@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.2

package/lib/commonjs/RcsbFvWeb/RcsbFvGroup/GroupTabs/GroupPfvApp.js

@@ -0,0 +1,135 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getReferenceFromGroupProvenance = exports.GroupPfvApp = void 0;
+const tslib_1 = require("tslib");
+const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
+const RcsbFvUniprotBuilder_1 = require("../../RcsbFvBuilder/RcsbFvUniprotBuilder");
+const GroupExternalTrackBuilder_1 = require("../../../RcsbUtils/TrackGenerators/GroupExternalTrackBuilder");
+const RcsbFvGroupBuilder_1 = require("../../RcsbFvBuilder/RcsbFvGroupBuilder");
+const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
+const AlignmentGlobalBindingSite_1 = require("../../../RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite");
+const RcsbTabs_1 = require("../../RcsbFvComponents/RcsbTabs");
+const GroupPfvUI_1 = require("../../../RcsbFvUI/GroupPfvUI");
+const ActionMethods_1 = require("../../../RcsbFvUI/Helper/ActionMethods");
+const PaginationItemComponent_1 = require("../../../RcsbFvUI/Components/PaginationItemComponent");
+var GroupPfvApp;
+(function (GroupPfvApp) {
+    function alignment(elementId, groupProvenanceId, groupId, entityCount, additionalConfig) {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            switch (groupProvenanceId) {
+                case DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession:
+                    return RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotMultipleEntitySequenceFv(elementId, elementId + RcsbTabs_1.RcsbTabs.SELECT_SUFFIX, groupId, {}, additionalConfig);
+                default:
+                    additionalConfig = Object.assign(Object.assign({}, additionalConfig), { externalTrackBuilder: (0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)() });
+                    // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
+                    const pfvArgs = [
+                        getReferenceFromGroupProvenance(groupProvenanceId),
+                        groupId,
+                        GqlTypes_1.SequenceReference.PdbEntity,
+                        GqlTypes_1.SequenceReference.Uniprot
+                    ];
+                    const pfv = yield RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAlignmentFv(elementId, ...pfvArgs, additionalConfig);
+                    const paginationCallback = ActionMethods_1.ActionMethods.paginationCallback();
+                    const uiComp = {
+                        component: PaginationItemComponent_1.PaginationItemComponent,
+                        props: {
+                            count: entityCount,
+                            after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : "0",
+                            first: (_d = (_c = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _c === void 0 ? void 0 : _c.first) !== null && _d !== void 0 ? _d : 50,
+                            stateChange: (state, prevState) => {
+                                paginationCallback(elementId, pfv, RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
+                                        first: state.first,
+                                        after: state.after.toString()
+                                    }, excludeLogo: true }));
+                            }
+                        }
+                    };
+                    GroupPfvUI_1.GroupPfvUI.fvUI(GroupPfvUI_1.GroupPfvUI.addBootstrapElement(elementId), (_f = (_e = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalUiComponents) === null || _e === void 0 ? void 0 : _e.replace) !== null && _f !== void 0 ? _f : (entityCount > ((_h = (_g = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _g === void 0 ? void 0 : _g.first) !== null && _h !== void 0 ? _h : 50) ? [uiComp] : []).concat(((_j = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalUiComponents) === null || _j === void 0 ? void 0 : _j.add) ? additionalConfig.externalUiComponents.add : []));
+                    return pfv;
+            }
+        });
+    }
+    GroupPfvApp.alignment = alignment;
+    function structure(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
+        var _a;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
+                        field: GqlTypes_1.FieldName.Type,
+                        values: [GqlTypes_1.Type.HelixP, GqlTypes_1.Type.Sheet, GqlTypes_1.Type.Cath, GqlTypes_1.Type.Scop],
+                        operation: GqlTypes_1.OperationType.Equals,
+                        source: GqlTypes_1.Source.PdbInstance
+                    }, {
+                        field: GqlTypes_1.FieldName.Type,
+                        values: [GqlTypes_1.Type.Pfam],
+                        operation: GqlTypes_1.OperationType.Equals,
+                        source: GqlTypes_1.Source.PdbEntity
+                    }], sources: [GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.PdbEntity], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: (0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)() });
+            // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
+            const pfvArgs = [
+                getReferenceFromGroupProvenance(groupProvenanceId),
+                groupId,
+                GqlTypes_1.SequenceReference.PdbEntity,
+                GqlTypes_1.SequenceReference.Uniprot
+            ];
+            return yield RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAnnotationFv(elementId, ...pfvArgs, additionalConfig);
+        });
+    }
+    GroupPfvApp.structure = structure;
+    function bindingSites(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
+        var _a;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
+                        field: GqlTypes_1.FieldName.Type,
+                        values: [GqlTypes_1.Type.BindingSite],
+                        operation: GqlTypes_1.OperationType.Equals,
+                        source: GqlTypes_1.Source.PdbInstance
+                    }], sources: [GqlTypes_1.Source.PdbInstance], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: (0, AlignmentGlobalBindingSite_1.alignmentGlobalLigandBindingSite)() });
+            // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
+            const pfvArgs = [
+                getReferenceFromGroupProvenance(groupProvenanceId),
+                groupId,
+                GqlTypes_1.SequenceReference.PdbEntity,
+                GqlTypes_1.SequenceReference.Uniprot
+            ];
+            return yield RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAnnotationFv(elementId, ...pfvArgs, additionalConfig);
+        });
+    }
+    GroupPfvApp.bindingSites = bindingSites;
+})(GroupPfvApp || (exports.GroupPfvApp = GroupPfvApp = {}));
+function annotationPositionFrequencyProcessing(nTargets) {
+    const targets = new Map();
+    return {
+        getAnnotationValue: (feature) => {
+            var _a, _b, _c, _d;
+            if (!targets.has(feature.type)) {
+                if (feature.d.value)
+                    targets.set(feature.type, feature.d.value);
+                return (_b = (_a = feature.p.values) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : 0;
+            }
+            else {
+                return (_d = (_c = feature.p.values) === null || _c === void 0 ? void 0 : _c[0]) !== null && _d !== void 0 ? _d : 0;
+            }
+        },
+        computeAnnotationValue: (annotationTracks) => {
+            annotationTracks.forEach((at, type) => {
+                const N = (type.includes(GqlTypes_1.Type.Cath) || type.includes(GqlTypes_1.Type.Scop) || type.includes(GqlTypes_1.Type.BindingSite) || type.includes(GqlTypes_1.Type.Pfam)) ? targets.get(type) : nTargets;
+                at.forEach((ann, positionKey) => {
+                    if (ann.source != GqlTypes_1.Source.PdbInterface)
+                        ann.value = Math.ceil(1000 * ann.value / (N !== null && N !== void 0 ? N : 1)) / 1000;
+                });
+            });
+        }
+    };
+}
+function getReferenceFromGroupProvenance(groupProvenanceId) {
+    switch (groupProvenanceId) {
+        case DwEnums_1.GroupProvenanceId.ProvenanceMatchingDepositGroupId:
+            throw `Undefined reference for provenance ${groupProvenanceId}`;
+        case DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity:
+            return GqlTypes_1.GroupReference.SequenceIdentity;
+        case DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession:
+            return GqlTypes_1.GroupReference.MatchingUniprotAccession;
+    }
+}
+exports.getReferenceFromGroupProvenance = getReferenceFromGroupProvenance;

package/lib/commonjs/RcsbFvWeb/RcsbFvGroup/RcsbFvGroupTabsBuilder.d.ts

@@ -0,0 +1,6 @@
+import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+import { RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
+export declare class RcsbFvGroupTabsBuilder {
+    static buildGroupTabs(elementId: string, groupProvenanceId: GroupProvenanceId, groupId: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig): void;
+}

package/lib/commonjs/RcsbFvWeb/RcsbFvGroup/RcsbFvGroupTabsBuilder.js

@@ -0,0 +1,16 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvGroupTabsBuilder = void 0;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const GroupPfvTabs_1 = require("./GroupPfvTabs");
+const client_1 = require("react-dom/client");
+const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
+var assertDefined = Assertions_1.Assertions.assertDefined;
+class RcsbFvGroupTabsBuilder {
+    static buildGroupTabs(elementId, groupProvenanceId, groupId, query, additionalConfig) {
+        const element = document.getElementById(elementId);
+        assertDefined(element);
+        (0, client_1.createRoot)(element).render((0, jsx_runtime_1.jsx)(GroupPfvTabs_1.GroupPfvTabs, { groupProvenanceId: groupProvenanceId, groupId: groupId, searchQuery: query, additionalConfig: additionalConfig }));
+    }
+}
+exports.RcsbFvGroupTabsBuilder = RcsbFvGroupTabsBuilder;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.d.ts

@@ -0,0 +1,47 @@
+import { RcsbFv } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFv";
+import { RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { AlignmentCollectorInterface } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
+import { AnnotationRequestContext, AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
+import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface } from "./RcsbFvModuleInterface";
+import { AlignmentResponse, AnnotationFeatures, Feature, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { TrackFactoryInterface } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryInterface";
+import { AlignmentRequestContextType } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
+import { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
+export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterface {
+    protected readonly rcsbFv: RcsbFv;
+    protected readonly elementId: string;
+    protected boardConfigData: RcsbFvBoardConfigInterface;
+    protected rowConfigData: Array<RcsbFvRowConfigInterface>;
+    protected polymerEntityInstance: PolymerEntityInstanceTranslate;
+    protected alignmentCollector: AlignmentCollectorInterface;
+    protected annotationCollector: AnnotationCollectorInterface;
+    protected referenceTrack: RcsbFvRowConfigInterface;
+    protected alignmentTracks: Array<RcsbFvRowConfigInterface>;
+    protected annotationTracks: Array<RcsbFvRowConfigInterface>;
+    protected buildConfig: RcsbFvModuleBuildInterface;
+    private rcsbFvRowUpdatePromise;
+    private activeDisplayFlag;
+    constructor(elementId: string, rcsbFv: RcsbFv);
+    setPolymerEntityInstanceTranslator(polymerEntityInstance: PolymerEntityInstanceTranslate): void;
+    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
+    display(): Promise<void>;
+    activeDisplay(): boolean;
+    getFv(): RcsbFv;
+    getTargets(): Promise<Array<string>>;
+    getAlignmentResponse(): Promise<AlignmentResponse>;
+    getFeatures(): Promise<Array<Feature>>;
+    getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
+    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    wait(): Promise<void>;
+    protected abstract protectedBuild(): Promise<void>;
+    protected abstract concatAlignmentAndAnnotationTracks(): void;
+    protected buildAlignmentTracks(alignmentRequestContext: AlignmentRequestContextType, alignmentResponse: AlignmentResponse, trackFactories?: {
+        alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
+        sequenceTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, string]>;
+    }): Promise<void>;
+    protected buildAnnotationsTrack(annotationsRequestContext: AnnotationRequestContext, annotationsFeatures: AnnotationFeatures[], annotationConfigMap?: AnnotationConfigInterface): Promise<void>;
+    protected getBoardConfig(): Promise<RcsbFvBoardConfigInterface>;
+    protected getRowsConfig(): Promise<Array<RcsbFvRowConfigInterface>>;
+    private buildExternalTracks;
+}

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.js

@@ -0,0 +1,147 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvAbstractModule = void 0;
+const tslib_1 = require("tslib");
+const AnnotationCollector_1 = require("../../RcsbCollectTools/AnnotationCollector/AnnotationCollector");
+const ComponentsManager_1 = require("../RcsbFvComponents/ComponentsManager");
+const SingletonMap_1 = require("../../RcsbUtils/Helpers/SingletonMap");
+const AlignmentCollector_1 = require("../../RcsbCollectTools/AlignmentCollector/AlignmentCollector");
+const AlignmentTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory");
+const SequenceTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory");
+const AlignmentBlockFactory_1 = require("../RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory");
+const AnnotationsBlockFactory_1 = require("../RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory");
+const AnnotationsTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory");
+const acm = tslib_1.__importStar(require("../../RcsbAnnotationConfig/RcsbAnnotationConfig.ac.json"));
+const AnnotationBlockManager_1 = require("../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager");
+const RcsbAnnotationConfig_1 = require("../../RcsbAnnotationConfig/RcsbAnnotationConfig");
+const AnnotationTrackManager_1 = require("../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager");
+class RcsbFvAbstractModule {
+    constructor(elementId, rcsbFv) {
+        this.boardConfigData = {
+            length: 0
+        };
+        this.rowConfigData = new Array();
+        this.alignmentCollector = new AlignmentCollector_1.AlignmentCollector();
+        this.annotationCollector = new AnnotationCollector_1.AnnotationCollector();
+        this.alignmentTracks = [];
+        this.annotationTracks = [];
+        this.activeDisplayFlag = false;
+        this.rcsbFv = rcsbFv;
+        this.elementId = elementId;
+        ComponentsManager_1.ComponentsManager.buildLoaderSpinner(elementId);
+    }
+    setPolymerEntityInstanceTranslator(polymerEntityInstance) {
+        this.polymerEntityInstance = polymerEntityInstance;
+    }
+    getPolymerEntityInstanceTranslator() {
+        return this.polymerEntityInstance;
+    }
+    display() {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            console.info(`Starting display ${this.elementId}`);
+            yield this.rcsbFv.updateBoardConfig({
+                boardConfigData: yield this.getBoardConfig(),
+                rowConfigData: []
+            });
+            ComponentsManager_1.ComponentsManager.unmountLoaderSpinner(this.elementId);
+            console.info(`Rendering tracks ${this.elementId}`);
+            this.rcsbFvRowUpdatePromise = this.rcsbFv.updateBoardConfig({
+                rowConfigData: yield this.getRowsConfig()
+            });
+            this.activeDisplayFlag = true;
+            return void 0;
+        });
+    }
+    activeDisplay() {
+        return this.activeDisplayFlag;
+    }
+    getFv() {
+        return this.rcsbFv;
+    }
+    getTargets() {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return yield this.alignmentCollector.getTargets();
+        });
+    }
+    getAlignmentResponse() {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return yield this.alignmentCollector.getAlignment();
+        });
+    }
+    getFeatures() {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            //return (await this.annotationCollector.getAnnotationFeatures()).map(af=>af.features).flat();
+            return yield this.annotationCollector.getFeatures();
+        });
+    }
+    getAnnotationConfigData() {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return this.annotationTracks;
+        });
+    }
+    build(buildConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            SingletonMap_1.SingletonMap.update(this.elementId, this);
+            this.buildConfig = buildConfig;
+            yield this.protectedBuild();
+            yield this.buildExternalTracks();
+            this.concatAlignmentAndAnnotationTracks();
+            yield this.display();
+            return void 0;
+        });
+    }
+    wait() {
+        return this.rcsbFvRowUpdatePromise;
+    }
+    buildAlignmentTracks(alignmentRequestContext, alignmentResponse, trackFactories) {
+        var _a, _b, _c, _d;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            const sequenceTrackFactory = (_a = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.sequenceTrackFactory) !== null && _a !== void 0 ? _a : new SequenceTrackFactory_1.SequenceTrackFactory(this.getPolymerEntityInstanceTranslator());
+            if (alignmentResponse.query_sequence)
+                this.referenceTrack = yield sequenceTrackFactory.getTrack(alignmentRequestContext, alignmentResponse.query_sequence);
+            const alignmentBlockFactory = new AlignmentBlockFactory_1.AlignmentBlockFactory((_b = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.alignmentTrackFactory) !== null && _b !== void 0 ? _b : new AlignmentTrackFactory_1.AlignmentTrackFactory(this.getPolymerEntityInstanceTranslator()), (_d = (_c = this.buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.trackConfigModifier) === null || _d === void 0 ? void 0 : _d.alignment);
+            this.alignmentTracks = yield alignmentBlockFactory.getBlock(alignmentRequestContext, alignmentResponse);
+        });
+    }
+    buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap) {
+        var _a, _b;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            const defaultAnnotationConfigMap = annotationConfigMap !== null && annotationConfigMap !== void 0 ? annotationConfigMap : acm;
+            const annotationsBlockFactory = new AnnotationsBlockFactory_1.AnnotationsBlockFactory(new AnnotationBlockManager_1.AnnotationBlockManager(new AnnotationTrackManager_1.AnnotationTrackManagerFactory(), new RcsbAnnotationConfig_1.RcsbAnnotationConfig(defaultAnnotationConfigMap), this.getPolymerEntityInstanceTranslator()), new AnnotationsTrackFactory_1.AnnotationsTrackFactory(), (_b = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.trackConfigModifier) === null || _b === void 0 ? void 0 : _b.annotations);
+            this.annotationTracks = yield annotationsBlockFactory.getBlock(annotationsRequestContext, annotationsFeatures);
+        });
+    }
+    getBoardConfig() {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return this.boardConfigData;
+        });
+    }
+    getRowsConfig() {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return this.rowConfigData;
+        });
+    }
+    buildExternalTracks() {
+        var _a, _b;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            const externalTrackBuilder = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder;
+            const rcsbContext = (_b = this.buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.rcsbContext;
+            if (!externalTrackBuilder)
+                return;
+            if (typeof externalTrackBuilder.processAlignmentAndFeatures === "function")
+                yield externalTrackBuilder.processAlignmentAndFeatures({
+                    annotations: yield this.annotationCollector.getAnnotationFeatures(),
+                    alignments: yield this.alignmentCollector.getAlignment(),
+                    rcsbContext: rcsbContext
+                });
+            if (typeof externalTrackBuilder.addTo === "function")
+                yield externalTrackBuilder.addTo({
+                    alignmentTracks: this.alignmentTracks,
+                    annotationTracks: this.annotationTracks,
+                    rcsbContext: rcsbContext
+                });
+            return void 0;
+        });
+    }
+}
+exports.RcsbFvAbstractModule = RcsbFvAbstractModule;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.d.ts

@@ -0,0 +1,49 @@
+import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
+export declare class RcsbFvChromosome extends RcsbFvAbstractModule {
+    private readonly targetAlignmentList;
+    private maxRange;
+    private minRange;
+    private alignmentCollectorQueue;
+    private nTasks;
+    private completeTasks;
+    private pdbEntityTrack;
+    private batchSize;
+    private beginView;
+    private endView;
+    private entityBegin;
+    private entityEnd;
+    private nonExonConfigData;
+    private featuresConfigData;
+    private targetCoverages;
+    private chrSet;
+    private targetFilterFlag;
+    private entityId;
+    private IDEOGRAM_DIV_ID;
+    private TITLE_CHR_DIV_ID;
+    private TITLE_CHR_REGION_ID;
+    private currentDisplayedChrId;
+    private elementSelectId;
+    private readonly buildSubject;
+    private readonly targetsSubject;
+    private buildPdbGenomeFv;
+    private buildFullGenomeRangeFv;
+    private collectPdbWorkerResults;
+    private buildChromosomeFv;
+    private plotChromosomeTitle;
+    private updateChromosomeTitleRegion;
+    private plotIdeogram;
+    private genomeSequenceTracks;
+    private collectChromosomeEntityRegion;
+    private collectChromosomeAlignments;
+    private collectChromosomeWorkerResults;
+    private collectExons;
+    private normalizeTargetAlignment;
+    private simplifyExonTracks;
+    private mergeExonTracks;
+    private addSequences;
+    private setDisplayView;
+    private plot;
+    protected protectedBuild(): Promise<void>;
+    getTargets(): Promise<Array<string>>;
+    protected concatAlignmentAndAnnotationTracks(): void;
+}