@jbrowse/plugin-wiggle 2.0.1 → 2.1.0

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js

@@ -0,0 +1,162 @@
+import React, { useState } from 'react';
+import { Button, Dialog, DialogContent, DialogActions, DialogTitle, IconButton, Paper, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { getStr, isUriLocation, measureGridWidth, useLocalStorage, } from '@jbrowse/core/util';
+import { DataGrid } from '@mui/x-data-grid';
+import Draggable from 'react-draggable';
+import clone from 'clone';
+// locals
+import ColorPicker, { ColorPopover } from '@jbrowse/core/ui/ColorPicker';
+import { UriLink } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import { moveUp, moveDown } from './util';
+// icons
+import CloseIcon from '@mui/icons-material/Close';
+import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp';
+import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrowDown';
+import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
+import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp';
+const useStyles = makeStyles()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+    content: {
+        minWidth: 800,
+    },
+}));
+// draggable dialog demo https://mui.com/material-ui/react-dialog/#draggable-dialog
+function PaperComponent(props) {
+    return (React.createElement(Draggable, { handle: "#draggable-dialog-title", cancel: '[class*="MuiDialogContent-root"]' },
+        React.createElement(Paper, { ...props })));
+}
+export default function SetColorDialog({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const { sources } = model;
+    const [currLayout, setCurrLayout] = useState(clone(sources || []));
+    const [showTipsTmp, setShowTips] = useLocalStorage('multiwiggle-showTips', 'true');
+    const showTips = showTipsTmp === 'true';
+    return (React.createElement(Dialog, { PaperComponent: PaperComponent, open: true, onClose: handleClose, maxWidth: "xl", "aria-labelledby": "draggable-dialog-title" // this area is important for the draggable functionality
+     },
+        React.createElement(DialogTitle, { style: { cursor: 'move' }, id: "draggable-dialog-title" },
+            "Multi-wiggle color/arrangement editor",
+            ' ',
+            React.createElement(IconButton, { className: classes.closeButton, onClick: handleClose },
+                React.createElement(CloseIcon, null))),
+        React.createElement(DialogContent, { className: classes.content },
+            React.createElement(Button, { variant: "contained", style: { float: 'right' }, onClick: () => setShowTips(showTips ? 'false' : 'true') }, showTips ? 'Hide tips' : 'Show tips'),
+            React.createElement("br", null),
+            showTips ? (React.createElement(React.Fragment, null,
+                "Helpful tips",
+                React.createElement("ul", null,
+                    React.createElement("li", null, "You can select rows in the table with the checkboxes"),
+                    React.createElement("li", null, "Multi-select is enabled with shift-click and control-click"),
+                    React.createElement("li", null, "The \"Move selected items up/down\" can re-arrange subtracks"),
+                    React.createElement("li", null, "Sorting the data grid itself can also re-arrange subtracks"),
+                    React.createElement("li", null, "Changes are applied when you hit Submit"),
+                    React.createElement("li", null, "You can click and drag the dialog box to move it on the screen"),
+                    React.createElement("li", null, "Columns in the table can be hidden using a vertical '...' menu on the right side of each column")))) : null,
+            React.createElement(SourcesGrid, { rows: currLayout, onChange: setCurrLayout, showTips: showTips })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", type: "submit", color: "inherit", onClick: () => {
+                    model.clearLayout();
+                    setCurrLayout(model.sources);
+                } }, "Clear custom settings"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                    setCurrLayout([...model.sources]);
+                } }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "primary", type: "submit", onClick: () => {
+                    model.setLayout(currLayout);
+                    handleClose();
+                } }, "Submit"))));
+}
+function SourcesGrid({ rows, onChange, showTips, }) {
+    const [anchorEl, setAnchorEl] = useState(null);
+    const [selected, setSelected] = useState([]);
+    // @ts-ignore
+    const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0];
+    // similar to BaseFeatureDetail data-grid for auto-measuring columns
+    const columns = [
+        {
+            field: 'color',
+            headerName: 'Color',
+            renderCell: (params) => {
+                const { value, id } = params;
+                return (React.createElement(ColorPicker, { color: value || 'blue', onChange: c => {
+                        const elt = rows.find(f => f.name === id);
+                        if (elt) {
+                            elt.color = c;
+                        }
+                        onChange([...rows]);
+                    } }));
+            },
+        },
+        {
+            field: 'name',
+            sortingOrder: [null],
+            headerName: 'Name',
+            width: measureGridWidth(rows.map(r => r.name)),
+        },
+        ...Object.keys(rest).map(val => ({
+            field: val,
+            sortingOrder: [null],
+            renderCell: (params) => {
+                const { value } = params;
+                return isUriLocation(value) ? React.createElement(UriLink, { value: value }) : getStr(value);
+            },
+            // @ts-ignore
+            width: measureGridWidth(rows.map(r => r[val])),
+        })),
+    ];
+    // this helps keep track of the selection, even though it is not used
+    // anywhere except inside the picker
+    const [widgetColor, setWidgetColor] = useState('blue');
+    const [currSort, setCurrSort] = useState({ idx: 0, field: null });
+    return (React.createElement("div", null,
+        React.createElement(Button, { disabled: !selected.length, onClick: event => setAnchorEl(event.currentTarget) }, "Change color of selected items"),
+        React.createElement(Button, { onClick: () => onChange(moveUp([...rows], selected)), disabled: !selected.length },
+            React.createElement(KeyboardArrowUpIcon, null),
+            showTips ? 'Move selected items up' : null),
+        React.createElement(Button, { onClick: () => onChange(moveDown([...rows], selected)), disabled: !selected.length },
+            React.createElement(KeyboardArrowDownIcon, null),
+            showTips ? 'Move selected items down' : null),
+        React.createElement(Button, { onClick: () => onChange(moveUp([...rows], selected, rows.length)), disabled: !selected.length },
+            React.createElement(KeyboardDoubleArrowUpIcon, null),
+            showTips ? 'Move selected items to top' : null),
+        React.createElement(Button, { onClick: () => onChange(moveDown([...rows], selected, rows.length)), disabled: !selected.length },
+            React.createElement(KeyboardDoubleArrowDownIcon, null),
+            showTips ? 'Move selected items to bottom' : null),
+        React.createElement(ColorPopover, { anchorEl: anchorEl, color: widgetColor, onChange: c => {
+                setWidgetColor(c);
+                selected.forEach(id => {
+                    const elt = rows.find(f => f.name === id);
+                    if (elt) {
+                        elt.color = c;
+                    }
+                });
+                onChange([...rows]);
+            }, onClose: () => setAnchorEl(null) }),
+        React.createElement("div", { style: { height: 400, width: '100%' } },
+            React.createElement(DataGrid, { getRowId: row => row.name, checkboxSelection: true, disableSelectionOnClick: true, onSelectionModelChange: arg => setSelected(arg), rows: rows, rowHeight: 25, headerHeight: 33, columns: columns, sortModel: [
+                /* we control the sort as a controlled component using onSortModelChange */
+                ], onSortModelChange: args => {
+                    const sort = args[0];
+                    const idx = (currSort.idx + 1) % 2;
+                    const field = (sort === null || sort === void 0 ? void 0 : sort.field) || currSort.field;
+                    setCurrSort({ idx, field });
+                    onChange(field
+                        ? [...rows].sort((a, b) => {
+                            // @ts-ignore
+                            const aa = getStr(a[field]);
+                            // @ts-ignore
+                            const bb = getStr(b[field]);
+                            return idx === 1
+                                ? aa.localeCompare(bb)
+                                : bb.localeCompare(aa);
+                        })
+                        : rows);
+                } }))));
+}
+//# sourceMappingURL=SetColorDialog.js.map

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js.map

@@ -0,0 +1 @@
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package/esm/MultiLinearWiggleDisplay/components/SetMinMaxDialog.d.ts

@@ -0,0 +1,11 @@
+/// <reference types="react" />
+export default function SetMinMaxDlg(props: {
+    model: {
+        minScore: number;
+        maxScore: number;
+        scaleType: string;
+        setMinScore: Function;
+        setMaxScore: Function;
+    };
+    handleClose: () => void;
+}): JSX.Element;

package/esm/MultiLinearWiggleDisplay/components/SetMinMaxDialog.js

@@ -0,0 +1,46 @@
+import React, { useState } from 'react';
+import { Button, Dialog, DialogContent, DialogTitle, IconButton, TextField, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import CloseIcon from '@mui/icons-material/Close';
+const useStyles = makeStyles()(theme => ({
+    root: {},
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+}));
+export default function SetMinMaxDlg(props) {
+    const { classes } = useStyles();
+    const { model, handleClose } = props;
+    const { minScore, maxScore, scaleType } = model;
+    const [min, setMin] = useState(`${minScore !== Number.MIN_VALUE ? minScore : ''}`);
+    const [max, setMax] = useState(`${maxScore !== Number.MAX_VALUE ? maxScore : ''}`);
+    const ok = min !== '' && max !== '' && !Number.isNaN(+min) && !Number.isNaN(+max)
+        ? +max > +min
+        : true;
+    const logOk = scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true;
+    return (React.createElement(Dialog, { open: true, onClose: handleClose },
+        React.createElement(DialogTitle, null,
+            "Set min/max score for track",
+            React.createElement(IconButton, { className: classes.closeButton, onClick: handleClose },
+                React.createElement(CloseIcon, null))),
+        React.createElement(DialogContent, { style: { overflowX: 'hidden' } },
+            React.createElement("div", { className: classes.root },
+                React.createElement(Typography, null, "Enter min/max score: "),
+                !ok ? (React.createElement(Typography, { color: "error" }, "Max is greater than or equal to min")) : null,
+                !logOk ? (React.createElement(Typography, { color: "error" }, "Min score should be greater than 0 for log scale")) : null,
+                React.createElement(TextField, { value: min, onChange: event => {
+                        setMin(event.target.value);
+                    }, placeholder: "Enter min score" }),
+                React.createElement(TextField, { value: max, onChange: event => {
+                        setMax(event.target.value);
+                    }, placeholder: "Enter max score" }),
+                React.createElement(Button, { variant: "contained", color: "primary", type: "submit", style: { marginLeft: 20 }, disabled: !ok, onClick: () => {
+                        model.setMinScore(min !== '' && !Number.isNaN(+min) ? +min : undefined);
+                        model.setMaxScore(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+                        handleClose();
+                    } }, "Submit")))));
+}
+//# sourceMappingURL=SetMinMaxDialog.js.map

package/esm/MultiLinearWiggleDisplay/components/SetMinMaxDialog.js.map

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package/esm/MultiLinearWiggleDisplay/components/Tooltip.d.ts

@@ -0,0 +1,25 @@
+import React from 'react';
+import { Feature } from '@jbrowse/core/util';
+import { Source } from '../../util';
+import Tooltip, { TooltipContentsComponent } from '../../Tooltip';
+declare const TooltipContents: React.ForwardRefExoticComponent<{
+    model: {
+        sources: Source[];
+    };
+    feature: Feature;
+} & React.RefAttributes<HTMLDivElement>>;
+declare type Coord = [number, number];
+declare const WiggleTooltip: (props: {
+    model: {
+        featureUnderMouse: Feature;
+        sources: Source[];
+        rowHeight: number;
+    };
+    height: number;
+    offsetMouseCoord: Coord;
+    clientMouseCoord: Coord;
+    clientRect?: DOMRect;
+    TooltipContents?: TooltipContentsComponent;
+}) => JSX.Element;
+export default WiggleTooltip;
+export { Tooltip };

package/esm/MultiLinearWiggleDisplay/components/Tooltip.js

@@ -0,0 +1,43 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+// locals
+import { toP } from '../../util';
+import Tooltip from '../../Tooltip';
+const en = (n) => n.toLocaleString('en-US');
+const TooltipContents = React.forwardRef(({ model, feature }, ref) => {
+    const start = feature.get('start');
+    const end = feature.get('end');
+    const refName = feature.get('refName');
+    const coord = start === end ? en(start) : `${en(start)}..${en(end)}`;
+    const sources = feature.get('sources');
+    const source = feature.get('source');
+    const summary = feature.get('summary');
+    const obj = Object.fromEntries(model.sources.map(ent => [ent.name, ent]));
+    return (React.createElement("div", { ref: ref },
+        [refName, coord].filter(f => !!f).join(':'),
+        React.createElement("br", null),
+        sources ? (React.createElement("table", null,
+            React.createElement("thead", null,
+                React.createElement("tr", null,
+                    React.createElement("th", null, "color"),
+                    React.createElement("th", null, "source"),
+                    React.createElement("th", null, "score"))),
+            React.createElement("tbody", null, Object.entries(sources).map(([source, data]) => {
+                var _a;
+                return (React.createElement("tr", { key: source },
+                    React.createElement("td", { style: { background: (_a = obj[source]) === null || _a === void 0 ? void 0 : _a.color } }, " "),
+                    React.createElement("td", null, source),
+                    React.createElement("td", null, toP(data.score))));
+            })))) : (React.createElement("span", null,
+            source,
+            ' ',
+            summary
+                ? `min:${toP(feature.get('minScore'))} avg:${toP(feature.get('score'))} max:${toP(feature.get('maxScore'))}`
+                : toP(feature.get('score'))))));
+});
+const WiggleTooltip = observer((props) => {
+    return React.createElement(Tooltip, { useClientY: true, TooltipContents: TooltipContents, ...props });
+});
+export default WiggleTooltip;
+export { Tooltip };
+//# sourceMappingURL=Tooltip.js.map

package/esm/MultiLinearWiggleDisplay/components/Tooltip.js.map

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

@@ -0,0 +1,13 @@
+/// <reference types="react" />
+import { WiggleDisplayModel } from '../models/model';
+import YScaleBar from './YScaleBar';
+export declare const StatBars: (props: {
+    model: WiggleDisplayModel;
+    orientation?: string;
+    exportSVG?: boolean;
+}) => JSX.Element | null;
+declare const LinearWiggleDisplay: (props: {
+    model: WiggleDisplayModel;
+}) => JSX.Element;
+export default LinearWiggleDisplay;
+export { YScaleBar };

package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js

@@ -0,0 +1,99 @@
+import React from 'react';
+import { measureText, getContainingView, getContainingTrack, } from '@jbrowse/core/util';
+import { getConf } from '@jbrowse/core/configuration';
+import { BaseLinearDisplayComponent, } from '@jbrowse/plugin-linear-genome-view';
+import { observer } from 'mobx-react';
+import YScaleBar from './YScaleBar';
+const trackLabelFontSize = 12.8;
+function getOffset(model) {
+    const { prefersOffset } = model;
+    const { trackLabels } = getContainingView(model);
+    const track = getContainingTrack(model);
+    const trackName = getConf(track, 'name');
+    return trackLabels === 'overlapping' && !prefersOffset
+        ? measureText(trackName, trackLabelFontSize) + 100
+        : 10;
+}
+const Wrapper = observer(({ children, model, exportSVG, }) => {
+    if (exportSVG) {
+        return React.createElement(React.Fragment, null, children);
+    }
+    else {
+        const { height } = model;
+        return (React.createElement("svg", { style: {
+                position: 'absolute',
+                top: 0,
+                left: 0,
+                pointerEvents: 'none',
+                height,
+                width: 1800,
+            } }, children));
+    }
+});
+const RectBg = (props) => {
+    const { color = 'rgb(255,255,255,0.8)' } = props;
+    return React.createElement("rect", { ...props, fill: color });
+};
+const ScoreLegend = observer(({ model }) => {
+    const { ticks, scaleType } = model;
+    const { width } = getContainingView(model);
+    const legend = `[${ticks.values[0]}-${ticks.values[1]}]` +
+        (scaleType === 'log' ? ' (log scale)' : '');
+    const len = measureText(legend, 14);
+    const padding = 25;
+    const xpos = width - len - padding;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(RectBg, { y: 0, x: xpos, width: len + 6, height: 16 }),
+        React.createElement("text", { y: 13, x: xpos }, legend)));
+});
+const ColorLegend = observer(({ model, rowHeight, labelWidth, exportSVG, }) => {
+    const { needsCustomLegend, needsScalebar, needsFullHeightScalebar, rowHeightTooSmallForScalebar, renderColorBoxes, sources, } = model;
+    const svgFontSize = Math.min(rowHeight, 12);
+    const canDisplayLabel = rowHeight > 11;
+    const colorBoxWidth = renderColorBoxes ? 15 : 0;
+    const legendWidth = labelWidth + colorBoxWidth + 5;
+    const svgOffset = exportSVG ? 10 : 0;
+    const extraOffset = svgOffset || (needsScalebar && !rowHeightTooSmallForScalebar ? 50 : 0);
+    return sources ? (React.createElement(React.Fragment, null,
+        /* 0.25 for hanging letters like g */
+        needsFullHeightScalebar ? (React.createElement(RectBg, { y: 0, x: extraOffset, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null,
+        sources.map((source, idx) => {
+            const boxHeight = Math.min(20, rowHeight);
+            return (React.createElement(React.Fragment, { key: source.name + '-' + idx },
+                !needsFullHeightScalebar ? (React.createElement(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: legendWidth, height: boxHeight })) : null,
+                source.color ? (React.createElement(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: colorBoxWidth, height: needsCustomLegend ? rowHeight : boxHeight, color: source.color })) : null,
+                canDisplayLabel ? (React.createElement("text", { y: idx * rowHeight + 13, x: extraOffset + colorBoxWidth + 2, fontSize: svgFontSize }, source.name)) : null));
+        }))) : null;
+});
+export const StatBars = observer((props) => {
+    const { model, orientation, exportSVG } = props;
+    const { stats, needsCustomLegend, needsFullHeightScalebar, rowHeightTooSmallForScalebar, rowHeight, sources, ticks, } = model;
+    const svgFontSize = Math.min(rowHeight, 12);
+    const canDisplayLabel = rowHeight > 11;
+    const { width: viewWidth } = getContainingView(model);
+    const minWidth = 20;
+    const ready = stats && sources;
+    if (!ready) {
+        return null;
+    }
+    const labelWidth = Math.max(...(sources
+        .map(s => measureText(s.name, svgFontSize))
+        .map(width => (canDisplayLabel ? width : minWidth)) || [0]));
+    return (React.createElement(Wrapper, { ...props }, needsFullHeightScalebar ? (React.createElement(React.Fragment, null,
+        React.createElement("g", { transform: `translate(${!exportSVG ? getOffset(model) : 0},0)` },
+            React.createElement(YScaleBar, { model: model, orientation: orientation })),
+        React.createElement("g", { transform: `translate(${viewWidth - labelWidth - 100},0)` },
+            React.createElement(ColorLegend, { exportSVG: exportSVG, model: model, rowHeight: 12, labelWidth: labelWidth })))) : (React.createElement(React.Fragment, null,
+        React.createElement(ColorLegend, { exportSVG: exportSVG, model: model, rowHeight: model.rowHeight, labelWidth: labelWidth }),
+        rowHeightTooSmallForScalebar || needsCustomLegend ? (React.createElement(ScoreLegend, { ...props })) : (sources.map((_source, idx) => (React.createElement("g", { transform: `translate(0 ${rowHeight * idx})`, key: JSON.stringify(ticks) + '-' + idx },
+            React.createElement(YScaleBar, { model: model, orientation: orientation })))))))));
+});
+const LinearWiggleDisplay = observer((props) => {
+    const { model } = props;
+    return (React.createElement("div", null,
+        React.createElement(BaseLinearDisplayComponent, { ...props }),
+        React.createElement(StatBars, { model: model })));
+});
+export default LinearWiggleDisplay;
+export { YScaleBar };
+//# sourceMappingURL=WiggleDisplayComponent.js.map

package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js.map

@@ -0,0 +1 @@
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package/esm/MultiLinearWiggleDisplay/components/YScaleBar.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { WiggleDisplayModel } from '../models/model';
+declare const YScaleBar: ({ model, orientation, }: {
+    model: WiggleDisplayModel;
+    orientation?: string | undefined;
+}) => JSX.Element | null;
+export default YScaleBar;

package/esm/MultiLinearWiggleDisplay/components/YScaleBar.js

@@ -0,0 +1,9 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { Axis, LEFT, RIGHT } from 'react-d3-axis-mod';
+const YScaleBar = observer(({ model, orientation, }) => {
+    const { ticks } = model;
+    return ticks ? (React.createElement(Axis, { ...ticks, shadow: 2, format: (n) => n, style: { orient: orientation === 'left' ? LEFT : RIGHT } })) : null;
+});
+export default YScaleBar;
+//# sourceMappingURL=YScaleBar.js.map

package/esm/MultiLinearWiggleDisplay/components/YScaleBar.js.map

@@ -0,0 +1 @@
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package/esm/MultiLinearWiggleDisplay/components/util.d.ts

@@ -0,0 +1,10 @@
+export declare function moveUp(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];
+export declare function moveDown(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];

package/esm/MultiLinearWiggleDisplay/components/util.js

@@ -0,0 +1,31 @@
+export 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 (let i = 0; i < idxs.length; i++) {
+        const old = idxs[i];
+        const idx = Math.max(lastIdx, old - by);
+        if (idx >= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx + 1;
+    }
+    return arr;
+}
+export 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 (let i = 0; i < idxs.length; i++) {
+        const old = idxs[i];
+        const idx = Math.min(lastIdx, old + by);
+        if (idx <= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx - 1;
+    }
+    return arr;
+}
+//# sourceMappingURL=util.js.map

package/esm/MultiLinearWiggleDisplay/components/util.js.map

@@ -0,0 +1 @@
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package/esm/MultiLinearWiggleDisplay/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/MultiLinearWiggleDisplay/index.js

@@ -0,0 +1,18 @@
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import configSchemaFactory from './models/configSchema';
+import modelFactory from './models/model';
+import ReactComponent from './components/WiggleDisplayComponent';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        return new DisplayType({
+            name: 'MultiLinearWiggleDisplay',
+            configSchema,
+            stateModel: modelFactory(pluginManager, configSchema),
+            trackType: 'MultiQuantitativeTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent,
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/MultiLinearWiggleDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MultiLinearWiggleDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,qCAAqC,CAAA;AAEhE,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/MultiLinearWiggleDisplay/models/configSchema.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/MultiLinearWiggleDisplay/models/configSchema.js

@@ -0,0 +1,74 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
+import { types } from 'mobx-state-tree';
+export default function WiggleConfigFactory(pluginManager) {
+    const MultiXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiXYPlotRenderer').configSchema;
+    const MultiDensityRendererConfigSchema = pluginManager.getRendererType('MultiDensityRenderer').configSchema;
+    const MultiRowXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiRowXYPlotRenderer').configSchema;
+    const MultiLineRendererConfigSchema = pluginManager.getRendererType('MultiLineRenderer').configSchema;
+    const MultiRowLineRendererConfigSchema = pluginManager.getRendererType('MultiRowLineRenderer').configSchema;
+    return ConfigurationSchema('MultiLinearWiggleDisplay', {
+        autoscale: {
+            type: 'stringEnum',
+            defaultValue: 'local',
+            model: types.enumeration('Autoscale type', [
+                'global',
+                'local',
+                'globalsd',
+                'localsd',
+                'zscore',
+            ]),
+            description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
+        },
+        minimalTicks: {
+            type: 'boolean',
+            defaultValue: false,
+            description: 'use the minimal amount of ticks',
+        },
+        minScore: {
+            type: 'number',
+            defaultValue: Number.MIN_VALUE,
+            description: 'minimum value for the y-scale',
+        },
+        maxScore: {
+            type: 'number',
+            description: 'maximum value for the y-scale',
+            defaultValue: Number.MAX_VALUE,
+        },
+        numStdDev: {
+            type: 'number',
+            description: 'number of standard deviations to use for autoscale types globalsd or localsd',
+            defaultValue: 3,
+        },
+        scaleType: {
+            type: 'stringEnum',
+            model: types.enumeration('Scale type', ['linear', 'log']),
+            description: 'The type of scale to use',
+            defaultValue: 'linear',
+        },
+        inverted: {
+            type: 'boolean',
+            description: 'draw upside down',
+            defaultValue: false,
+        },
+        defaultRendering: {
+            type: 'stringEnum',
+            model: types.enumeration('Rendering', [
+                'multirowxy',
+                'xyplot',
+                'multirowdensity',
+                'multiline',
+                'multirowline',
+            ]),
+            defaultValue: 'multirowxy',
+        },
+        renderers: ConfigurationSchema('RenderersConfiguration', {
+            MultiXYPlotRenderer: MultiXYPlotRendererConfigSchema,
+            MultiDensityRenderer: MultiDensityRendererConfigSchema,
+            MultiRowXYPlotRenderer: MultiRowXYPlotRendererConfigSchema,
+            MultiLineRenderer: MultiLineRendererConfigSchema,
+            MultiRowLineRenderer: MultiRowLineRendererConfigSchema,
+        }),
+    }, { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true });
+}
+//# sourceMappingURL=configSchema.js.map