@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbUtils/TrackGenerators/Logo.js

@@ -1,45 +0,0 @@
-import { Assertions } from "../Helpers/Assertions";
-var assertElementListDefined = Assertions.assertElementListDefined;
-var assertDefined = Assertions.assertDefined;
-export class Logo {
-    constructor(logo) {
-        this.symbols = Object();
-        this.n = 0;
-        assertElementListDefined(logo);
-        logo.forEach(s => {
-            assertDefined(s.symbol);
-            assertDefined(s.value);
-            this.symbols[s.symbol] = s.value;
-            this.n += s.value;
-        });
-    }
-    aaTypes() {
-        return Object.keys(this.symbols);
-    }
-    /*add(aa: T): void{
-        this.symbols[aa] ++;
-        this.n ++;
-    }*/
-    get(aa) {
-        const n = this.symbols[aa];
-        assertDefined(n);
-        return n;
-    }
-    total() {
-        return this.n;
-    }
-    forEach(callback) {
-        this.aaTypes().forEach((aa, n) => {
-            callback(aa, n);
-        });
-    }
-    mode() {
-        return this.aaTypes().sort((a, b) => (this.symbols[b] - this.symbols[a]))[0];
-    }
-    frequency() {
-        return this.aaTypes().sort((a, b) => (this.symbols[b] - this.symbols[a])).map(a => ({ symbol: a, value: this.get(a) / this.n }));
-    }
-    entropy() {
-        return -this.aaTypes().map(aa => (this.get(aa) != 0 ? (this.get(aa) / this.n) * (Math.log(this.get(aa) / this.n) / Math.log(this.aaTypes().length)) : 0)).reduce((p, v) => (p + v));
-    }
-}

package/lib/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.d.ts

@@ -1,14 +0,0 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
-import { RcsbFvTooltipInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvTooltip/RcsbFvTooltipInterface";
-import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
-export declare function addUnmodeledTrackBuilder(unmodeledTrackBuilder: UnmodeledTrackBuilder, externalTrackBuilder?: ExternalTrackBuilderInterface): ExternalTrackBuilderInterface;
-export declare class UnmodeledTrackBuilder {
-    private readonly unmodeledDescription;
-    filterFeatures(data: {
-        annotations: Array<AnnotationFeatures>;
-        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<Array<AnnotationFeatures>>;
-    getTooltip(): RcsbFvTooltipInterface;
-    private buildUnobserved;
-}

package/lib/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.js

@@ -1,100 +0,0 @@
-import { __awaiter } from "tslib";
-import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { range } from "lodash";
-import { rcsbRequestCtxManager } from "../../RcsbRequest/RcsbRequestContextManager";
-import { RcsbFvTooltip } from "../../RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip";
-export function addUnmodeledTrackBuilder(unmodeledTrackBuilder, externalTrackBuilder) {
-    const trackBuilder = (data) => __awaiter(this, void 0, void 0, function* () {
-        var _a, _b;
-        return [
-            ...(_b = yield ((_a = externalTrackBuilder === null || externalTrackBuilder === void 0 ? void 0 : externalTrackBuilder.filterFeatures) === null || _a === void 0 ? void 0 : _a.call(externalTrackBuilder, data))) !== null && _b !== void 0 ? _b : [],
-            ...yield unmodeledTrackBuilder.filterFeatures(data)
-        ];
-    });
-    return Object.assign(Object.assign({}, externalTrackBuilder), { filterFeatures: (data) => __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
-            (_a = externalTrackBuilder === null || externalTrackBuilder === void 0 ? void 0 : externalTrackBuilder.filterFeatures) === null || _a === void 0 ? void 0 : _a.call(externalTrackBuilder, data);
-            return trackBuilder({
-                annotations: (_c = yield ((_b = externalTrackBuilder === null || externalTrackBuilder === void 0 ? void 0 : externalTrackBuilder.filterFeatures) === null || _b === void 0 ? void 0 : _b.call(externalTrackBuilder, data))) !== null && _c !== void 0 ? _c : data.annotations,
-                rcsbContext: data.rcsbContext
-            });
-        }) });
-}
-export class UnmodeledTrackBuilder {
-    constructor() {
-        this.unmodeledDescription = new Map();
-    }
-    filterFeatures(data) {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (!data.rcsbContext)
-                return data.annotations;
-            return [
-                ...yield this.buildUnobserved(data.annotations, data.rcsbContext),
-                ...filterUnobserved(data.annotations)
-            ];
-        });
-    }
-    getTooltip() {
-        return new UnobservedToolTip(this.unmodeledDescription);
-    }
-    buildUnobserved(annotations, rcsbContext) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            const nInstances = (yield rcsbRequestCtxManager.getEntityProperties((_a = rcsbContext.entityId) !== null && _a !== void 0 ? _a : "none"))[0].instances.length;
-            const featurePositions = Array.from(annotations.filter(ann => {
-                var _a, _b, _c;
-                return (_c = (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.UnobservedResidueXyz)) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0 > 0;
-            }).map(ann => {
-                var _a, _b;
-                return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter((f) => (f === null || f === void 0 ? void 0 : f.type) == Type.UnobservedResidueXyz)) !== null && _b !== void 0 ? _b : [];
-            }).flat().map(feature => {
-                var _a, _b;
-                return (_b = (_a = feature.feature_positions) === null || _a === void 0 ? void 0 : _a.filter((p) => typeof p != "undefined")) !== null && _b !== void 0 ? _b : [];
-            }).flat().map(p => p.beg_seq_id && p.end_seq_id ? range(p.beg_seq_id, p.end_seq_id + 1) : []).flat().reduce((map, idx) => { var _a; return map.set(idx, ((_a = map.get(idx)) !== null && _a !== void 0 ? _a : 0) + 1); }, new Map).entries()).map(([idx, unobserved]) => {
-                this.unmodeledDescription.set(`${rcsbContext.entityId}:${idx}`, [unobserved, nInstances]);
-                return {
-                    beg_seq_id: idx,
-                    values: [Math.round(unobserved / nInstances * 100) / 100]
-                };
-            });
-            return [{
-                    source: Source.PdbEntity,
-                    target_id: rcsbContext.entityId,
-                    features: [{
-                            type: UNMODELED,
-                            feature_positions: featurePositions
-                        }]
-                }];
-        });
-    }
-}
-class UnobservedToolTip {
-    constructor(trackDescription) {
-        this.regularTooltip = new RcsbFvTooltip();
-        this.trackDescription = trackDescription;
-    }
-    showTooltip(d) {
-        return this.regularTooltip.showTooltip(d);
-    }
-    showTooltipDescription(d) {
-        if (d.title == UNMODELED)
-            return this.overloadTooltipDescription(d);
-        return this.regularTooltip.showTooltipDescription(d);
-    }
-    overloadTooltipDescription(d) {
-        var _a;
-        if (!this.trackDescription.has(`${d.sourceId}:${d.begin}`))
-            return undefined;
-        const tooltipDescriptionDiv = document.createElement("div");
-        const [unobserved, total] = (_a = this.trackDescription.get(`${d.sourceId}:${d.begin}`)) !== null && _a !== void 0 ? _a : [0, 0];
-        tooltipDescriptionDiv.append(`Unmodeled in ${unobserved} of ${total} chains`);
-        return tooltipDescriptionDiv;
-    }
-}
-function filterUnobserved(annotations) {
-    return annotations.map(ann => {
-        var _a;
-        return Object.assign(Object.assign({}, ann), { features: (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) != Type.UnobservedResidueXyz && (f === null || f === void 0 ? void 0 : f.type) != Type.UnobservedAtomXyz) });
-    });
-}
-const UNMODELED = "UNMODELED";

package/lib/RcsbUtils/Translators/AssemblyInterfacesTranslate.d.ts

@@ -1,8 +0,0 @@
-import { AssemblyInterfacesInterface } from "../../RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector";
-export declare class AssemblyInterfacesTranslate {
-    private readonly rawData;
-    private interfaceMap;
-    constructor(data: Array<AssemblyInterfacesInterface>);
-    getInterfaces(assemblyId: string): Array<string> | undefined;
-    getRawData(): Array<AssemblyInterfacesInterface>;
-}

package/lib/RcsbUtils/Translators/AssemblyInterfacesTranslate.js

@@ -1,15 +0,0 @@
-export class AssemblyInterfacesTranslate {
-    constructor(data) {
-        this.interfaceMap = new Map();
-        this.rawData = data;
-        data.forEach(d => {
-            this.interfaceMap.set(d.rcsbId, d.interfaceIds);
-        });
-    }
-    getInterfaces(assemblyId) {
-        return this.interfaceMap.get(assemblyId);
-    }
-    getRawData() {
-        return this.rawData;
-    }
-}

package/lib/RcsbUtils/Translators/EntryAssemblyTranslate.d.ts

@@ -1,6 +0,0 @@
-import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
-export declare class EntryAssemblyTranslate {
-    private readonly rawData;
-    constructor(data: Map<string, Array<PolymerEntityInstanceInterface>>);
-    getData(): Map<string, Array<PolymerEntityInstanceInterface>>;
-}

package/lib/RcsbUtils/Translators/EntryAssemblyTranslate.js

@@ -1,8 +0,0 @@
-export class EntryAssemblyTranslate {
-    constructor(data) {
-        this.rawData = data;
-    }
-    getData() {
-        return this.rawData;
-    }
-}

package/lib/RcsbUtils/Translators/InterfaceInstanceTranslate.d.ts

@@ -1,10 +0,0 @@
-import { InterfaceInstanceInterface } from "../../RcsbCollectTools/DataCollectors/InterfaceInstanceCollector";
-export declare class InterfaceInstanceTranslate {
-    private readonly rawData;
-    private readonly instances;
-    private readonly operatorsIds;
-    constructor(data: Array<InterfaceInstanceInterface>);
-    getInstances(rcsbId: string): [string, string] | undefined;
-    getOperatorIds(rcsbId: string): [Array<Array<string>>, Array<Array<string>>] | undefined;
-    getRawData(): Array<InterfaceInstanceInterface>;
-}

package/lib/RcsbUtils/Translators/InterfaceInstanceTranslate.js

@@ -1,20 +0,0 @@
-export class InterfaceInstanceTranslate {
-    constructor(data) {
-        this.instances = new Map();
-        this.operatorsIds = new Map();
-        this.rawData = data;
-        data.forEach(d => {
-            this.instances.set(d.rcsbId, d.asymIds);
-            this.operatorsIds.set(d.rcsbId, d.operatorIds);
-        });
-    }
-    getInstances(rcsbId) {
-        return this.instances.get(rcsbId);
-    }
-    getOperatorIds(rcsbId) {
-        return this.operatorsIds.get(rcsbId);
-    }
-    getRawData() {
-        return this.rawData;
-    }
-}

package/lib/RcsbUtils/Translators/MultipleEntityInstanceTranslate.d.ts

@@ -1,10 +0,0 @@
-import { PolymerEntityInstanceTranslate } from "./PolymerEntityInstanceTranslate";
-import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
-export declare class MultipleEntityInstanceTranslate {
-    private readonly entityInstanceTranslateMap;
-    add(data: Array<PolymerEntityInstanceInterface>): void;
-    getEntity(entityId: string): PolymerEntityInstanceTranslate | undefined;
-    getEntities(): Array<string>;
-    getEntries(): Array<string>;
-    getInstances(): Array<string>;
-}

package/lib/RcsbUtils/Translators/MultipleEntityInstanceTranslate.js

@@ -1,33 +0,0 @@
-import { PolymerEntityInstanceTranslate } from "./PolymerEntityInstanceTranslate";
-import { Operator } from "../Helpers/Operator";
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class MultipleEntityInstanceTranslate {
-    constructor() {
-        this.entityInstanceTranslateMap = new Map();
-    }
-    add(data) {
-        const entryEntityInstanceMapList = new Map();
-        data.forEach(d => {
-            var _a;
-            const entityId = d.entryId + TagDelimiter.entity + d.entityId;
-            if (!entryEntityInstanceMapList.has(entityId))
-                entryEntityInstanceMapList.set(entityId, new Array());
-            (_a = entryEntityInstanceMapList.get(entityId)) === null || _a === void 0 ? void 0 : _a.push(d);
-        });
-        entryEntityInstanceMapList.forEach((v, entityId) => {
-            this.entityInstanceTranslateMap.set(entityId, new PolymerEntityInstanceTranslate(v));
-        });
-    }
-    getEntity(entityId) {
-        return this.entityInstanceTranslateMap.get(entityId);
-    }
-    getEntities() {
-        return Array.from(this.entityInstanceTranslateMap.keys());
-    }
-    getEntries() {
-        return Operator.uniqueValues(Array.from(this.entityInstanceTranslateMap.keys()).map(entityId => TagDelimiter.parseEntity(entityId).entryId));
-    }
-    getInstances() {
-        return Operator.uniqueValues(Array.from(this.entityInstanceTranslateMap.values()).map(peit => peit.getData()).flat().map(e => e.asymId));
-    }
-}

package/lib/RcsbUtils/Translators/PolymerEntityChromosomeTranslate.d.ts

@@ -1,5 +0,0 @@
-export declare class PolymerEntityChromosomeTranslate {
-    private readonly rawData;
-    constructor(entityMap: Map<string, Array<string>>);
-    getData(): Map<string, Array<string>>;
-}

package/lib/RcsbUtils/Translators/PolymerEntityChromosomeTranslate.js

@@ -1,8 +0,0 @@
-export class PolymerEntityChromosomeTranslate {
-    constructor(entityMap) {
-        this.rawData = entityMap;
-    }
-    getData() {
-        return this.rawData;
-    }
-}

package/lib/RcsbUtils/Translators/PolymerEntityInstanceTranslate.d.ts

@@ -1,29 +0,0 @@
-import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
-import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export interface AlignmentContextInterface {
-    queryId: string;
-    targetId: string;
-    from: SequenceReference | undefined;
-    to: SequenceReference | Source | undefined;
-    targetSequenceLength?: number;
-    querySequenceLength?: number;
-}
-export declare class PolymerEntityInstanceTranslate {
-    private readonly rawData;
-    private readonly instanceAsymToAuth;
-    private readonly instanceAuthToAsym;
-    private readonly instanceAsymToEntity;
-    private readonly entityToAsym;
-    private readonly instanceAuthResIds;
-    private readonly INDEX_NAME;
-    constructor(data: Array<PolymerEntityInstanceInterface>);
-    getData(): Array<PolymerEntityInstanceInterface>;
-    translateEntityToAsym(id: string): string[] | undefined;
-    translateAsymToEntity(id: string): string | undefined;
-    translateAsymToAuth(id: string): string | undefined;
-    translateAuthToAsym(id: string): string | undefined;
-    translateAuthResId(asymId: string, index: number): string | undefined;
-    addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
-    private helperAddAuthorResIds;
-}

package/lib/RcsbUtils/Translators/PolymerEntityInstanceTranslate.js

@@ -1,92 +0,0 @@
-import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class PolymerEntityInstanceTranslate {
-    constructor(data) {
-        this.instanceAsymToAuth = new Map();
-        this.instanceAuthToAsym = new Map();
-        this.instanceAsymToEntity = new Map();
-        this.entityToAsym = new Map();
-        this.instanceAuthResIds = new Map();
-        this.INDEX_NAME = "auth";
-        this.rawData = data;
-        data.forEach(d => {
-            var _a;
-            this.instanceAsymToAuth.set(d.asymId, d.authId);
-            this.instanceAuthToAsym.set(d.authId, d.asymId);
-            this.instanceAuthResIds.set(d.asymId, d.authResId);
-            this.instanceAsymToEntity.set(d.asymId, d.entityId);
-            if (!this.entityToAsym.has(d.entityId))
-                this.entityToAsym.set(d.entityId, new Set());
-            (_a = this.entityToAsym.get(d.entityId)) === null || _a === void 0 ? void 0 : _a.add(d.asymId);
-        });
-    }
-    getData() {
-        return this.rawData;
-    }
-    translateEntityToAsym(id) {
-        const asymIds = this.entityToAsym.get(id);
-        if (asymIds)
-            return Array.from(asymIds);
-    }
-    translateAsymToEntity(id) {
-        return this.instanceAsymToEntity.get(id);
-    }
-    translateAsymToAuth(id) {
-        return this.instanceAsymToAuth.get(id);
-    }
-    translateAuthToAsym(id) {
-        return this.instanceAuthToAsym.get(id);
-    }
-    translateAuthResId(asymId, index) {
-        const autReaIds = this.instanceAuthResIds.get(asymId);
-        if (!autReaIds)
-            return undefined;
-        else if (index > autReaIds.length)
-            return undefined;
-        else if (autReaIds[index - 1])
-            return undefined;
-        else
-            return autReaIds[index - 1];
-    }
-    addAuthorResIds(e, alignmentContext) {
-        let o = e;
-        if (alignmentContext.from === SequenceReference.PdbInstance && alignmentContext.to) {
-            const asymId = alignmentContext.queryId.split(TagDelimiter.instance)[1];
-            this.helperAddAuthorResIds(o, alignmentContext.from, alignmentContext.to, asymId);
-            o.indexName = this.INDEX_NAME;
-        }
-        else if (alignmentContext.to === SequenceReference.PdbInstance && alignmentContext.from) {
-            const asymId = alignmentContext.targetId.split(TagDelimiter.instance)[1];
-            this.helperAddAuthorResIds(o, alignmentContext.from, alignmentContext.to, asymId);
-            o.indexName = this.INDEX_NAME;
-        }
-        return o;
-    }
-    helperAddAuthorResIds(e, reference, source, asymId) {
-        let out = e;
-        const authResIds = this.instanceAuthResIds.get(asymId);
-        if (!authResIds)
-            return out;
-        if (reference === SequenceReference.PdbInstance || (reference === SequenceReference.PdbEntity && source === Source.PdbInstance)) {
-            const x = authResIds[e.begin - 1];
-            if (typeof e.end === "number" && authResIds[e.end - 1] != x) {
-                out.beginName = x;
-                out.endName = authResIds[e.end - 1];
-            }
-            else if (typeof e.end != "number" || authResIds[e.end - 1] == x) {
-                out.beginName = x;
-            }
-        }
-        else if (source === Source.PdbInstance && e.oriBegin) {
-            const x = authResIds[e.oriBegin - 1];
-            if (typeof e.oriEnd === "number" && authResIds[e.oriEnd - 1] != x) {
-                out.oriBeginName = x;
-                out.oriEndName = authResIds[e.oriEnd - 1];
-            }
-            else if (typeof e.oriEnd != "number" || authResIds[e.oriEnd - 1] == x) {
-                out.oriBeginName = x;
-            }
-        }
-        return out;
-    }
-}

package/lib/app.d.ts

@@ -1,11 +0,0 @@
-export { buildEntryChromosome, buildFullChromosome, buildEntityChromosome, buildChromosome, buildEntityFv, buildEntitySummaryFv, buildSingleEntitySummaryFv, buildInstanceFv, buildInstanceSequenceFv, buildMultipleInstanceSequenceFv, buildAssemblySequenceFv, buildPairwiseAlignment, buildPfv, buildMultipleAlignmentSequenceFv, buildUniprotEntityFv, buildUniprotEntityInstanceFv, buildUniprotFv, buildGroupFv, buildSequenceIdentityAlignmentFv, buildUniprotAlignmentFv, buildDataProviderFv, unmount } from "./RcsbFvWeb/RcsbFvBuilder";
-export { rcsbRequestCtxManager as RcsbRequestContextManager } from "./RcsbRequest/RcsbRequestContextManager";
-export { RcsbFvUI } from "./RcsbExport/RcsbFvUI";
-export { FeatureType } from "./RcsbExport/FeatureType";
-export { SequenceTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory";
-export { PositionalScoreAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory";
-export { PlainObservedAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory";
-export { PlainAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory";
-export { MsaAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
-export { AnnotationsTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory";
-export { AlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";

package/lib/app.js

@@ -1,11 +0,0 @@
-export { buildEntryChromosome, buildFullChromosome, buildEntityChromosome, buildChromosome, buildEntityFv, buildEntitySummaryFv, buildSingleEntitySummaryFv, buildInstanceFv, buildInstanceSequenceFv, buildMultipleInstanceSequenceFv, buildAssemblySequenceFv, buildPairwiseAlignment, buildPfv, buildMultipleAlignmentSequenceFv, buildUniprotEntityFv, buildUniprotEntityInstanceFv, buildUniprotFv, buildGroupFv, buildSequenceIdentityAlignmentFv, buildUniprotAlignmentFv, buildDataProviderFv, unmount } from "./RcsbFvWeb/RcsbFvBuilder";
-export { rcsbRequestCtxManager as RcsbRequestContextManager } from "./RcsbRequest/RcsbRequestContextManager";
-export { RcsbFvUI } from "./RcsbExport/RcsbFvUI";
-export { FeatureType } from "./RcsbExport/FeatureType";
-export { SequenceTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory";
-export { PositionalScoreAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory";
-export { PlainObservedAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory";
-export { PlainAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory";
-export { MsaAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
-export { AnnotationsTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory";
-export { AlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";

package/lib/commonjs/ExternalResources/NcbiData/NcbiGenomeSequenceData.d.ts

@@ -1,7 +0,0 @@
-import { RcsbFvTrackData } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { LocationViewInterface } from "@rcsb/rcsb-saguaro/lib/RcsbBoard/RcsbBoard";
-export declare class NcbiGenomeSequenceData {
-    private static readonly urlPrefix;
-    private static readonly urlSuffix;
-    static update(ncbiId: string, strand: number, reverse: boolean, trackWidth?: number): ((where: LocationViewInterface) => Promise<RcsbFvTrackData>);
-}

package/lib/commonjs/ExternalResources/NcbiData/NcbiGenomeSequenceData.js

@@ -1,70 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.NcbiGenomeSequenceData = void 0;
-const tslib_1 = require("tslib");
-const rxjs_1 = require("rxjs");
-const web_resources_json_1 = tslib_1.__importDefault(require("../../RcsbServerConfig/web.resources.json"));
-class NcbiGenomeSequenceData {
-    static update(ncbiId, strand, reverse, trackWidth) {
-        let process = null;
-        return (where) => {
-            if (process)
-                process.unsubscribe();
-            return new Promise((resolve, reject) => {
-                const delta = trackWidth ? trackWidth / (where.to - where.from) : 1000 / (where.to - where.from);
-                if (delta > 4) {
-                    let N = 0;
-                    const timeout = 5000;
-                    const getGenomeSequence = () => {
-                        const Http = new XMLHttpRequest();
-                        Http.timeout = timeout;
-                        const url = NcbiGenomeSequenceData.urlPrefix + 'id=' + ncbiId + '&from=' + where.from + '&to=' + where.to + '&strand=' + strand + NcbiGenomeSequenceData.urlSuffix;
-                        Http.open("GET", url);
-                        Http.send();
-                        Http.onloadend = (e) => {
-                            const sequence = Http.responseText.split("\n").slice(1).join("");
-                            if (sequence.length < 1) {
-                                N++;
-                                console.warn("HTTP error while access URL: " + url + " - empty sequence - " + N);
-                                if (N < 4) {
-                                    process = rxjs_1.asyncScheduler.schedule(() => {
-                                        getGenomeSequence();
-                                    }, timeout);
-                                }
-                                else {
-                                    reject("HTTP error while access URL: " + url + " - No more attempts after " + N);
-                                }
-                            }
-                            else {
-                                const selectedOption = [{
-                                        begin: where.from,
-                                        label: reverse ? sequence.split("").reverse().join("") : sequence
-                                    }];
-                                resolve(selectedOption);
-                            }
-                        };
-                        Http.onerror = (e) => {
-                            N++;
-                            console.warn("HTTP error while access URL: " + url + " - " + N);
-                            if (N < 4) {
-                                process = rxjs_1.asyncScheduler.schedule(() => {
-                                    getGenomeSequence();
-                                }, timeout);
-                            }
-                            else {
-                                reject("HTTP error while access URL: " + url + " - No more attempts after " + N);
-                            }
-                        };
-                    };
-                    getGenomeSequence();
-                }
-                else {
-                    resolve([]);
-                }
-            });
-        };
-    }
-}
-exports.NcbiGenomeSequenceData = NcbiGenomeSequenceData;
-NcbiGenomeSequenceData.urlPrefix = web_resources_json_1.default.ncbi_genome_sequence.url;
-NcbiGenomeSequenceData.urlSuffix = web_resources_json_1.default.ncbi_genome_sequence.url_suffix;

package/lib/commonjs/ExternalResources/NcbiData/NcbiSummary.d.ts

@@ -1,24 +0,0 @@
-export interface ChromosomeMetadataInterface {
-    ncbiId: string;
-    title: string;
-    organism: string;
-    extra: string;
-    taxid: number;
-    length: number;
-    subtype: string;
-    subname: string;
-    uid: number;
-}
-export interface TaxonomyMetadataInterface {
-    scientificname: string;
-    commonname: string;
-    taxid: number;
-    uid: number;
-}
-export declare class NcbiSummary {
-    private static timeout;
-    private static httpTimeout;
-    private static jobTask;
-    static requestChromosomeData(chrId: string): Promise<ChromosomeMetadataInterface>;
-    static requestTaxonomyData(taxId: string): Promise<TaxonomyMetadataInterface>;
-}

package/lib/commonjs/ExternalResources/NcbiData/NcbiSummary.js

@@ -1,86 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.NcbiSummary = void 0;
-const tslib_1 = require("tslib");
-const rxjs_1 = require("rxjs");
-const web_resources_json_1 = tslib_1.__importDefault(require("../../RcsbServerConfig/web.resources.json"));
-//TODO are static attributes/methods safe in this case ?
-//TODO change `XMLHttpRequest` to `fetch`
-class NcbiSummary {
-    static requestChromosomeData(chrId) {
-        if (NcbiSummary.jobTask)
-            NcbiSummary.jobTask.unsubscribe();
-        const urlPrefix = web_resources_json_1.default.ncbi_summary_nuccore.url;
-        const urlSuffix = web_resources_json_1.default.ncbi_summary_nuccore.url_suffix;
-        return new Promise((resolve, reject) => {
-            const recursiveRequest = () => {
-                const url = urlPrefix + chrId + urlSuffix;
-                const Http = new XMLHttpRequest();
-                Http.timeout = NcbiSummary.httpTimeout;
-                Http.open("GET", url);
-                Http.send();
-                Http.onloadend = (e) => {
-                    var _a;
-                    if (Http.responseText.length == 0) {
-                        NcbiSummary.jobTask = rxjs_1.asyncScheduler.schedule(() => {
-                            recursiveRequest();
-                        }, NcbiSummary.timeout);
-                    }
-                    else {
-                        const jsonResult = JSON.parse(Http.responseText);
-                        const uid = (_a = jsonResult === null || jsonResult === void 0 ? void 0 : jsonResult.result) === null || _a === void 0 ? void 0 : _a.uids[0];
-                        const out = jsonResult.result[uid];
-                        out.ncbiId = chrId;
-                        resolve(out);
-                    }
-                };
-                Http.onerror = (e) => {
-                    if (NcbiSummary.jobTask)
-                        NcbiSummary.jobTask.unsubscribe();
-                    NcbiSummary.jobTask = rxjs_1.asyncScheduler.schedule(() => {
-                        recursiveRequest();
-                    }, NcbiSummary.timeout);
-                };
-            };
-            recursiveRequest();
-        });
-    }
-    static requestTaxonomyData(taxId) {
-        if (NcbiSummary.jobTask)
-            NcbiSummary.jobTask.unsubscribe();
-        const urlPrefix = web_resources_json_1.default.ncbi_summary_taxonomy.url;
-        const urlSuffix = web_resources_json_1.default.ncbi_summary_taxonomy.url_suffix;
-        return new Promise((resolve, reject) => {
-            const recursiveRequest = () => {
-                const url = urlPrefix + taxId + urlSuffix;
-                const Http = new XMLHttpRequest();
-                Http.timeout = NcbiSummary.httpTimeout;
-                Http.open("GET", url);
-                Http.send();
-                Http.onloadend = (e) => {
-                    var _a;
-                    if (Http.responseText.length == 0) {
-                        NcbiSummary.jobTask = rxjs_1.asyncScheduler.schedule(() => {
-                            recursiveRequest();
-                        }, NcbiSummary.timeout);
-                    }
-                    else {
-                        const jsonResult = JSON.parse(Http.responseText);
-                        const uid = (_a = jsonResult === null || jsonResult === void 0 ? void 0 : jsonResult.result) === null || _a === void 0 ? void 0 : _a.uids[0];
-                        resolve(jsonResult.result[uid]);
-                    }
-                };
-                Http.onerror = (e) => {
-                    NcbiSummary.jobTask = rxjs_1.asyncScheduler.schedule(() => {
-                        recursiveRequest();
-                    }, NcbiSummary.timeout);
-                };
-            };
-            recursiveRequest();
-        });
-    }
-}
-exports.NcbiSummary = NcbiSummary;
-NcbiSummary.timeout = 3000;
-NcbiSummary.httpTimeout = 10000;
-NcbiSummary.jobTask = null;