@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/commonjs/RcsbChartWeb/AbsractChartComponent.d.ts

@@ -1,21 +0,0 @@
-import { ChartObjectInterface } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
-import React from "react";
-import { ChartInterface, ChartState } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartComponent";
-interface AbstractChartInterface extends Omit<ChartInterface, "chartComponentImplementation" | "dataProvider"> {
-    attributeName: string;
-}
-interface AbstractChartState extends Partial<ChartState> {
-    data: ChartObjectInterface[][];
-}
-export declare abstract class AbstractChartComponent extends React.Component<AbstractChartInterface, AbstractChartState> {
-    private asyncSubscription;
-    private subscription;
-    readonly state: AbstractChartState;
-    componentDidMount(): void;
-    componentWillUnmount(): void;
-    private unsubscribe;
-    private subscribe;
-    private updateChartMap;
-    private asyncUpdate;
-}
-export {};

package/lib/commonjs/RcsbChartWeb/AbsractChartComponent.js

@@ -1,53 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AbstractChartComponent = void 0;
-const tslib_1 = require("tslib");
-const rxjs_1 = require("rxjs");
-const react_1 = tslib_1.__importDefault(require("react"));
-const SearchQueryContextManager_1 = require("../RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/SearchQueryContextManager");
-class AbstractChartComponent extends react_1.default.Component {
-    constructor() {
-        super(...arguments);
-        this.state = {
-            data: this.props.data,
-            chartConfig: this.props.chartConfig
-        };
-    }
-    componentDidMount() {
-        this.subscribe();
-    }
-    componentWillUnmount() {
-        this.unsubscribe();
-    }
-    unsubscribe() {
-        var _a, _b;
-        (_b = (_a = this.subscription) === null || _a === void 0 ? void 0 : _a.unsubscribe) === null || _b === void 0 ? void 0 : _b.call(_a);
-    }
-    subscribe() {
-        this.subscription = SearchQueryContextManager_1.SearchQueryContextManager.dataSubscription((o) => {
-            this.updateChartMap(o);
-        });
-    }
-    updateChartMap(sqData) {
-        if (!sqData.chartMap)
-            return;
-        if (this.props.attributeName === sqData.attributeName) {
-            this.asyncUpdate(sqData);
-        }
-        else {
-            this.asyncUpdate(sqData, 10);
-        }
-    }
-    asyncUpdate(sqData, x) {
-        var _a;
-        (_a = this.asyncSubscription) === null || _a === void 0 ? void 0 : _a.unsubscribe();
-        this.asyncSubscription = rxjs_1.asyncScheduler.schedule(() => {
-            const data = sqData.chartMap.get(this.props.attributeName);
-            if (data)
-                this.setState({
-                    data
-                });
-        }, x);
-    }
-}
-exports.AbstractChartComponent = AbstractChartComponent;

package/lib/commonjs/RcsbChartWeb/BarChartComponent.d.ts

@@ -1,4 +0,0 @@
-import { AbstractChartComponent } from "./AbsractChartComponent";
-export declare class BarChartComponent extends AbstractChartComponent {
-    render(): import("react/jsx-runtime").JSX.Element;
-}

package/lib/commonjs/RcsbChartWeb/BarChartComponent.js

@@ -1,14 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.BarChartComponent = void 0;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const AbsractChartComponent_1 = require("./AbsractChartComponent");
-const ChartComponent_1 = require("@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartComponent");
-const BarChartDataProvider_1 = require("@rcsb/rcsb-charts/lib/RcsbChartDataProvider/BarChartDataProvider");
-const ChartJsBarComponent_1 = require("@rcsb/rcsb-charts/lib/RcsbChartImplementations/ChatJsImplementations/ChartJsBarComponent");
-class BarChartComponent extends AbsractChartComponent_1.AbstractChartComponent {
-    render() {
-        return ((0, jsx_runtime_1.jsx)(ChartComponent_1.ChartComponent, { data: this.state.data, chartComponentImplementation: ChartJsBarComponent_1.ChartJsBarComponent, dataProvider: new BarChartDataProvider_1.BarChartDataProvider(), chartConfig: this.props.chartConfig }));
-    }
-}
-exports.BarChartComponent = BarChartComponent;

package/lib/commonjs/RcsbChartWeb/HistogramChartComponent.d.ts

@@ -1,4 +0,0 @@
-import { AbstractChartComponent } from "./AbsractChartComponent";
-export declare class HistogramChartComponent extends AbstractChartComponent {
-    render(): JSX.Element;
-}

package/lib/commonjs/RcsbChartWeb/HistogramChartComponent.js

@@ -1,14 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.HistogramChartComponent = void 0;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const AbsractChartComponent_1 = require("./AbsractChartComponent");
-const ChartComponent_1 = require("@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartComponent");
-const HistogramChartDataProvider_1 = require("@rcsb/rcsb-charts/lib/RcsbChartDataProvider/HistogramChartDataProvider");
-const ChartJsHistogramComponent_1 = require("@rcsb/rcsb-charts/lib/RcsbChartImplementations/ChatJsImplementations/ChartJsHistogramComponent");
-class HistogramChartComponent extends AbsractChartComponent_1.AbstractChartComponent {
-    render() {
-        return ((0, jsx_runtime_1.jsx)(ChartComponent_1.ChartComponent, { data: this.state.data.map(d => d.map(d => { var _a, _b; return (Object.assign(Object.assign({}, d), { label: (parseFloat(d.label.toString()) + ((_b = (_a = this.props.chartConfig) === null || _a === void 0 ? void 0 : _a.histogramBinIncrement) !== null && _b !== void 0 ? _b : 0) * 0.5) })); })), chartComponentImplementation: ChartJsHistogramComponent_1.ChartJsHistogramComponent, dataProvider: new HistogramChartDataProvider_1.HistogramChartDataProvider(), chartConfig: this.props.chartConfig }));
-    }
-}
-exports.HistogramChartComponent = HistogramChartComponent;

package/lib/commonjs/RcsbCollectTools/AlignmentCollector/AlignmentCollector.d.ts

@@ -1,17 +0,0 @@
-import { AlignmentCollectConfig, AlignmentCollectorInterface } from "./AlignmentCollectorInterface";
-import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare class AlignmentCollector implements AlignmentCollectorInterface {
-    private requestStatus;
-    readonly rcsbFvQuery: RcsbClient;
-    private readonly targetsSubject;
-    private alignmentResponse;
-    private readonly alignmentResponseSubject;
-    private readonly alignmentLengthSubject;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
-    getTargets(): Promise<Array<string>>;
-    getAlignment(): Promise<AlignmentResponse>;
-    getAlignmentLength(): Promise<number>;
-    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<AlignmentResponse>;
-    private complete;
-}

package/lib/commonjs/RcsbCollectTools/AlignmentCollector/AlignmentCollector.js

@@ -1,108 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AlignmentCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const rxjs_1 = require("rxjs");
-const ObservableHelper_1 = require("../../RcsbUtils/Helpers/ObservableHelper");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertElementListDefined = Assertions_1.Assertions.assertElementListDefined;
-class AlignmentCollector {
-    constructor() {
-        this.requestStatus = "complete";
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-        this.targetsSubject = new rxjs_1.Subject();
-        this.alignmentResponseSubject = new rxjs_1.Subject();
-        this.alignmentLengthSubject = new rxjs_1.Subject();
-    }
-    collect(requestConfig, filter) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f;
-            this.requestStatus = "pending";
-            this.alignmentResponse = yield this.requestAlignment(requestConfig);
-            const targetAlignment = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) !== null && _b !== void 0 ? _b : (_e = (_d = (_c = this.alignmentResponse) === null || _c === void 0 ? void 0 : _c.target_alignment_subset) === null || _d === void 0 ? void 0 : _d.edges) === null || _e === void 0 ? void 0 : _e.map(e => e === null || e === void 0 ? void 0 : e.node);
-            if (targetAlignment) {
-                assertElementListDefined(targetAlignment);
-                this.alignmentResponse.target_alignment = !filter ? targetAlignment : targetAlignment === null || targetAlignment === void 0 ? void 0 : targetAlignment.filter(ta => { var _a; return filter.includes((_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "not-included"); });
-            }
-            this.alignmentResponse = typeof ((_f = requestConfig.externalTrackBuilder) === null || _f === void 0 ? void 0 : _f.filterAlignments) === "function" ? yield requestConfig.externalTrackBuilder.filterAlignments({ alignments: this.alignmentResponse }) : this.alignmentResponse;
-            this.complete();
-            return this.alignmentResponse;
-        });
-    }
-    getTargets() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                var _a, _b;
-                if (this.requestStatus === "complete") {
-                    const targetIds = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) === null || _b === void 0 ? void 0 : _b.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
-                    assertElementListDefined(targetIds);
-                    resolve(targetIds);
-                }
-                else {
-                    ObservableHelper_1.ObservableHelper.oneTimeSubscription(resolve, this.targetsSubject);
-                }
-            });
-        });
-    }
-    getAlignment() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                if (this.requestStatus === "complete") {
-                    resolve(this.alignmentResponse);
-                }
-                else {
-                    ObservableHelper_1.ObservableHelper.oneTimeSubscription(resolve, this.alignmentResponseSubject);
-                }
-            });
-        });
-    }
-    getAlignmentLength() {
-        return new Promise((resolve, reject) => {
-            var _a, _b, _c;
-            if (this.requestStatus === "complete") {
-                resolve((_c = ((_b = (_a = this.alignmentResponse.query_sequence) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : this.alignmentResponse.alignment_length)) !== null && _c !== void 0 ? _c : -1);
-            }
-            else {
-                ObservableHelper_1.ObservableHelper.oneTimeSubscription(resolve, this.alignmentLengthSubject);
-            }
-        });
-    }
-    requestAlignment(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            this.requestStatus = "pending";
-            if (requestConfig.queryId) {
-                return yield this.rcsbFvQuery.requestAlignment({
-                    queryId: requestConfig.queryId,
-                    from: requestConfig.from,
-                    to: requestConfig.to
-                });
-            }
-            else {
-                if (requestConfig.group && requestConfig.page) {
-                    return yield this.rcsbFvQuery.requestGroupAlignment({
-                        group: requestConfig.group,
-                        groupId: requestConfig.groupId,
-                        page: requestConfig.page,
-                        excludeLogo: requestConfig.excludeLogo,
-                        filter: requestConfig.filter
-                    });
-                }
-                else {
-                    return {};
-                }
-            }
-        });
-    }
-    complete() {
-        var _a, _b, _c, _d, _e;
-        this.requestStatus = "complete";
-        const targetIds = (_b = (_a = this.alignmentResponse.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id)) !== null && _b !== void 0 ? _b : [];
-        assertElementListDefined(targetIds);
-        this.targetsSubject.next(targetIds);
-        this.alignmentResponseSubject.next(this.alignmentResponse);
-        this.alignmentLengthSubject.next((_e = ((_d = (_c = this.alignmentResponse.query_sequence) === null || _c === void 0 ? void 0 : _c.length) !== null && _d !== void 0 ? _d : this.alignmentResponse.alignment_length)) !== null && _e !== void 0 ? _e : -1);
-        console.info("Alignment Processing Complete");
-    }
-}
-exports.AlignmentCollector = AlignmentCollector;

package/lib/commonjs/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.d.ts

@@ -1,29 +0,0 @@
-import { AlignmentResponse, QueryAlignmentArgs, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbQueryGroupAlignmentArguments } from "../../RcsbGraphQL/RcsbQueryAlignment";
-import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
-interface CommonAlignmentInterface {
-    externalTrackBuilder?: ExternalTrackBuilderInterface;
-    filterByTargetContains?: string;
-    dynamicDisplay?: boolean;
-    excludeAlignmentLinks?: boolean;
-    fitTitleWidth?: boolean;
-    excludeFirstRowLink?: boolean;
-}
-type QueryAlignmentArgsTypes = {
-    [K in keyof QueryAlignmentArgs]: NonNullable<QueryAlignmentArgs[K]>;
-};
-export interface CollectAlignmentInterface extends QueryAlignmentArgsTypes, CommonAlignmentInterface {
-}
-export interface CollectGroupAlignmentInterface extends RcsbQueryGroupAlignmentArguments, CommonAlignmentInterface {
-    sequencePrefix: string;
-    from?: SequenceReference;
-    to?: SequenceReference;
-}
-export type AlignmentCollectConfig = Partial<CollectAlignmentInterface & CollectGroupAlignmentInterface>;
-export interface AlignmentCollectorInterface {
-    getTargets(): Promise<Array<string>>;
-    getAlignment(): Promise<AlignmentResponse>;
-    getAlignmentLength(): Promise<number>;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
-}
-export {};

package/lib/commonjs/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/lib/commonjs/RcsbCollectTools/AnnotationCollector/AnnotationCollector.d.ts

@@ -1,16 +0,0 @@
-import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { AnnotationRequestContext, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
-export declare class AnnotationCollector implements AnnotationCollectorInterface {
-    readonly rcsbFvQuery: RcsbClient;
-    private requestStatus;
-    private rawFeatures;
-    private annotationFeatures;
-    private readonly rawFeaturesSubject;
-    private readonly annotationFeaturesSubject;
-    collect(requestConfig: AnnotationRequestContext): Promise<Array<AnnotationFeatures>>;
-    getFeatures(): Promise<Array<Feature>>;
-    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
-    private requestAnnotations;
-    private complete;
-}

package/lib/commonjs/RcsbCollectTools/AnnotationCollector/AnnotationCollector.js

@@ -1,87 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AnnotationCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const rxjs_1 = require("rxjs");
-const ObservableHelper_1 = require("../../RcsbUtils/Helpers/ObservableHelper");
-class AnnotationCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-        this.requestStatus = "complete";
-        this.rawFeaturesSubject = new rxjs_1.Subject();
-        this.annotationFeaturesSubject = new rxjs_1.Subject();
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a;
-            this.requestStatus = "pending";
-            this.annotationFeatures = yield this.requestAnnotations(requestConfig);
-            if (typeof (requestConfig === null || requestConfig === void 0 ? void 0 : requestConfig.annotationGenerator) === "function") {
-                const generatedFeatures = yield requestConfig.annotationGenerator(this.annotationFeatures);
-                if (generatedFeatures && generatedFeatures.filter((f) => (f != null)).length > 0)
-                    this.annotationFeatures = this.annotationFeatures.concat(generatedFeatures.filter((f) => (f != null)));
-            }
-            if (typeof (requestConfig === null || requestConfig === void 0 ? void 0 : requestConfig.annotationFilter) === "function") {
-                this.annotationFeatures = yield requestConfig.annotationFilter(this.annotationFeatures);
-            }
-            if (typeof ((_a = requestConfig === null || requestConfig === void 0 ? void 0 : requestConfig.externalTrackBuilder) === null || _a === void 0 ? void 0 : _a.filterFeatures) === "function")
-                this.annotationFeatures = yield requestConfig.externalTrackBuilder.filterFeatures({ annotations: this.annotationFeatures, rcsbContext: requestConfig.rcsbContext });
-            this.rawFeatures = [].concat.apply([], this.annotationFeatures.map(af => af.features));
-            this.complete();
-            return this.annotationFeatures;
-        });
-    }
-    getFeatures() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                if (this.requestStatus === "complete") {
-                    resolve(this.rawFeatures);
-                }
-                else {
-                    ObservableHelper_1.ObservableHelper.oneTimeSubscription(resolve, this.rawFeaturesSubject);
-                }
-            });
-        });
-    }
-    getAnnotationFeatures() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                if (this.requestStatus === "complete") {
-                    resolve(this.annotationFeatures);
-                }
-                else {
-                    ObservableHelper_1.ObservableHelper.oneTimeSubscription(resolve, this.annotationFeaturesSubject);
-                }
-            });
-        });
-    }
-    requestAnnotations(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            if (requestConfig.queryId)
-                return yield this.rcsbFvQuery.requestRcsbPdbAnnotations({
-                    queryId: requestConfig.queryId,
-                    reference: requestConfig.reference,
-                    sources: requestConfig.sources,
-                    filters: requestConfig.filters,
-                    range: requestConfig.range
-                });
-            else if (requestConfig.group && requestConfig.groupId)
-                return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotations({
-                    group: requestConfig.group,
-                    groupId: requestConfig.groupId,
-                    sources: requestConfig.sources,
-                    filters: requestConfig.filters,
-                    histogram: requestConfig.histogram
-                });
-            throw new Error(`Annotation query error`);
-        });
-    }
-    complete() {
-        this.requestStatus = "complete";
-        this.annotationFeaturesSubject.next(this.annotationFeatures);
-        this.rawFeaturesSubject.next(this.rawFeatures);
-        console.info("Features Processing Complete");
-    }
-}
-exports.AnnotationCollector = AnnotationCollector;

package/lib/commonjs/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.d.ts

@@ -1,37 +0,0 @@
-import { AnnotationFeatures, Feature, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { FeaturePositionGaps } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
-import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
-import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
-import { TrackManagerInterface } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-export type IncreaseAnnotationValueType = (feature: {
-    type: string;
-    targetId: string;
-    positionKey: string;
-    d: Feature;
-    p: FeaturePositionGaps;
-}) => number;
-export interface AnnotationProcessingInterface {
-    getAnnotationValue?: IncreaseAnnotationValueType;
-    computeAnnotationValue?: (annotationTracks: Map<string, TrackManagerInterface>) => void;
-    addTrackElementCallback?: IncreaseAnnotationValueType;
-}
-export interface CommonAnnotationInterface {
-    rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    annotationProcessing?: AnnotationProcessingInterface;
-    externalTrackBuilder?: ExternalTrackBuilderInterface;
-    annotationGenerator?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
-    annotationFilter?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
-    titleSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
-    trackTitle?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
-    typeSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
-}
-export interface AnnotationsCollectConfig extends QueryAnnotationsArgs, CommonAnnotationInterface {
-}
-export interface CollectGroupAnnotationsInterface extends QueryGroup_AnnotationsArgs, CommonAnnotationInterface {
-}
-export type AnnotationRequestContext = Partial<AnnotationsCollectConfig & CollectGroupAnnotationsInterface>;
-export interface AnnotationCollectorInterface {
-    collect(requestConfig: AnnotationsCollectConfig | CollectGroupAnnotationsInterface): Promise<Array<AnnotationFeatures>>;
-    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
-    getFeatures(): Promise<Array<Feature>>;
-}

package/lib/commonjs/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/lib/commonjs/RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector.d.ts

@@ -1,9 +0,0 @@
-import { QueryAssembliesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-export interface AssemblyInterfacesInterface {
-    rcsbId: string;
-    interfaceIds: Array<string>;
-}
-export declare class AssemblyInterfacesCollector {
-    private readonly rcsbFvQuery;
-    collect(requestConfig: QueryAssembliesArgs): Promise<Array<AssemblyInterfacesInterface>>;
-}

package/lib/commonjs/RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector.js

@@ -1,35 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AssemblyInterfacesCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-class AssemblyInterfacesCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            try {
-                const result = yield this.rcsbFvQuery.requestAssemblyInterfaces(requestConfig);
-                return result.map(r => parseAssemblyInterfaces(r));
-            }
-            catch (error) {
-                console.log(error);
-                throw error;
-            }
-        });
-    }
-}
-exports.AssemblyInterfacesCollector = AssemblyInterfacesCollector;
-function parseAssemblyInterfaces(assemblyInterfaces) {
-    var _a, _b;
-    return {
-        rcsbId: assemblyInterfaces.rcsb_id,
-        interfaceIds: (_b = (_a = assemblyInterfaces.interfaces) === null || _a === void 0 ? void 0 : _a.map(i => {
-            assertDefined(i === null || i === void 0 ? void 0 : i.rcsb_id);
-            return i.rcsb_id;
-        })) !== null && _b !== void 0 ? _b : []
-    };
-}

package/lib/commonjs/RcsbCollectTools/DataCollectors/DataCollectorInterface.d.ts

@@ -1,7 +0,0 @@
-export type DataCollectorArgsType<K extends string> = Record<K, string | Array<string>>;
-export interface MultipleDocumentPropertyCollectorInterface<K extends string, T> {
-    collect(args: DataCollectorArgsType<K>): Promise<Array<T>>;
-}
-export interface SingleDocumentPropertyCollectorInterface<K extends string, T> {
-    collect(args: DataCollectorArgsType<K>): Promise<T>;
-}

package/lib/commonjs/RcsbCollectTools/DataCollectors/DataCollectorInterface.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/lib/commonjs/RcsbCollectTools/DataCollectors/EntryAssembliesCollector.d.ts

@@ -1,10 +0,0 @@
-import { QueryEntryArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
-export declare class EntryAssembliesCollector {
-    private readonly rcsbFvQuery;
-    static readonly modelKey: string;
-    collect(requestConfig: QueryEntryArgs): Promise<Map<string, Array<PolymerEntityInstanceInterface>>>;
-    private static getEntryAssemblies;
-    private static parsePolymerEntityInstances;
-    private static parsePolymerEntityAssemblies;
-}

package/lib/commonjs/RcsbCollectTools/DataCollectors/EntryAssembliesCollector.js

@@ -1,96 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.EntryAssembliesCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertElementListDefined = Assertions_1.Assertions.assertElementListDefined;
-var assertDefined = Assertions_1.Assertions.assertDefined;
-class EntryAssembliesCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            try {
-                const coreEntry = yield this.rcsbFvQuery.requestEntityInstances(requestConfig);
-                return EntryAssembliesCollector.getEntryAssemblies(coreEntry);
-            }
-            catch (error) {
-                console.log(error);
-                throw error;
-            }
-        });
-    }
-    static getEntryAssemblies(entry) {
-        const out = new Map();
-        out.set(EntryAssembliesCollector.modelKey, new Array());
-        const asymInstanceMap = new Map();
-        if ((entry === null || entry === void 0 ? void 0 : entry.polymer_entities) instanceof Array) {
-            entry.polymer_entities.forEach(entity => {
-                if ((entity === null || entity === void 0 ? void 0 : entity.polymer_entity_instances) && Array.isArray(entity === null || entity === void 0 ? void 0 : entity.polymer_entity_instances)) {
-                    assertElementListDefined(entity.polymer_entity_instances);
-                    EntryAssembliesCollector.parsePolymerEntityInstances(entity.polymer_entity_instances, asymInstanceMap, out);
-                }
-            });
-        }
-        if ((entry === null || entry === void 0 ? void 0 : entry.assemblies) instanceof Array) {
-            entry.assemblies.forEach(assembly => {
-                if (assembly)
-                    EntryAssembliesCollector.parsePolymerEntityAssemblies(assembly, asymInstanceMap, out);
-            });
-        }
-        return out;
-    }
-    static parsePolymerEntityInstances(polymerEntityInstances, asymInstanceMap, out) {
-        polymerEntityInstances.forEach(instance => {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q, _r, _s, _t, _u, _v, _w, _x, _y, _z, _0, _1, _2, _3;
-            const taxIds = new Set();
-            if (((_a = instance === null || instance === void 0 ? void 0 : instance.polymer_entity) === null || _a === void 0 ? void 0 : _a.rcsb_entity_source_organism) instanceof Array)
-                instance.polymer_entity.rcsb_entity_source_organism.forEach(sO => {
-                    if (typeof (sO === null || sO === void 0 ? void 0 : sO.ncbi_scientific_name) === "string" && sO.ncbi_scientific_name.length > 0)
-                        taxIds.add(sO.ncbi_scientific_name);
-                });
-            const o = instance.rcsb_polymer_entity_instance_container_identifiers;
-            assertDefined(o), assertDefined(o === null || o === void 0 ? void 0 : o.entry_id), assertDefined(o === null || o === void 0 ? void 0 : o.entity_id), assertDefined(o === null || o === void 0 ? void 0 : o.entity_id), assertDefined(o === null || o === void 0 ? void 0 : o.asym_id), assertDefined(o === null || o === void 0 ? void 0 : o.auth_asym_id), assertElementListDefined(o === null || o === void 0 ? void 0 : o.auth_to_entity_poly_seq_mapping);
-            assertDefined((_c = (_b = instance.polymer_entity) === null || _b === void 0 ? void 0 : _b.entity_poly) === null || _c === void 0 ? void 0 : _c.rcsb_sample_sequence_length);
-            assertDefined((_d = instance.polymer_entity.entry) === null || _d === void 0 ? void 0 : _d.rcsb_entry_info.structure_determination_methodology);
-            const d = {
-                rcsbId: instance.rcsb_id,
-                entryId: o.entry_id,
-                entityId: o.entity_id,
-                asymId: o.asym_id,
-                authId: o.auth_asym_id,
-                authResId: o.auth_to_entity_poly_seq_mapping,
-                name: (_m = ((_j = (_h = (_g = (_f = (_e = instance.polymer_entity) === null || _e === void 0 ? void 0 : _e.rcsb_polymer_entity) === null || _f === void 0 ? void 0 : _f.rcsb_polymer_name_combined) === null || _g === void 0 ? void 0 : _g.names) === null || _h === void 0 ? void 0 : _h.join(", ")) !== null && _j !== void 0 ? _j : (_l = (_k = instance.polymer_entity) === null || _k === void 0 ? void 0 : _k.rcsb_polymer_entity) === null || _l === void 0 ? void 0 : _l.pdbx_description)) !== null && _m !== void 0 ? _m : "NA",
-                taxNames: Array.from(taxIds),
-                experimentalMethod: (_q = (_p = (_o = instance.polymer_entity) === null || _o === void 0 ? void 0 : _o.entry) === null || _p === void 0 ? void 0 : _p.rcsb_entry_info.experimental_method) !== null && _q !== void 0 ? _q : "NA",
-                resolution: (_u = (_t = (_s = (_r = instance.polymer_entity) === null || _r === void 0 ? void 0 : _r.entry) === null || _s === void 0 ? void 0 : _s.rcsb_entry_info.resolution_combined) === null || _t === void 0 ? void 0 : _t[0]) !== null && _u !== void 0 ? _u : undefined,
-                sequenceLength: (_w = (_v = instance.polymer_entity) === null || _v === void 0 ? void 0 : _v.entity_poly) === null || _w === void 0 ? void 0 : _w.rcsb_sample_sequence_length,
-                entityMolecularWeight: (_y = (_x = instance.polymer_entity.rcsb_polymer_entity) === null || _x === void 0 ? void 0 : _x.formula_weight) !== null && _y !== void 0 ? _y : undefined,
-                entryMolecularWeight: (_0 = (_z = instance.polymer_entity.entry) === null || _z === void 0 ? void 0 : _z.rcsb_entry_info.molecular_weight) !== null && _0 !== void 0 ? _0 : undefined,
-                structureDeterminationMethodology: instance.polymer_entity.entry.rcsb_entry_info.structure_determination_methodology
-            };
-            (_1 = out.get(EntryAssembliesCollector.modelKey)) === null || _1 === void 0 ? void 0 : _1.push(d);
-            if ((_2 = instance === null || instance === void 0 ? void 0 : instance.rcsb_polymer_entity_instance_container_identifiers) === null || _2 === void 0 ? void 0 : _2.asym_id)
-                asymInstanceMap.set((_3 = instance === null || instance === void 0 ? void 0 : instance.rcsb_polymer_entity_instance_container_identifiers) === null || _3 === void 0 ? void 0 : _3.asym_id, d);
-        });
-    }
-    static parsePolymerEntityAssemblies(assembly, asymInstanceMap, out) {
-        var _a;
-        out.set(assembly.rcsb_assembly_container_identifiers.assembly_id, new Array());
-        (_a = assembly.pdbx_struct_assembly_gen) === null || _a === void 0 ? void 0 : _a.forEach(assemblyGen => {
-            var _a;
-            (_a = assemblyGen === null || assemblyGen === void 0 ? void 0 : assemblyGen.asym_id_list) === null || _a === void 0 ? void 0 : _a.forEach(asymId => {
-                var _a;
-                if (!asymId)
-                    return;
-                const o = asymInstanceMap.get(asymId);
-                if (o)
-                    (_a = out.get(assembly.rcsb_assembly_container_identifiers.assembly_id)) === null || _a === void 0 ? void 0 : _a.push(o);
-            });
-        });
-    }
-}
-exports.EntryAssembliesCollector = EntryAssembliesCollector;
-EntryAssembliesCollector.modelKey = "Model";

package/lib/commonjs/RcsbCollectTools/DataCollectors/GroupMemberCollector.d.ts

@@ -1,6 +0,0 @@
-import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
-export declare class GroupMemberCollector {
-    private readonly rcsbFvQuery;
-    collect(requestConfig: QueryPolymer_Entity_GroupArgs): Promise<Array<PolymerEntityInstanceInterface>>;
-}

package/lib/commonjs/RcsbCollectTools/DataCollectors/GroupMemberCollector.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.GroupMemberCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const MultipleEntityInstancesCollector_1 = require("./MultipleEntityInstancesCollector");
-class GroupMemberCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const result = yield this.rcsbFvQuery.requestGroupInfo(requestConfig);
-            if (result.rcsb_group_info.group_members_granularity === "polymer_entity") {
-                const multipleEntityInstancesCollector = new MultipleEntityInstancesCollector_1.MultipleEntityInstancesCollector();
-                return yield multipleEntityInstancesCollector.collect({ entity_ids: result.rcsb_group_container_identifiers.group_member_ids.filter((x) => x != null) });
-            }
-            else {
-                console.error(`Group granularity ${result.rcsb_group_info.group_members_granularity} not supported`);
-                throw new Error(`Group granularity ${result.rcsb_group_info.group_members_granularity} not supported`);
-            }
-        });
-    }
-}
-exports.GroupMemberCollector = GroupMemberCollector;

package/lib/commonjs/RcsbCollectTools/DataCollectors/GroupPropertyCollector.d.ts

@@ -1,10 +0,0 @@
-import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-export interface GroupPropertyInterface {
-    groupName: string;
-    groupDescription: string;
-}
-export declare class GroupPropertyCollector {
-    private readonly rcsbFvQuery;
-    collect(requestConfig: QueryPolymer_Entity_GroupArgs): Promise<GroupPropertyInterface>;
-    private static getGroupProperties;
-}