@jbrowse/core 3.7.0 → 4.0.0

package/ui/theme.js

@@ -1,381 +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.defaultThemes = void 0;
-exports.createJBrowseBaseTheme = createJBrowseBaseTheme;
-exports.createJBrowseTheme = createJBrowseTheme;
-const material_1 = require("@mui/material");
-const colors_1 = require("@mui/material/colors");
-const deepmerge_1 = __importDefault(require("deepmerge"));
-const refTheme = (0, material_1.createTheme)();
-const midnight = refTheme.palette.augmentColor({ color: { main: '#0D233F' } });
-const grape = refTheme.palette.augmentColor({ color: { main: '#721E63' } });
-const forest = refTheme.palette.augmentColor({ color: { main: '#135560' } });
-const mandarin = refTheme.palette.augmentColor({ color: { main: '#FFB11D' } });
-const lightgrey = refTheme.palette.augmentColor({ color: { main: '#aaa' } });
-const bases = {
-    A: refTheme.palette.augmentColor({ color: colors_1.green }),
-    C: refTheme.palette.augmentColor({ color: colors_1.blue }),
-    G: refTheme.palette.augmentColor({ color: colors_1.orange }),
-    T: refTheme.palette.augmentColor({ color: colors_1.red }),
-};
-const framesCDS = [
-    null,
-    refTheme.palette.augmentColor({ color: { main: '#FF8080' } }),
-    refTheme.palette.augmentColor({ color: { main: '#80FF80' } }),
-    refTheme.palette.augmentColor({ color: { main: '#8080FF' } }),
-    refTheme.palette.augmentColor({ color: { main: '#8080FF' } }),
-    refTheme.palette.augmentColor({ color: { main: '#80FF80' } }),
-    refTheme.palette.augmentColor({ color: { main: '#FF8080' } }),
-];
-const frames = [
-    null,
-    refTheme.palette.augmentColor({ color: { main: '#8f8f8f' } }),
-    refTheme.palette.augmentColor({ color: { main: '#adadad' } }),
-    refTheme.palette.augmentColor({ color: { main: '#d8d8d8' } }),
-    refTheme.palette.augmentColor({ color: { main: '#d8d8d8' } }),
-    refTheme.palette.augmentColor({ color: { main: '#adadad' } }),
-    refTheme.palette.augmentColor({ color: { main: '#8f8f8f' } }),
-];
-const stopCodon = '#e22';
-const startCodon = '#3e3';
-const insertion = '#800080';
-const deletion = '#808080';
-const hardclip = '#f00';
-const softclip = '#00f';
-const skip = '#97b8c9';
-const defaults = {
-    primary: midnight,
-    secondary: grape,
-    tertiary: forest,
-    quaternary: mandarin,
-    highlight: mandarin,
-    stopCodon,
-    startCodon,
-    insertion,
-    deletion,
-    softclip,
-    hardclip,
-    bases,
-    frames,
-    framesCDS,
-    skip,
-};
-function stockTheme() {
-    return {
-        palette: {
-            ...defaults,
-            mode: undefined,
-        },
-        components: {
-            MuiLink: {
-                styleOverrides: {
-                    root: ({ theme }) => ({
-                        color: theme.palette.tertiary.main,
-                    }),
-                },
-            },
-        },
-    };
-}
-function getDefaultTheme() {
-    return {
-        ...stockTheme(),
-        name: 'Default (from config)',
-    };
-}
-function getLightStockTheme() {
-    return {
-        ...stockTheme(),
-        name: 'Light (stock)',
-    };
-}
-function getDarkStockTheme() {
-    return {
-        name: 'Dark (stock)',
-        palette: {
-            ...defaults,
-            mode: 'dark',
-        },
-        components: {
-            MuiAppBar: {
-                defaultProps: {
-                    enableColorOnDark: true,
-                },
-                styleOverrides: {
-                    root: ({ theme }) => theme.palette.primary.main,
-                },
-            },
-        },
-    };
-}
-function getDarkMinimalTheme() {
-    return {
-        name: 'Dark (minimal)',
-        palette: {
-            ...defaults,
-            mode: 'dark',
-            primary: { main: colors_1.grey[700] },
-            secondary: { main: colors_1.grey[800] },
-            tertiary: refTheme.palette.augmentColor({ color: { main: colors_1.grey[900] } }),
-        },
-    };
-}
-function getMinimalTheme() {
-    return {
-        name: 'Light (minimal)',
-        palette: {
-            ...defaults,
-            primary: { main: colors_1.grey[900] },
-            secondary: { main: colors_1.grey[800] },
-            tertiary: refTheme.palette.augmentColor({ color: { main: colors_1.grey[900] } }),
-        },
-    };
-}
-exports.defaultThemes = {
-    default: getDefaultTheme(),
-    lightStock: getLightStockTheme(),
-    lightMinimal: getMinimalTheme(),
-    darkMinimal: getDarkMinimalTheme(),
-    darkStock: getDarkStockTheme(),
-};
-function overwriteArrayMerge(_, sourceArray) {
-    return sourceArray;
-}
-function createJBrowseBaseTheme(theme) {
-    var _a, _b, _c, _d, _e, _f;
-    const themeP = {
-        palette: theme === null || theme === void 0 ? void 0 : theme.palette,
-        typography: {
-            fontSize: 12,
-        },
-        spacing: 4,
-        components: {
-            MuiTooltip: {
-                styleOverrides: {
-                    tooltip: {
-                        fontSize: 12,
-                    },
-                },
-            },
-            MuiButton: {
-                defaultProps: {
-                    size: 'small',
-                },
-                styleOverrides: {
-                    root: ({ theme }) => theme.palette.mode === 'dark'
-                        ? {
-                            color: theme.palette.text.primary,
-                        }
-                        : undefined,
-                },
-            },
-            MuiAccordion: {
-                defaultProps: {
-                    disableGutters: true,
-                    slotProps: {
-                        transition: {
-                            timeout: 150,
-                            unmountOnExit: true,
-                        },
-                    },
-                },
-            },
-            MuiFilledInput: {
-                defaultProps: {
-                    margin: 'dense',
-                },
-            },
-            MuiFormControl: {
-                defaultProps: {
-                    margin: 'dense',
-                    size: 'small',
-                },
-            },
-            MuiFormHelperText: {
-                defaultProps: {
-                    margin: 'dense',
-                },
-            },
-            MuiIconButton: {
-                defaultProps: {
-                    size: 'small',
-                },
-            },
-            MuiInputBase: {
-                defaultProps: {
-                    margin: 'dense',
-                },
-            },
-            MuiAutocomplete: {
-                defaultProps: {
-                    size: 'small',
-                },
-            },
-            MuiInputLabel: {
-                defaultProps: {
-                    margin: 'dense',
-                },
-            },
-            MuiToolbar: {
-                defaultProps: {
-                    variant: 'dense',
-                },
-            },
-            MuiListItem: {
-                defaultProps: {
-                    dense: true,
-                },
-            },
-            MuiOutlinedInput: {
-                defaultProps: {
-                    margin: 'dense',
-                },
-            },
-            MuiFab: {
-                defaultProps: {
-                    size: 'small',
-                },
-                styleOverrides: {
-                    secondary: {
-                        backgroundColor: (_b = (_a = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _a === void 0 ? void 0 : _a.quaternary) === null || _b === void 0 ? void 0 : _b.main,
-                    },
-                },
-            },
-            MuiTable: {
-                defaultProps: {
-                    size: 'small',
-                },
-            },
-            MuiPopover: {
-                defaultProps: {
-                    transitionDuration: 0,
-                },
-            },
-            MuiMenu: {
-                defaultProps: {
-                    transitionDuration: 0,
-                },
-            },
-            MuiMenuItem: {
-                defaultProps: {
-                    dense: true,
-                },
-            },
-            MuiTextField: {
-                defaultProps: {
-                    margin: 'dense',
-                    variant: 'standard',
-                },
-            },
-            MuiLink: {
-                styleOverrides: {
-                    root: ({ theme }) => ({
-                        color: theme.palette.text.secondary,
-                    }),
-                },
-            },
-            MuiCheckbox: {
-                styleOverrides: {
-                    root: ({ theme }) => theme.palette.mode === 'dark'
-                        ? {
-                            color: theme.palette.text.secondary,
-                            '&.Mui-checked': {
-                                color: theme.palette.text.secondary,
-                            },
-                        }
-                        : undefined,
-                },
-            },
-            MuiRadio: {
-                styleOverrides: {
-                    root: ({ theme }) => theme.palette.mode === 'dark'
-                        ? {
-                            color: theme.palette.text.secondary,
-                            '&.Mui-checked': {
-                                color: theme.palette.text.secondary,
-                            },
-                        }
-                        : undefined,
-                },
-            },
-            MuiFormLabel: {
-                styleOverrides: {
-                    root: ({ theme }) => theme.palette.mode === 'dark'
-                        ? {
-                            color: theme.palette.text.secondary,
-                            '&.Mui-focused': {
-                                color: theme.palette.text.secondary,
-                            },
-                        }
-                        : undefined,
-                },
-            },
-            MuiAccordionSummary: {
-                styleOverrides: {
-                    root: {
-                        backgroundColor: (_d = (_c = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _c === void 0 ? void 0 : _c.tertiary) === null || _d === void 0 ? void 0 : _d.main,
-                    },
-                    content: {
-                        color: (_f = (_e = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _e === void 0 ? void 0 : _e.tertiary) === null || _f === void 0 ? void 0 : _f.contrastText,
-                    },
-                },
-            },
-            MuiToggleButtonGroup: {
-                defaultProps: {
-                    size: 'small',
-                },
-            },
-        },
-    };
-    return (0, deepmerge_1.default)(themeP, theme || {}, { arrayMerge: overwriteArrayMerge });
-}
-function createJBrowseTheme(configTheme = {}, themes = exports.defaultThemes, themeName = 'default') {
-    return (0, material_1.createTheme)(createJBrowseBaseTheme(themeName === 'default'
-        ? (0, deepmerge_1.default)(themes.default, augmentThemeColors(configTheme), {
-            arrayMerge: overwriteArrayMerge,
-        })
-        : addMissingColors(themes[themeName])));
-}
-function augmentThemeColors(theme = {}) {
-    var _a;
-    for (const entry of [
-        'primary',
-        'secondary',
-        'tertiary',
-        'quaternary',
-        'highlight',
-    ]) {
-        if ((_a = theme.palette) === null || _a === void 0 ? void 0 : _a[entry]) {
-            theme = (0, deepmerge_1.default)(theme, {
-                palette: {
-                    [entry]: refTheme.palette.augmentColor('color' in theme.palette[entry]
-                        ? theme.palette[entry]
-                        : {
-                            color: theme.palette[entry],
-                        }),
-                },
-            });
-        }
-    }
-    return theme;
-}
-function addMissingColors(theme = {}) {
-    const { palette } = theme;
-    return augmentThemeColors((0, deepmerge_1.default)(theme, {
-        palette: {
-            quaternary: (palette === null || palette === void 0 ? void 0 : palette.quaternary) || lightgrey,
-            tertiary: (palette === null || palette === void 0 ? void 0 : palette.tertiary) || lightgrey,
-            highlight: (palette === null || palette === void 0 ? void 0 : palette.highlight) || mandarin,
-            insertion: (palette === null || palette === void 0 ? void 0 : palette.insertion) || insertion,
-            softclip: (palette === null || palette === void 0 ? void 0 : palette.softclip) || softclip,
-            skip: (palette === null || palette === void 0 ? void 0 : palette.skip) || skip,
-            hardclip: (palette === null || palette === void 0 ? void 0 : palette.hardclip) || hardclip,
-            deletion: (palette === null || palette === void 0 ? void 0 : palette.deletion) || deletion,
-            startCodon: (palette === null || palette === void 0 ? void 0 : palette.startCodon) || startCodon,
-            stopCodon: (palette === null || palette === void 0 ? void 0 : palette.stopCodon) || stopCodon,
-        },
-    }));
-}

package/ui/useEvent.js

@@ -1,47 +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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.useEvent = useEvent;
-const React = __importStar(require("react"));
-function useEvent(handler) {
-    const handlerRef = React.useRef(null);
-    React.useLayoutEffect(() => {
-        handlerRef.current = handler;
-    });
-    return React.useCallback((...args) => {
-        var _a;
-        (_a = handlerRef.current) === null || _a === void 0 ? void 0 : _a.call(handlerRef, ...args);
-    }, []);
-}

package/util/Base1DUtils.d.ts

@@ -1,38 +0,0 @@
-import type { ViewSnap } from './index';
-export interface BpOffset {
-    refName?: string;
-    index: number;
-    offset: number;
-    start?: number;
-    end?: number;
-}
-export declare function moveTo(self: ViewSnap & {
-    zoomTo: (arg: number) => number;
-    scrollTo: (arg: number) => void;
-}, start?: BpOffset, end?: BpOffset): void;
-export declare function pxToBp(self: ViewSnap, px: number): {
-    coord: number;
-    index: number;
-    refName: string;
-    oob: boolean;
-    assemblyName: string;
-    offset: number;
-    start: number;
-    end: number;
-    reversed?: boolean;
-};
-export declare function bpToPx({ refName, coord, regionNumber, self, }: {
-    refName: string;
-    coord: number;
-    regionNumber?: number;
-    self: ViewSnap;
-}): {
-    index: number;
-    offsetPx: number;
-} | undefined;
-export declare function bpToPxMap({ refName, coord, regionNumber, self, }: {
-    refName: string;
-    coord: number;
-    regionNumber?: number;
-    self: ViewSnap;
-}): {};

package/util/Base1DUtils.js

@@ -1,198 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.moveTo = moveTo;
-exports.pxToBp = pxToBp;
-exports.bpToPx = bpToPx;
-exports.bpToPxMap = bpToPxMap;
-function lengthBetween(self, start, end) {
-    let bpSoFar = 0;
-    const { displayedRegions } = self;
-    if (start.index === end.index) {
-        bpSoFar += end.offset - start.offset;
-    }
-    else {
-        const s = displayedRegions[start.index];
-        bpSoFar += s.end - s.start - start.offset;
-        if (end.index - start.index >= 2) {
-            for (let i = start.index + 1; i < end.index; i++) {
-                const region = displayedRegions[i];
-                const len = region.end - region.start;
-                bpSoFar += len;
-            }
-        }
-        bpSoFar += end.offset;
-    }
-    return bpSoFar;
-}
-function moveTo(self, start, end) {
-    if (!start || !end) {
-        return;
-    }
-    const { width, interRegionPaddingWidth, displayedRegions, bpPerPx, minimumBlockWidth, } = self;
-    const len = lengthBetween(self, start, end);
-    let numBlocksWideEnough = 0;
-    for (let i = start.index; i < end.index; i++) {
-        const r = displayedRegions[i];
-        if ((r.end - r.start) / bpPerPx > minimumBlockWidth) {
-            numBlocksWideEnough++;
-        }
-    }
-    const targetBpPerPx = len / (width - interRegionPaddingWidth * numBlocksWideEnough);
-    const newBpPerPx = self.zoomTo(targetBpPerPx);
-    let extraBp = 0;
-    if (targetBpPerPx < newBpPerPx) {
-        extraBp = ((newBpPerPx - targetBpPerPx) * self.width) / 2;
-    }
-    let bpToStart = -extraBp;
-    for (let i = 0; i < self.displayedRegions.length; i++) {
-        const region = self.displayedRegions[i];
-        if (start.index === i) {
-            bpToStart += start.offset;
-            break;
-        }
-        else {
-            bpToStart += region.end - region.start;
-        }
-    }
-    self.scrollTo(Math.round(bpToStart / self.bpPerPx));
-}
-function coord(r, bp) {
-    return Math.floor(r.reversed ? r.end - bp : r.start + bp) + 1;
-}
-function pxToBp(self, px) {
-    var _a;
-    let bpSoFar = 0;
-    const { bpPerPx, offsetPx, displayedRegions, interRegionPaddingWidth, staticBlocks, } = self;
-    const blocks = staticBlocks.contentBlocks;
-    const bp = (offsetPx + px) * bpPerPx;
-    if (bp < 0) {
-        const r = displayedRegions[0];
-        const snap = r;
-        return {
-            ...snap,
-            oob: true,
-            coord: coord(r, bp),
-            offset: bp,
-            index: 0,
-        };
-    }
-    const interRegionPaddingBp = interRegionPaddingWidth * bpPerPx;
-    let currBlock = 0;
-    for (let i = 0; i < displayedRegions.length; i++) {
-        const r = displayedRegions[i];
-        const len = r.end - r.start;
-        const offset = bp - bpSoFar;
-        if (len + bpSoFar > bp && bpSoFar <= bp) {
-            const snap = r;
-            return {
-                ...snap,
-                oob: false,
-                offset,
-                coord: coord(r, offset),
-                index: i,
-            };
-        }
-        if (((_a = blocks[currBlock]) === null || _a === void 0 ? void 0 : _a.regionNumber) === i) {
-            bpSoFar += len + interRegionPaddingBp;
-            currBlock++;
-        }
-        else {
-            bpSoFar += len;
-        }
-    }
-    if (bp >= bpSoFar && displayedRegions.length > 0) {
-        const r = displayedRegions.at(-1);
-        const len = r.end - r.start;
-        const offset = bp - bpSoFar + len;
-        const snap = r;
-        return {
-            ...snap,
-            oob: true,
-            offset,
-            coord: coord(r, offset),
-            index: displayedRegions.length - 1,
-        };
-    }
-    return {
-        coord: 0,
-        index: 0,
-        refName: '',
-        oob: true,
-        assemblyName: '',
-        offset: 0,
-        start: 0,
-        end: 0,
-        reversed: false,
-    };
-}
-function bpToPx({ refName, coord, regionNumber, self, }) {
-    var _a;
-    let bpSoFar = 0;
-    const { interRegionPaddingWidth, bpPerPx, displayedRegions, staticBlocks } = self;
-    const blocks = staticBlocks.contentBlocks;
-    const interRegionPaddingBp = interRegionPaddingWidth * bpPerPx;
-    let currBlock = 0;
-    let i = 0;
-    for (; i < displayedRegions.length; i++) {
-        const r = displayedRegions[i];
-        const len = r.end - r.start;
-        if (refName === r.refName &&
-            coord >= r.start &&
-            coord <= r.end &&
-            (regionNumber ? regionNumber === i : true)) {
-            bpSoFar += r.reversed ? r.end - coord : coord - r.start;
-            break;
-        }
-        if (((_a = blocks[currBlock]) === null || _a === void 0 ? void 0 : _a.regionNumber) === i) {
-            bpSoFar += len + interRegionPaddingBp;
-            currBlock++;
-        }
-        else {
-            bpSoFar += len;
-        }
-    }
-    const found = displayedRegions[i];
-    if (found) {
-        return {
-            index: i,
-            offsetPx: Math.round(bpSoFar / bpPerPx),
-        };
-    }
-    return undefined;
-}
-function bpToPxMap({ refName, coord, regionNumber, self, }) {
-    var _a;
-    let bpSoFar = 0;
-    const { interRegionPaddingWidth, bpPerPx, displayedRegions, staticBlocks } = self;
-    const blocks = staticBlocks.contentBlocks;
-    const interRegionPaddingBp = interRegionPaddingWidth * bpPerPx;
-    const map = {};
-    let currBlock = 0;
-    let i = 0;
-    for (; i < displayedRegions.length; i++) {
-        const r = displayedRegions[i];
-        const len = r.end - r.start;
-        if (refName === r.refName &&
-            coord >= r.start &&
-            coord <= r.end &&
-            (regionNumber === undefined ? true : regionNumber === i)) {
-            bpSoFar += r.reversed ? r.end - coord : coord - r.start;
-            break;
-        }
-        if (((_a = blocks[currBlock]) === null || _a === void 0 ? void 0 : _a.regionNumber) === i) {
-            bpSoFar += len + interRegionPaddingBp;
-            currBlock++;
-        }
-        else {
-            bpSoFar += len;
-        }
-    }
-    const found = displayedRegions[i];
-    if (found) {
-        return {
-            index: i,
-            offsetPx: Math.round(bpSoFar / bpPerPx),
-        };
-    }
-    return map;
-}