@jbrowse/plugin-wiggle 2.17.0 → 2.18.0

package/esm/MultiDensityRenderer/MultiDensityRenderer.d.ts

@@ -1,6 +1,7 @@
-import { Feature } from '@jbrowse/core/util';
-import WiggleBaseRenderer, { MultiRenderArgsDeserialized as MultiArgs } from '../WiggleBaseRenderer';
-export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+import type { MultiRenderArgsDeserialized as MultiArgs } from '../WiggleBaseRenderer';
+import type { Feature } from '@jbrowse/core/util';
+export default class MultiDensityPlotRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: MultiArgs): Promise<{
         reducedFeatures: Feature[];
     }>;

package/esm/MultiDensityRenderer/MultiDensityRenderer.js

@@ -1,8 +1,7 @@
 import { groupBy } from '@jbrowse/core/util';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 import { drawDensity } from '../drawDensity';
-export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
-    // @ts-expect-error
+export default class MultiDensityPlotRenderer extends WiggleBaseRenderer {
     async draw(ctx, props) {
         const { sources, features } = props;
         const groups = groupBy(features.values(), f => f.get('source'));

package/esm/MultiDensityRenderer/configSchema.js

@@ -1,13 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import baseWiggleRendererConfigSchema from '../configSchema';
-/**
- * #config MultiDensityRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('MultiDensityRenderer', {}, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: baseWiggleRendererConfigSchema,
     explicitlyTyped: true,
 });

package/esm/MultiDensityRenderer/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MultiDensityRendererF(pluginManager: PluginManager): void;

package/esm/MultiLineRenderer/MultiLineRenderer.d.ts

@@ -1,5 +1,6 @@
-import { Feature } from '@jbrowse/core/util';
-import WiggleBaseRenderer, { MultiRenderArgsDeserialized as MultiArgs } from '../WiggleBaseRenderer';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+import type { MultiRenderArgsDeserialized as MultiArgs } from '../WiggleBaseRenderer';
+import type { Feature } from '@jbrowse/core/util';
 export default class MultiLineRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: MultiArgs): Promise<{
         reducedFeatures: Feature[];

package/esm/MultiLineRenderer/MultiLineRenderer.js

@@ -1,8 +1,7 @@
 import { groupBy } from '@jbrowse/core/util';
-import { drawLine } from '../drawLine';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
+import { drawLine } from '../drawLine';
 export default class MultiLineRenderer extends WiggleBaseRenderer {
-    // @ts-expect-error
     async draw(ctx, props) {
         const { sources, features } = props;
         const groups = groupBy(features.values(), f => f.get('source'));

package/esm/MultiLineRenderer/configSchema.d.ts

@@ -1,15 +1,9 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     displayCrossHatches: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     summaryScoreMode: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;

package/esm/MultiLineRenderer/configSchema.js

@@ -1,22 +1,13 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
 import baseWiggleRendererConfigSchema from '../configSchema';
-/**
- * #config MultiLineRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('MultiLineRenderer', {
-    /**
-     * #slot
-     */
     displayCrossHatches: {
         type: 'boolean',
         description: 'choose to draw cross hatches (sideways lines)',
         defaultValue: false,
     },
-    /**
-     * #slot
-     */
     summaryScoreMode: {
         type: 'stringEnum',
         model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
@@ -24,9 +15,6 @@ const configSchema = ConfigurationSchema('MultiLineRenderer', {
         defaultValue: 'avg',
     },
 }, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: baseWiggleRendererConfigSchema,
     explicitlyTyped: true,
 });

package/esm/MultiLineRenderer/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MultiLineRendererF(pluginManager: PluginManager): void;

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../model';
+import type { WiggleDisplayModel } from '../model';
 declare const ColorLegend: ({ model, rowHeight, labelWidth, exportSVG, }: {
     model: WiggleDisplayModel;
     rowHeight: number;

package/esm/MultiLinearWiggleDisplay/components/ColorLegend.js

@@ -10,7 +10,6 @@ const ColorLegend = observer(function ({ model, rowHeight, labelWidth, exportSVG
     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);

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { DialogProps } from '@mui/material';
+import type { DialogProps } from '@mui/material';
 declare const DraggableDialog: (props: DialogProps & {
     title: string;
 }) => React.JSX.Element;

package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.js

@@ -1,10 +1,9 @@
 import React, { useRef } from 'react';
-import { Dialog, DialogTitle, IconButton, Divider, Paper, ScopedCssBaseline, } from '@mui/material';
+import CloseIcon from '@mui/icons-material/Close';
+import { Dialog, DialogTitle, Divider, IconButton, Paper, ScopedCssBaseline, } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
 import Draggable from 'react-draggable';
-// icons
-import CloseIcon from '@mui/icons-material/Close';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     closeButton: {
         position: 'absolute',
@@ -15,9 +14,7 @@ const useStyles = makeStyles()(theme => ({
 }));
 function PaperComponent(props) {
     const ref = useRef(null);
-    return (React.createElement(Draggable, { nodeRef: ref, cancel: '[class*="MuiDialogContent-root"]', 
-        // @ts-expect-error
-        onStart: arg => { var _a, _b; return (_b = (_a = arg.target) === null || _a === void 0 ? void 0 : _a.className) === null || _b === void 0 ? void 0 : _b.includes('MuiDialogTitle'); } },
+    return (React.createElement(Draggable, { nodeRef: ref, cancel: '[class*="MuiDialogContent-root"]', onStart: arg => { var _a, _b; return (_b = (_a = arg.target) === null || _a === void 0 ? void 0 : _a.className) === null || _b === void 0 ? void 0 : _b.includes('MuiDialogTitle'); } },
         React.createElement(Paper, { ref: ref, ...props })));
 }
 const DraggableDialog = observer(function DraggableDialog(props) {
@@ -28,7 +25,6 @@ const DraggableDialog = observer(function DraggableDialog(props) {
             React.createElement(DialogTitle, { style: { cursor: 'move' } },
                 title,
                 onClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => {
-                        // @ts-expect-error
                         onClose();
                     } },
                     React.createElement(CloseIcon, null))) : null),

package/esm/MultiLinearWiggleDisplay/components/RectBg.js

@@ -1,5 +1,5 @@
-import { getFillProps } from '@jbrowse/core/util';
 import React from 'react';
+import { getFillProps } from '@jbrowse/core/util';
 const RectBg = (props) => {
     const { color = 'rgb(255,255,255,0.8)' } = props;
     return React.createElement("rect", { ...props, ...getFillProps(color) });

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../model';
+import type { WiggleDisplayModel } from '../model';
 declare const ScoreLegend: ({ model }: {
     model: WiggleDisplayModel;
 }) => React.JSX.Element;

package/esm/MultiLinearWiggleDisplay/components/ScoreLegend.js

@@ -1,5 +1,5 @@
 import React from 'react';
-import { measureText, getContainingView } from '@jbrowse/core/util';
+import { getContainingView, measureText } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import RectBg from './RectBg';
 const ScoreLegend = observer(({ model }) => {

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Source } from '../../util';
+import type { Source } from '../../util';
 export default function SetColorDialog({ model, handleClose, }: {
     model: {
         sources?: Source[];

package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js

@@ -1,9 +1,7 @@
 import React, { useState } from 'react';
-import { Button, DialogContent, DialogActions } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 import { useLocalStorage } from '@jbrowse/core/util';
-import clone from 'clone';
-// locals
+import { Button, DialogActions, DialogContent } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
 import DraggableDialog from './DraggableDialog';
 import SourcesGrid from './SourcesGrid';
 const useStyles = makeStyles()({
@@ -14,8 +12,8 @@ const useStyles = makeStyles()({
 export default function SetColorDialog({ model, handleClose, }) {
     const { classes } = useStyles();
     const { sources } = model;
-    const [currLayout, setCurrLayout] = useState(clone(sources || []));
-    const [showTips, setShowTips] = useLocalStorage('multiwiggle-showTips', true);
+    const [currLayout, setCurrLayout] = useState(structuredClone(sources || []));
+    const [showTips, setShowTips] = useLocalStorage('multiwiggle-showTips', false);
     return (React.createElement(DraggableDialog, { open: true, onClose: handleClose, maxWidth: "xl", title: 'Multi-wiggle color/arrangement editor' },
         React.createElement(DialogContent, { className: classes.content },
             React.createElement(Button, { variant: "contained", style: { float: 'right' }, onClick: () => {

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Source } from '../../util';
+import type { Source } from '../../util';
 declare function SourcesGrid({ rows, onChange, showTips, }: {
     rows: Source[];
     onChange: (arg: Source[]) => void;

package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.js

@@ -1,17 +1,15 @@
 import React, { useState } from 'react';
-import { Button } from '@mui/material';
-import { getStr, measureGridWidth } from '@jbrowse/core/util';
-import { DataGrid } from '@mui/x-data-grid';
-import { makeStyles } from 'tss-react/mui';
-import ColorPicker, { ColorPopover } from '@jbrowse/core/ui/ColorPicker';
 import { SanitizedHTML } from '@jbrowse/core/ui';
-// locals
-import { moveUp, moveDown } from './util';
-// icons
-import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp';
-import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrowDown';
+import ColorPicker, { ColorPopover } from '@jbrowse/core/ui/ColorPicker';
+import { getStr, measureGridWidth } from '@jbrowse/core/util';
 import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
 import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp';
+import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrowDown';
+import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp';
+import { Button } from '@mui/material';
+import { DataGrid } from '@mui/x-data-grid';
+import { makeStyles } from 'tss-react/mui';
+import { moveDown, moveUp } from './util';
 const useStyles = makeStyles()({
     cell: {
         whiteSpace: 'nowrap',
@@ -72,16 +70,13 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                     {
                         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]);
-                                } }));
-                        },
+                        renderCell: ({ value, id }) => (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',
@@ -94,14 +89,8 @@ function SourcesGrid({ rows, onChange, showTips, }) {
                             React.createElement(SanitizedHTML, { html: getStr(value) }))),
                         width: measureGridWidth(rows.map(r => `${r[val]}`)),
                     })),
-                ], sortModel: [
-                /* we control the sort as a controlled component using onSortModelChange */
-                ], onSortModelChange: args => {
+                ], sortModel: [], onSortModelChange: args => {
                     const sort = args[0];
-                    // this idx%2 flip flops the sorting order, we could inspect args
-                    // for sort direction asc or desc but this is just a simplified
-                    // thing since we are controlling sort instead of the default data
-                    // grid sort anyways
                     const idx = (currSort.idx + 1) % 2;
                     const field = sort.field || currSort.field;
                     setCurrSort({ idx, field });

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

@@ -1,7 +1,7 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-import { Source } from '../../util';
-import { TooltipContentsComponent } from '../../Tooltip';
+import type { TooltipContentsComponent } from '../../Tooltip';
+import type { Source } from '../../util';
+import type { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const WiggleTooltip: (props: {
     model: {

package/esm/MultiLinearWiggleDisplay/components/Tooltip.js

@@ -1,8 +1,7 @@
 import React from 'react';
 import { observer } from 'mobx-react';
-// locals
-import { toP } from '../../util';
 import Tooltip from '../../Tooltip';
+import { toP } from '../../util';
 const en = (n) => n.toLocaleString('en-US');
 const TooltipContents = React.forwardRef(function TooltipContents2({ model, feature }, ref) {
     const start = feature.get('start');

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

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

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

@@ -1,5 +1,5 @@
 import React from 'react';
-import { WiggleDisplayModel } from '../model';
+import type { WiggleDisplayModel } from '../model';
 export declare const YScaleBars: (props: {
     model: WiggleDisplayModel;
     orientation?: string;

package/esm/MultiLinearWiggleDisplay/components/YScaleBars.js

@@ -1,10 +1,10 @@
 import React from 'react';
-import { measureText, getContainingView } from '@jbrowse/core/util';
+import { getContainingView, measureText } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import YScaleBar from '../../shared/YScaleBar';
 import ColorLegend from './ColorLegend';
 import ScoreLegend from './ScoreLegend';
 import { getOffset } from './util';
+import YScaleBar from '../../shared/YScaleBar';
 const Wrapper = observer(function ({ children, model, exportSVG, }) {
     const { height } = model;
     return exportSVG ? (children) : (React.createElement("svg", { style: {

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

@@ -1,4 +1,4 @@
-import { WiggleDisplayModel } from '../model';
+import type { WiggleDisplayModel } from '../model';
 export declare function moveUp(arr: {
     name: string;
 }[], sel: string[], by?: number): {

package/esm/MultiLinearWiggleDisplay/components/util.js

@@ -1,5 +1,5 @@
-import { getContainingTrack, getContainingView, measureText, } from '@jbrowse/core/util';
 import { getConf } from '@jbrowse/core/configuration';
+import { getContainingTrack, getContainingView, measureText, } from '@jbrowse/core/util';
 export function moveUp(arr, sel, by = 1) {
     const idxs = sel
         .map(l => arr.findIndex(v => v.name === l))

package/esm/MultiLinearWiggleDisplay/configSchema.d.ts

@@ -1,16 +1,10 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     defaultRendering: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         MultiXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         MultiDensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
@@ -18,9 +12,6 @@ export default function WiggleConfigFactory(pluginManager: PluginManager): impor
         MultiLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         MultiRowLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     height: {
         type: string;
         defaultValue: number;

package/esm/MultiLinearWiggleDisplay/configSchema.js

@@ -1,13 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-// locals
 import sharedWiggleConfigFactory from '../shared/SharedWiggleConfigSchema';
-/**
- * #config MultiLinearWiggleDisplay
- * extends
- * - [SharedWiggleDisplay](../sharedwiggledisplay)
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 export default function WiggleConfigFactory(pluginManager) {
     const MultiXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiXYPlotRenderer').configSchema;
     const MultiDensityRendererConfigSchema = pluginManager.getRendererType('MultiDensityRenderer').configSchema;
@@ -15,9 +9,6 @@ export default function WiggleConfigFactory(pluginManager) {
     const MultiLineRendererConfigSchema = pluginManager.getRendererType('MultiLineRenderer').configSchema;
     const MultiRowLineRendererConfigSchema = pluginManager.getRendererType('MultiRowLineRenderer').configSchema;
     return ConfigurationSchema('MultiLinearWiggleDisplay', {
-        /**
-         * #slot
-         */
         defaultRendering: {
             type: 'stringEnum',
             model: types.enumeration('Rendering', [
@@ -29,9 +20,6 @@ export default function WiggleConfigFactory(pluginManager) {
             ]),
             defaultValue: 'multirowxy',
         },
-        /**
-         * #slot
-         */
         renderers: ConfigurationSchema('RenderersConfiguration', {
             MultiXYPlotRenderer: MultiXYPlotRendererConfigSchema,
             MultiDensityRenderer: MultiDensityRendererConfigSchema,
@@ -39,17 +27,11 @@ export default function WiggleConfigFactory(pluginManager) {
             MultiLineRenderer: MultiLineRendererConfigSchema,
             MultiRowLineRenderer: MultiRowLineRendererConfigSchema,
         }),
-        /**
-         * #slot
-         */
         height: {
             type: 'number',
             defaultValue: 200,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: sharedWiggleConfigFactory(),
         explicitlyTyped: true,
     });

package/esm/MultiLinearWiggleDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MultiLinearWiggleDisplayF(pluginManager: PluginManager): void;

package/esm/MultiLinearWiggleDisplay/index.js

@@ -1,7 +1,7 @@
+import { lazy } from 'react';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaFactory from './configSchema';
 import modelFactory from './model';
-import { lazy } from 'react';
 export default function MultiLinearWiggleDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);