@rcsb/rcsb-saguaro-app 6.2.2 → 6.2.3

package/lib/RcsbAnnotationConfig/RcsbAnnotationConfig.js

@@ -40,8 +40,8 @@ export class RcsbAnnotationConfig {
     }
     //TODO refactor how title and type are defined. Can this be split in two different methods ?
     getAnnotationType(requestConfig, ann, feature) {
+        var _a, _b, _c;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
             const trackTitle = typeof requestConfig.trackTitle === "function" ? (yield requestConfig.trackTitle(ann, feature)) : undefined;
             const titleSuffix = typeof requestConfig.titleSuffix === "function" ? (yield requestConfig.titleSuffix(ann, feature)) : undefined;
             const typeSuffix = typeof requestConfig.typeSuffix === "function" ? (yield requestConfig.typeSuffix(ann, feature)) : undefined;

package/lib/RcsbChartWeb/HistogramChartComponent.d.ts

@@ -1,3 +1,4 @@
+/// <reference types="react" />
 import { AbstractChartComponent } from "./AbsractChartComponent";
 export declare class HistogramChartComponent extends AbstractChartComponent {
     render(): JSX.Element;

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollector.js

@@ -13,8 +13,8 @@ export class AlignmentCollector {
         this.alignmentLengthSubject = new Subject();
     }
     collect(requestConfig, filter) {
+        var _a, _b, _c, _d, _e, _f;
         return __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);

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollector.js

@@ -10,8 +10,8 @@ export class AnnotationCollector {
         this.annotationFeaturesSubject = new Subject();
     }
     collect(requestConfig) {
+        var _a;
         return __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") {

package/lib/RcsbCollectTools/FeatureTools/FeatureTools.js

@@ -44,15 +44,15 @@ export class FeatureTools {
     static mergeTrackBuilders(builderA, builderB) {
         return {
             addTo(tracks) {
+                var _a, _b;
                 return __awaiter(this, void 0, void 0, function* () {
-                    var _a, _b;
                     yield ((_a = builderA.addTo) === null || _a === void 0 ? void 0 : _a.call(builderA, tracks));
                     yield ((_b = builderB === null || builderB === void 0 ? void 0 : builderB.addTo) === null || _b === void 0 ? void 0 : _b.call(builderB, tracks));
                 });
             },
             processAlignmentAndFeatures(data) {
+                var _a, _b;
                 return __awaiter(this, void 0, void 0, function* () {
-                    var _a, _b;
                     yield ((_a = builderA.processAlignmentAndFeatures) === null || _a === void 0 ? void 0 : _a.call(builderA, data));
                     yield ((_b = builderB === null || builderB === void 0 ? void 0 : builderB.processAlignmentAndFeatures) === null || _b === void 0 ? void 0 : _b.call(builderB, data));
                 });

package/lib/RcsbFvExamples/ExternalDataProvider.js

@@ -882,8 +882,8 @@ class RcsbStructuralAlignmentProvider {
     }
 }
 function alignmentTransform(alignment) {
+    var _a, _b;
     return __awaiter(this, void 0, void 0, function* () {
-        var _a, _b;
         const alignmentRef = mergeAlignments(alignment.results);
         const out = alignmentRef.buildAlignments();
         const instance_ids = (_a = out.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);

package/lib/RcsbFvUI/Components/FilterItemComponent.d.ts

@@ -1,3 +1,4 @@
+/// <reference types="react" />
 import { AbstractMenuItemComponent } from "../AbstractMenuItemComponent";
 interface FilterItemProps {
     elements: string[];

package/lib/RcsbFvUI/Components/PaginationItemComponent.d.ts

@@ -1,3 +1,4 @@
+/// <reference types="react" />
 import { AbstractMenuItemComponent } from "../AbstractMenuItemComponent";
 export interface PaginationItemState {
     after: number;

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvCoreBuilder.js

@@ -35,8 +35,8 @@ export class RcsbFvCoreBuilder {
      * @description This method implements a centralized point where PFVs are created. All PFV should be created using this method directly or through <CreateFvInterface.getPolymerEntityInstanceMapAndBuildFv>. In any case PFV should be built using a custom implementation.
      * */
     static createFv(createFvI) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             const elementId = createFvI.elementId;
             const fvModuleI = createFvI.fvModuleI;
             const config = createFvI.config;

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupAlignmentBuilder.js

@@ -23,8 +23,8 @@ export class RcsbFvGroupAlignmentBuilder {
         });
     }
     static buildGroupAlignmentFv(elementId, groupProvenance, groupId, query, additionalConfig) {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
             let entityCount = -1;
             let filterEntities = undefined;
             if (query && query.query) {

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.d.ts

@@ -1,3 +1,4 @@
+/// <reference types="react" />
 import { RcsbContextType, RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
 import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 import { SelectOptionProps } from "../RcsbFvComponents/SelectButton";

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.js

@@ -6,8 +6,8 @@ import { rcsbRequestCtxManager } from "../../RcsbRequest/RcsbRequestContextManag
 import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
 //TODO Find a better structure for change callbacks
 export class RcsbFvInstanceBuilder {
-    static buildMultipleInstanceSequenceFv(elementFvId_1, elementEntrySelectId_1, elementInstanceSelectId_1, entryIdList_1) {
-        return __awaiter(this, arguments, void 0, function* (elementFvId, elementEntrySelectId, elementInstanceSelectId, entryIdList, config = {}, additionalConfig) {
+    static buildMultipleInstanceSequenceFv(elementFvId, elementEntrySelectId, elementInstanceSelectId, entryIdList, config = {}, additionalConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
             RcsbFvCoreBuilder.buildSelectButton(elementFvId, elementEntrySelectId, entryIdList.map(entryId => {
                 return {
                     label: entryId,
@@ -35,8 +35,8 @@ export class RcsbFvInstanceBuilder {
         });
     }
     static buildSelectorInstanceFv(instanceList, elementFvId, elementSelectId, entryId, config, additionalConfig) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             const filteredInstanceList = instanceList.filter(i => (config.filterInstances == null || config.filterInstances.has(i.asymId)));
             const groupedInstances = new Map();
             filteredInstanceList.forEach((instance) => {

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.js

@@ -4,8 +4,8 @@ import { RcsbFvProteinSequence } from "../RcsbFvModule/RcsbFvProteinSequence";
 import { RcsbFvCoreBuilder } from "./RcsbFvCoreBuilder";
 export class RcsbFvProteinSequenceBuilder {
     static buildPfv(elementId, config) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             const alignmentSource = (_a = config.alignmentSource) !== null && _a !== void 0 ? _a : config.reference;
             const sources = [Source.Uniprot];
             if (config.reference == SequenceReference.PdbEntity)

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvUniprotBuilder.js

@@ -9,8 +9,8 @@ import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter"
 const ALL = "ALL";
 //TODO Find a better structure for change callbacks
 export class RcsbFvUniprotBuilder {
-    static buildUniprotMultipleEntitySequenceFv(elementFvId_1, elementSelectId_1, upAcc_1) {
-        return __awaiter(this, arguments, void 0, function* (elementFvId, elementSelectId, upAcc, config = {}, additionalConfig) {
+    static buildUniprotMultipleEntitySequenceFv(elementFvId, elementSelectId, upAcc, config = {}, additionalConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
             return new Promise((resolve, reject) => __awaiter(this, void 0, void 0, function* () {
                 let externalContext;
                 if (typeof config.beforeChangeCallback === "function")

package/lib/RcsbFvWeb/RcsbFvComponents/ComponentsManager.d.ts

@@ -1,3 +1,4 @@
+/// <reference types="react" />
 import { GroupedOptionsInterface, SelectOptionInterface, SelectOptionProps } from "./SelectButton";
 export interface SelectButtonConfigInterface {
     addTitle?: boolean;

package/lib/RcsbFvWeb/RcsbFvComponents/MountableComponent.d.ts

@@ -1,6 +1,6 @@
 import { ReactNode } from "react";
 export declare class MountableComponent {
-    private readonly element;
+    private static readonly ROOT;
     private root;
     constructor(element: HTMLElement);
     render(node: ReactNode): void;

package/lib/RcsbFvWeb/RcsbFvComponents/MountableComponent.js

@@ -1,8 +1,10 @@
 import { createRoot } from "react-dom/client";
 export class MountableComponent {
     constructor(element) {
-        this.element = element;
-        this.root = createRoot(this.element);
+        var _a;
+        if (!MountableComponent.ROOT.has(element.id))
+            MountableComponent.ROOT.set(element.id, createRoot(element));
+        this.root = (_a = MountableComponent.ROOT.get(element.id)) !== null && _a !== void 0 ? _a : createRoot(element);
     }
     render(node) {
         this.unmount();
@@ -12,3 +14,4 @@ export class MountableComponent {
         this.root.render(undefined);
     }
 }
+MountableComponent.ROOT = new Map();

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory.js

@@ -5,18 +5,18 @@ export class AlignmentBlockFactory {
         this.trackConfigModifier = trackModifier;
     }
     getBlock(alignmentRequestContext, alignmentData) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             alignmentRequestContext = Object.assign(Object.assign({}, alignmentRequestContext), { querySequence: (_a = alignmentData.query_sequence) !== null && _a !== void 0 ? _a : undefined });
             if (!alignmentData.target_alignment)
                 return [];
             return (yield Promise.all(alignmentData.target_alignment.map((alignment, index) => __awaiter(this, void 0, void 0, function* () {
-                var _a, _b;
-                if (alignmentRequestContext.filterByTargetContains != null && !((_a = alignment === null || alignment === void 0 ? void 0 : alignment.target_id) === null || _a === void 0 ? void 0 : _a.includes(alignmentRequestContext.filterByTargetContains)))
+                var _b, _c;
+                if (alignmentRequestContext.filterByTargetContains != null && !((_b = alignment === null || alignment === void 0 ? void 0 : alignment.target_id) === null || _b === void 0 ? void 0 : _b.includes(alignmentRequestContext.filterByTargetContains)))
                     return;
                 if ((alignment === null || alignment === void 0 ? void 0 : alignment.target_sequence) == null)
                     return;
-                return Object.assign(Object.assign({}, yield this.trackFactory.getTrack(alignmentRequestContext, alignment)), yield ((_b = this.trackConfigModifier) === null || _b === void 0 ? void 0 : _b.call(this, alignmentRequestContext, alignment, alignmentData, index)));
+                return Object.assign(Object.assign({}, yield this.trackFactory.getTrack(alignmentRequestContext, alignment)), yield ((_c = this.trackConfigModifier) === null || _c === void 0 ? void 0 : _c.call(this, alignmentRequestContext, alignment, alignmentData, index)));
             })))).filter((x) => x != undefined);
         });
     }

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager.js

@@ -33,8 +33,8 @@ export class AnnotationBlockManager {
         ].flat();
     }
     processAnnotations(requestConfig, data) {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
             yield Promise.all(data.map(ann => {
                 var _a, _b;
                 return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.map((feature) => __awaiter(this, void 0, void 0, function* () {
@@ -46,8 +46,8 @@ export class AnnotationBlockManager {
         });
     }
     addFeature(requestConfig, ann, feature) {
+        var _a, _b, _c, _d, _e;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
             if (feature.type && ((_a = this.rcsbAnnotationConfig.getConfig(feature.type)) === null || _a === void 0 ? void 0 : _a.ignore))
                 return;
             const type = yield this.rcsbAnnotationConfig.getAnnotationType(requestConfig, ann, feature);

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory.js

@@ -12,8 +12,8 @@ export class SequenceTrackFactory {
         this.trackTitleFactory = trackTitleFactory !== null && trackTitleFactory !== void 0 ? trackTitleFactory : new SequenceTrackTitleFactory(entityInstanceTranslator);
     }
     getTrack(alignmentQueryContext, querySequence) {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
             const queryId = (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : alignmentQueryContext.groupId;
             assertDefined(queryId);
             return {

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AnnotationsTrackTitleFactory.js

@@ -9,8 +9,8 @@ export class AnnotationsTrackTitleFactory {
         });
     }
     getTrackTitleFlagColor(trackManager) {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
             const provenance = Array.from((_b = (_a = trackManager.getConfig()) === null || _a === void 0 ? void 0 : _a.provenanceList) !== null && _b !== void 0 ? _b : []);
             if (provenance.length == 1
                 &&
@@ -23,8 +23,8 @@ export class AnnotationsTrackTitleFactory {
         });
     }
     getTrackTitlePrefix(trackManager) {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
             return (_b = (_a = trackManager.getConfig()) === null || _a === void 0 ? void 0 : _a.prefix) !== null && _b !== void 0 ? _b : "";
         });
     }

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/SequenceTrackTitleFactory.js

@@ -12,8 +12,8 @@ export class SequenceTrackTitleFactory {
         this.entityInstanceTranslator = entityInstanceTranslator;
     }
     getTrackTitle(alignmentQueryContext) {
+        var _a, _b, _c;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
             let rowTitle;
             if (!alignmentQueryContext.excludeFirstRowLink && alignmentQueryContext.from === SequenceReference.Uniprot) {
                 rowTitle = {
@@ -45,14 +45,14 @@ export class SequenceTrackTitleFactory {
         });
     }
     getTrackTitlePrefix(alignmentQueryContext) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             return (alignmentQueryContext.from && !alignmentQueryContext.from.includes("PDB")) ? alignmentQueryContext.from.replace("_", " ") + " " + TagDelimiter.sequenceTitle : ((_a = alignmentQueryContext.sequencePrefix) !== null && _a !== void 0 ? _a : "");
         });
     }
     getTrackTitleFlagColor(alignmentQueryContext) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             const queryId = (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : alignmentQueryContext.groupId;
             assertDefined(queryId), assertDefined(alignmentQueryContext.from);
             return TrackUtils.getProvenanceConfigFormTarget(queryId, alignmentQueryContext.from).color;

package/lib/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.js

@@ -76,8 +76,8 @@ export class GroupPfvTabs extends React.Component {
         });
     }
     renderPositionalFeatureViewer(tabKey) {
+        var _a, _b, _c, _d, _e;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
             switch (tabKey) {
                 case ALIGNMENT:
                     this.featureViewers.set(tabKey, yield GPA.alignment(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_a = this.entityCount) !== null && _a !== void 0 ? _a : 0, Object.assign(Object.assign({ page: { first: 50, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.filterEntities })));

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

@@ -12,8 +12,8 @@ import { PaginationItemComponent } from "../../../RcsbFvUI/Components/Pagination
 export var GroupPfvApp;
 (function (GroupPfvApp) {
     function alignment(elementId, groupProvenanceId, groupId, entityCount, additionalConfig) {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
             switch (groupProvenanceId) {
                 case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
                     return RcsbFvUniprotBuilder.buildUniprotMultipleEntitySequenceFv(elementId, elementId + RcsbTabs.SELECT_SUFFIX, groupId, {}, additionalConfig);
@@ -49,8 +49,8 @@ export var GroupPfvApp;
     }
     GroupPfvApp.alignment = alignment;
     function structure(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
                         field: FieldName.Type,
                         values: [Type.HelixP, Type.Sheet, Type.Cath, Type.Scop],
@@ -74,8 +74,8 @@ export var GroupPfvApp;
     }
     GroupPfvApp.structure = structure;
     function bindingSites(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
                         field: FieldName.Type,
                         values: [Type.BindingSite],

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.js

@@ -91,8 +91,8 @@ export class RcsbFvAbstractModule {
         return this.rcsbFvRowUpdatePromise;
     }
     buildAlignmentTracks(alignmentRequestContext, alignmentResponse, trackFactories) {
+        var _a, _b, _c, _d;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d;
             const sequenceTrackFactory = (_a = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.sequenceTrackFactory) !== null && _a !== void 0 ? _a : new SequenceTrackFactory(this.getPolymerEntityInstanceTranslator());
             if (alignmentResponse.query_sequence)
                 this.referenceTrack = yield sequenceTrackFactory.getTrack(alignmentRequestContext, alignmentResponse.query_sequence);
@@ -101,8 +101,8 @@ export class RcsbFvAbstractModule {
         });
     }
     buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap) {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
             const defaultAnnotationConfigMap = annotationConfigMap !== null && annotationConfigMap !== void 0 ? annotationConfigMap : acm;
             const annotationsBlockFactory = new AnnotationsBlockFactory(new AnnotationBlockManager(new AnnotationTrackManagerFactory(), new RcsbAnnotationConfig(defaultAnnotationConfigMap), this.getPolymerEntityInstanceTranslator()), new 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);
@@ -119,8 +119,8 @@ export class RcsbFvAbstractModule {
         });
     }
     buildExternalTracks() {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
             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)

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.js

@@ -139,8 +139,8 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
         this.collectChromosomeAlignments(chrId, SequenceReference.NcbiProtein);
     }
     collectPdbWorkerResults(ar, pdbEntityId, chrId) {
+        var _c, _d;
         return __awaiter(this, void 0, void 0, function* () {
-            var _c, _d;
             assertElementListDefined(ar.target_alignment);
             const exonTracks = this.collectExons(ar.target_alignment, "target", RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, SequenceReference.PdbEntity, chrId);
             this.pdbEntityTrack = this.mergeExonTracks(exonTracks, SequenceReference.PdbEntity)[0];
@@ -621,8 +621,8 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
         });
     }
     setDisplayView() {
+        var _c, _d, _e, _f, _g, _h, _j;
         return __awaiter(this, void 0, void 0, function* () {
-            var _c, _d, _e, _f, _g, _h, _j;
             if (this.entityBegin == 0 && this.entityEnd == 0 && ((_e = (_d = (_c = this.pdbEntityTrack) === null || _c === void 0 ? void 0 : _c.displayConfig) === null || _d === void 0 ? void 0 : _d.length) !== null && _e !== void 0 ? _e : 0) > 0) {
                 const d = (_f = this.pdbEntityTrack.displayConfig) === null || _f === void 0 ? void 0 : _f[0].displayData;
                 if (!d)
@@ -659,8 +659,8 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
         });
     }
     plot() {
+        var _c, _d, _e, _f;
         return __awaiter(this, void 0, void 0, function* () {
-            var _c, _d, _e, _f;
             console.log("PROCESSING");
             let tracks = new Array();
             let ncbiTracks = new Array();

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvDataProvider.js

@@ -3,8 +3,8 @@ import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { PlainAlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory";
 export class RcsbFvDataProvider extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o;
             if ((_b = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.dataProvider) === null || _b === void 0 ? void 0 : _b.alignments) {
                 this.alignmentCollector = this.buildConfig.additionalConfig.dataProvider.alignments.collector;
                 const alignmentResponse = yield this.alignmentCollector.collect(Object.assign({}, (_d = (_c = this.buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.dataProvider) === null || _d === void 0 ? void 0 : _d.alignments.context), (_e = this.buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.alignmentFilter);

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvEntity.js

@@ -11,8 +11,8 @@ export class RcsbFvEntity extends RcsbFvAbstractModule {
         this.unmodeledTrackBuilder = new UnmodeledTrackBuilder();
     }
     protectedBuild() {
+        var _a, _b, _c, _d, _e, _f, _g;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g;
             const buildConfig = this.buildConfig;
             assertDefined(buildConfig.entityId);
             const alignmentRequestContext = {

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAlignment.js

@@ -9,8 +9,8 @@ import { Operator } from "../../RcsbUtils/Helpers/Operator";
 import { rcsbRequestCtxManager } from "../../RcsbRequest/RcsbRequestContextManager";
 export class RcsbFvGroupAlignment extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
             const buildConfig = this.buildConfig;
             assertDefined(buildConfig.groupId), assertDefined(buildConfig.group), assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page);
             const alignmentRequestContext = {

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAnnotation.js

@@ -7,8 +7,8 @@ var assertDefined = Assertions.assertDefined;
 const annotationConfigMap = acm;
 export class RcsbFvGroupAnnotation extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
             const buildConfig = this.buildConfig;
             assertDefined(buildConfig.group), assertDefined(buildConfig.groupId), assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page);
             const alignmentRequestContext = {

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInstance.js

@@ -8,8 +8,8 @@ import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
 export class RcsbFvInstance extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c, _d;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d;
             const buildConfig = this.buildConfig;
             const instanceId = buildConfig.instanceId;
             assertDefined(instanceId);

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.js

@@ -14,8 +14,8 @@ import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter"
 const annotationConfigMap = acm;
 export class RcsbFvInterface extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c, _d, _e;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
             const buildConfig = this.buildConfig;
             const instanceId = buildConfig.instanceId;
             assertDefined(instanceId);
@@ -60,8 +60,8 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
                     this.alignmentTracks.concat(this.annotationTracks);
     }
     typeSuffix(ann, d) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             if (ann.source === Source.PdbInterface && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_id)) {
                 return ann.target_identifiers.interface_id + "|" + ann.target_identifiers.interface_partner_index;
             }

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvPairwiseAlignment.js

@@ -5,8 +5,8 @@ import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
 export class RcsbFvPairwiseAlignment extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             const buildConfig = this.buildConfig;
             assertDefined(buildConfig.psa);
             const pab = new PairwiseAlignmentBuilder(buildConfig.psa);

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvProteinSequence.js

@@ -5,8 +5,8 @@ import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
 export class RcsbFvProteinSequence extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c, _d, _e;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
             const buildConfig = this.buildConfig;
             const queryId = buildConfig.queryId;
             assertDefined(queryId);

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprot.js

@@ -7,8 +7,8 @@ import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
 export class RcsbFvUniprot extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c, _d;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d;
             const buildConfig = this.buildConfig;
             const upAcc = buildConfig.upAcc;
             assertDefined(upAcc);

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotAlignment.js

@@ -7,8 +7,8 @@ import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
 export class RcsbFvUniprotAlignment extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
             const buildConfig = this.buildConfig;
             assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page), assertDefined(buildConfig.upAcc);
             const alignmentRequestContext = {

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotEntity.js

@@ -11,8 +11,8 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
         this.unmodeledTrackBuilder = new UnmodeledTrackBuilder();
     }
     protectedBuild() {
+        var _a, _b, _c;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
             const buildConfig = this.buildConfig;
             const upAcc = buildConfig.upAcc;
             const entityId = buildConfig.entityId;
@@ -62,8 +62,8 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
         this.rowConfigData = [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks);
     }
     titleSuffix(ann, d) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             if (this.polymerEntityInstance != null && ann.source === Source.PdbInstance) {
                 const labelAsymId = (_a = ann.target_id) === null || _a === void 0 ? void 0 : _a.split(TagDelimiter.instance)[1];
                 if (!labelAsymId)

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotInstance.js

@@ -6,8 +6,8 @@ import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
 export class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
     protectedBuild() {
+        var _a, _b, _c;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
             const buildConfig = this.buildConfig;
             const upAcc = buildConfig.upAcc;
             const entityId = buildConfig.entityId;

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartTools.js

@@ -8,8 +8,8 @@ import { rcsbRequestCtxManager } from "../../../RcsbRequest/RcsbRequestContextMa
 export var GroupChartMap;
 (function (GroupChartMap) {
     function getChartMap(groupProvenanceId, groupId, searchQuery) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             const facetStore = SQT.getFacetStoreFromGroupProvenance(groupProvenanceId);
             let facets = [];
             for (const service of facetStore.getServices()) {
@@ -45,8 +45,8 @@ export var GroupChartMap;
     }
     GroupChartMap.getChartMap = getChartMap;
     function subtractSearchQuery(chartData, groupProvenanceId, groupId, searchQuery) {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
             const facetStore = SQT.getFacetStoreFromGroupProvenance(groupProvenanceId);
             let subData;
             let partialFacets = [];

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbGroupChartComponent.js

@@ -23,8 +23,8 @@ export class RcsbGroupChartComponent extends React.Component {
         }
     }
     updateState() {
+        var _a, _b, _c;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
             const layout = (_a = this.props.facetLayoutGrid) !== null && _a !== void 0 ? _a : SQT.getFacetStoreFromGroupProvenance(this.props.groupProvenanceId).facetLayoutGrid;
             const chartMap = yield GDCM.getChartMap(this.props.groupProvenanceId, this.props.groupId, this.props.searchQuery);
             if ((_b = this.props.additionalProperties) === null || _b === void 0 ? void 0 : _b.layoutConfig)

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupContent/RcsbGroupContentComponent.js

@@ -18,8 +18,8 @@ export class RcsbGroupContentComponent extends React.Component {
         };
     }
     componentDidMount() {
+        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
             this.subscribe();
             const fullGroupMembers = (_a = (yield searchRequest(this.props.groupProvenanceId, this.props.groupId))) === null || _a === void 0 ? void 0 : _a.total_count;
             const subGroupMembers = (_b = (yield searchRequest(this.props.groupProvenanceId, this.props.groupId, this.props.searchQuery))) === null || _b === void 0 ? void 0 : _b.total_count;
@@ -44,8 +44,8 @@ export class RcsbGroupContentComponent extends React.Component {
         return ((_a = this.props.displayNumber) !== null && _a !== void 0 ? _a : Operator.digitGrouping)(x);
     }
     updateGroupContent(o) {
+        var _a;
         return __awaiter(this, void 0, void 0, function* () {
-            var _a;
             const subGroupMembers = (_a = (yield searchRequest(this.props.groupProvenanceId, this.props.groupId, o.searchQuery))) === null || _a === void 0 ? void 0 : _a.total_count;
             if (subGroupMembers)
                 this.setState({ subGroupMembers, searchQuery: o.searchQuery });

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMembersGrid.js

@@ -71,8 +71,8 @@ export class GroupMembersGrid extends React.Component {
     }
 }
 function searchRequest(groupProvenanceId, groupId, start, rows, searchQuery) {
+    var _a, _b, _c, _d, _e, _f, _g, _h;
     return __awaiter(this, void 0, void 0, function* () {
-        var _a, _b, _c, _d, _e, _f, _g, _h;
         return yield rcsbRequestCtxManager.getSearchQuery({
             query: (searchQuery === null || searchQuery === void 0 ? void 0 : searchQuery.query) ? SQT.addGroupNodeToSearchQuery(groupProvenanceId, groupId, searchQuery.query) : SQT.searchGroupQuery(groupProvenanceId, groupId),
             request_options: {

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/RcsbGroupSeacrhQueryComponent.d.ts

@@ -1,3 +1,4 @@
+/// <reference types="react" />
 import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
 import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
 export declare class SearchQueryComponentFactory {