-    chainLocation?: undefined;
-    mcscanAnchorsLocation?: undefined;
-    bed1Location?: undefined;
-    bed2Location?: undefined;
-    assemblyNames?: undefined;
-    mcscanSimpleAnchorsLocation?: undefined;
-    pifGzLocation?: undefined;
-    index?: undefined;
-} | {
-    type: string;
-    chainLocation: FileLocation | undefined;
-    queryAssembly: string;
-    targetAssembly: string;
-    pafLocation?: undefined;
-    outLocation?: undefined;
-    deltaLocation?: undefined;
-    mcscanAnchorsLocation?: undefined;
-    bed1Location?: undefined;
-    bed2Location?: undefined;
-    assemblyNames?: undefined;
-    mcscanSimpleAnchorsLocation?: undefined;
-    pifGzLocation?: undefined;
-    index?: undefined;
-} | {
-    type: string;
-    mcscanAnchorsLocation: FileLocation | undefined;
-    bed1Location: FileLocation | undefined;
-    bed2Location: FileLocation | undefined;
-    assemblyNames: string[];
-    pafLocation?: undefined;
-    queryAssembly?: undefined;
-    targetAssembly?: undefined;
-    outLocation?: undefined;
-    deltaLocation?: undefined;
-    chainLocation?: undefined;
-    mcscanSimpleAnchorsLocation?: undefined;
-    pifGzLocation?: undefined;
-    index?: undefined;
-} | {
-    type: string;
-    mcscanSimpleAnchorsLocation: FileLocation | undefined;
-    bed1Location: FileLocation | undefined;
-    bed2Location: FileLocation | undefined;
-    assemblyNames: string[];
-    pafLocation?: undefined;
-    queryAssembly?: undefined;
-    targetAssembly?: undefined;
-    outLocation?: undefined;
-    deltaLocation?: undefined;
-    chainLocation?: undefined;
-    mcscanAnchorsLocation?: undefined;
-    pifGzLocation?: undefined;
-    index?: undefined;
-} | {
-    type: string;
-    pifGzLocation: FileLocation | undefined;
-    index: {
-        location: FileLocation | undefined;
-    };
-    assemblyNames: string[];
-    pafLocation?: undefined;
-    queryAssembly?: undefined;
-    targetAssembly?: undefined;
-    outLocation?: undefined;
-    deltaLocation?: undefined;
-    chainLocation?: undefined;
-    mcscanAnchorsLocation?: undefined;
-    bed1Location?: undefined;
-    bed2Location?: undefined;
-    mcscanSimpleAnchorsLocation?: undefined;
-};

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

@@ -1,68 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getAdapter = getAdapter;
-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)`);
-    }
-}

package/dist/LinearSyntenyView/components/ImportForm/selectors/AnchorsSelector.d.ts

@@ -1,3 +0,0 @@
-import type { SelectorProps } from './SelectorTypes';
-declare const AnchorsSelector: ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, bed1Location, setBed1Location, bed2Location, setBed2Location, radioOption, }: SelectorProps) => import("react/jsx-runtime").JSX.Element;
-export default AnchorsSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/AnchorsSelector.js

@@ -1,13 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const mobx_react_1 = require("mobx-react");
-const SwapAssemblies_1 = __importDefault(require("./SwapAssemblies"));
-const AnchorsSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, bed1Location = undefined, setBed1Location = () => { }, bed2Location = undefined, setBed2Location = () => { }, radioOption, }) {
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: { margin: 20 }, children: ["Open the ", radioOption, " and .bed files for both genome assemblies from the MCScan (Python version) pipeline", ' ', (0, jsx_runtime_1.jsx)("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)", children: "(more info)" })] }), (0, jsx_runtime_1.jsxs)("div", { style: { maxWidth: 400, margin: '0 auto' }, children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: radioOption, location: fileLocation, setLocation: setFileLocation }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: setBed1Location }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: setBed2Location }), (0, jsx_runtime_1.jsx)(SwapAssemblies_1.default, { swap: swap, radioOption: radioOption, assembly1: assembly1, assembly2: assembly2, setSwap: setSwap, text1: "bed 1 assembly", text2: "bed 2 assembly" })] })] }));
-});
-exports.default = AnchorsSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/PifGzSelector.d.ts

@@ -1,3 +0,0 @@
-import type { SelectorProps } from './SelectorTypes';
-declare const PifGzSelector: ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, indexFileLocation, setIndexFileLocation, radioOption, }: SelectorProps) => import("react/jsx-runtime").JSX.Element;
-export default PifGzSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/PifGzSelector.js

@@ -1,13 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const mobx_react_1 = require("mobx-react");
-const SwapAssemblies_1 = __importDefault(require("./SwapAssemblies"));
-const PifGzSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, indexFileLocation = undefined, setIndexFileLocation = () => { }, radioOption, }) {
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: { margin: 20 }, children: ["Open the ", radioOption, " and .pif.gz and index file (.pif.gz.tbi or .pif.gz.csi) files for created by `jbrowse make-pif`"] }), (0, jsx_runtime_1.jsxs)("div", { style: { maxWidth: 400, margin: '0 auto' }, children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${radioOption} location`, inline: true, description: "", location: fileLocation, setLocation: setFileLocation }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${radioOption} index location`, inline: true, description: "", location: indexFileLocation, setLocation: setIndexFileLocation }), (0, jsx_runtime_1.jsx)(SwapAssemblies_1.default, { swap: swap, radioOption: radioOption, assembly1: assembly1, assembly2: assembly2, setSwap: setSwap, text1: "query assembly", text2: "target assembly" })] })] }));
-});
-exports.default = PifGzSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/SelectorTypes.d.ts

@@ -1,19 +0,0 @@
-import type { FileLocation } from '@jbrowse/core/util/types';
-export interface SelectorProps {
-    assembly1: string;
-    assembly2: string;
-    swap: boolean;
-    setSwap?: (swap: boolean) => void;
-    fileLocation: FileLocation | undefined;
-    setFileLocation: (location: FileLocation | undefined) => void;
-    indexFileLocation?: FileLocation | undefined;
-    setIndexFileLocation?: (location: FileLocation | undefined) => void;
-    bed1Location?: FileLocation | undefined;
-    setBed1Location?: (location: FileLocation | undefined) => void;
-    bed2Location?: FileLocation | undefined;
-    setBed2Location?: (location: FileLocation | undefined) => void;
-    radioOption: string;
-}
-export type SetLocationFunction = (location: FileLocation | undefined) => void;
-export type HelpStrings = Record<string, string>;
-export declare const helpStrings: HelpStrings;

package/dist/LinearSyntenyView/components/ImportForm/selectors/SelectorTypes.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.helpStrings = void 0;
-exports.helpStrings = {
-    '.paf': 'minimap2 target.fa query.fa',
-    '.pif.gz': 'minimap2 target.fa query.fa',
-    '.out': 'mashmap target.fa query.fa',
-    '.delta': 'mummer target.fa query.fa',
-    '.chain': 'e.g. queryToTarget.chain',
-};

package/dist/LinearSyntenyView/components/ImportForm/selectors/StandardFormatSelector.d.ts

@@ -1,3 +0,0 @@
-import type { SelectorProps } from './SelectorTypes';
-declare const StandardFormatSelector: ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, radioOption, }: SelectorProps) => import("react/jsx-runtime").JSX.Element;
-export default StandardFormatSelector;

package/dist/LinearSyntenyView/components/ImportForm/selectors/StandardFormatSelector.js

@@ -1,20 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const Help_1 = __importDefault(require("@mui/icons-material/Help"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const SelectorTypes_1 = require("./SelectorTypes");
-const SwapAssemblies_1 = __importDefault(require("./SwapAssemblies"));
-const StandardFormatSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, radioOption, }) {
-    return ((0, jsx_runtime_1.jsxs)("div", { style: {
-            display: 'flex',
-            flexDirection: 'column',
-            gap: 10,
-        }, children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${radioOption} location`, inline: true, description: "", location: fileLocation, setLocation: setFileLocation }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { children: ["Verify or click swap", (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: (0, jsx_runtime_1.jsx)("code", { children: SelectorTypes_1.helpStrings[radioOption] }), children: (0, jsx_runtime_1.jsx)(Help_1.default, {}) })] }), (0, jsx_runtime_1.jsx)(SwapAssemblies_1.default, { swap: swap, radioOption: radioOption, assembly1: assembly1, assembly2: assembly2, setSwap: setSwap, text1: "query assembly", text2: "target assembly" })] })] }));
-});
-exports.default = StandardFormatSelector;