@jbrowse/plugin-dotplot-view 2.18.0 → 3.0.0

package/dist/DotplotView/components/ImportForm/ImportCustomTrack.js

@@ -1,194 +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 ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const util_1 = require("./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 ${radioOption} from filename (select radio button to clarify)`);
-    }
-}
-const ImportCustomTrack = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, setSessionTrackData, }) {
-    const [bed2Location, setBed2Location] = (0, react_1.useState)();
-    const [bed1Location, setBed1Location] = (0, react_1.useState)();
-    const [fileLocation, setFileLocation] = (0, react_1.useState)();
-    const [indexFileLocation, setIndexFileLocation] = (0, react_1.useState)();
-    const [value, setValue] = (0, react_1.useState)('');
-    const [error, setError] = (0, react_1.useState)();
-    const fileName = (0, util_1.getName)(fileLocation);
-    const radioOption = value || (fileName ? (0, util_1.extName)((0, util_1.stripGz)(fileName)) : '');
-    (0, react_1.useEffect)(() => {
-        try {
-            if (fileLocation) {
-                const fn = fileName ? (0, util_1.basename)(fileName) : 'MyTrack';
-                const trackId = `${fn}-${Date.now()}`;
-                setError(undefined);
-                setSessionTrackData({
-                    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,
-        setSessionTrackData,
-    ]);
-    return (react_1.default.createElement(material_1.Paper, { style: { padding: 12 } },
-        error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
-        react_1.default.createElement(material_1.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_1.default.createElement(material_1.RadioGroup, { value: radioOption, onChange: event => {
-                setValue(event.target.value);
-            } },
-            react_1.default.createElement(material_1.Grid, { container: true, justifyContent: "center" },
-                react_1.default.createElement(material_1.Grid, { item: true },
-                    react_1.default.createElement(material_1.FormControlLabel, { value: ".paf", control: react_1.default.createElement(material_1.Radio, null), label: ".paf" })),
-                react_1.default.createElement(material_1.Grid, { item: true },
-                    react_1.default.createElement(material_1.FormControlLabel, { value: ".out", control: react_1.default.createElement(material_1.Radio, null), label: ".out" })),
-                react_1.default.createElement(material_1.Grid, { item: true },
-                    react_1.default.createElement(material_1.FormControlLabel, { value: ".delta", control: react_1.default.createElement(material_1.Radio, null), label: ".delta" })),
-                react_1.default.createElement(material_1.Grid, { item: true },
-                    react_1.default.createElement(material_1.FormControlLabel, { value: ".chain", control: react_1.default.createElement(material_1.Radio, null), label: ".chain" })),
-                react_1.default.createElement(material_1.Grid, { item: true },
-                    react_1.default.createElement(material_1.FormControlLabel, { value: ".anchors", control: react_1.default.createElement(material_1.Radio, null), label: ".anchors" })),
-                react_1.default.createElement(material_1.Grid, { item: true },
-                    react_1.default.createElement(material_1.FormControlLabel, { value: ".anchors.simple", control: react_1.default.createElement(material_1.Radio, null), label: ".anchors.simple" })),
-                react_1.default.createElement(material_1.Grid, { item: true },
-                    react_1.default.createElement(material_1.FormControlLabel, { value: ".pif.gz", control: react_1.default.createElement(material_1.Radio, null), label: ".pif.gz" })))),
-        react_1.default.createElement(material_1.Grid, { container: true, justifyContent: "center" },
-            react_1.default.createElement(material_1.Grid, { item: true }, value === '.anchors' || value === '.anchors.simple' ? (react_1.default.createElement("div", null,
-                react_1.default.createElement("div", { style: { margin: 20 } },
-                    "Open the ",
-                    value,
-                    " and .bed files for both genome assemblies from the MCScan (Python version) pipeline",
-                    ' ',
-                    react_1.default.createElement("a", { href: "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)" }, "(more info)")),
-                react_1.default.createElement("div", { style: { display: 'flex' } },
-                    react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: ".anchors file", description: "", location: fileLocation, setLocation: loc => {
-                                setFileLocation(loc);
-                            } })),
-                    react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => {
-                                setBed1Location(loc);
-                            } })),
-                    react_1.default.createElement("div", null,
-                        react_1.default.createElement(ui_1.FileSelector, { name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
-                                setBed2Location(loc);
-                            } }))))) : value === '.pif.gz' ? (react_1.default.createElement("div", { style: { display: 'flex' } },
-                react_1.default.createElement("div", null,
-                    react_1.default.createElement(ui_1.FileSelector, { name: `${value} location`, description: "", location: fileLocation, setLocation: loc => {
-                            setFileLocation(loc);
-                        } })),
-                react_1.default.createElement("div", null,
-                    react_1.default.createElement(ui_1.FileSelector, { name: `${value} index location`, description: "", location: indexFileLocation, setLocation: loc => {
-                            setIndexFileLocation(loc);
-                        } })))) : (react_1.default.createElement(ui_1.FileSelector, { name: value ? `${value} location` : '', description: "", location: fileLocation, setLocation: loc => {
-                    setFileLocation(loc);
-                } }))))));
-});
-exports.default = ImportCustomTrack;

package/esm/DotplotView/components/ImportForm/ImportCustomTrack.d.ts

@@ -1,11 +0,0 @@
-import React from 'react';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { SnapshotIn } from 'mobx-state-tree';
-type Conf = SnapshotIn<AnyConfigurationModel>;
-declare const ImportCustomTrack: ({ assembly1, assembly2, setSessionTrackData, }: {
-    sessionTrackData: Conf;
-    assembly1: string;
-    assembly2: string;
-    setSessionTrackData: (arg: Conf) => void;
-}) => React.JSX.Element;
-export default ImportCustomTrack;

package/esm/DotplotView/components/ImportForm/ImportCustomTrack.js

@@ -1,169 +0,0 @@
-import React, { useEffect, useState } from 'react';
-import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
-import { FormControlLabel, Grid, Paper, Radio, RadioGroup, Typography, } from '@mui/material';
-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 ${radioOption} from filename (select radio button to clarify)`);
-    }
-}
-const ImportCustomTrack = observer(function ({ assembly1, assembly2, setSessionTrackData, }) {
-    const [bed2Location, setBed2Location] = useState();
-    const [bed1Location, setBed1Location] = useState();
-    const [fileLocation, setFileLocation] = useState();
-    const [indexFileLocation, setIndexFileLocation] = useState();
-    const [value, setValue] = useState('');
-    const [error, setError] = useState();
-    const fileName = getName(fileLocation);
-    const radioOption = value || (fileName ? extName(stripGz(fileName)) : '');
-    useEffect(() => {
-        try {
-            if (fileLocation) {
-                const fn = fileName ? basename(fileName) : 'MyTrack';
-                const trackId = `${fn}-${Date.now()}`;
-                setError(undefined);
-                setSessionTrackData({
-                    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,
-        setSessionTrackData,
-    ]);
-    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;