@jbrowse/plugin-wiggle 2.0.0 → 2.1.2

package/esm/BigWigAdapter/BigWigAdapter.js

@@ -3,32 +3,36 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import { openLocation } from '@jbrowse/core/util/io';
 import { updateStatus } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { map, mergeAll } from 'rxjs/operators';
-import { readConfObject } from '@jbrowse/core/configuration';
 import { rectifyStats } from '@jbrowse/core/util/stats';
 export default class BigWigAdapter extends BaseFeatureDataAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        this.bigwig = new BigWig({
-            filehandle: openLocation(readConfObject(config, 'bigWigLocation'), this.pluginManager),
+    async setupPre(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        const bigwig = new BigWig({
+            filehandle: openLocation(this.getConf('bigWigLocation'), this.pluginManager),
         });
+        const header = await updateStatus('Downloading bigwig header', statusCallback, () => bigwig.getHeader(opts));
+        return { bigwig, header };
     }
     async setup(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return updateStatus('Downloading bigwig header', statusCallback, () => this.bigwig.getHeader(opts));
+        if (!this.setupP) {
+            this.setupP = this.setupPre(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
     }
     async getRefNames(opts) {
-        const { refsByName } = await this.setup(opts);
+        const { header: { refsByName }, } = await this.setup(opts);
         return Object.keys(refsByName);
     }
     async refIdToName(refId) {
         var _a;
-        const { refsByNumber } = await this.setup();
+        const { header: { refsByNumber }, } = await this.setup();
         return (_a = refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
     }
     async getGlobalStats(opts) {
-        const { totalSummary } = await this.setup(opts);
+        const { header: { totalSummary }, } = await this.setup(opts);
         return rectifyStats(totalSummary);
     }
     getFeatures(region, opts = {}) {
@@ -36,16 +40,31 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
         const { bpPerPx = 0, signal, resolution = 1, statusCallback = () => { }, } = opts;
         return ObservableCreate(async (observer) => {
             statusCallback('Downloading bigwig data');
-            const ob = await this.bigwig.getFeatureStream(refName, start, end, {
+            const source = this.getConf('source');
+            const { bigwig } = await this.setup(opts);
+            const feats = await bigwig.getFeatures(refName, start, end, {
                 ...opts,
                 basesPerSpan: bpPerPx / resolution,
             });
-            ob.pipe(mergeAll(), map(record => {
-                return new SimpleFeature({
-                    id: `${refName}:${record.start}-${record.end}`,
-                    data: { ...record, refName },
+            for (let i = 0; i < feats.length; i++) {
+                const data = feats[i];
+                if (source) {
+                    // @ts-ignore
+                    data.source = source;
+                }
+                const uniqueId = `${source}:${region.refName}:${data.start}-${data.end}`;
+                // @ts-ignore
+                data.refName = refName;
+                data.uniqueId = uniqueId;
+                observer.next({
+                    // @ts-ignore
+                    get: (str) => data[str],
+                    id: () => uniqueId,
+                    // @ts-ignore
+                    toJSON: () => data,
                 });
-            })).subscribe(observer);
+            }
+            observer.complete();
         }, signal);
     }
     // always render bigwig instead of calculating a feature density for it

package/esm/BigWigAdapter/BigWigAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BigWigAdapter.js","sourceRoot":"","sources":["../../src/BigWigAdapter/BigWigAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAA;AAClC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,YAAY,EAAW,MAAM,oBAAoB,CAAA;AAC1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,YAAY,EAA2B,MAAM,0BAA0B,CAAA;AAMhF,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IAUvD,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC;YACxB,UAAU,EAAE,YAAY,CACtB,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,EAC9B,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;QACF,MAAM,MAAM,GAAG,MAAM,YAAY,CAC/B,2BAA2B,EAC3B,cAAc,EACd,GAAG,EAAE,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,CAC7B,CAAA;QACD,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,CAAA;IAC3B,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EACJ,MAAM,EAAE,EAAE,UAAU,EAAE,GACvB,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1B,OAAO,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;IAChC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,KAAa;;QACpC,MAAM,EACJ,MAAM,EAAE,EAAE,YAAY,EAAE,GACzB,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtB,OAAO,MAAA,YAAY,CAAC,KAAK,CAAC,0CAAE,IAAI,CAAA;IAClC,CAAC;IAEM,KAAK,CAAC,cAAc,CAAC,IAAkB;QAC5C,MAAM,EACJ,MAAM,EAAE,EAAE,YAAY,EAAE,GACzB,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1B,OAAO,YAAY,CAAC,YAAuC,CAAC,CAAA;IAC9D,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAsB,EAAE;QACzD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,MAAM,EACJ,OAAO,GAAG,CAAC,EACX,MAAM,EACN,UAAU,GAAG,CAAC,EACd,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,GAC1B,GAAG,IAAI,CAAA;QACR,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,cAAc,CAAC,yBAAyB,CAAC,CAAA;YACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;YACrC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACzC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBAC1D,GAAG,IAAI;gBACP,YAAY,EAAE,OAAO,GAAG,UAAU;aACnC,CAAC,CAAA;YAEF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBACrB,IAAI,MAAM,EAAE;oBACV,aAAa;oBACb,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;iBACrB;gBACD,MAAM,QAAQ,GAAG,GAAG,MAAM,IAAI,MAAM,CAAC,OAAO,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;gBACxE,aAAa;gBACb,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;gBACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;gBACxB,QAAQ,CAAC,IAAI,CAAC;oBACZ,aAAa;oBACb,GAAG,EAAE,CAAC,GAAW,EAAE,EAAE,CAAE,IAAgC,CAAC,GAAG,CAAC;oBAC5D,EAAE,EAAE,GAAG,EAAE,CAAC,QAAQ;oBAClB,aAAa;oBACb,MAAM,EAAE,GAAG,EAAE,CAAC,IAAI;iBACnB,CAAC,CAAA;aACH;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAED,uEAAuE;IACvE,KAAK,CAAC,oBAAoB,CAAC,QAAkB;QAC3C,OAAO,EAAE,cAAc,EAAE,CAAC,EAAE,CAAA;IAC9B,CAAC;IAEM,aAAa,KAAU,CAAC;;AAjGjB,0BAAY,GAAG;IAC3B,eAAe;IACf,eAAe;IACf,gBAAgB;CACjB,CAAA"}

package/esm/BigWigAdapter/configSchema.js

@@ -7,5 +7,10 @@ export default ConfigurationSchema('BigWigAdapter', {
             locationType: 'UriLocation',
         },
     },
+    source: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Used for multiwiggle',
+    },
 }, { explicitlyTyped: true });
 //# sourceMappingURL=configSchema.js.map

package/esm/BigWigAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigWigAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigWigAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,sBAAsB;KACpC;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/BigWigAdapter/index.d.ts

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

package/esm/BigWigAdapter/index.js

@@ -1,2 +1,15 @@
-export { default as configSchema } from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BigWigAdapter',
+        configSchema,
+        adapterCapabilities: [
+            'hasResolution',
+            'hasLocalStats',
+            'hasGlobalStats',
+        ],
+        getAdapterClass: () => import('./BigWigAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/BigWigAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigWigAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigWigAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,eAAe;QACrB,YAAY;QACZ,mBAAmB,EAAE;YACnB,eAAe;YACf,eAAe;YACf,gBAAgB;SACjB;QACD,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACtE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/CreateMultiWiggleExtension/ConfirmDialog.d.ts

@@ -0,0 +1,9 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+declare const ConfirmDialog: ({ tracks, onClose, }: {
+    tracks: AnyConfigurationModel[];
+    onClose: (arg: boolean, arg1?: {
+        name: string;
+    }) => void;
+}) => JSX.Element;
+export default ConfirmDialog;

package/esm/CreateMultiWiggleExtension/ConfirmDialog.js

@@ -0,0 +1,26 @@
+import React, { useState } from 'react';
+import { Button, Dialog, DialogActions, DialogContent, DialogTitle, TextField, Typography, } from '@mui/material';
+import { readConfObject, } from '@jbrowse/core/configuration';
+const ConfirmDialog = ({ tracks, onClose, }) => {
+    const [val, setVal] = useState('MultiWiggle ' + Date.now());
+    const allQuant = tracks.every(t => t.type === 'QuantitativeTrack');
+    return (React.createElement(Dialog, { open: true, onClose: () => onClose(false) },
+        React.createElement(DialogTitle, null, "Confirm multi-wiggle track create"),
+        React.createElement(DialogContent, null,
+            React.createElement(Typography, null,
+                !allQuant
+                    ? 'Not every track looks like a QuantitativeTrack. This could have unexpected behavior, confirm if it looks ok.'
+                    : null,
+                "Listing:"),
+            React.createElement("ul", null, tracks.map(track => (React.createElement("li", { key: track.trackId },
+                readConfObject(track, 'name'),
+                " - ",
+                track.type)))),
+            React.createElement(TextField, { value: val, onChange: event => setVal(event.target.value), helperText: "Track name" }),
+            React.createElement(Typography, null, "Confirm creation of track?")),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { onClick: () => onClose(false), color: "primary" }, "Cancel"),
+            React.createElement(Button, { onClick: () => onClose(true, { name: val }), color: "primary", variant: "contained", autoFocus: true }, "Submit"))));
+};
+export default ConfirmDialog;
+//# sourceMappingURL=ConfirmDialog.js.map

package/esm/CreateMultiWiggleExtension/ConfirmDialog.js.map

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

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function (pm: PluginManager): void;

package/esm/CreateMultiWiggleExtension/index.js

@@ -0,0 +1,51 @@
+import { lazy } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+const ConfirmDialog = lazy(() => import('./ConfirmDialog'));
+export default function (pm) {
+    pm.addToExtensionPoint('TrackSelector-multiTrackMenuItems', () => {
+        return [
+            {
+                label: 'Create multi-wiggle track',
+                onClick: (model) => {
+                    const tracks = model.selection;
+                    const trackIds = tracks.map(c => readConfObject(c, 'name'));
+                    function makeTrack(arg) {
+                        const subadapters = tracks
+                            .map(c => readConfObject(c, 'adapter'))
+                            .map((c, idx) => ({ ...c, source: trackIds[idx] }));
+                        const assemblyNames = [
+                            ...new Set(tracks.map(c => readConfObject(c, 'assemblyNames')).flat()),
+                        ];
+                        const now = +Date.now();
+                        const trackId = `multitrack-${now}-sessionTrack`;
+                        getSession(model).addTrackConf({
+                            type: 'MultiQuantitativeTrack',
+                            trackId,
+                            name: arg.name,
+                            assemblyNames,
+                            adapter: {
+                                type: 'MultiWiggleAdapter',
+                                subadapters,
+                            },
+                        });
+                        model.view.showTrack(trackId);
+                    }
+                    getSession(model).queueDialog(handleClose => [
+                        ConfirmDialog,
+                        {
+                            tracks,
+                            onClose: (arg, arg1) => {
+                                if (arg) {
+                                    makeTrack(arg1);
+                                }
+                                handleClose();
+                            },
+                        },
+                    ]);
+                },
+            },
+        ];
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/CreateMultiWiggleExtension/index.js.map

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package/esm/DensityRenderer/DensityRenderer.d.ts

@@ -0,0 +1,6 @@
+import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
+export default class DensityRenderer extends WiggleBaseRenderer {
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
+        reducedFeatures: import("@jbrowse/core/util").Feature[];
+    }>;
+}

package/esm/DensityRenderer/DensityRenderer.js

@@ -0,0 +1,8 @@
+import { drawDensity } from '../drawxy';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+export default class DensityRenderer extends WiggleBaseRenderer {
+    async draw(ctx, props) {
+        return drawDensity(ctx, props);
+    }
+}
+//# sourceMappingURL=DensityRenderer.js.map

package/esm/DensityRenderer/DensityRenderer.js.map

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

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/DensityRenderer/configSchema.js

@@ -0,0 +1,5 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import ConfigSchema from '../configSchema';
+const configSchema = ConfigurationSchema('DensityRenderer', {}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/DensityRenderer/configSchema.js.map

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

@@ -1,6 +1,3 @@
-import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
-export { default as ReactComponent } from '../WiggleRendering';
-export default class DensityRenderer extends WiggleBaseRenderer {
-    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
-}
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/DensityRenderer/index.js

@@ -1,39 +1,12 @@
-import { readConfObject, ConfigurationSchema, } from '@jbrowse/core/configuration';
-import { featureSpanPx } from '@jbrowse/core/util';
-import { getScale } from '../util';
-import ConfigSchema from '../configSchema';
-import WiggleBaseRenderer from '../WiggleBaseRenderer';
-export { default as ReactComponent } from '../WiggleRendering';
-export default class DensityRenderer extends WiggleBaseRenderer {
-    async draw(ctx, props) {
-        const { features, regions, bpPerPx, scaleOpts, height, config } = props;
-        const [region] = regions;
-        const pivot = readConfObject(config, 'bicolorPivot');
-        const pivotValue = readConfObject(config, 'bicolorPivotValue');
-        const negColor = readConfObject(config, 'negColor');
-        const posColor = readConfObject(config, 'posColor');
-        const color = readConfObject(config, 'color');
-        let colorCallback;
-        if (color === '#f0f') {
-            const colorScale = pivot !== 'none'
-                ? getScale({
-                    ...scaleOpts,
-                    pivotValue,
-                    range: [negColor, 'white', posColor],
-                })
-                : getScale({ ...scaleOpts, range: ['white', posColor] });
-            colorCallback = (feature) => colorScale(feature.get('score'));
-        }
-        else {
-            colorCallback = (feature) => readConfObject(config, 'color', { feature });
-        }
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-            const w = rightPx - leftPx + 0.3; // fudge factor for subpixel rendering
-            ctx.fillStyle = colorCallback(feature);
-            ctx.fillRect(leftPx, 0, w, height);
-        }
-    }
-}
-export const configSchema = ConfigurationSchema('DensityRenderer', {}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+import configSchema from './configSchema';
+import DensityRenderer from './DensityRenderer';
+import ReactComponent from '../WiggleRendering';
+export default (pluginManager) => {
+    pluginManager.addRendererType(() => new DensityRenderer({
+        name: 'DensityRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/DensityRenderer/index.js.map

@@ -1 +1 @@
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package/esm/LinePlotRenderer/LinePlotRenderer.d.ts

@@ -1,4 +1,6 @@
+import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
 export default class LinePlotRenderer extends WiggleBaseRenderer {
-    draw(ctx: any, props: any): Promise<void>;
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
+        reducedFeatures: import("@jbrowse/core/util").Feature[];
+    }>;
 }
-import WiggleBaseRenderer from "../WiggleBaseRenderer";

package/esm/LinePlotRenderer/LinePlotRenderer.js

@@ -1,71 +1,13 @@
-import { readConfObject } from '@jbrowse/core/configuration';
-import { featureSpanPx } from '@jbrowse/core/util';
-import { getScale } from '../util';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
-import { YSCALEBAR_LABEL_OFFSET } from '../LinearWiggleDisplay/models/model';
+import { YSCALEBAR_LABEL_OFFSET } from '../util';
+import { drawLine } from '../drawxy';
 export default class LinePlotRenderer extends WiggleBaseRenderer {
     async draw(ctx, props) {
-        const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, config, } = props;
-        const [region] = regions;
-        const width = (region.end - region.start) / bpPerPx;
-        const offset = YSCALEBAR_LABEL_OFFSET;
-        // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
-        // wiggle display, and makes the height of the actual drawn area add
-        // "padding" to the top and bottom of the display
-        const height = unadjustedHeight - offset * 2;
-        const clipColor = readConfObject(config, 'clipColor');
-        const highlightColor = readConfObject(config, 'highlightColor');
-        const scale = getScale({ ...scaleOpts, range: [0, height] });
-        const [niceMin, niceMax] = scale.domain();
-        const toY = rawscore => height - scale(rawscore) + offset;
-        const colorCallback = readConfObject(config, 'color') === '#f0f'
-            ? () => 'grey'
-            : feature => readConfObject(config, 'color', { feature });
-        let lastVal;
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-            const score = feature.get('score');
-            const lowClipping = score < niceMin;
-            const highClipping = score > niceMax;
-            const w = rightPx - leftPx + 0.3; // fudge factor for subpixel rendering
-            const c = colorCallback(feature);
-            ctx.strokeStyle = c;
-            ctx.beginPath();
-            if (!region.reversed) {
-                ctx.moveTo(leftPx, toY(typeof lastVal !== 'undefined' ? lastVal : score));
-                ctx.lineTo(leftPx, toY(score));
-                ctx.lineTo(rightPx, toY(score));
-            }
-            else {
-                ctx.moveTo(rightPx, toY(typeof lastVal !== 'undefined' ? lastVal : score));
-                ctx.lineTo(rightPx, toY(score));
-                ctx.lineTo(leftPx, toY(score));
-            }
-            ctx.stroke();
-            lastVal = score;
-            if (highClipping) {
-                ctx.fillStyle = clipColor;
-                ctx.fillRect(leftPx, 0, w, 4);
-            }
-            else if (lowClipping && scaleOpts.scaleType !== 'log') {
-                ctx.fillStyle = clipColor;
-                ctx.fillRect(leftPx, height - 4, w, height);
-            }
-            if (feature.get('highlighted')) {
-                ctx.fillStyle = highlightColor;
-                ctx.fillRect(leftPx, 0, w, height);
-            }
-        }
-        if (displayCrossHatches) {
-            ctx.lineWidth = 1;
-            ctx.strokeStyle = 'rgba(200,200,200,0.8)';
-            values.forEach(tick => {
-                ctx.beginPath();
-                ctx.moveTo(0, Math.round(toY(tick)));
-                ctx.lineTo(width, Math.round(toY(tick)));
-                ctx.stroke();
-            });
-        }
+        return drawLine(ctx, {
+            ...props,
+            offset: YSCALEBAR_LABEL_OFFSET,
+            colorCallback: () => 'grey',
+        });
     }
 }
 //# sourceMappingURL=LinePlotRenderer.js.map

package/esm/LinePlotRenderer/LinePlotRenderer.js.map

@@ -1 +1 @@
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package/esm/LinePlotRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/LinePlotRenderer/configSchema.js

@@ -0,0 +1,11 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import ConfigSchema from '../configSchema';
+const configSchema = ConfigurationSchema('LinePlotRenderer', {
+    displayCrossHatches: {
+        type: 'boolean',
+        description: 'choose to draw cross hatches (sideways lines)',
+        defaultValue: false,
+    },
+}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/LinePlotRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinePlotRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,YAAY,MAAM,iBAAiB,CAAA;AAE1C,MAAM,YAAY,GAAG,mBAAmB,CACtC,kBAAkB,EAClB;IACE,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,+CAA+C;QAC5D,YAAY,EAAE,KAAK;KACpB;CACF,EACD,EAAE,iBAAiB,EAAE,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA;AAED,eAAe,YAAY,CAAA"}

package/esm/LinePlotRenderer/index.d.ts

@@ -1,3 +1,3 @@
-export { default as ReactComponent } from "../WiggleRendering";
-export { default } from "./LinePlotRenderer";
-export const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LinePlotRenderer/index.js

@@ -1,12 +1,12 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import ConfigSchema from '../configSchema';
-export { default as ReactComponent } from '../WiggleRendering';
-export { default } from './LinePlotRenderer';
-export const configSchema = ConfigurationSchema('LinePlotRenderer', {
-    displayCrossHatches: {
-        type: 'boolean',
-        description: 'choose to draw cross hatches (sideways lines)',
-        defaultValue: false,
-    },
-}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+import configSchema from './configSchema';
+import ReactComponent from '../WiggleRendering';
+import LinePlotRenderer from './LinePlotRenderer';
+export default (pluginManager) => {
+    pluginManager.addRendererType(() => new LinePlotRenderer({
+        name: 'LinePlotRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/LinePlotRenderer/index.js.map

@@ -1 +1 @@
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package/esm/LinearWiggleDisplay/components/SetColorDialog.d.ts

@@ -1,10 +1,14 @@
 /// <reference types="react" />
-export default function SetColorDialog({ model, handleClose, }: {
+declare function SetColorDialog({ model, handleClose, }: {
     model: {
-        color: number;
+        color?: string;
+        posColor?: string;
+        negColor?: string;
         setColor: (arg?: string) => void;
         setPosColor: (arg?: string) => void;
         setNegColor: (arg?: string) => void;
     };
     handleClose: () => void;
 }): JSX.Element;
+declare const _default: typeof SetColorDialog;
+export default _default;

package/esm/LinearWiggleDisplay/components/SetColorDialog.js

@@ -1,8 +1,9 @@
 import React, { useState } from 'react';
+import { observer } from 'mobx-react';
 import { Button, Dialog, DialogContent, DialogActions, DialogTitle, FormControlLabel, IconButton, Radio, Typography, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import CloseIcon from '@mui/icons-material/Close';
-import { CompactPicker } from 'react-color';
+import { ColorPicker } from '@jbrowse/core/ui/ColorPicker';
 const useStyles = makeStyles()(theme => ({
     closeButton: {
         position: 'absolute',
@@ -11,16 +12,7 @@ const useStyles = makeStyles()(theme => ({
         color: theme.palette.grey[500],
     },
 }));
-// this is needed because passing a entire color object into the react-color
-// for alpha, can't pass in an rgba string for example
-function serialize(color) {
-    if (color instanceof Object) {
-        const { r, g, b } = color;
-        return `rgb(${r},${g},${b})`;
-    }
-    return color;
-}
-export default function SetColorDialog({ model, handleClose, }) {
+function SetColorDialog({ model, handleClose, }) {
     const { classes } = useStyles();
     const [posneg, setPosNeg] = useState(false);
     return (React.createElement(Dialog, { open: true, onClose: handleClose },
@@ -33,17 +25,17 @@ export default function SetColorDialog({ model, handleClose, }) {
             React.createElement(FormControlLabel, { checked: posneg, onClick: () => setPosNeg(true), control: React.createElement(Radio, null), label: 'Positive/negative color' }),
             posneg ? (React.createElement(React.Fragment, null,
                 React.createElement(Typography, null, "Positive color"),
-                React.createElement(CompactPicker, { onChange: event => {
-                        model.setPosColor(serialize(event.rgb));
+                React.createElement(ColorPicker, { color: model.posColor || 'black', onChange: event => {
+                        model.setPosColor(event);
                         model.setColor(undefined);
                     } }),
                 React.createElement(Typography, null, "Negative color"),
-                React.createElement(CompactPicker, { onChange: event => {
-                        model.setNegColor(serialize(event.rgb));
+                React.createElement(ColorPicker, { color: model.negColor || 'black', onChange: event => {
+                        model.setNegColor(event);
                         model.setColor(undefined);
                     } }))) : (React.createElement(React.Fragment, null,
                 React.createElement(Typography, null, "Overall color"),
-                React.createElement(CompactPicker, { onChange: event => model.setColor(serialize(event.rgb)) })))),
+                React.createElement(ColorPicker, { color: model.color || 'black', onChange: event => model.setColor(event) })))),
         React.createElement(DialogActions, null,
             React.createElement(Button, { onClick: () => {
                     model.setPosColor(undefined);
@@ -52,4 +44,5 @@ export default function SetColorDialog({ model, handleClose, }) {
                 }, color: "secondary", variant: "contained" }, "Restore default"),
             React.createElement(Button, { variant: "contained", color: "primary", type: "submit", onClick: () => handleClose() }, "Submit"))));
 }
+export default observer(SetColorDialog);
 //# sourceMappingURL=SetColorDialog.js.map