jbrowse-plugin-protein3d 0.0.3 → 0.0.5

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/HighlightComponents.d.ts

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

package/dist/AddHighlightModel/HighlightComponents.js.map

@@ -1 +1 @@
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+{"version":3,"file":"HighlightComponents.js","sourceRoot":"","sources":["../../src/AddHighlightModel/HighlightComponents.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,SAAS;AACT,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,wBAAwB,MAAM,4BAA4B,CAAA;AAEjE,MAAM,mBAAmB,GAAG,QAAQ,CAAC,SAAS,SAAS,CAAC,EACtD,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,6BAA6B,IAAC,KAAK,EAAE,KAAK,GAAI;QAC/C,oBAAC,6BAA6B,IAAC,KAAK,EAAE,KAAK,GAAI;QAC/C,oBAAC,wBAAwB,IAAC,KAAK,EAAE,KAAK,GAAI,CACzC,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,mBAAmB,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 @@
-{"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,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,GAAG,EACnC,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":"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 @@
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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 @@
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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 @@
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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 @@
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