@jbrowse/plugin-wiggle 3.7.0 → 4.0.0

package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.js

@@ -1,153 +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 tracks_1 = require("@jbrowse/core/util/tracks");
-const material_1 = require("@mui/material");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const file_saver_1 = require("file-saver");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-    mgap: {
-        display: 'flex',
-        flexDirection: 'column',
-        gap: theme.spacing(4),
-    },
-}));
-const WiggleClusterDialogManuals = (0, mobx_react_1.observer)(function ({ model, handleClose, children, }) {
-    const { classes } = useStyles();
-    const [paste, setPaste] = (0, react_1.useState)('');
-    const [ret, setRet] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    const [loading, setLoading] = (0, react_1.useState)(false);
-    const [showAdvanced, setShowAdvanced] = (0, util_1.useLocalStorage)('cluster-showAdvanced', false);
-    const [clusterMethod, setClusterMethod] = (0, react_1.useState)('single');
-    const [samplesPerPixel, setSamplesPerPixel] = (0, react_1.useState)('1');
-    (0, react_1.useEffect)(() => {
-        ;
-        (async () => {
-            try {
-                setError(undefined);
-                setRet(undefined);
-                setLoading(true);
-                const view = (0, util_1.getContainingView)(model);
-                const { dynamicBlocks, bpPerPx } = view;
-                const { rpcManager } = (0, util_1.getSession)(model);
-                const { sourcesWithoutLayout, adapterConfig } = model;
-                const sessionId = (0, tracks_1.getRpcSessionId)(model);
-                const ret = (await rpcManager.call(sessionId, 'MultiWiggleGetScoreMatrix', {
-                    regions: dynamicBlocks.contentBlocks,
-                    sources: sourcesWithoutLayout,
-                    sessionId,
-                    adapterConfig,
-                    bpPerPx: bpPerPx / +samplesPerPixel,
-                }));
-                setRet(ret);
-            }
-            catch (e) {
-                if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(model)) {
-                    console.error(e);
-                    setError(e);
-                }
-            }
-            finally {
-                setLoading(false);
-            }
-        })();
-    }, [model, samplesPerPixel]);
-    const results = ret
-        ? String.raw `inputMatrix<-matrix(c(${Object.values(ret)
-            .map(val => val.join(','))
-            .join(',\n')}
-),nrow=${Object.values(ret).length},byrow=TRUE)
-rownames(inputMatrix)<-c(${Object.keys(ret)
-            .map(key => `'${key}'`)
-            .join(',')})
-resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
-cat(resultClusters$order,sep='\n')`
-        : undefined;
-    const resultsTsv = ret
-        ? Object.entries(ret)
-            .map(([key, val]) => [key, ...val].join('\t'))
-            .join('\n')
-        : undefined;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [children, (0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 50 }, children: [(0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: {
-                                            display: 'flex',
-                                            gap: '8px',
-                                            flexWrap: 'wrap',
-                                            marginBottom: '16px',
-                                        }, children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, file_saver_1.saveAs)(new Blob([results || ''], {
-                                                        type: 'text/plain;charset=utf-8',
-                                                    }), 'cluster.R');
-                                                }, children: "Download Rscript" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, copy_to_clipboard_1.default)(results || '');
-                                                }, children: "Copy Rscript to clipboard" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, file_saver_1.saveAs)(new Blob([resultsTsv || ''], {
-                                                        type: 'text/plain;charset=utf-8',
-                                                    }), 'scores.tsv');
-                                                }, children: "Download TSV" })] }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                setShowAdvanced(!showAdvanced);
-                                            }, children: showAdvanced
-                                                ? 'Hide advanced options'
-                                                : 'Show advanced options' }) }), showAdvanced ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "h6", children: "Advanced options" }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { children: Object.entries({
-                                                    single: 'Single',
-                                                    complete: 'Complete',
-                                                }).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Radio, { checked: clusterMethod === key, onChange: () => {
-                                                            setClusterMethod(key);
-                                                        } }), label: val }, key))) }), (0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 20 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This procedure samples the data at each 'pixel' across the visible by default" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Samples per pixel (>1 for denser sampling, between 0-1 for sparser sampling)", variant: "outlined", size: "small", value: samplesPerPixel, onChange: event => {
-                                                            setSamplesPerPixel(event.target.value);
-                                                        } })] })] })) : null, results ? ((0, jsx_runtime_1.jsx)("div", {})) : loading ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { variant: "h6", message: "Generating score matrix" })) : error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : null] }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "subtitle2", gutterBottom: true, style: { marginTop: '16px' }, children: "Clustering Results:" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
-                                            setPaste(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", onClick: () => {
-                            var _a;
-                            const { sourcesWithoutLayout } = model;
-                            if (sourcesWithoutLayout) {
-                                try {
-                                    const currentLayout = ((_a = model.layout) === null || _a === void 0 ? void 0 : _a.length)
-                                        ? model.layout
-                                        : sourcesWithoutLayout;
-                                    const sourcesByName = Object.fromEntries(currentLayout.map((s) => [s.name, s]));
-                                    model.setLayout(paste
-                                        .split('\n')
-                                        .map(t => t.trim())
-                                        .filter(f => !!f)
-                                        .map(r => +r)
-                                        .map(idx => {
-                                        const sourceItem = sourcesWithoutLayout[idx - 1];
-                                        if (!sourceItem) {
-                                            throw new Error(`out of bounds at ${idx}`);
-                                        }
-                                        return {
-                                            ...sourceItem,
-                                            ...sourcesByName[sourceItem.name],
-                                        };
-                                    }));
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    (0, util_1.getSession)(model).notifyError(`${e}`, e);
-                                }
-                            }
-                            handleClose();
-                        }, children: "Apply clustering" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-exports.default = WiggleClusterDialogManuals;

package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.d.ts

@@ -1,8 +0,0 @@
-import type { Source } from '../../../util';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export interface ReducedModel {
-    sourcesWithoutLayout?: Source[];
-    layout?: Source[];
-    adapterConfig: AnyConfigurationModel;
-    setLayout: (arg: Source[]) => void;
-}

package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts

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

package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.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 plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_react_1 = require("mobx-react");
-const YScaleBars_1 = __importDefault(require("./YScaleBars"));
-const MultiLinearWiggleDisplayComponent = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }), (0, jsx_runtime_1.jsx)(YScaleBars_1.default, { model: model })] }));
-});
-exports.default = MultiLinearWiggleDisplayComponent;

package/dist/MultiLinearWiggleDisplay/components/YScaleBars.d.ts

@@ -1,7 +0,0 @@
-import type { WiggleDisplayModel } from '../model';
-export declare const YScaleBars: (props: {
-    model: WiggleDisplayModel;
-    orientation?: string;
-    exportSVG?: boolean;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default YScaleBars;

package/dist/MultiLinearWiggleDisplay/components/YScaleBars.js

@@ -1,28 +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.YScaleBars = void 0;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const mobx_react_1 = require("mobx-react");
-const FullHeightScaleBar_1 = __importDefault(require("./FullHeightScaleBar"));
-const IndividualScaleBars_1 = __importDefault(require("./IndividualScaleBars"));
-const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSVG, }) {
-    const { height } = model;
-    return exportSVG ? (children) : ((0, jsx_runtime_1.jsx)("svg", { style: {
-            position: 'absolute',
-            top: 0,
-            left: 0,
-            pointerEvents: 'none',
-            height,
-            width: (0, util_1.getContainingView)(model).width,
-        }, children: children }));
-});
-exports.YScaleBars = (0, mobx_react_1.observer)(function (props) {
-    const { model, orientation, exportSVG } = props;
-    const { showSidebar, stats, needsFullHeightScalebar, sources } = model;
-    return stats && sources ? ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, children: showSidebar ? (needsFullHeightScalebar ? ((0, jsx_runtime_1.jsx)(FullHeightScaleBar_1.default, { model: model, orientation: orientation, exportSVG: exportSVG })) : ((0, jsx_runtime_1.jsx)(IndividualScaleBars_1.default, { model: model, orientation: orientation, exportSVG: exportSVG }))) : null })) : null;
-});
-exports.default = exports.YScaleBars;

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

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

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

@@ -1,42 +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 !== 'source' &&
-        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/MultiLinearWiggleDisplay/components/util.d.ts

@@ -1,9 +0,0 @@
-import type { WiggleDisplayModel } from '../model';
-import type { GridRowId } from '@mui/x-data-grid';
-export declare function moveUp<T extends {
-    name: string;
-}>(arr: T[], sel: GridRowId[], by?: number): T[];
-export declare function moveDown<T extends {
-    name: string;
-}>(arr: T[], sel: GridRowId[], by?: number): T[];
-export declare function getOffset(model: WiggleDisplayModel): number;

package/dist/MultiLinearWiggleDisplay/components/util.js

@@ -1,45 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.moveUp = moveUp;
-exports.moveDown = moveDown;
-exports.getOffset = getOffset;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-function moveUp(arr, sel, by = 1) {
-    const idxs = sel
-        .map(l => arr.findIndex(v => v.name === l))
-        .sort((a, b) => a - b);
-    let lastIdx = 0;
-    for (const old of idxs) {
-        const idx = Math.max(lastIdx, old - by);
-        if (idx >= lastIdx) {
-            arr.splice(idx, 0, arr.splice(old, 1)[0]);
-        }
-        lastIdx = lastIdx + 1;
-    }
-    return arr;
-}
-function moveDown(arr, sel, by = 1) {
-    const idxs = sel
-        .map(l => arr.findIndex(v => v.name === l))
-        .sort((a, b) => b - a);
-    let lastIdx = arr.length - 1;
-    for (const old of idxs) {
-        const idx = Math.min(lastIdx, old + by);
-        if (idx <= lastIdx) {
-            arr.splice(idx, 0, arr.splice(old, 1)[0]);
-        }
-        lastIdx = lastIdx - 1;
-    }
-    return arr;
-}
-const trackLabelFontSize = 12.8;
-function getOffset(model) {
-    const { prefersOffset } = model;
-    const { trackLabels } = (0, util_1.getContainingView)(model);
-    const track = (0, util_1.getContainingTrack)(model);
-    const trackName = (0, configuration_1.getConf)(track, 'name');
-    return trackLabels === 'overlapping' && !prefersOffset
-        ? (0, util_1.measureText)(trackName, trackLabelFontSize) + 100
-        : 10;
-}

package/dist/MultiLinearWiggleDisplay/configSchema.d.ts

@@ -1,84 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    defaultRendering: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        defaultValue: string;
-    };
-    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        MultiXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        MultiDensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        MultiRowXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        MultiLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        MultiRowLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    height: {
-        type: string;
-        defaultValue: number;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    autoscale: {
-        type: string;
-        defaultValue: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-    };
-    minimalTicks: {
-        type: string;
-        defaultValue: boolean;
-        description: string;
-    };
-    minScore: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    maxScore: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    numStdDev: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    scaleType: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
-    };
-    inverted: {
-        type: string;
-        description: string;
-        defaultValue: boolean;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;