jbrowse-plugin-protein3d 0.0.3 → 0.0.4

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js

@@ -3,18 +3,12 @@ import { observer } from 'mobx-react';
 import { getSession } from '@jbrowse/core/util';
 // locals
 import Highlight from './Highlight';
+import { checkHovered } from '../ProteinView/util';
 const GenomeMouseoverHighlight = observer(function ({ model, }) {
-    const { hovered } = getSession(model);
-    return hovered &&
-        typeof hovered === 'object' &&
-        'hoverPosition' in hovered ? (React.createElement(HoverHighlight, { model: model })) : null;
-});
-const HoverHighlight = observer(function ({ model, }) {
     const session = getSession(model);
-    if (session.views.some(s => s.type === 'ProteinView')) {
-        const { hovered } = session;
+    const { views, hovered } = session;
+    if (checkHovered(hovered) && views.some(s => s.type === 'ProteinView')) {
         const { assemblyNames } = model;
-        // @ts-expect-error
         const { coord, refName } = hovered.hoverPosition;
         return (React.createElement(Highlight, { model: model, start: coord - 1, end: coord, refName: refName, assemblyName: assemblyNames[0] }));
     }

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

@@ -1 +1 @@
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+{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,SAAS;AACT,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAA;AAElD,MAAM,wBAAwB,GAAG,QAAQ,CAAC,UAAU,EAClD,KAAK,GAGN;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;IAClC,IAAI,YAAY,CAAC,OAAO,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CAAC,EAAE,CAAC;QACvE,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;QAC/B,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;QAChD,OAAO,CACL,oBAAC,SAAS,IACR,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,KAAK,GAAG,CAAC,EAChB,GAAG,EAAE,KAAK,EACV,OAAO,EAAE,OAAO,EAChB,YAAY,EAAE,aAAa,CAAC,CAAC,CAAE,GAC/B,CACH,CAAA;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA;AAEF,eAAe,wBAAwB,CAAA"}

package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js

@@ -5,9 +5,10 @@ import Highlight from './Highlight';
 const ProteinToGenomeClickHighlight = observer(function ({ model, }) {
     const { assemblyManager, views } = getSession(model);
     const { assemblyNames } = model;
-    const p = views.find(f => f.type === 'ProteinView');
-    const assembly = assemblyManager.get(assemblyNames[0]);
-    return assembly ? (React.createElement(React.Fragment, null, p?.clickGenomeHighlights.map((r, idx) => (React.createElement(Highlight, { key: `${JSON.stringify(r)}-${idx}}`, start: r.start, end: r.end, refName: r.refName, assemblyName: assemblyNames[0], model: model }))))) : null;
+    const proteinView = views.find(f => f.type === 'ProteinView');
+    const assemblyName = assemblyNames[0];
+    const assembly = assemblyManager.get(assemblyName);
+    return assembly ? (React.createElement(React.Fragment, null, proteinView?.structures.map(structure => structure.clickGenomeHighlights.map((r, idx) => (React.createElement(Highlight, { key: `${JSON.stringify(r)}-${idx}}`, start: r.start, end: r.end, refName: r.refName, assemblyName: assemblyName, model: model })))))) : null;
 });
 export default ProteinToGenomeClickHighlight;
 //# sourceMappingURL=ProteinToGenomeClickHighlight.js.map

package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ProteinToGenomeClickHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/ProteinToGenomeClickHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAI/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAInC,MAAM,6BAA6B,GAAG,QAAQ,CAAC,UAAU,EACvD,KAAK,GAGN;IACC,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CAE/C,CAAA;IACb,MAAM,YAAY,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;IACtC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,WAAW,EAAE,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CACvC,SAAS,CAAC,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAC9C,oBAAC,SAAS,IACR,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,GAAG,EACnC,KAAK,EAAE,CAAC,CAAC,KAAK,EACd,GAAG,EAAE,CAAC,CAAC,GAAG,EACV,OAAO,EAAE,CAAC,CAAC,OAAO,EAClB,YAAY,EAAE,YAAY,EAC1B,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CACH,CACA,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,6BAA6B,CAAA"}

package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.d.ts

@@ -1,7 +1,6 @@
 import React from 'react';
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-type LGV = LinearGenomeViewModel;
 declare const ProteinToGenomeHoverHighlight: ({ model, }: {
-    model: LGV;
+    model: LinearGenomeViewModel;
 }) => React.JSX.Element | null;
 export default ProteinToGenomeHoverHighlight;

package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js

@@ -5,9 +5,10 @@ import Highlight from './Highlight';
 const ProteinToGenomeHoverHighlight = observer(function ({ model, }) {
     const { assemblyManager, views } = getSession(model);
     const { assemblyNames } = model;
-    const p = views.find(f => f.type === 'ProteinView');
-    const assembly = assemblyManager.get(assemblyNames[0]);
-    return assembly ? (React.createElement(React.Fragment, null, p?.hoverGenomeHighlights.map((r, idx) => (React.createElement(Highlight, { key: `${JSON.stringify(r)}-${idx}`, start: r.start, end: r.end, refName: r.refName, assemblyName: assemblyNames[0], model: model }))))) : null;
+    const proteinView = views.find(f => f.type === 'ProteinView');
+    const assemblyName = assemblyNames[0];
+    const assembly = assemblyManager.get(assemblyName);
+    return assembly ? (React.createElement(React.Fragment, null, proteinView?.structures.map(structure => structure.hoverGenomeHighlights.map((r, idx) => (React.createElement(Highlight, { key: `${JSON.stringify(r)}-${idx}`, start: r.start, end: r.end, refName: r.refName, assemblyName: assemblyName, model: model })))))) : null;
 });
 export default ProteinToGenomeHoverHighlight;
 //# sourceMappingURL=ProteinToGenomeHoverHighlight.js.map

package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js.map

@@ -1 +1 @@
-{"version":3,"file":"ProteinToGenomeHoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/ProteinToGenomeHoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAI/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAInC,MAAM,6BAA6B,GAAG,QAAQ,CAAC,UAAU,EACvD,KAAK,GAGN;IACC,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,MAAM,CAAC,GAAG,KAAK,CAAC,IAAI,CAClB,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CACG,CAAA;IAClC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA;IACtD,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,CAAC,EAAE,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CACxC,oBAAC,SAAS,IACR,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,EAClC,KAAK,EAAE,CAAC,CAAC,KAAK,EACd,GAAG,EAAE,CAAC,CAAC,GAAG,EACV,OAAO,EAAE,CAAC,CAAC,OAAO,EAClB,YAAY,EAAE,aAAa,CAAC,CAAC,CAAC,EAC9B,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,6BAA6B,CAAA"}
+{"version":3,"file":"ProteinToGenomeHoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/ProteinToGenomeHoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAI/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,MAAM,6BAA6B,GAAG,QAAQ,CAAC,UAAU,EACvD,KAAK,GAGN;IACC,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CAE/C,CAAA;IACb,MAAM,YAAY,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;IACtC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,WAAW,EAAE,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CACvC,SAAS,CAAC,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAC9C,oBAAC,SAAS,IACR,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,EAClC,KAAK,EAAE,CAAC,CAAC,KAAK,EACd,GAAG,EAAE,CAAC,CAAC,GAAG,EACV,OAAO,EAAE,CAAC,CAAC,OAAO,EAClB,YAAY,EAAE,YAAY,EAC1B,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CACH,CACA,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,6BAA6B,CAAA"}

package/dist/AddHighlightModel/util.js

@@ -5,7 +5,7 @@ export const useStyles = makeStyles()({
         background: 'rgba(255,255,0,0.2)',
         border: '1px solid rgba(50,50,0,0.2)',
         position: 'absolute',
-        zIndex: 1000,
+        zIndex: 99,
         textAlign: 'center',
         pointerEvents: 'none',
         overflow: 'hidden',

package/dist/AddHighlightModel/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,EAAE;QACV,SAAS,EAAE,QAAQ;QACnB,aAAa,EAAE,MAAM;QACrB,QAAQ,EAAE,QAAQ;KACnB;IACD,UAAU,EAAE;QACV,MAAM,EAAE,iBAAiB;KAC1B;CACF,CAAC,CAAA"}

package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.d.ts

@@ -0,0 +1,16 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+export default class AlphaFoldConfidenceAdapter extends BaseFeatureDataAdapter {
+    static capabilities: string[];
+    feats: Promise<{
+        uniqueId: string;
+        start: number;
+        end: number;
+        score: number;
+    }[]> | undefined;
+    private loadDataP;
+    private loadData;
+    getRefNames(_opts?: BaseOptions): Promise<never[]>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js

@@ -0,0 +1,43 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { doesIntersect2, SimpleFeature, } from '@jbrowse/core/util';
+export default class AlphaFoldConfidenceAdapter extends BaseFeatureDataAdapter {
+    static capabilities = ['getFeatures', 'getRefNames'];
+    feats;
+    async loadDataP() {
+        const scores = JSON.parse(await openLocation(this.getConf('location')).readFile('utf8'));
+        return scores.residueNumber.map((value, idx) => ({
+            uniqueId: `feat-${idx}`,
+            start: value,
+            end: value + 1,
+            score: scores.confidenceScore[idx],
+        }));
+    }
+    async loadData(_opts = {}) {
+        if (!this.feats) {
+            this.feats = this.loadDataP().catch((e) => {
+                this.feats = undefined;
+                throw e;
+            });
+        }
+        return this.feats;
+    }
+    async getRefNames(_opts = {}) {
+        return [];
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { start, end, refName } = query;
+            const data = await this.loadData();
+            for (const f of data) {
+                if (doesIntersect2(f.start, f.end, start, end)) {
+                    observer.next(new SimpleFeature({ ...f, refName }));
+                }
+            }
+            observer.complete();
+        }, opts.signal);
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=AlphaFoldConfidenceAdapter.js.map

package/dist/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.js.map

@@ -0,0 +1 @@
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package/dist/AlphaFoldConfidenceAdapter/configSchema.d.ts

@@ -0,0 +1,13 @@
+declare const AlphaFoldConfidenceAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default AlphaFoldConfidenceAdapter;

package/dist/AlphaFoldConfidenceAdapter/configSchema.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config AlphaFoldConfidenceAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const AlphaFoldConfidenceAdapter = ConfigurationSchema('AlphaFoldConfidenceAdapter', {
+    /**
+     * #slot
+     */
+    location: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+export default AlphaFoldConfidenceAdapter;
+//# sourceMappingURL=configSchema.js.map

package/dist/AlphaFoldConfidenceAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/AlphaFoldConfidenceAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,0BAA0B,GAAG,mBAAmB,CACpD,4BAA4B,EAC5B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,0BAA0B,CAAA"}

package/dist/AlphaFoldConfidenceAdapter/index.d.ts

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

package/dist/AlphaFoldConfidenceAdapter/index.js

@@ -0,0 +1,11 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default function AlphaFoldConfidenceAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'AlphaFoldConfidenceAdapter',
+        displayName: 'AlphaFoldConfidence adapter',
+        configSchema,
+        getAdapterClass: () => import('./AlphaFoldConfidenceAdapter').then(r => r.default),
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/AlphaFoldConfidenceAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlphaFoldConfidenceAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,2BAA2B,CACjD,aAA4B;IAE5B,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,4BAA4B;QAClC,WAAW,EAAE,6BAA6B;QAC1C,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,8BAA8B,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KAC9D,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.d.ts

@@ -0,0 +1,30 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+export default class AlphaMissensePathogenicityAdapter extends BaseFeatureDataAdapter {
+    static capabilities: string[];
+    feats: Promise<{
+        uniqueId: string;
+        start: number;
+        end: number;
+        score: number;
+        ref: string;
+        variant: string;
+        am_class: string;
+    }[]> | undefined;
+    private loadDataP;
+    private loadData;
+    getGlobalStats(_opts?: BaseOptions): Promise<{
+        scoreMin: number;
+        scoreMax: number;
+    }>;
+    getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
+        featureDensity: number;
+    }>;
+    getRefNames(_opts?: BaseOptions): Promise<never[]>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getSources(): Promise<{
+        name: string;
+        __name: string;
+    }[]>;
+    freeResources(): void;
+}

package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js

@@ -0,0 +1,78 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { doesIntersect2, SimpleFeature, max, min, } from '@jbrowse/core/util';
+export default class AlphaMissensePathogenicityAdapter extends BaseFeatureDataAdapter {
+    static capabilities = ['getFeatures', 'getRefNames'];
+    feats;
+    async loadDataP() {
+        const scores = await openLocation(this.getConf('location')).readFile('utf8');
+        return scores
+            .split('\n')
+            .slice(1)
+            .map(f => f.trim())
+            .filter(f => !!f)
+            .map((row, idx) => {
+            const [protein_variant, score, am_class] = row.split(',');
+            const ref = protein_variant[0];
+            const variant = protein_variant.at(-1);
+            const coord = protein_variant.slice(1, -1);
+            return {
+                uniqueId: `feat-${idx}`,
+                ref: ref,
+                variant: variant,
+                start: +coord,
+                end: +coord + 1,
+                score: +score,
+                am_class: am_class,
+            };
+        });
+    }
+    async loadData(_opts = {}) {
+        if (!this.feats) {
+            this.feats = this.loadDataP().catch((e) => {
+                this.feats = undefined;
+                throw e;
+            });
+        }
+        return this.feats;
+    }
+    async getGlobalStats(_opts) {
+        const data = await this.loadData();
+        const scoreMin = min(data.map(s => s.score));
+        const scoreMax = max(data.map(s => s.score));
+        return { scoreMin, scoreMax };
+    }
+    // always render bigwig instead of calculating a feature density for it
+    async getMultiRegionFeatureDensityStats(_regions) {
+        return { featureDensity: 0 };
+    }
+    async getRefNames(_opts = {}) {
+        return [];
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { start, end, refName } = query;
+            const data = await this.loadData();
+            for (const f of data) {
+                if (doesIntersect2(f.start, f.end, start, end)) {
+                    observer.next(new SimpleFeature({ ...f, refName, source: f.variant }));
+                }
+            }
+            observer.complete();
+        }, opts.signal);
+    }
+    async getSources() {
+        const sources = new Set();
+        const data = await this.loadData();
+        for (const f of data) {
+            sources.add(f.variant);
+        }
+        return [...sources].map(s => ({
+            name: s,
+            __name: s,
+        }));
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=AlphaMissensePathogenicityAdapter.js.map

package/dist/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.js.map

@@ -0,0 +1 @@
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package/dist/AlphaMissensePathogenicityAdapter/configSchema.d.ts

@@ -0,0 +1,13 @@
+declare const AlphaMissensePathogenicityAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default AlphaMissensePathogenicityAdapter;

package/dist/AlphaMissensePathogenicityAdapter/configSchema.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config AlphaMissensePathogenicityAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const AlphaMissensePathogenicityAdapter = ConfigurationSchema('AlphaMissensePathogenicityAdapter', {
+    /**
+     * #slot
+     */
+    location: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+export default AlphaMissensePathogenicityAdapter;
+//# sourceMappingURL=configSchema.js.map

package/dist/AlphaMissensePathogenicityAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/AlphaMissensePathogenicityAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,iCAAiC,GAAG,mBAAmB,CAC3D,mCAAmC,EACnC;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,iCAAiC,CAAA"}

package/dist/AlphaMissensePathogenicityAdapter/index.d.ts

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

package/dist/AlphaMissensePathogenicityAdapter/index.js

@@ -0,0 +1,11 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default function AlphaMissensePathogenicityAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'AlphaMissensePathogenicityAdapter',
+        displayName: 'AlphaMissensePathogenicity adapter',
+        configSchema,
+        getAdapterClass: () => import('./AlphaMissensePathogenicityAdapter').then(r => r.default),
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/AlphaMissensePathogenicityAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlphaMissensePathogenicityAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,kCAAkC,CACxD,aAA4B;IAE5B,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,mCAAmC;QACzC,WAAW,EAAE,oCAAoC;QACjD,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,qCAAqC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrE,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js

@@ -2,7 +2,7 @@ import React, { useEffect, useState } from 'react';
 import { observer } from 'mobx-react';
 import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import { getContainingView, getSession, } from '@jbrowse/core/util';
+import { getContainingView, getSession, isSessionWithAddTracks, } from '@jbrowse/core/util';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 // locals
 import { getDisplayName, getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from './util';
@@ -42,8 +42,9 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
     const url = uniprotId
         ? `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-model_v4.cif`
         : undefined;
-    const { seq: structureSequence, isLoading: isRemoteStructureSequenceLoading, error: remoteStructureSequenceError, } = useRemoteStructureFileSequence({ url });
+    const { sequences: structureSequences, isLoading: isRemoteStructureSequenceLoading, error: remoteStructureSequenceError, } = useRemoteStructureFileSequence({ url });
     const e = myGeneError || isoformProteinSequencesError || remoteStructureSequenceError;
+    const structureSequence = structureSequences?.[0];
     useEffect(() => {
         if (isoformSequences !== undefined) {
             const ret = options.find(f => isoformSequences[f.id()]?.seq.replaceAll('*', '') ==
@@ -59,30 +60,179 @@ const AlphaFoldDBSearch = observer(function ({ feature, model, handleClose, }) {
                 ' ',
                 React.createElement(HelpButton, null)),
             isRemoteStructureSequenceLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Loading sequence from remote structure file" })) : null,
-            isMyGeneLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Looking up UniProt ID from mygene.info" })) : !uniprotId ? (React.createElement("div", null,
+            isMyGeneLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Looking up UniProt ID from mygene.info" })) : uniprotId ? null : (React.createElement("div", null,
                 "UniProt ID not found. Search sequence on AlphaFoldDB",
                 ' ',
                 React.createElement("a", { href: `https://alphafold.ebi.ac.uk/search/sequence/${userSelectedProteinSequence?.seq.replaceAll('*', '')}`, target: "_blank", rel: "noreferrer" }, "here"),
                 ' ',
                 React.createElement("br", null),
-                "After visiting the above link, then paste the structure URL into the Manual tab")) : null,
+                "After visiting the above link, then paste the structure URL into the Manual tab")),
             isIsoformProteinSequencesLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Loading protein sequences from transcript isoforms" })) : null,
             isoformSequences && structureSequence && selectedTranscript ? (React.createElement(React.Fragment, null,
                 React.createElement(TranscriptSelector, { val: userSelection ?? '', setVal: setUserSelection, structureSequence: structureSequence, feature: feature, isoforms: options, isoformSequences: isoformSequences }),
                 React.createElement(AlphaFoldDBSearchStatus, { uniprotId: uniprotId, selectedTranscript: selectedTranscript, structureSequence: structureSequence, isoformSequences: isoformSequences }))) : null),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", disabled: !uniprotId || !userSelectedProteinSequence || !selectedTranscript, onClick: () => {
                     session.addView('ProteinView', {
                         type: 'ProteinView',
-                        url,
-                        seq2: userSelectedProteinSequence?.seq,
-                        feature: selectedTranscript?.toJSON(),
-                        connectedViewId: view.id,
-                        displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+                        isFloating: true,
+                        structures: [
+                            {
+                                url,
+                                userProvidedTranscriptSequence: userSelectedProteinSequence?.seq,
+                                feature: selectedTranscript?.toJSON(),
+                                connectedViewId: view.id,
+                            },
+                        ],
+                        displayName: [
+                            'Protein view',
+                            uniprotId,
+                            getGeneDisplayName(feature),
+                            getTranscriptDisplayName(selectedTranscript),
+                        ].join(' - '),
                     });
                     handleClose();
-                } }, "Submit"))));
+                } }, "Launch 3-D protein structure view"),
+            React.createElement(Button, { variant: "contained", disabled: !uniprotId || !userSelectedProteinSequence || !selectedTranscript, onClick: () => {
+                    if (uniprotId && isSessionWithAddTracks(session)) {
+                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                        ;
+                        (async () => {
+                            try {
+                                session.addTemporaryAssembly?.({
+                                    name: uniprotId,
+                                    sequence: {
+                                        type: 'ReferenceSequenceTrack',
+                                        trackId: `${uniprotId}-ReferenceSequenceTrack`,
+                                        sequenceType: 'pep',
+                                        adapter: {
+                                            type: 'UnindexedFastaAdapter',
+                                            rewriteRefNames: "jexl:split(refName,'|')[1]",
+                                            fastaLocation: {
+                                                uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.fasta`,
+                                            },
+                                        },
+                                    },
+                                });
+                                const url = `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`;
+                                const res = await fetch(url);
+                                if (!res.ok) {
+                                    throw new Error(`HTTP ${res.status} fetching ${url}`);
+                                }
+                                const data = await res.text();
+                                const types = [
+                                    ...new Set(data
+                                        .split('\n')
+                                        .filter(f => !f.startsWith('#'))
+                                        .map(f => f.trim())
+                                        .filter(f => !!f)
+                                        .map(f => f.split('\t')[2])),
+                                ];
+                                types.forEach(type => {
+                                    const s = `${uniprotId}-${type}`;
+                                    session.addTrackConf({
+                                        type: 'FeatureTrack',
+                                        trackId: s,
+                                        name: type,
+                                        adapter: {
+                                            type: 'Gff3Adapter',
+                                            gffLocation: {
+                                                uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`,
+                                            },
+                                        },
+                                        assemblyNames: [uniprotId],
+                                        displays: [
+                                            {
+                                                displayId: `${type}-LinearBasicDisplay`,
+                                                type: 'LinearBasicDisplay',
+                                                jexlFilters: [`get(feature,'type')=='${type}'`],
+                                            },
+                                        ],
+                                    });
+                                });
+                                session.addTrackConf({
+                                    type: 'FeatureTrack',
+                                    trackId: 'Antigen',
+                                    name: 'Antigen',
+                                    adapter: {
+                                        type: 'Gff3Adapter',
+                                        gffLocation: {
+                                            uri: `https://www.ebi.ac.uk/proteins/api/antigen/${uniprotId}?format=gff`,
+                                        },
+                                    },
+                                    assemblyNames: [uniprotId],
+                                });
+                                session.addTrackConf({
+                                    type: 'FeatureTrack',
+                                    trackId: 'Variation',
+                                    name: 'Variation',
+                                    adapter: {
+                                        type: 'UniProtVariationAdapter',
+                                        location: {
+                                            uri: `https://www.ebi.ac.uk/proteins/api/variation/${uniprotId}.json`,
+                                        },
+                                    },
+                                    assemblyNames: [uniprotId],
+                                });
+                                session.addTrackConf({
+                                    type: 'QuantitativeTrack',
+                                    trackId: 'AlphaFold confidence',
+                                    name: 'AlphaFold confidence',
+                                    adapter: {
+                                        type: 'AlphaFoldConfidenceAdapter',
+                                        location: {
+                                            uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-confidence_v4.json`,
+                                        },
+                                    },
+                                    assemblyNames: [uniprotId],
+                                });
+                                session.addTrackConf({
+                                    type: 'MultiQuantitativeTrack',
+                                    trackId: 'AlphaMissense scores',
+                                    name: 'AlphaMissense scores',
+                                    assemblyNames: [uniprotId],
+                                    adapter: {
+                                        type: 'AlphaMissensePathogenicityAdapter',
+                                        location: {
+                                            uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-aa-substitutions.csv`,
+                                        },
+                                    },
+                                    displays: [
+                                        {
+                                            type: 'MultiLinearWiggleDisplay',
+                                            displayId: 'AlphaMissense scores-MultiLinearWiggleDisplay',
+                                            defaultRendering: 'multirowdensity',
+                                            renderers: {
+                                                MultiDensityRenderer: {
+                                                    type: 'MultiDensityRenderer',
+                                                    bicolorPivotValue: 0.5,
+                                                },
+                                            },
+                                        },
+                                    ],
+                                });
+                                const view = session.addView('LinearGenomeView', {
+                                    type: 'LinearGenomeView',
+                                    displayName: [
+                                        'Protein view',
+                                        uniprotId,
+                                        getGeneDisplayName(feature),
+                                        getTranscriptDisplayName(selectedTranscript),
+                                    ].join(' - '),
+                                });
+                                await view.navToLocString(uniprotId, uniprotId);
+                            }
+                            catch (e) {
+                                console.error(e);
+                                session.notifyError(`${e}`, e);
+                            }
+                        })();
+                    }
+                    handleClose();
+                } }, "Launch linear protein annotation view"))));
 });
 export default AlphaFoldDBSearch;
 //# sourceMappingURL=AlphaFoldDBSearch.js.map