@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/shared/components/SourcesDataGrid.js

@@ -1,68 +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 = SourcesDataGrid;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const ColorPicker_1 = __importDefault(require("@jbrowse/core/ui/ColorPicker"));
-const util_1 = require("@jbrowse/core/util");
-const x_data_grid_1 = require("@mui/x-data-grid");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
-    cell: {
-        whiteSpace: 'nowrap',
-        overflow: 'hidden',
-        textOverflow: 'ellipsis',
-    },
-});
-function SourcesDataGrid({ rows, onChange, setSelected, }) {
-    const { classes } = useStyles();
-    const { id: _id, name: _name, label: _label, color: _color, baseUri: _baseUri, HP: _HP, ...rest } = rows[0];
-    const [currSort, setCurrSort] = (0, react_1.useState)({
-        idx: 0,
-        field: null,
-    });
-    return ((0, jsx_runtime_1.jsx)("div", { style: { height: 400, width: '100%' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { checkboxSelection: true, disableRowSelectionOnClick: true, onRowSelectionModelChange: arg => {
-                setSelected([...arg.ids]);
-            }, rows: rows, rowHeight: 25, columnHeaderHeight: 33, columns: [
-                {
-                    field: 'color',
-                    headerName: 'Color',
-                    renderCell: params => {
-                        const { value, id } = params;
-                        return ((0, jsx_runtime_1.jsx)(ColorPicker_1.default, { color: value || 'blue', onChange: c => {
-                                const elt = rows.find(f => f.name === id);
-                                if (elt) {
-                                    elt.color = c;
-                                }
-                                onChange([...rows]);
-                            } }));
-                    },
-                },
-                {
-                    field: 'label',
-                    headerName: 'Name',
-                    width: (0, util_1.measureGridWidth)(rows.map(r => r.label)),
-                },
-                ...Object.keys(rest).map(val => ({
-                    field: val,
-                    renderCell: ({ value }) => ((0, jsx_runtime_1.jsx)("div", { className: classes.cell, children: (0, jsx_runtime_1.jsx)(ui_1.SanitizedHTML, { html: (0, util_1.getStr)(value) }) })),
-                    width: (0, util_1.measureGridWidth)(rows.map(r => `${r[val]}`)),
-                })),
-            ], sortModel: [], onSortModelChange: args => {
-                const sort = args[0];
-                const idx = (currSort.idx + 1) % 2;
-                const field = sort.field || currSort.field;
-                setCurrSort({ idx, field });
-                onChange(field
-                    ? [...rows].sort((a, b) => {
-                        const aa = (0, util_1.getStr)(a[field]);
-                        const bb = (0, util_1.getStr)(b[field]);
-                        return idx === 1 ? aa.localeCompare(bb) : bb.localeCompare(aa);
-                    })
-                    : rows);
-            } }) }));
-}

package/dist/shared/components/SourcesGrid.d.ts

@@ -1,7 +0,0 @@
-import type { Source } from '../types';
-declare function SourcesGrid({ rows, onChange, showTips, }: {
-    rows: Source[];
-    onChange: (arg: Source[]) => void;
-    showTips: boolean;
-}): import("react/jsx-runtime").JSX.Element;
-export default SourcesGrid;

package/dist/shared/components/SourcesGrid.js

@@ -1,14 +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 SourcesDataGrid_1 = __importDefault(require("./SourcesDataGrid"));
-const SourcesGridHeader_1 = __importDefault(require("./SourcesGridHeader"));
-function SourcesGrid({ rows, onChange, showTips, }) {
-    const [selected, setSelected] = (0, react_1.useState)([]);
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(SourcesGridHeader_1.default, { selected: selected, rows: rows, showTips: showTips, onChange: onChange }), rows.length ? ((0, jsx_runtime_1.jsx)(SourcesDataGrid_1.default, { rows: rows, onChange: onChange, setSelected: setSelected })) : ((0, jsx_runtime_1.jsx)("div", { children: "No rows" }))] }));
-}
-exports.default = SourcesGrid;

package/dist/shared/components/SourcesGridHeader.d.ts

@@ -1,8 +0,0 @@
-import type { Source } from '../types';
-import type { GridRowId } from '@mui/x-data-grid';
-export default function SourcesGridHeader({ selected, onChange, rows, showTips, }: {
-    onChange: (arg: Source[]) => void;
-    rows: Source[];
-    selected: GridRowId[];
-    showTips: boolean;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/components/SourcesGridHeader.js

@@ -1,41 +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 = SourcesGridHeader;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ColorPicker_1 = require("@jbrowse/core/ui/ColorPicker");
-const KeyboardArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardArrowDown"));
-const KeyboardArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardArrowUp"));
-const KeyboardDoubleArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowDown"));
-const KeyboardDoubleArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowUp"));
-const material_1 = require("@mui/material");
-const sourcesGridUtils_1 = require("../sourcesGridUtils");
-function SourcesGridHeader({ selected, onChange, rows, showTips, }) {
-    const [anchorEl, setAnchorEl] = (0, react_1.useState)(null);
-    const [widgetColor, setWidgetColor] = (0, react_1.useState)('blue');
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !selected.length, onClick: event => {
-                    setAnchorEl(event.currentTarget);
-                }, children: "Change color of selected items" }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
-                    onChange((0, sourcesGridUtils_1.moveUp)([...rows], selected));
-                }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardArrowUp_1.default, {}), showTips ? 'Move selected items up' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
-                    onChange((0, sourcesGridUtils_1.moveDown)([...rows], selected));
-                }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardArrowDown_1.default, {}), showTips ? 'Move selected items down' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
-                    onChange((0, sourcesGridUtils_1.moveUp)([...rows], selected, rows.length));
-                }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardDoubleArrowUp_1.default, {}), showTips ? 'Move selected items to top' : null] }), (0, jsx_runtime_1.jsxs)(material_1.Button, { onClick: () => {
-                    onChange((0, sourcesGridUtils_1.moveDown)([...rows], selected, rows.length));
-                }, disabled: !selected.length, children: [(0, jsx_runtime_1.jsx)(KeyboardDoubleArrowDown_1.default, {}), showTips ? 'Move selected items to bottom' : null] }), (0, jsx_runtime_1.jsx)(ColorPicker_1.ColorPopover, { anchorEl: anchorEl, color: widgetColor, onChange: c => {
-                    setWidgetColor(c);
-                    for (const id of selected) {
-                        const elt = rows.find(f => f.name === id);
-                        if (elt) {
-                            elt.color = c;
-                        }
-                    }
-                    onChange([...rows]);
-                }, onClose: () => {
-                    setAnchorEl(null);
-                } })] }));
-}

package/dist/shared/components/ui/SetColorDialog.d.ts

@@ -1,31 +0,0 @@
-interface SetColorDialogProps {
-    model: {
-        sources?: {
-            name: string;
-            [key: string]: unknown;
-        }[];
-        setLayout: (s: {
-            name: string;
-            [key: string]: unknown;
-        }[]) => void;
-        clearLayout: () => void;
-    };
-    handleClose: () => void;
-    title?: string;
-    enableBulkEdit?: boolean;
-    enableRowPalettizer?: boolean;
-    showTipsStorageKey?: string;
-    SourcesGridComponent: React.ComponentType<{
-        rows: {
-            name: string;
-            [key: string]: unknown;
-        }[];
-        onChange: (rows: {
-            name: string;
-            [key: string]: unknown;
-        }[]) => void;
-        showTips: boolean;
-    }>;
-}
-export default function SetColorDialog({ model, handleClose, title, enableBulkEdit, enableRowPalettizer, showTipsStorageKey, SourcesGridComponent, }: SetColorDialogProps): import("react/jsx-runtime").JSX.Element;
-export {};

package/dist/shared/components/ui/SetColorDialog.js

@@ -1,51 +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 = SetColorDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const DraggableDialog_1 = __importDefault(require("@jbrowse/core/ui/DraggableDialog"));
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const SetColorDialogBulkEditPanel_1 = __importDefault(require("./SetColorDialogBulkEditPanel"));
-const SetColorDialogHelpfulTips_1 = __importDefault(require("./SetColorDialogHelpfulTips"));
-const SetColorDialogRowPalettizer_1 = __importDefault(require("./SetColorDialogRowPalettizer"));
-const useStyles = (0, mui_1.makeStyles)()({
-    content: {
-        minWidth: 800,
-    },
-    fr: {
-        float: 'right',
-        display: 'flex',
-        gap: 8,
-    },
-});
-function SetColorDialog({ model, handleClose, title = 'Color/arrangement editor', enableBulkEdit = false, enableRowPalettizer = false, showTipsStorageKey = 'setColorDialog-showTips', SourcesGridComponent, }) {
-    const { classes } = useStyles();
-    const { sources } = model;
-    const [showBulkEditor, setShowBulkEditor] = (0, react_1.useState)(false);
-    const [currLayout, setCurrLayout] = (0, react_1.useState)(structuredClone(sources || []));
-    const [showTips, setShowTips] = (0, util_1.useLocalStorage)(showTipsStorageKey, false);
-    return ((0, jsx_runtime_1.jsx)(DraggableDialog_1.default, { open: true, onClose: handleClose, maxWidth: "xl", title: title, children: showBulkEditor && enableBulkEdit ? ((0, jsx_runtime_1.jsx)(SetColorDialogBulkEditPanel_1.default, { currLayout: currLayout, onClose: arg => {
-                if (arg) {
-                    setCurrLayout(arg);
-                }
-                setShowBulkEditor(false);
-            } })) : ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.content, children: [(0, jsx_runtime_1.jsxs)("div", { className: classes.fr, children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                        setShowTips(!showTips);
-                                    }, children: showTips ? 'Hide tips' : 'Show tips' }), enableBulkEdit ? ((0, jsx_runtime_1.jsx)(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
-                                        setShowBulkEditor(!showBulkEditor);
-                                    }, children: "Show Bulk row editor" })) : null] }), showTips ? (0, jsx_runtime_1.jsx)(SetColorDialogHelpfulTips_1.default, {}) : null, enableRowPalettizer ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("br", {}), (0, jsx_runtime_1.jsx)(SetColorDialogRowPalettizer_1.default, { currLayout: currLayout, setCurrLayout: setCurrLayout })] })) : null, (0, jsx_runtime_1.jsx)(SourcesGridComponent, { rows: currLayout, onChange: setCurrLayout, showTips: showTips })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", type: "submit", color: "inherit", onClick: () => {
-                                model.clearLayout();
-                                setCurrLayout(model.sources || []);
-                            }, children: "Clear custom settings" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                                handleClose();
-                                setCurrLayout([...(model.sources || [])]);
-                            }, children: "Cancel" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: () => {
-                                model.setLayout(currLayout);
-                                handleClose();
-                            }, children: "Submit" })] })] })) }));
-}

package/dist/shared/components/ui/SetColorDialogBulkEditPanel.d.ts

@@ -1,10 +0,0 @@
-export default function SetColorDialogBulkEditPanel({ onClose, currLayout, }: {
-    currLayout: {
-        name: string;
-        [key: string]: unknown;
-    }[];
-    onClose: (arg?: {
-        name: string;
-        [key: string]: unknown;
-    }[]) => void;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/components/ui/SetColorDialogBulkEditPanel.js

@@ -1,84 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetColorDialogBulkEditPanel;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-});
-function SetColorDialogBulkEditPanel({ onClose, currLayout, }) {
-    const { classes } = useStyles();
-    const [val, setVal] = (0, react_1.useState)('');
-    const [error, setError] = (0, react_1.useState)();
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Paste CSV or TSV. If a header column is present. First line is a header. If a column called \"name\" is present, it uses that to connect to IDs in the table, otherwise it uses the first column no." }), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, placeholder: 'name,population\nHG00098,GBR\nHG00101,GBR\nHG00459,CHS\n...', maxRows: 10, fullWidth: true, value: val, onChange: event => {
-                            setVal(event.target.value);
-                        }, slotProps: {
-                            input: {
-                                classes: {
-                                    input: classes.textAreaFont,
-                                },
-                            },
-                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            const lines = val
-                                .split('\n')
-                                .map(f => f.trim())
-                                .filter(f => !!f);
-                            const fields = lines[0].split(/[,\t]/gm);
-                            if (fields.includes('name')) {
-                                setError('');
-                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
-                                const newData = Object.fromEntries(lines.slice(1).map(line => {
-                                    const cols = line.split(/[,\t]/gm);
-                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
-                                    return [
-                                        newRecord.name,
-                                        {
-                                            ...newRecord,
-                                            ...oldLayout[newRecord.name],
-                                        },
-                                    ];
-                                }));
-                                onClose(currLayout.map(record => ({
-                                    ...record,
-                                    ...newData[record.name],
-                                })));
-                            }
-                            else {
-                                setError(new Error('No "name" column found on line 1'));
-                            }
-                        }, children: "Update rows" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
-                            const lines = val
-                                .split('\n')
-                                .map(f => f.trim())
-                                .filter(f => !!f);
-                            const fields = lines[0].split(/[,\t]/gm);
-                            if (fields.includes('name')) {
-                                setError('');
-                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
-                                const newData = Object.fromEntries(lines.slice(1).map(line => {
-                                    const cols = line.split(/[,\t]/gm);
-                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
-                                    return [
-                                        newRecord.name,
-                                        {
-                                            ...newRecord,
-                                            ...oldLayout[newRecord.name],
-                                        },
-                                    ];
-                                }));
-                                onClose(currLayout.map(record => ({
-                                    ...newData[record.name],
-                                })));
-                            }
-                            else {
-                                setError(new Error('No "name" column found on line 1'));
-                            }
-                        }, children: "Replace rows" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
-                            onClose();
-                        }, children: "Cancel" })] })] }));
-}

package/dist/shared/components/ui/SetColorDialogHelpfulTips.d.ts

@@ -1 +0,0 @@
-export default function SetColorDialogHelpfulTips(): import("react/jsx-runtime").JSX.Element;

package/dist/shared/components/ui/SetColorDialogHelpfulTips.js

@@ -1,7 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetColorDialogHelpfulTips;
-const jsx_runtime_1 = require("react/jsx-runtime");
-function SetColorDialogHelpfulTips() {
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: ["Helpful tips", (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsx)("li", { children: "You can select rows in the table with the checkboxes" }), (0, jsx_runtime_1.jsx)("li", { children: "Multi-select is enabled with shift-click and control-click" }), (0, jsx_runtime_1.jsx)("li", { children: "The \"Move selected items up/down\" can re-arrange subtracks" }), (0, jsx_runtime_1.jsx)("li", { children: "Sorting the data grid itself can also re-arrange subtracks" }), (0, jsx_runtime_1.jsx)("li", { children: "Changes are applied when you hit Submit" }), (0, jsx_runtime_1.jsx)("li", { children: "You can click and drag the dialog box to move it on the screen" }), (0, jsx_runtime_1.jsx)("li", { children: "Columns in the table can be hidden using a vertical '...' menu on the right side of each column" })] })] }));
-}

package/dist/shared/components/ui/SetColorDialogRowPalettizer.d.ts

@@ -1,10 +0,0 @@
-export default function SetColorDialogRowPalettizer({ setCurrLayout, currLayout, }: {
-    currLayout: {
-        name: string;
-        [key: string]: unknown;
-    }[];
-    setCurrLayout: (arg: {
-        name: string;
-        [key: string]: unknown;
-    }[]) => void;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/shared/components/ui/SetColorDialogRowPalettizer.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SetColorDialogRowPalettizer;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const colors_1 = require("@jbrowse/core/ui/colors");
-const color_1 = require("@jbrowse/core/util/color");
-const material_1 = require("@mui/material");
-function SetColorDialogRowPalettizer({ setCurrLayout, currLayout, }) {
-    if (!currLayout.length || !currLayout[0]) {
-        return null;
-    }
-    const fields = Object.keys(currLayout[0]).filter(f => f !== 'name' &&
-        f !== 'color' &&
-        f !== 'label' &&
-        f !== 'id' &&
-        f !== 'HP');
-    return ((0, jsx_runtime_1.jsxs)("div", { children: ["Create color palette based on...", fields.map(r => ((0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
-                    const map = new Map();
-                    for (const row of currLayout) {
-                        const val = map.get(row[r]);
-                        if (!val) {
-                            map.set(row[r], 1);
-                        }
-                        else {
-                            map.set(row[r], val + 1);
-                        }
-                    }
-                    const ret = Object.fromEntries([...map.entries()]
-                        .sort((a, b) => a[1] - b[1])
-                        .map((r, idx) => [r[0], colors_1.set1[idx] || (0, color_1.randomColor)(r[0])]));
-                    setCurrLayout(currLayout.map(row => ({
-                        ...row,
-                        color: ret[row[r]],
-                    })));
-                }, children: r }, r))), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
-                    setCurrLayout(currLayout.map(row => ({
-                        ...row,
-                        color: undefined,
-                    })));
-                }, children: "Clear colors" })] }));
-}

package/dist/shared/constants.d.ts

@@ -1,2 +0,0 @@
-export declare const fudgeFactor = 0.6;
-export declare const f2: number;

package/dist/shared/constants.js

@@ -1,5 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.f2 = exports.fudgeFactor = void 0;
-exports.fudgeFactor = 0.6;
-exports.f2 = exports.fudgeFactor / 2;

package/dist/shared/drawAlleleCount.d.ts

@@ -1,2 +0,0 @@
-export declare function getColorAlleleCount(ref: number, alt: number, alt2: number, uncalled: number, total: number, drawReference?: boolean): any;
-export declare function drawColorAlleleCount(c: string, ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, featureType?: string, featureStrand?: number, alpha?: number): void;

package/dist/shared/drawAlleleCount.js

@@ -1,50 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getColorAlleleCount = getColorAlleleCount;
-exports.drawColorAlleleCount = drawColorAlleleCount;
-const colord_1 = require("@jbrowse/core/util/colord");
-const constants_1 = require("./constants");
-function getColorAlleleCount(ref, alt, alt2, uncalled, total, drawReference = true) {
-    if (ref === total) {
-        return drawReference ? '#ccc' : '';
-    }
-    else {
-        let a1;
-        if (alt) {
-            a1 = (0, colord_1.colord)(`hsl(200,50%,${80 - (alt / total) * 50}%)`);
-        }
-        if (alt2) {
-            const l = `hsla(0,100%,20%,${alt2 / total})`;
-            a1 = a1 ? a1.mix(l) : (0, colord_1.colord)(l);
-        }
-        if (uncalled) {
-            const l = `hsl(50,50%,50%,${uncalled / total})`;
-            a1 = a1 ? a1.mix(l) : (0, colord_1.colord)(l);
-        }
-        return (a1 === null || a1 === void 0 ? void 0 : a1.toHex()) || 'black';
-    }
-}
-function drawColorAlleleCount(c, ctx, x, y, w, h, featureType = '', featureStrand, alpha = 1) {
-    ctx.fillStyle = alpha !== 1 ? (0, colord_1.colord)(c).alpha(alpha).toHex() : c;
-    if (featureType === 'inversion') {
-        if (featureStrand === 1) {
-            ctx.beginPath();
-            ctx.moveTo(x - constants_1.f2, y - constants_1.f2);
-            ctx.lineTo(x - constants_1.f2, y + h + constants_1.f2);
-            ctx.lineTo(x + w + constants_1.f2, y + h / 2);
-            ctx.closePath();
-            ctx.fill();
-        }
-        else {
-            ctx.beginPath();
-            ctx.moveTo(x + w + constants_1.f2, y - constants_1.f2);
-            ctx.lineTo(x + w + constants_1.f2, y + h + constants_1.f2);
-            ctx.lineTo(x - constants_1.f2, y + h / 2);
-            ctx.closePath();
-            ctx.fill();
-        }
-    }
-    else {
-        ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
-    }
-}

package/dist/shared/drawPhased.d.ts

@@ -1 +0,0 @@
-export declare function drawPhased(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, HP: number, PS?: string, drawReference?: boolean, alpha?: number): string | undefined;

package/dist/shared/drawPhased.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawPhased = drawPhased;
-const colors_1 = require("@jbrowse/core/ui/colors");
-const colord_1 = require("@jbrowse/core/util/colord");
-const constants_1 = require("./constants");
-const util_1 = require("./util");
-function getColorPhased(alleles, HP, drawReference = true) {
-    const c = +alleles[HP];
-    return c ? colors_1.set1[c - 1] || 'black' : drawReference ? '#ccc' : undefined;
-}
-function getColorPhasedWithPhaseSet(alleles, HP, PS, drawReference = true) {
-    const c = +alleles[HP];
-    return c ? (0, util_1.colorify)(+PS) || 'black' : drawReference ? '#ccc' : undefined;
-}
-function drawPhased(alleles, ctx, x, y, w, h, HP, PS, drawReference = true, alpha = 1) {
-    const c = PS !== undefined
-        ? getColorPhasedWithPhaseSet(alleles, HP, PS, drawReference)
-        : getColorPhased(alleles, HP, drawReference);
-    if (c) {
-        ctx.fillStyle = alpha !== 1 ? (0, colord_1.colord)(c).alpha(alpha).toHex() : c;
-        ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
-    }
-    return c;
-}

package/dist/shared/findSecondLargestNumber.js

@@ -1 +0,0 @@
-"use strict";

package/dist/shared/getSources.d.ts

@@ -1,15 +0,0 @@
-import type { SampleInfo, Source } from './types';
-export declare function getSources({ sources, layout, renderingMode, sampleInfo, }: {
-    sources: Source[];
-    layout?: Source[];
-    renderingMode: string;
-    sampleInfo?: Record<string, SampleInfo>;
-}): {
-    label: string;
-    id: string;
-    baseUri?: string;
-    name: string;
-    color?: string;
-    group?: string;
-    HP?: number;
-}[];

package/dist/shared/getSources.js

@@ -1,34 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSources = getSources;
-function getSources({ sources, layout = sources, renderingMode, sampleInfo, }) {
-    const rows = [];
-    const sourceMap = Object.fromEntries(sources.map(s => [s.name, s]));
-    for (const row of layout) {
-        if (renderingMode === 'phased') {
-            const info = sampleInfo === null || sampleInfo === void 0 ? void 0 : sampleInfo[row.name];
-            if (info === null || info === void 0 ? void 0 : info.isPhased) {
-                const ploidy = info.maxPloidy;
-                for (let i = 0; i < ploidy; i++) {
-                    const id = `${row.name} HP${i}`;
-                    rows.push({
-                        ...sourceMap[row.name],
-                        ...row,
-                        label: id,
-                        HP: i,
-                        id: id,
-                    });
-                }
-            }
-        }
-        else {
-            rows.push({
-                ...sourceMap[row.name],
-                ...row,
-                label: row.name,
-                id: row.name,
-            });
-        }
-    }
-    return rows;
-}

package/dist/shared/minorAlleleFrequencyUtils.d.ts

@@ -1,14 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function findSecondLargestNumber(arr: Iterable<number>): number;
-export declare function calculateAlleleCounts(feat: Feature): Record<string, number>;
-export declare function calculateMinorAlleleFrequency(alleleCounts: Record<string, number>): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopToken, }: {
-    features: Iterable<Feature>;
-    minorAlleleFrequencyFilter: number;
-    lengthCutoffFilter: number;
-    stopToken?: string;
-}): {
-    feature: Feature;
-    mostFrequentAlt: string;
-    alleleCounts: Record<string, number>;
-}[];

package/dist/shared/minorAlleleFrequencyUtils.js

@@ -1,72 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.findSecondLargestNumber = findSecondLargestNumber;
-exports.calculateAlleleCounts = calculateAlleleCounts;
-exports.calculateMinorAlleleFrequency = calculateMinorAlleleFrequency;
-exports.getFeaturesThatPassMinorAlleleFrequencyFilter = getFeaturesThatPassMinorAlleleFrequencyFilter;
-const util_1 = require("@jbrowse/core/util");
-function findSecondLargestNumber(arr) {
-    let firstMax = 0;
-    let secondMax = 0;
-    for (const num of arr) {
-        if (num > firstMax) {
-            secondMax = firstMax;
-            firstMax = num;
-        }
-        else if (num > secondMax && num !== firstMax) {
-            secondMax = num;
-        }
-    }
-    return secondMax;
-}
-function calculateAlleleCounts(feat) {
-    var _a;
-    const genotypes = feat.get('genotypes');
-    const alleleCounts = { 0: 0, 1: 0, '.': 0 };
-    const cacheSplit = {};
-    const vals = Object.values(genotypes);
-    const len = vals.length;
-    for (let i = 0; i < len; i++) {
-        const genotype = vals[i];
-        const alleles = cacheSplit[genotype] || (cacheSplit[genotype] = genotype.split(/[/|]/));
-        for (let i = 0, len = alleles.length; i < len; i++) {
-            const a = alleles[i];
-            alleleCounts[a] = ((_a = alleleCounts[a]) !== null && _a !== void 0 ? _a : 0) + 1;
-        }
-    }
-    return alleleCounts;
-}
-function calculateMinorAlleleFrequency(alleleCounts) {
-    return (findSecondLargestNumber(Object.values(alleleCounts)) /
-        ((0, util_1.sum)(Object.values(alleleCounts)) || 1));
-}
-function getMostFrequentAlt(alleleCounts) {
-    let mostFrequentAlt;
-    let max = 0;
-    for (const [alt, altCount] of Object.entries(alleleCounts)) {
-        if (alt !== '.' && alt !== '0') {
-            if (altCount > max) {
-                mostFrequentAlt = alt;
-                max = altCount;
-            }
-        }
-    }
-    return mostFrequentAlt;
-}
-function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopToken, }) {
-    const results = [];
-    (0, util_1.forEachWithStopTokenCheck)(features, stopToken, feature => {
-        if (feature.get('end') - feature.get('start') <= lengthCutoffFilter) {
-            const alleleCounts = calculateAlleleCounts(feature);
-            if (calculateMinorAlleleFrequency(alleleCounts) >=
-                minorAlleleFrequencyFilter) {
-                results.push({
-                    feature,
-                    mostFrequentAlt: getMostFrequentAlt(alleleCounts),
-                    alleleCounts,
-                });
-            }
-        }
-    });
-    return results;
-}

package/dist/shared/sourcesGridUtils.d.ts

@@ -1,11 +0,0 @@
-import type { GridRowId } from '@mui/x-data-grid';
-export declare function moveUp(arr: {
-    name: string;
-}[], sel: GridRowId[], by?: number): {
-    name: string;
-}[];
-export declare function moveDown(arr: {
-    name: string;
-}[], sel: GridRowId[], by?: number): {
-    name: string;
-}[];