jbrowse-plugin-protein3d 0.0.3 → 0.0.4

package/dist/ProteinView/util.js

@@ -15,18 +15,20 @@ export function getMolstarStructureSelection({ structure, selectedResidue, }) {
         'group-by': Q.struct.atomProperty.macromolecular.residueKey(),
     }), structure);
 }
-export function toStr(r) {
+export function toStr({ chain, code, structureSeqPos, }) {
     return [
-        `Position: ${r.structureSeqPos}`,
-        r.code
-            ? `Letter: ${r.code} (${proteinAbbreviationMapping[r.code]?.singleLetterCode})`
+        structureSeqPos === undefined ? '' : `Position: ${structureSeqPos}`,
+        code
+            ? `Letter: ${code} (${proteinAbbreviationMapping[code]?.singleLetterCode})`
             : '',
-        r.chain ? `Chain: ${r.chain}` : '',
+        chain ? `Chain: ${chain}` : '',
     ]
         .filter(f => !!f)
         .join(', ');
 }
 export function invertMap(arg) {
-    return Object.fromEntries(Object.entries(arg).map(([a, b]) => [b, a]));
+    return Object.fromEntries(Object.entries(arg)
+        .map(([a, b]) => [b, +a])
+        .filter(f => f[0] !== undefined));
 }
 //# sourceMappingURL=util.js.map

package/dist/ProteinView/util.js.map

@@ -1 +1 @@
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package/dist/UniProtVariationAdapter/UniProtVariationAdapter.d.ts

@@ -0,0 +1,15 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+export default class UniProtVariationAdapter extends BaseFeatureDataAdapter {
+    static capabilities: string[];
+    feats: Promise<{
+        uniqueId: string;
+        start: number;
+        end: number;
+    }[]> | undefined;
+    private loadDataP;
+    private loadData;
+    getRefNames(_opts?: BaseOptions): Promise<never[]>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/UniProtVariationAdapter/UniProtVariationAdapter.js

@@ -0,0 +1,55 @@
+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 UniProtVariationAdapter extends BaseFeatureDataAdapter {
+    static capabilities = ['getFeatures', 'getRefNames'];
+    feats;
+    async loadDataP() {
+        const { features } = JSON.parse(await openLocation(this.getConf('location')).readFile('utf8'));
+        const scoreField = this.getConf('scoreField');
+        return features.map(({ begin, end, ...rest }, idx) => ({
+            ...rest,
+            uniqueId: `feat-${idx}`,
+            start: +begin,
+            end: +end + 1,
+            score: scoreField === 'population_frequency'
+                ? rest.populationFrequencies?.[0]?.frequency
+                : scoreField === 'variant_impact_score'
+                    ? rest.predictions?.[0]?.score
+                    : undefined,
+            description: rest.descriptions?.map(d => d.value).join(','),
+            name: [
+                rest.mutatedType
+                    ? `${rest.wildType}->${rest.mutatedType}`
+                    : `${rest.wildType}->del`,
+            ],
+        }));
+    }
+    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=UniProtVariationAdapter.js.map

package/dist/UniProtVariationAdapter/UniProtVariationAdapter.js.map

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

@@ -0,0 +1,17 @@
+declare const UniProtVariationAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    scoreField: {
+        type: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default UniProtVariationAdapter;

package/dist/UniProtVariationAdapter/configSchema.js

@@ -0,0 +1,20 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config UniProtVariationAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const UniProtVariationAdapter = ConfigurationSchema('UniProtVariationAdapter', {
+    /**
+     * #slot
+     */
+    location: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+    scoreField: {
+        type: 'string',
+        defaultValue: '',
+    },
+}, { explicitlyTyped: true });
+export default UniProtVariationAdapter;
+//# sourceMappingURL=configSchema.js.map

package/dist/UniProtVariationAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/UniProtVariationAdapter/index.d.ts

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

package/dist/UniProtVariationAdapter/index.js

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

package/dist/UniProtVariationAdapter/index.js.map

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

@@ -1,7 +1,7 @@
 import { Feature } from '@jbrowse/core/util';
 export declare function genomeToTranscriptMapping(feature: Feature): {
-    g2p: Record<number, number | undefined>;
-    p2g: Record<number, number | undefined>;
+    g2p: Record<number, number>;
+    p2g: Record<number, number>;
     refName: string;
     strand: number;
 };

package/dist/genomeToTranscriptMapping.js

@@ -9,9 +9,9 @@ export function genomeToTranscriptMapping(feature) {
     const g2p = {};
     const p2g = {};
     let proteinCounter = 0;
-    if (strand !== -1) {
+    if (strand === -1) {
         for (const f of cds) {
-            for (let genomePos = f.get('start'); genomePos < f.get('end'); genomePos++) {
+            for (let genomePos = f.get('end'); genomePos > f.get('start'); genomePos--) {
                 const proteinPos = Math.floor(proteinCounter++ / 3);
                 g2p[genomePos] = proteinPos;
                 if (!p2g[proteinPos]) {
@@ -22,7 +22,7 @@ export function genomeToTranscriptMapping(feature) {
     }
     else {
         for (const f of cds) {
-            for (let genomePos = f.get('end'); genomePos > f.get('start'); genomePos--) {
+            for (let genomePos = f.get('start'); genomePos < f.get('end'); genomePos++) {
                 const proteinPos = Math.floor(proteinCounter++ / 3);
                 g2p[genomePos] = proteinPos;
                 if (!p2g[proteinPos]) {

package/dist/genomeToTranscriptMapping.js.map

@@ -1 +1 @@
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package/dist/index.js

@@ -4,6 +4,9 @@ import { version } from '../package.json';
 import ProteinViewF from './ProteinView';
 import LaunchProteinViewF from './LaunchProteinView';
 import AddHighlightModelF from './AddHighlightModel';
+import AlphaFoldConfidenceAdapterF from './AlphaFoldConfidenceAdapter';
+import UniProtVariationAdapterF from './UniProtVariationAdapter';
+import AlphaMissensePathogenicityAdapterF from './AlphaMissensePathogenicityAdapter';
 export default class ProteinViewer extends Plugin {
     name = 'ProteinViewer';
     version = version;
@@ -11,6 +14,9 @@ export default class ProteinViewer extends Plugin {
         ProteinViewF(pluginManager);
         LaunchProteinViewF(pluginManager);
         AddHighlightModelF(pluginManager);
+        AlphaFoldConfidenceAdapterF(pluginManager);
+        AlphaMissensePathogenicityAdapterF(pluginManager);
+        UniProtVariationAdapterF(pluginManager);
     }
     configure(_pluginManager) { }
 }

package/dist/index.js.map

@@ -1 +1 @@
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