@jbrowse/plugin-dotplot-view 3.7.0 → 4.0.0

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

@@ -1,75 +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.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/MinLengthSlider.d.ts

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

package/dist/DotplotView/components/MinLengthSlider.js

@@ -1,44 +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 mui_1 = require("tss-react/mui");
-const SliderTooltip_1 = __importDefault(require("./SliderTooltip"));
-const useStyles = (0, mui_1.makeStyles)()({
-    container: {
-        display: 'flex',
-        alignItems: 'center',
-        marginLeft: 16,
-        marginRight: 16,
-        minWidth: 150,
-    },
-});
-const MinLengthSlider = (0, mobx_react_1.observer)(function ({ model, }) {
-    var _a, _b;
-    const { classes } = useStyles();
-    const firstDisplay = (_a = model.tracks[0]) === null || _a === void 0 ? void 0 : _a.displays[0];
-    const minAlignmentLength = (_b = firstDisplay === null || firstDisplay === void 0 ? void 0 : firstDisplay.minAlignmentLength) !== null && _b !== void 0 ? _b : 0;
-    const [minLengthValue, setMinLengthValue] = (0, react_1.useState)(Math.log2(Math.max(1, minAlignmentLength)) * 100);
-    (0, react_1.useEffect)(() => {
-        setMinLengthValue(Math.log2(Math.max(1, minAlignmentLength)) * 100);
-    }, [minAlignmentLength]);
-    return ((0, jsx_runtime_1.jsxs)("span", { className: classes.container, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "body2", style: { marginRight: 8 }, children: "Min length:" }), (0, jsx_runtime_1.jsx)(material_1.Slider, { value: minLengthValue, onChange: (_, val) => {
-                    setMinLengthValue(val);
-                }, onChangeCommitted: () => {
-                    const newMinLength = Math.round(2 ** (minLengthValue / 100));
-                    for (const track of model.tracks) {
-                        for (const display of track.displays) {
-                            ;
-                            display.setMinAlignmentLength(newMinLength);
-                        }
-                    }
-                }, min: 0, max: Math.log2(1000000) * 100, valueLabelDisplay: "auto", valueLabelFormat: newValue => Math.round(2 ** (newValue / 100)).toLocaleString(), size: "small", style: { minWidth: 100 }, slots: {
-                    valueLabel: SliderTooltip_1.default,
-                } })] }));
-});
-exports.default = MinLengthSlider;

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

@@ -1,17 +0,0 @@
-import type { DotplotViewModel } from '../model';
-type Coord = [number, number] | undefined;
-interface MouseInteractionLayerProps {
-    model: DotplotViewModel;
-    ctrlKeyDown: boolean;
-    cursorMode: string;
-    validSelect: boolean;
-    mousedown: Coord;
-    mouserect: Coord;
-    xdistance: number;
-    ydistance: number;
-    setMouseDownClient: (coord: Coord) => void;
-    setMouseCurrClient: (coord: Coord) => void;
-    setCtrlKeyWasUsed: (wasUsed: boolean) => void;
-}
-export default function MouseInteractionLayer({ model, ctrlKeyDown, cursorMode, validSelect, mousedown, mouserect, xdistance, ydistance, setMouseDownClient, setMouseCurrClient, setCtrlKeyWasUsed, }: MouseInteractionLayerProps): import("react/jsx-runtime").JSX.Element;
-export {};

package/dist/DotplotView/components/MouseInteractionLayer.js

@@ -1,18 +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 = MouseInteractionLayer;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const Grid_1 = __importDefault(require("./Grid"));
-function MouseInteractionLayer({ model, ctrlKeyDown, cursorMode, validSelect, mousedown, mouserect, xdistance, ydistance, setMouseDownClient, setMouseCurrClient, setCtrlKeyWasUsed, }) {
-    return ((0, jsx_runtime_1.jsx)("div", { style: { cursor: ctrlKeyDown ? 'pointer' : cursorMode }, onMouseDown: event => {
-            if (event.button === 0) {
-                const { clientX, clientY } = event;
-                setMouseDownClient([clientX, clientY]);
-                setMouseCurrClient([clientX, clientY]);
-                setCtrlKeyWasUsed(ctrlKeyDown);
-            }
-        }, children: (0, jsx_runtime_1.jsx)(Grid_1.default, { model: model, children: validSelect && mousedown && mouserect ? ((0, jsx_runtime_1.jsx)("rect", { fill: "rgba(255,0,0,0.3)", x: Math.min(mouserect[0], mousedown[0]), y: Math.min(mouserect[1], mousedown[1]), width: Math.abs(xdistance), height: Math.abs(ydistance) })) : null }) }));
-}

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

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

package/dist/DotplotView/components/OpacitySlider.js

@@ -1,43 +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 material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const SliderTooltip_1 = __importDefault(require("./SliderTooltip"));
-const useStyles = (0, mui_1.makeStyles)()({
-    container: {
-        display: 'flex',
-        alignItems: 'center',
-        marginLeft: 16,
-        marginRight: 16,
-        minWidth: 150,
-    },
-});
-const OpacitySlider = (0, mobx_react_1.observer)(function ({ model, }) {
-    var _a, _b;
-    const { classes } = useStyles();
-    const firstDisplay = (_a = model.tracks[0]) === null || _a === void 0 ? void 0 : _a.displays[0];
-    const alpha = (_b = firstDisplay === null || firstDisplay === void 0 ? void 0 : firstDisplay.alpha) !== null && _b !== void 0 ? _b : 1;
-    const exponent = 3;
-    const alphaToSlider = (a) => Math.pow(a, 1 / exponent);
-    const sliderToAlpha = (s) => Math.pow(s, exponent);
-    const sliderValue = alphaToSlider(alpha);
-    const handleAlphaChange = (_event, value) => {
-        const sliderVal = typeof value === 'number' ? value : value[0];
-        const newAlpha = sliderToAlpha(sliderVal);
-        for (const track of model.tracks) {
-            for (const display of track.displays) {
-                ;
-                display.setAlpha(newAlpha);
-            }
-        }
-    };
-    return ((0, jsx_runtime_1.jsxs)("span", { className: classes.container, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "body2", style: { marginRight: 8 }, children: "Opacity:" }), (0, jsx_runtime_1.jsx)(material_1.Slider, { value: sliderValue, onChange: handleAlphaChange, min: 0, max: 1, step: 0.01, valueLabelDisplay: "auto", size: "small", style: { minWidth: 100 }, slots: {
-                    valueLabel: SliderTooltip_1.default,
-                }, valueLabelFormat: value => sliderToAlpha(value).toFixed(3) })] }));
-});
-exports.default = OpacitySlider;

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/SelectionContextMenu.d.ts

@@ -1,13 +0,0 @@
-import type { DotplotViewModel } from '../model';
-type Coord = [number, number] | undefined;
-interface SelectionContextMenuProps {
-    model: DotplotViewModel;
-    mouseup: Coord;
-    mouseupClient: Coord;
-    mousedown: Coord;
-    setMouseUpClient: (coord: Coord) => void;
-    setMouseDownClient: (coord: Coord) => void;
-    setMouseOvered: (isOvered: boolean) => void;
-}
-export default function SelectionContextMenu({ model, mouseup, mouseupClient, mousedown, setMouseUpClient, setMouseDownClient, setMouseOvered, }: SelectionContextMenuProps): import("react/jsx-runtime").JSX.Element;
-export {};

package/dist/DotplotView/components/SelectionContextMenu.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SelectionContextMenu;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-function getSelectionMenuItems(model, mousedown, mouseup, setMouseOvered) {
-    return [
-        {
-            label: 'Zoom in',
-            onClick: () => {
-                if (mousedown && mouseup) {
-                    model.zoomInToMouseCoords(mousedown, mouseup);
-                }
-                setMouseOvered(false);
-            },
-        },
-        {
-            label: 'Open linear synteny view',
-            onClick: () => {
-                if (mousedown && mouseup) {
-                    model.onDotplotView(mousedown, mouseup);
-                }
-                setMouseOvered(false);
-            },
-        },
-    ];
-}
-function SelectionContextMenu({ model, mouseup, mouseupClient, mousedown, setMouseUpClient, setMouseDownClient, setMouseOvered, }) {
-    return ((0, jsx_runtime_1.jsx)(ui_1.Menu, { open: Boolean(mouseup), onMenuItemClick: (_, callback) => {
-            callback();
-            setMouseUpClient(undefined);
-            setMouseDownClient(undefined);
-        }, onClose: () => {
-            setMouseUpClient(undefined);
-            setMouseDownClient(undefined);
-        }, anchorReference: "anchorPosition", anchorPosition: mouseupClient
-            ? {
-                top: mouseupClient[1] + 50,
-                left: mouseupClient[0] + 50,
-            }
-            : undefined, style: { zIndex: 11000 }, menuItems: getSelectionMenuItems(model, mousedown, mouseup, setMouseOvered) }));
-}

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

@@ -1,2 +0,0 @@
-import type { SliderValueLabelProps } from '@mui/material';
-export default function SliderTooltip(props: SliderValueLabelProps): import("react/jsx-runtime").JSX.Element;