@jbrowse/plugin-wiggle 2.5.0 → 2.6.1

package/esm/shared/modelShared.js

@@ -0,0 +1,454 @@
+import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { getEnv, getSession, isSelectionContainer, } from '@jbrowse/core/util';
+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 SetMinMaxDlg = 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(() => ({
+        message: undefined,
+        stats: undefined,
+        statsFetchInProgress: undefined,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        updateQuantitativeStats(stats) {
+            const { scoreMin, scoreMax } = stats;
+            const EPSILON = 0.000001;
+            if (!self.stats) {
+                self.stats = { scoreMin, scoreMax };
+            }
+            else if (Math.abs(self.stats.scoreMax - scoreMax) > EPSILON ||
+                Math.abs(self.stats.scoreMin - scoreMin) > EPSILON) {
+                self.stats = { scoreMin, scoreMax };
+            }
+        },
+        /**
+         * #action
+         */
+        setColor(color) {
+            self.color = color;
+        },
+        /**
+         * #action
+         */
+        setPosColor(color) {
+            self.posColor = color;
+        },
+        /**
+         * #action
+         */
+        setNegColor(color) {
+            self.negColor = color;
+        },
+        /**
+         * #action
+         */
+        setLoading(aborter) {
+            const { statsFetchInProgress: statsFetch } = self;
+            if (statsFetch !== undefined && !statsFetch.signal.aborted) {
+                statsFetch.abort();
+            }
+            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
+         */
+        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;
+                self.minSize = 0;
+            }
+            else if (fill === 1) {
+                self.fill = false;
+                self.minSize = 1;
+            }
+            else if (fill === 2) {
+                self.fill = false;
+                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]) || {};
+            return self.rendererType.configSchema.create({
+                ...configBlob,
+                ...(scaleType ? { scaleType } : {}),
+                ...(fill !== undefined ? { filled: fill } : {}),
+                ...(displayCrossHatches !== undefined
+                    ? { displayCrossHatches }
+                    : {}),
+                ...(summaryScoreMode !== undefined ? { summaryScoreMode } : {}),
+                ...(color !== undefined ? { color } : {}),
+                ...(negColor !== undefined ? { negColor } : {}),
+                ...(posColor !== undefined ? { posColor } : {}),
+                ...(minSize !== undefined ? { minSize } : {}),
+            }, getEnv(self));
+        },
+        /**
+         * #getter
+         */
+        get autoscaleType() {
+            var _a;
+            return (_a = self.autoscale) !== null && _a !== void 0 ? _a : getConf(self, 'autoscale');
+        },
+    }))
+        .views(self => {
+        let oldDomain = [0, 0];
+        return {
+            /**
+             * #getter
+             */
+            get domain() {
+                const { stats, scaleType, minScore, maxScore } = self;
+                if (!stats) {
+                    return undefined;
+                }
+                const ret = getNiceDomain({
+                    domain: [stats.scoreMin, stats.scoreMax],
+                    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;
+                }
+                return oldDomain;
+            },
+        };
+    })
+        .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,
+                stats: self.stats,
+                autoscaleType: self.autoscaleType,
+                scaleType: self.scaleType,
+                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
+                    ? [
+                        {
+                            label: 'Resolution',
+                            subMenu: [
+                                {
+                                    label: 'Finer resolution',
+                                    onClick: () => self.setResolution(self.resolution * 5),
+                                },
+                                {
+                                    label: 'Coarser resolution',
+                                    onClick: () => self.setResolution(self.resolution / 5),
+                                },
+                            ],
+                        },
+                        {
+                            label: 'Summary score mode',
+                            subMenu: ['min', 'max', 'avg', 'whiskers'].map(elt => ({
+                                label: elt,
+                                type: 'radio',
+                                checked: self.summaryScoreModeSetting === elt,
+                                onClick: () => self.setSummaryScoreMode(elt),
+                            })),
+                        },
+                    ]
+                    : []),
+                {
+                    label: self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',
+                    onClick: () => self.toggleLogScale(),
+                },
+                {
+                    label: 'Autoscale type',
+                    subMenu: [
+                        ['local', 'Local'],
+                        ...(self.hasGlobalStats
+                            ? [
+                                ['global', 'Global'],
+                                ['globalsd', 'Global ± 3σ'],
+                            ]
+                            : []),
+                        ['localsd', 'Local ± 3σ'],
+                    ].map(([val, label]) => ({
+                        label,
+                        type: 'radio',
+                        checked: self.autoscaleType === val,
+                        onClick: () => self.setAutoscale(val),
+                    })),
+                },
+                {
+                    label: 'Set min/max score',
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            SetMinMaxDlg,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
+            ];
+        },
+    }))
+        .actions(self => {
+        const { reload: superReload } = self;
+        return {
+            /**
+             * #action
+             */
+            async reload() {
+                self.setError();
+                superReload();
+            },
+        };
+    });
+}
+//# sourceMappingURL=modelShared.js.map

package/esm/shared/modelShared.js.map

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

@@ -47,9 +47,6 @@ export declare function getNiceDomain({ scaleType, domain, bounds, }: {
     domain: readonly [number, number];
     bounds: readonly [number | undefined, number | undefined];
 }): [number, number];
-export declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
-    [key: string]: T[];
-};
 export declare function getQuantitativeStats(self: {
     adapterConfig: AnyConfigurationModel;
     configuration: AnyConfigurationModel;

package/esm/util.js

@@ -126,15 +126,6 @@ export function getNiceDomain({ scaleType, domain, bounds, }) {
     scale.nice();
     return scale.domain();
 }
-export function groupBy(array, predicate) {
-    var _a;
-    const result = {};
-    for (const value of array) {
-        const entry = (result[_a = predicate(value)] || (result[_a] = []));
-        entry.push(value);
-    }
-    return result;
-}
 export async function getQuantitativeStats(self, opts) {
     const { rpcManager } = getSession(self);
     const nd = getConf(self, 'numStdDev') || 3;

package/esm/util.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "2.5.0",
+  "version": "2.6.1",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bbi": "^3.0.0",
+    "@gmod/bbi": "^4.0.0",
     "@mui/icons-material": "^5.0.2",
     "@popperjs/core": "^2.11.0",
     "clone": "^2.1.2",
@@ -69,5 +69,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
 }

package/src/BigWigAdapter/BigWigAdapter.ts

@@ -28,11 +28,9 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
 
   private async setupPre(opts?: BaseOptions) {
     const { statusCallback = () => {} } = opts || {}
+    const pm = this.pluginManager
     const bigwig = new BigWig({
-      filehandle: openLocation(
-        this.getConf('bigWigLocation'),
-        this.pluginManager,
-      ),
+      filehandle: openLocation(this.getConf('bigWigLocation'), pm),
     })
     const header = await updateStatus(
       'Downloading bigwig header',

package/src/LinearWiggleDisplay/index.ts

@@ -3,7 +3,7 @@ import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
 
 import configSchemaFactory from './models/configSchema'
 import modelFactory from './models/model'
-import ReactComponent from './components/WiggleDisplayComponent'
+import { lazy } from 'react'
 
 export default (pluginManager: PluginManager) => {
   pluginManager.addDisplayType(() => {
@@ -16,7 +16,7 @@ export default (pluginManager: PluginManager) => {
       stateModel,
       trackType: 'QuantitativeTrack',
       viewType: 'LinearGenomeView',
-      ReactComponent,
+      ReactComponent: lazy(() => import('./components/WiggleDisplayComponent')),
     })
   })
 }