@jbrowse/plugin-wiggle 2.17.0 → 3.0.0

package/esm/shared/SharedWiggleMixin.js

@@ -1,96 +1,38 @@
+import { lazy } from 'react';
 import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { getEnv, getSession, isSelectionContainer, } from '@jbrowse/core/util';
+import { getEnv, getSession, isSelectionContainer } from '@jbrowse/core/util';
+import { stopStopToken } from '@jbrowse/core/util/stopToken';
 import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
 import { types } from 'mobx-state-tree';
-// locals
 import { getNiceDomain } from '../util';
-import { lazy } from 'react';
-// lazies
 const SetMinMaxDialog = lazy(() => import('./SetMinMaxDialog'));
-/**
- * #stateModel SharedWiggleMixin
- */
 export default function SharedWiggleMixin(configSchema) {
     return types
         .compose(BaseLinearDisplay, types.model({
-        /**
-         * #property
-         */
         selectedRendering: types.optional(types.string, ''),
-        /**
-         * #property
-         */
         resolution: types.optional(types.number, 1),
-        /**
-         * #property
-         */
         fill: types.maybe(types.boolean),
-        /**
-         * #property
-         */
         minSize: types.maybe(types.number),
-        /**
-         * #property
-         */
         color: types.maybe(types.string),
-        /**
-         * #property
-         */
         posColor: types.maybe(types.string),
-        /**
-         * #property
-         */
         negColor: types.maybe(types.string),
-        /**
-         * #property
-         */
         summaryScoreMode: types.maybe(types.string),
-        /**
-         * #property
-         */
         rendererTypeNameState: types.maybe(types.string),
-        /**
-         * #property
-         */
         scale: types.maybe(types.string),
-        /**
-         * #property
-         */
         autoscale: types.maybe(types.string),
-        /**
-         * #property
-         */
         displayCrossHatches: types.maybe(types.boolean),
-        /**
-         * #property
-         */
         constraints: types.optional(types.model({
             max: types.maybe(types.number),
             min: types.maybe(types.number),
         }), {}),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
     }))
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         message: undefined,
-        /**
-         * #volatile
-         */
         stats: undefined,
-        /**
-         * #volatile
-         */
         statsFetchInProgress: undefined,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         updateQuantitativeStats(stats) {
             const { currStatsBpPerPx, scoreMin, scoreMax } = stats;
             const EPSILON = 0.000001;
@@ -104,55 +46,30 @@ export default function SharedWiggleMixin(configSchema) {
                 };
             }
         },
-        /**
-         * #action
-         */
         setColor(color) {
             self.color = color;
         },
-        /**
-         * #action
-         */
         setPosColor(color) {
             self.posColor = color;
         },
-        /**
-         * #action
-         */
         setNegColor(color) {
             self.negColor = color;
         },
-        /**
-         * #action
-         */
-        setStatsLoading(aborter) {
-            if (self.statsFetchInProgress !== undefined &&
-                !self.statsFetchInProgress.signal.aborted) {
-                self.statsFetchInProgress.abort();
+        setStatsLoading(arg) {
+            if (self.statsFetchInProgress) {
+                stopStopToken(self.statsFetchInProgress);
             }
-            self.statsFetchInProgress = aborter;
-        },
-        /**
-         * #action
-         * this overrides the BaseLinearDisplayModel to avoid popping up a
-         * feature detail display, but still sets the feature selection on the
-         * model so listeners can detect a click
-         */
+            self.statsFetchInProgress = arg;
+        },
         selectFeature(feature) {
             const session = getSession(self);
             if (isSelectionContainer(session)) {
                 session.setSelection(feature);
             }
         },
-        /**
-         * #action
-         */
         setResolution(res) {
             self.resolution = res;
         },
-        /**
-         * #action
-         */
         setFill(fill) {
             if (fill === 0) {
                 self.fill = true;
@@ -167,116 +84,64 @@ export default function SharedWiggleMixin(configSchema) {
                 self.minSize = 2;
             }
         },
-        /**
-         * #action
-         */
         toggleLogScale() {
             self.scale = self.scale === 'log' ? 'linear' : 'log';
         },
-        /**
-         * #action
-         */
         setScaleType(scale) {
             self.scale = scale;
         },
-        /**
-         * #action
-         */
         setSummaryScoreMode(val) {
             self.summaryScoreMode = val;
         },
-        /**
-         * #action
-         */
         setAutoscale(val) {
             self.autoscale = val;
         },
-        /**
-         * #action
-         */
         setMaxScore(val) {
             self.constraints.max = val;
         },
-        /**
-         * #action
-         */
         setRendererType(val) {
             self.rendererTypeNameState = val;
         },
-        /**
-         * #action
-         */
         setMinScore(val) {
             self.constraints.min = val;
         },
-        /**
-         * #action
-         */
         toggleCrossHatches() {
             self.displayCrossHatches = !self.displayCrossHatches;
         },
-        /**
-         * #action
-         */
         setCrossHatches(cross) {
             self.displayCrossHatches = cross;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get adapterTypeName() {
             return self.adapterConfig.type;
         },
-        /**
-         * #getter
-         */
         get rendererTypeNameSimple() {
             var _a;
             return (_a = self.rendererTypeNameState) !== null && _a !== void 0 ? _a : getConf(self, 'defaultRendering');
         },
-        /**
-         * #getter
-         * subclasses can define these, as snpcoverage track does
-         */
         get filters() {
             return undefined;
         },
-        /**
-         * #getter
-         */
         get scaleType() {
             var _a;
             return (_a = self.scale) !== null && _a !== void 0 ? _a : getConf(self, 'scaleType');
         },
-        /**
-         * #getter
-         */
         get maxScore() {
             var _a;
             return (_a = self.constraints.max) !== null && _a !== void 0 ? _a : getConf(self, 'maxScore');
         },
-        /**
-         * #getter
-         */
         get minScore() {
             var _a;
             return (_a = self.constraints.min) !== null && _a !== void 0 ? _a : getConf(self, 'minScore');
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get adapterCapabilities() {
             const type = self.adapterTypeName;
             const { pluginManager } = getEnv(self);
             return pluginManager.getAdapterType(type).adapterCapabilities;
         },
-        /**
-         * #getter
-         */
         get rendererConfig() {
             const { color, displayCrossHatches, fill, minSize, negColor, posColor, summaryScoreMode, scaleType, rendererTypeName, } = self;
             const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
@@ -294,9 +159,6 @@ export default function SharedWiggleMixin(configSchema) {
                 ...(minSize !== undefined ? { minSize } : {}),
             }, getEnv(self));
         },
-        /**
-         * #getter
-         */
         get autoscaleType() {
             var _a;
             return (_a = self.autoscale) !== null && _a !== void 0 ? _a : getConf(self, 'autoscale');
@@ -305,9 +167,6 @@ export default function SharedWiggleMixin(configSchema) {
         .views(self => {
         let oldDomain = [0, 0];
         return {
-            /**
-             * #getter
-             */
             get domain() {
                 const { stats, scaleType, minScore, maxScore } = self;
                 if (!stats) {
@@ -318,11 +177,9 @@ export default function SharedWiggleMixin(configSchema) {
                     bounds: [minScore, maxScore],
                     scaleType,
                 });
-                // avoid weird scalebar if log value and empty region displayed
                 if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {
                     return [0, Number.MIN_VALUE];
                 }
-                // avoid returning a new object if it matches the old value
                 if (JSON.stringify(oldDomain) !== JSON.stringify(ret)) {
                     oldDomain = ret;
                 }
@@ -331,23 +188,14 @@ export default function SharedWiggleMixin(configSchema) {
         };
     })
         .views(self => ({
-        /**
-         * #getter
-         */
         get filled() {
             const { fill, rendererConfig } = self;
             return fill !== null && fill !== void 0 ? fill : readConfObject(rendererConfig, 'filled');
         },
-        /**
-         * #getter
-         */
         get summaryScoreModeSetting() {
             const { summaryScoreMode: mode, rendererConfig } = self;
             return mode !== null && mode !== void 0 ? mode : readConfObject(rendererConfig, 'summaryScoreMode');
         },
-        /**
-         * #getter
-         */
         get scaleOpts() {
             return {
                 domain: self.domain,
@@ -357,36 +205,21 @@ export default function SharedWiggleMixin(configSchema) {
                 inverted: getConf(self, 'inverted'),
             };
         },
-        /**
-         * #getter
-         */
         get canHaveFill() {
             return self.rendererTypeName === 'XYPlotRenderer';
         },
-        /**
-         * #getter
-         */
         get displayCrossHatchesSetting() {
             const { displayCrossHatches: hatches, rendererConfig } = self;
             return hatches !== null && hatches !== void 0 ? hatches : readConfObject(rendererConfig, 'displayCrossHatches');
         },
-        /**
-         * #getter
-         */
         get hasResolution() {
             return self.adapterCapabilities.includes('hasResolution');
         },
-        /**
-         * #getter
-         */
         get hasGlobalStats() {
             return self.adapterCapabilities.includes('hasGlobalStats');
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         scoreTrackMenuItems() {
             return [
                 ...(self.hasResolution
@@ -462,9 +295,6 @@ export default function SharedWiggleMixin(configSchema) {
         .actions(self => {
         const { reload: superReload } = self;
         return {
-            /**
-             * #action
-             */
             async reload() {
                 self.setError();
                 superReload();

package/esm/shared/YScaleBar.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { axisPropsFromTickScale } from 'react-d3-axis-mod';
 type Ticks = ReturnType<typeof axisPropsFromTickScale>;
 declare const YScaleBar: ({ model, orientation, }: {
@@ -6,5 +5,5 @@ declare const YScaleBar: ({ model, orientation, }: {
         ticks?: Ticks;
     };
     orientation?: string;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default YScaleBar;

package/esm/shared/YScaleBar.js

@@ -1,10 +1,10 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import { Axis, LEFT, RIGHT } from 'react-d3-axis-mod';
 const YScaleBar = observer(function ({ model, orientation, }) {
     const { ticks } = model;
     const theme = useTheme();
-    return ticks ? (React.createElement(Axis, { ...ticks, shadow: 2, format: (n) => n, style: { orient: orientation === 'left' ? LEFT : RIGHT }, bg: theme.palette.background.default, fg: theme.palette.text.primary })) : null;
+    return ticks ? (_jsx(Axis, { ...ticks, shadow: 2, format: (n) => n, style: { orient: orientation === 'left' ? LEFT : RIGHT }, bg: theme.palette.background.default, fg: theme.palette.text.primary })) : null;
 });
 export default YScaleBar;

package/esm/util.d.ts

@@ -12,36 +12,8 @@ export interface Source {
     color?: string;
     group?: string;
 }
-/**
- * produces a d3-scale from arguments. applies a "nice domain" adjustment
- *
- * @param object - containing attributes
- *   - domain [min,max]
- *   - range [min,max]
- *   - bounds [min,max]
- *   - scaleType (linear or log)
- *   - pivotValue (number)
- *   - inverted (boolean)
- */
 export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleLogarithmic<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
-/**
- * gets the origin for drawing the graph. for linear this is 0, for log this is
- * arbitrarily set to log(1)==0
- *
- * @param scaleType -
- */
 export declare function getOrigin(scaleType: string): 1 | 0;
-/**
- * produces a "nice" domain that actually rounds down to 0 for the min or 0 to
- * the max depending on if all values are positive or negative
- *
- * @param object - containing attributes
- *   - domain [min,max]
- *   - bounds [min,max]
- *   - mean
- *   - stddev
- *   - scaleType (linear or log)
- */
 export declare function getNiceDomain({ scaleType, domain, bounds, }: {
     scaleType: string;
     domain: readonly [number, number];

package/esm/util.js

@@ -1,16 +1,5 @@
 import { scaleLinear, scaleLog, scaleQuantize, } from '@mui/x-charts-vendor/d3-scale';
 export const YSCALEBAR_LABEL_OFFSET = 5;
-/**
- * produces a d3-scale from arguments. applies a "nice domain" adjustment
- *
- * @param object - containing attributes
- *   - domain [min,max]
- *   - range [min,max]
- *   - bounds [min,max]
- *   - scaleType (linear or log)
- *   - pivotValue (number)
- *   - inverted (boolean)
- */
 export function getScale({ domain = [], range = [], scaleType, pivotValue, inverted, }) {
     let scale;
     const [min, max] = domain;
@@ -38,41 +27,12 @@ export function getScale({ domain = [], range = [], scaleType, pivotValue, inver
     scale.range(inverted ? range.slice().reverse() : range);
     return scale;
 }
-/**
- * gets the origin for drawing the graph. for linear this is 0, for log this is
- * arbitrarily set to log(1)==0
- *
- * @param scaleType -
- */
-export function getOrigin(scaleType /* , pivot, stats */) {
-    // if (pivot) {
-    //   if (pivot === 'mean') {
-    //     return stats.scoreMean || 0
-    //   }
-    //   if (pivot === 'zero') {
-    //     return 0
-    //   }
-    //   return parseFloat()
-    // }
-    // if (scaleType === 'z_score') {
-    //   return stats.scoreMean || 0
-    // }
+export function getOrigin(scaleType) {
     if (scaleType === 'log') {
         return 1;
     }
     return 0;
 }
-/**
- * produces a "nice" domain that actually rounds down to 0 for the min or 0 to
- * the max depending on if all values are positive or negative
- *
- * @param object - containing attributes
- *   - domain [min,max]
- *   - bounds [min,max]
- *   - mean
- *   - stddev
- *   - scaleType (linear or log)
- */
 export function getNiceDomain({ scaleType, domain, bounds, }) {
     const [minScore, maxScore] = bounds;
     let [min, max] = domain;
@@ -85,9 +45,6 @@ export function getNiceDomain({ scaleType, domain, bounds, }) {
         }
     }
     if (scaleType === 'log') {
-        // for min>0 and max>1, set log min to 1, which works for most coverage
-        // types tracks. if max is not >1, might be like raw p-values so then it'll
-        // display negative values
         if (min >= 0 && max > 1) {
             min = 1;
         }
@@ -123,7 +80,6 @@ export function toP(s = 0) {
 export function round(value) {
     return Math.round(value * 1e5) / 1e5;
 }
-// avoid drawing negative width features for SVG exports
 export function fillRectCtx(x, y, width, height, ctx, color) {
     if (width < 0) {
         x += width;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,14 +36,11 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@floating-ui/react": "^0.26.3",
-    "@gmod/bbi": "^5.0.0",
+    "@gmod/bbi": "^6.0.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/x-charts-vendor": "^7.12.0",
     "@mui/x-data-grid": "^7.0.0",
-    "clone": "^2.1.2",
     "fast-deep-equal": "^3.1.3",
-    "is-object": "^1.0.1",
     "react-d3-axis-mod": "^0.1.9",
     "react-draggable": "^4.4.5"
   },
@@ -65,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }

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

@@ -1,6 +0,0 @@
-import React from 'react';
-import { DialogProps } from '@mui/material';
-declare const DraggableDialog: (props: DialogProps & {
-    title: string;
-}) => React.JSX.Element;
-export default DraggableDialog;

package/dist/MultiLinearWiggleDisplay/components/DraggableDialog.js

@@ -1,66 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const react_draggable_1 = __importDefault(require("react-draggable"));
-// icons
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
-function PaperComponent(props) {
-    const ref = (0, react_1.useRef)(null);
-    return (react_1.default.createElement(react_draggable_1.default, { 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'); } },
-        react_1.default.createElement(material_1.Paper, { ref: ref, ...props })));
-}
-const DraggableDialog = (0, mobx_react_1.observer)(function DraggableDialog(props) {
-    const { classes } = useStyles();
-    const { title, children, onClose } = props;
-    return (react_1.default.createElement(material_1.Dialog, { ...props, PaperComponent: PaperComponent },
-        react_1.default.createElement(material_1.ScopedCssBaseline, null,
-            react_1.default.createElement(material_1.DialogTitle, { style: { cursor: 'move' } },
-                title,
-                onClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => {
-                        // @ts-expect-error
-                        onClose();
-                    } },
-                    react_1.default.createElement(Close_1.default, null))) : null),
-            react_1.default.createElement(material_1.Divider, null),
-            children)));
-});
-exports.default = DraggableDialog;

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

@@ -1,6 +0,0 @@
-import React from 'react';
-import { DialogProps } from '@mui/material';
-declare const DraggableDialog: (props: DialogProps & {
-    title: string;
-}) => React.JSX.Element;
-export default DraggableDialog;

package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.js

@@ -1,38 +0,0 @@
-import React, { useRef } from 'react';
-import { Dialog, DialogTitle, IconButton, Divider, 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';
-const useStyles = makeStyles()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
-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'); } },
-        React.createElement(Paper, { ref: ref, ...props })));
-}
-const DraggableDialog = observer(function DraggableDialog(props) {
-    const { classes } = useStyles();
-    const { title, children, onClose } = props;
-    return (React.createElement(Dialog, { ...props, PaperComponent: PaperComponent },
-        React.createElement(ScopedCssBaseline, null,
-            React.createElement(DialogTitle, { style: { cursor: 'move' } },
-                title,
-                onClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => {
-                        // @ts-expect-error
-                        onClose();
-                    } },
-                    React.createElement(CloseIcon, null))) : null),
-            React.createElement(Divider, null),
-            children)));
-});
-export default DraggableDialog;