@jbrowse/plugin-dotplot-view 3.6.5 → 4.0.0

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

@@ -1,23 +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 material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const ImportSyntenyOpenCustomTrack_1 = __importDefault(require("./ImportSyntenyOpenCustomTrack"));
-const ImportSyntenyTrackSelector_1 = __importDefault(require("./ImportSyntenyTrackSelector"));
-const TrackSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, model, }) {
-    const [choice, setChoice] = (0, react_1.useState)('tracklist');
-    (0, react_1.useEffect)(() => {
-        if (choice === 'none') {
-            model.setImportFormSyntenyTrack(0, { type: 'none' });
-        }
-    }, [model, choice]);
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.FormControl, { children: [(0, jsx_runtime_1.jsx)(material_1.FormLabel, { id: "group-label", children: "(Optional) Select or add a synteny track" }), (0, jsx_runtime_1.jsxs)(material_1.RadioGroup, { row: true, value: choice, onChange: event => {
-                            setChoice(event.target.value);
-                        }, "aria-labelledby": "group-label", 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, assembly2: assembly2, assembly1: assembly1 })) : null, choice === 'tracklist' ? ((0, jsx_runtime_1.jsx)(ImportSyntenyTrackSelector_1.default, { model: model, assembly1: assembly1, assembly2: assembly2 })) : null] }));
-});
-exports.default = TrackSelector;

package/dist/DotplotView/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/DotplotView/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/DotplotView/components/ImportForm/index.d.ts

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

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

@@ -1,76 +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_1 = require("mobx");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const TrackSelector_1 = __importDefault(require("./TrackSelector"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    importFormContainer: {
-        padding: theme.spacing(4),
-        margin: '0 auto',
-    },
-    assemblySelector: {
-        width: '75%',
-        margin: '0 auto',
-    },
-}));
-function doSubmit({ model, assembly1, assembly2, }) {
-    const session = (0, util_1.getSession)(model);
-    const { importFormSyntenyTrackSelections } = model;
-    model.setError(undefined);
-    (0, mobx_1.transaction)(() => {
-        if ((0, util_1.isSessionWithAddTracks)(session)) {
-            (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);
-                }
-                else if (f.type === 'preConfigured') {
-                    model.showTrack(f.value, idx);
-                }
-            });
-        }
-        model.showAllRegions();
-        model.setAssemblyNames(assembly2, assembly1);
-    });
-}
-const DotplotImportForm = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    const session = (0, util_1.getSession)(model);
-    const { assemblyNames } = session;
-    const [assembly2, setAssembly2] = (0, react_1.useState)(assemblyNames[0] || '');
-    const [assembly1, setAssembly1] = (0, react_1.useState)(assemblyNames[0] || '');
-    const [error, setError] = (0, react_1.useState)();
-    const displayError = error || model.error;
-    return ((0, jsx_runtime_1.jsxs)(material_1.Container, { className: classes.importFormContainer, children: [displayError ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: displayError }) : null, (0, jsx_runtime_1.jsxs)(material_1.Paper, { style: { padding: 12 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { style: { textAlign: 'center' }, children: "Select assemblies for dotplot view" }), (0, jsx_runtime_1.jsxs)(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center", children: [(0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "x-axis assembly", selected: assembly2, session: session, onChange: val => {
-                                    setAssembly2(val);
-                                } }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { helperText: "y-axis assembly", selected: assembly1, session: session, onChange: val => {
-                                    setAssembly1(val);
-                                } }), (0, jsx_runtime_1.jsx)(material_1.FormControl, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                                        ;
-                                        (async () => {
-                                            try {
-                                                setError(undefined);
-                                                doSubmit({
-                                                    assembly1,
-                                                    assembly2,
-                                                    model,
-                                                });
-                                            }
-                                            catch (e) {
-                                                console.error(e);
-                                                setError(e);
-                                            }
-                                        })();
-                                    }, variant: "contained", color: "primary", children: "Launch" }) })] }), (0, jsx_runtime_1.jsx)(TrackSelector_1.default, { assembly2: assembly2, assembly1: assembly1, model: model })] })] }));
-});
-exports.default = DotplotImportForm;

package/dist/DotplotView/components/ImportForm/selectors/AnchorsFileSelector.d.ts

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

package/dist/DotplotView/components/ImportForm/selectors/AnchorsFileSelector.js

@@ -1,23 +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 AnchorsFileSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, bed1Location, setBed1Location, bed2Location, 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", { children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: radioOption, location: fileLocation, setLocation: loc => {
-                            setFileLocation(loc);
-                        } }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "genome 1 .bed (left column of anchors file)", description: "", location: bed1Location, setLocation: loc => {
-                            if (setBed1Location) {
-                                setBed1Location(loc);
-                            }
-                        } }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "genome 2 .bed (right column of anchors file)", description: "", location: bed2Location, setLocation: loc => {
-                            if (setBed2Location) {
-                                setBed2Location(loc);
-                            }
-                        } })] }), (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 = AnchorsFileSelector;

package/dist/DotplotView/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/DotplotView/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 (.tbi or .csi)`, 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/DotplotView/components/ImportForm/selectors/SelectorTypes.d.ts

@@ -1,23 +0,0 @@
-import type { FileLocation } from '@jbrowse/core/util/types';
-export declare const helpStrings: {
-    readonly '.paf': "minimap2 target.fa query.fa";
-    readonly '.pif.gz': "minimap2 target.fa query.fa";
-    readonly '.out': "mashmap target.fa query.fa";
-    readonly '.delta': "mummer target.fa query.fa";
-    readonly '.chain': "e.g. queryToTarget.chain";
-};
-export interface SelectorProps {
-    assembly1?: string;
-    assembly2?: string;
-    swap?: boolean;
-    setSwap?: (arg: boolean) => void;
-    fileLocation?: FileLocation;
-    setFileLocation: (arg: FileLocation) => void;
-    indexFileLocation?: FileLocation;
-    setIndexFileLocation?: (arg: FileLocation) => void;
-    bed1Location?: FileLocation;
-    setBed1Location?: (arg: FileLocation) => void;
-    bed2Location?: FileLocation;
-    setBed2Location?: (arg: FileLocation) => void;
-    radioOption: string;
-}

package/dist/DotplotView/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/DotplotView/components/ImportForm/selectors/SwapAssemblies.d.ts

@@ -1,13 +0,0 @@
-import type { ReactNode } from 'react';
-export interface SwapAssembliesProps {
-    assembly1?: string;
-    assembly2?: string;
-    swap?: boolean;
-    setSwap?: (arg: boolean) => void;
-    radioOption: string;
-    helpContent?: ReactNode;
-    text1: string;
-    text2: string;
-}
-declare const SwapAssemblies: ({ assembly1, assembly2, swap, setSwap, radioOption, helpContent, text1, text2, }: SwapAssembliesProps) => import("react/jsx-runtime").JSX.Element;
-export default SwapAssemblies;

package/dist/DotplotView/components/ImportForm/selectors/SwapAssemblies.js

@@ -1,32 +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 Help_1 = __importDefault(require("@mui/icons-material/Help"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const SelectorTypes_1 = require("./SelectorTypes");
-const useStyles = (0, mui_1.makeStyles)()({
-    row: {
-        display: 'flex',
-        gap: 20,
-    },
-    swap: {
-        display: 'grid',
-        gridTemplateColumns: '1fr 1fr',
-        gap: 4,
-        alignItems: 'center',
-    },
-});
-const SwapAssemblies = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, radioOption, helpContent, text1, text2, }) {
-    const { classes } = useStyles();
-    return ((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: helpContent || ((0, jsx_runtime_1.jsx)("code", { children: SelectorTypes_1.helpStrings[radioOption] })), children: (0, jsx_runtime_1.jsx)(Help_1.default, {}) })] }), (0, jsx_runtime_1.jsxs)("div", { className: classes.row, children: [(0, jsx_runtime_1.jsxs)("div", { className: classes.swap, children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("i", { children: swap ? assembly2 : assembly1 }) }), (0, jsx_runtime_1.jsx)("div", { children: text1 }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)("i", { children: swap ? assembly1 : assembly2 }) }), (0, jsx_runtime_1.jsx)("div", { children: text2 })] }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                            if (setSwap) {
-                                setSwap(!swap);
-                            }
-                        }, children: "Swap?" })] })] }));
-});
-exports.default = SwapAssemblies;

package/dist/DotplotView/components/ImportForm/selectors/SyntenyFileSelector.d.ts

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

package/dist/DotplotView/components/ImportForm/selectors/SyntenyFileSelector.js

@@ -1,24 +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 mui_1 = require("tss-react/mui");
-const SwapAssemblies_1 = __importDefault(require("./SwapAssemblies"));
-const useStyles = (0, mui_1.makeStyles)()({
-    container: {
-        display: 'flex',
-        flexDirection: 'column',
-        gap: 10,
-    },
-});
-const SyntenyFileSelector = (0, mobx_react_1.observer)(function ({ assembly1, assembly2, swap, setSwap, fileLocation, setFileLocation, radioOption, }) {
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsxs)("div", { className: classes.container, children: [(0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: `${radioOption} location`, inline: true, description: "", location: fileLocation, setLocation: loc => {
-                    setFileLocation(loc);
-                } }), (0, jsx_runtime_1.jsx)(SwapAssemblies_1.default, { assembly1: assembly1, assembly2: assembly2, swap: swap, setSwap: setSwap, radioOption: radioOption, text1: "query assembly", text2: "target assembly" })] }));
-});
-exports.default = SyntenyFileSelector;

package/dist/DotplotView/components/ImportForm/selectors/index.d.ts

@@ -1,3 +0,0 @@
-export { default as AnchorsFileSelector } from './AnchorsFileSelector';
-export { default as PifGzSelector } from './PifGzSelector';
-export { default as SyntenyFileSelector } from './SyntenyFileSelector';

package/dist/DotplotView/components/ImportForm/selectors/index.js

@@ -1,12 +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.SyntenyFileSelector = exports.PifGzSelector = exports.AnchorsFileSelector = void 0;
-var AnchorsFileSelector_1 = require("./AnchorsFileSelector");
-Object.defineProperty(exports, "AnchorsFileSelector", { enumerable: true, get: function () { return __importDefault(AnchorsFileSelector_1).default; } });
-var PifGzSelector_1 = require("./PifGzSelector");
-Object.defineProperty(exports, "PifGzSelector", { enumerable: true, get: function () { return __importDefault(PifGzSelector_1).default; } });
-var SyntenyFileSelector_1 = require("./SyntenyFileSelector");
-Object.defineProperty(exports, "SyntenyFileSelector", { enumerable: true, get: function () { return __importDefault(SyntenyFileSelector_1).default; } });

package/dist/DotplotView/components/ImportForm/util.d.ts

@@ -1,10 +0,0 @@
-export declare function getName(sessionTrackData?: {
-    uri: string;
-} | {
-    localPath: string;
-} | {
-    name: string;
-}): any;
-export declare function stripGz(fileName: string): string;
-export declare function basename(str: string): string | undefined;
-export declare function extName(str: string): string;

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

@@ -1,24 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getName = getName;
-exports.stripGz = stripGz;
-exports.basename = basename;
-exports.extName = extName;
-function getName(sessionTrackData) {
-    return sessionTrackData
-        ?
-            sessionTrackData.uri ||
-                sessionTrackData.localPath ||
-                sessionTrackData.name
-        : undefined;
-}
-function stripGz(fileName) {
-    return fileName.endsWith('.gz') ? fileName.slice(0, -3) : fileName;
-}
-function basename(str) {
-    return str.split('#')[0].split('?')[0].split('/').pop();
-}
-function extName(str) {
-    const r = str.split('.').pop();
-    return r ? `.${r}` : '';
-}

package/dist/DotplotView/components/PanButtons.d.ts

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

package/dist/DotplotView/components/PanButtons.js

@@ -1,47 +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 ArrowDropDown_1 = __importDefault(require("@mui/icons-material/ArrowDropDown"));
-const ArrowDropUp_1 = __importDefault(require("@mui/icons-material/ArrowDropUp"));
-const ArrowLeft_1 = __importDefault(require("@mui/icons-material/ArrowLeft"));
-const ArrowRight_1 = __importDefault(require("@mui/icons-material/ArrowRight"));
-const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
-const ZoomOut_1 = __importDefault(require("@mui/icons-material/ZoomOut"));
-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)()({
-    dpad: {
-        display: 'grid',
-        gridTemplateColumns: 'repeat(3, 1fr)',
-        margin: 0,
-        position: 'absolute',
-        right: 50,
-        zIndex: 500,
-        top: 50,
-    },
-    icon: {
-        padding: 0,
-        margin: 0,
-    },
-});
-const PanButtons = (0, mobx_react_1.observer)(function PanButtons({ model, }) {
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { className: classes.dpad, elevation: 6, children: [(0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
-                    model.vview.scroll(100);
-                }, children: (0, jsx_runtime_1.jsx)(ArrowDropUp_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
-                    model.hview.scroll(-100);
-                }, children: (0, jsx_runtime_1.jsx)(ArrowLeft_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
-                    model.hview.scroll(100);
-                }, children: (0, jsx_runtime_1.jsx)(ArrowRight_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
-                    model.vview.scroll(-100);
-                }, children: (0, jsx_runtime_1.jsx)(ArrowDropDown_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
-                    model.zoomIn();
-                }, children: (0, jsx_runtime_1.jsx)(ZoomIn_1.default, {}) }), (0, jsx_runtime_1.jsx)("div", {}), (0, jsx_runtime_1.jsx)(material_1.IconButton, { className: classes.icon, onClick: () => {
-                    model.zoomOut();
-                }, children: (0, jsx_runtime_1.jsx)(ZoomOut_1.default, {}) })] }));
-});
-exports.default = PanButtons;

package/dist/DotplotView/components/WarningDialog.d.ts

@@ -1,16 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-interface Warning {
-    message: string;
-    effect: string;
-}
-interface TrackWarning {
-    configuration: AnyConfigurationModel;
-    displays: {
-        warnings: Warning[];
-    }[];
-}
-declare const WarningDialog: ({ trackWarnings, handleClose, }: {
-    handleClose: () => void;
-    trackWarnings: TrackWarning[];
-}) => import("react/jsx-runtime").JSX.Element;
-export default WarningDialog;

package/dist/DotplotView/components/WarningDialog.js

@@ -1,39 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const configuration_1 = require("@jbrowse/core/configuration");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const x_data_grid_1 = require("@mui/x-data-grid");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
-    content: {
-        minWidth: 600,
-    },
-});
-function getTrackWarnings({ trackWarnings, }) {
-    const rows = [];
-    for (const [i, trackWarning] of trackWarnings.entries()) {
-        const track = trackWarning;
-        const name = (0, configuration_1.getConf)(track, 'name');
-        const d = track.displays[0];
-        for (let j = 0; j < d.warnings.length; j++) {
-            const warning = d.warnings[j];
-            rows.push({ name, ...warning, id: `${i}_${j}` });
-        }
-    }
-    return rows;
-}
-const WarningDialog = (0, mobx_react_1.observer)(function WarningDialog({ trackWarnings, handleClose, }) {
-    const { classes } = useStyles();
-    const rows = getTrackWarnings({ trackWarnings });
-    const columns = [
-        { field: 'name' },
-        { field: 'message', width: (0, util_1.measureGridWidth)(rows.map(r => r.message)) },
-        { field: 'effect', width: (0, util_1.measureGridWidth)(rows.map(r => r.effect)) },
-    ];
-    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Dotplot rendered with warnings", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.content, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContentText, { children: "Found warnings while rendering the dotplot. This is often due to out-of-bound features that may indicate the wrong assemblies are being used. Check that the query and target are configured correctly, and that the right assemblies are being compared." }), (0, jsx_runtime_1.jsx)("div", { style: { height: 600, width: '100%', overflow: 'auto' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: rows, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }) })] }) }));
-});
-exports.default = WarningDialog;

package/dist/DotplotView/components/util.d.ts

@@ -1,14 +0,0 @@
-import type { Dotplot1DViewModel } from '../model';
-import type { BaseBlock } from '@jbrowse/core/util/blockTypes';
-export declare function locstr(px: number, view: Dotplot1DViewModel, includeAsm?: boolean): string;
-export declare function getBlockLabelKeysToHide(blocks: BaseBlock[], length: number, viewOffsetPx: number): Set<string>;
-export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
-    majorPitch: number;
-    minorPitch: number;
-};
-export declare function makeTicks(regions: BaseBlock[], bpPerPx: number, emitMajor?: boolean, emitMinor?: boolean): {
-    type: string;
-    base: number;
-    index: number;
-    refName: string;
-}[];