@rcsb/rcsb-saguaro-app 6.2.3 → 6.2.5-dev-js-seqcoord.1

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

@@ -16,16 +16,16 @@ class AlignmentCollector {
         this.alignmentLengthSubject = new rxjs_1.Subject();
     }
     collect(requestConfig, filter) {
-        var _a, _b, _c, _d, _e, _f;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             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);
+            const targetAlignment = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignments;
             if (targetAlignment) {
                 assertElementListDefined(targetAlignment);
-                this.alignmentResponse.target_alignment = !filter ? targetAlignment : targetAlignment === null || targetAlignment === void 0 ? void 0 : targetAlignment.filter(ta => { var _a; return filter.includes((_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "not-included"); });
+                this.alignmentResponse.target_alignments = !filter ? targetAlignment : targetAlignment === null || targetAlignment === void 0 ? void 0 : targetAlignment.filter(ta => { var _a; return filter.includes((_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "not-included"); });
             }
-            this.alignmentResponse = typeof ((_f = requestConfig.externalTrackBuilder) === null || _f === void 0 ? void 0 : _f.filterAlignments) === "function" ? yield requestConfig.externalTrackBuilder.filterAlignments({ alignments: this.alignmentResponse }) : this.alignmentResponse;
+            this.alignmentResponse = typeof ((_b = requestConfig.externalTrackBuilder) === null || _b === void 0 ? void 0 : _b.filterAlignments) === "function" ? yield requestConfig.externalTrackBuilder.filterAlignments({ alignments: this.alignmentResponse }) : this.alignmentResponse;
             this.complete();
             return this.alignmentResponse;
         });
@@ -35,7 +35,7 @@ class AlignmentCollector {
             return new Promise((resolve, reject) => {
                 var _a, _b;
                 if (this.requestStatus === "complete") {
-                    const targetIds = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) === null || _b === void 0 ? void 0 : _b.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
+                    const targetIds = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignments) === null || _b === void 0 ? void 0 : _b.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
                     assertElementListDefined(targetIds);
                     resolve(targetIds);
                 }
@@ -71,7 +71,7 @@ class AlignmentCollector {
     requestAlignment(requestConfig) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             this.requestStatus = "pending";
-            if (requestConfig.queryId) {
+            if (requestConfig.queryId && requestConfig.from && requestConfig.to) {
                 return yield this.rcsbFvQuery.requestAlignment({
                     queryId: requestConfig.queryId,
                     from: requestConfig.from,
@@ -79,7 +79,7 @@ class AlignmentCollector {
                 });
             }
             else {
-                if (requestConfig.group && requestConfig.page) {
+                if (requestConfig.group && requestConfig.groupId && requestConfig.page) {
                     return yield this.rcsbFvQuery.requestGroupAlignment({
                         group: requestConfig.group,
                         groupId: requestConfig.groupId,
@@ -97,7 +97,7 @@ class AlignmentCollector {
     complete() {
         var _a, _b, _c, _d, _e;
         this.requestStatus = "complete";
-        const targetIds = (_b = (_a = this.alignmentResponse.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id)) !== null && _b !== void 0 ? _b : [];
+        const targetIds = (_b = (_a = this.alignmentResponse.target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id)) !== null && _b !== void 0 ? _b : [];
         assertElementListDefined(targetIds);
         this.targetsSubject.next(targetIds);
         this.alignmentResponseSubject.next(this.alignmentResponse);

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

@@ -1,4 +1,4 @@
-import { AlignmentResponse, QueryAlignmentArgs, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, QueryAlignmentsArgs, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbQueryGroupAlignmentArguments } from "../../RcsbGraphQL/RcsbQueryAlignment";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 interface CommonAlignmentInterface {
@@ -10,7 +10,7 @@ interface CommonAlignmentInterface {
     excludeFirstRowLink?: boolean;
 }
 type QueryAlignmentArgsTypes = {
-    [K in keyof QueryAlignmentArgs]: NonNullable<QueryAlignmentArgs[K]>;
+    [K in keyof QueryAlignmentsArgs]: NonNullable<QueryAlignmentsArgs[K]>;
 };
 export interface CollectAlignmentInterface extends QueryAlignmentArgsTypes, CommonAlignmentInterface {
 }
@@ -22,8 +22,8 @@ export interface CollectGroupAlignmentInterface extends RcsbQueryGroupAlignmentA
 export type AlignmentCollectConfig = Partial<CollectAlignmentInterface & CollectGroupAlignmentInterface>;
 export interface AlignmentCollectorInterface {
     getTargets(): Promise<Array<string>>;
-    getAlignment(): Promise<AlignmentResponse>;
+    getAlignment(): Promise<SequenceAlignments>;
     getAlignmentLength(): Promise<number>;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<SequenceAlignments>;
 }
 export {};

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

@@ -1,4 +1,4 @@
-import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations, Features } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AnnotationRequestContext, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
 export declare class AnnotationCollector implements AnnotationCollectorInterface {
@@ -8,9 +8,9 @@ export declare class AnnotationCollector implements AnnotationCollectorInterface
     private annotationFeatures;
     private readonly rawFeaturesSubject;
     private readonly annotationFeaturesSubject;
-    collect(requestConfig: AnnotationRequestContext): Promise<Array<AnnotationFeatures>>;
-    getFeatures(): Promise<Array<Feature>>;
-    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
+    collect(requestConfig: AnnotationRequestContext): Promise<Array<SequenceAnnotations>>;
+    getFeatures(): Promise<Array<Features>>;
+    getAnnotationFeatures(): Promise<Array<SequenceAnnotations>>;
     private requestAnnotations;
     private complete;
 }

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

@@ -13,8 +13,8 @@ class AnnotationCollector {
         this.annotationFeaturesSubject = new rxjs_1.Subject();
     }
     collect(requestConfig) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a;
             this.requestStatus = "pending";
             this.annotationFeatures = yield this.requestAnnotations(requestConfig);
             if (typeof (requestConfig === null || requestConfig === void 0 ? void 0 : requestConfig.annotationGenerator) === "function") {
@@ -58,7 +58,22 @@ class AnnotationCollector {
     }
     requestAnnotations(requestConfig) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            if (requestConfig.queryId)
+            if (requestConfig.group && requestConfig.groupId && requestConfig.sources)
+                if (requestConfig.isSummary)
+                    return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotationsSummary({
+                        group: requestConfig.group,
+                        groupId: requestConfig.groupId,
+                        sources: requestConfig.sources,
+                        filters: requestConfig.filters
+                    });
+                else
+                    return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotations({
+                        group: requestConfig.group,
+                        groupId: requestConfig.groupId,
+                        sources: requestConfig.sources,
+                        filters: requestConfig.filters
+                    });
+            else if (requestConfig.queryId && requestConfig.reference && requestConfig.sources)
                 return yield this.rcsbFvQuery.requestRcsbPdbAnnotations({
                     queryId: requestConfig.queryId,
                     reference: requestConfig.reference,
@@ -66,14 +81,6 @@ class AnnotationCollector {
                     filters: requestConfig.filters,
                     range: requestConfig.range
                 });
-            else if (requestConfig.group && requestConfig.groupId)
-                return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotations({
-                    group: requestConfig.group,
-                    groupId: requestConfig.groupId,
-                    sources: requestConfig.sources,
-                    filters: requestConfig.filters,
-                    histogram: requestConfig.histogram
-                });
             throw new Error(`Annotation query error`);
         });
     }

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

@@ -1,4 +1,4 @@
-import { AnnotationFeatures, Feature, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations, Features, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { FeaturePositionGaps } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
@@ -7,7 +7,7 @@ export type IncreaseAnnotationValueType = (feature: {
     type: string;
     targetId: string;
     positionKey: string;
-    d: Feature;
+    d: Features;
     p: FeaturePositionGaps;
 }) => number;
 export interface AnnotationProcessingInterface {
@@ -19,19 +19,20 @@ export interface CommonAnnotationInterface {
     rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     annotationProcessing?: AnnotationProcessingInterface;
     externalTrackBuilder?: ExternalTrackBuilderInterface;
-    annotationGenerator?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
-    annotationFilter?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
-    titleSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
-    trackTitle?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
-    typeSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+    annotationGenerator?(annotations: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
+    annotationFilter?(annotations: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
+    titleSuffix?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
+    trackTitle?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
+    typeSuffix?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
 }
 export interface AnnotationsCollectConfig extends QueryAnnotationsArgs, CommonAnnotationInterface {
 }
 export interface CollectGroupAnnotationsInterface extends QueryGroup_AnnotationsArgs, CommonAnnotationInterface {
+    isSummary: boolean;
 }
 export type AnnotationRequestContext = Partial<AnnotationsCollectConfig & CollectGroupAnnotationsInterface>;
 export interface AnnotationCollectorInterface {
-    collect(requestConfig: AnnotationsCollectConfig | CollectGroupAnnotationsInterface): Promise<Array<AnnotationFeatures>>;
-    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
-    getFeatures(): Promise<Array<Feature>>;
+    collect(requestConfig: AnnotationsCollectConfig | CollectGroupAnnotationsInterface): Promise<Array<SequenceAnnotations>>;
+    getAnnotationFeatures(): Promise<Array<SequenceAnnotations>>;
+    getFeatures(): Promise<Array<Features>>;
 }

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

@@ -16,7 +16,7 @@ class PolymerEntityChromosomeCollector {
             }));
             result.forEach((alignment, n) => {
                 var _a;
-                (_a = alignment.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
+                (_a = alignment.target_alignments) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
                     var _a, _b, _c;
                     if (((_b = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0) {
                         if (!entityMap.has(entityIds[n]))

package/lib/commonjs/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.d.ts

@@ -1,20 +1,20 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
 export interface ExternalTrackBuilderInterface {
     processAlignmentAndFeatures?(data: {
-        annotations?: Array<AnnotationFeatures>;
-        alignments?: AlignmentResponse;
+        annotations?: Array<SequenceAnnotations>;
+        alignments?: SequenceAlignments;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     }): Promise<void>;
     filterAlignments?(data: {
-        alignments: AlignmentResponse;
+        alignments: SequenceAlignments;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<AlignmentResponse>;
+    }): Promise<SequenceAlignments>;
     filterFeatures?(data: {
-        annotations: Array<AnnotationFeatures>;
+        annotations: Array<SequenceAnnotations>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<Array<AnnotationFeatures>>;
+    }): Promise<Array<SequenceAnnotations>>;
     addTo?(tracks: {
         alignmentTracks?: Array<RcsbFvRowConfigInterface>;
         annotationTracks?: Array<RcsbFvRowConfigInterface>;

package/lib/commonjs/RcsbCollectTools/FeatureTools/FeatureTools.js

@@ -47,15 +47,15 @@ class FeatureTools {
     static mergeTrackBuilders(builderA, builderB) {
         return {
             addTo(tracks) {
-                var _a, _b;
                 return tslib_1.__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 tslib_1.__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/commonjs/RcsbExport/FeatureType.d.ts

@@ -1,9 +1,9 @@
-import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 declare const ExtendedTypes: {
-    BurialFraction: Type;
-    BuriedResidues: Type;
+    BurialFraction: FeaturesType;
+    BuriedResidues: FeaturesType;
 };
-type MergedType = typeof Type & typeof ExtendedTypes;
+type MergedType = typeof FeaturesType & typeof ExtendedTypes;
 declare const MergedType: MergedType;
 type FeatureType = typeof MergedType;
 export declare const FeatureType: FeatureType;

package/lib/commonjs/RcsbExport/FeatureType.js

@@ -8,5 +8,5 @@ const ExtendedTypes = {
     BurialFraction: BURIAL_FRACTION,
     BuriedResidues: BURIED_RESIDUES
 };
-const MergedType = Object.assign(Object.assign({}, GqlTypes_1.Type), ExtendedTypes);
+const MergedType = Object.assign(Object.assign({}, GqlTypes_1.FeaturesType), ExtendedTypes);
 exports.FeatureType = MergedType;

package/lib/commonjs/RcsbFvExamples/ExternalDataProvider.js

@@ -861,7 +861,7 @@ class RcsbStructuralAlignmentProvider {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             return new Promise((resolve) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a, _b;
-                resolve((_b = (_a = (yield this.data()).target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a; return (_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "NA"; })) !== null && _b !== void 0 ? _b : []);
+                resolve((_b = (_a = (yield this.data()).target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a; return (_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "NA"; })) !== null && _b !== void 0 ? _b : []);
             }));
         });
     }
@@ -869,7 +869,7 @@ class RcsbStructuralAlignmentProvider {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             return new Promise((resolve) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a;
-                const ends = (_a = (yield this.data()).target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a, _b, _c; return (_c = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a[((_b = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _b === void 0 ? void 0 : _b.length) - 1]) === null || _c === void 0 ? void 0 : _c.query_end; });
+                const ends = (_a = (yield this.data()).target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a, _b, _c; return (_c = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a[((_b = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _b === void 0 ? void 0 : _b.length) - 1]) === null || _c === void 0 ? void 0 : _c.query_end; });
                 assertElementListDefined(ends);
                 resolve(Math.max(...ends));
             }));
@@ -884,14 +884,14 @@ class RcsbStructuralAlignmentProvider {
     }
 }
 function alignmentTransform(alignment) {
-    var _a, _b;
     return tslib_1.__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);
+        const instance_ids = (_a = out.target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
         assertElementListDefined(instance_ids);
         const seqs = yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getInstanceSequences(instance_ids);
-        (_b = out.target_alignment) === null || _b === void 0 ? void 0 : _b.forEach(ta => {
+        (_b = out.target_alignments) === null || _b === void 0 ? void 0 : _b.forEach(ta => {
             var _a;
             const seq = (_a = seqs.find(s => s.rcsbId === (ta === null || ta === void 0 ? void 0 : ta.target_id))) === null || _a === void 0 ? void 0 : _a.sequence;
             if (seq && ta)

package/lib/commonjs/RcsbFvExamples/InstanceSequenceFv.js

@@ -36,7 +36,7 @@ function externalTrackBuilder() {
                     var _a;
                     (_a = a.features) === null || _a === void 0 ? void 0 : _a.forEach(f => {
                         var _a, _b;
-                        if (f != null && f.type === GqlTypes_1.Type.RegionOfInterest) {
+                        if (f != null && f.type === GqlTypes_1.FeaturesType.RegionOfInterest) {
                             if (f.feature_positions)
                                 (_a = myComputedTrack.trackData) === null || _a === void 0 ? void 0 : _a.push(...(_b = f.feature_positions) === null || _b === void 0 ? void 0 : _b.map(p => {
                                     var _a, _b;

package/lib/commonjs/RcsbFvExamples/SequenceIdentityGroupAlignmentFv.js

@@ -22,7 +22,7 @@ class UiComponent extends react_1.default.Component {
     },
     page: {
         first: 200,
-        after: "0"
+        after: 0
     },
     externalTrackBuilder: {
         filterAlignments: (data) => {

package/lib/commonjs/RcsbFvExamples/UniprotGroupFv.js

@@ -2,7 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const RcsbFvBuilder_1 = require("../RcsbFvWeb/RcsbFvBuilder");
 const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
-const query = {
+// import {SearchQuery} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+/* const query: SearchQuery = {
     "query": {
         "type": "group",
         "nodes": [
@@ -66,7 +67,7 @@ const query = {
             "experimental"
         ]
     }
-};
-//buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "Q8WZ42");
-(0, RcsbFvBuilder_1.buildGroupFv)("pfv", DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession, "P69905", query);
-//buildGroupFv("pfv",GroupProvenanceId.ProvenanceSequenceIdentity, "1_30");
+}*/
+// buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "Q8WZ42");
+// buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "P69905", query);
+(0, RcsbFvBuilder_1.buildGroupFv)("pfv", DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity, "10_30");

package/lib/commonjs/RcsbFvExamples/utils/events.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.onLoad = exports.getJsonFromUrl = void 0;
+exports.getJsonFromUrl = getJsonFromUrl;
+exports.onLoad = onLoad;
 function getJsonFromUrl() {
     const url = location.search;
     var query = url.substring(1);
@@ -11,10 +12,8 @@ function getJsonFromUrl() {
     });
     return result;
 }
-exports.getJsonFromUrl = getJsonFromUrl;
 function onLoad(f) {
     document.addEventListener("DOMContentLoaded", function (event) {
         f();
     });
 }
-exports.onLoad = onLoad;

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

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

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AbstractMenuItemComponent } from "../AbstractMenuItemComponent";
 export interface PaginationItemState {
     after: number;
@@ -6,7 +5,7 @@ export interface PaginationItemState {
 }
 export interface PaginationItemProps {
     count: number;
-    after: string;
+    after: number;
     first: number;
     stateChange(state: PaginationItemState, prevState: PaginationItemState): void;
 }

package/lib/commonjs/RcsbFvUI/Components/PaginationItemComponent.js

@@ -7,7 +7,7 @@ class PaginationItemComponent extends AbstractMenuItemComponent_1.AbstractMenuIt
     constructor() {
         super(...arguments);
         this.state = {
-            after: parseInt(this.props.after),
+            after: this.props.after,
             first: this.props.first > this.props.count ? this.props.count : this.props.first
         };
     }

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvCoreBuilder.js

@@ -38,8 +38,8 @@ 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 tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a;
             const elementId = createFvI.elementId;
             const fvModuleI = createFvI.fvModuleI;
             const config = createFvI.config;

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvEntityBuilder.js

@@ -36,7 +36,7 @@ class RcsbFvEntityBuilder {
                                     yield RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotEntityFv(elementFvId, t, entityId, Object.assign({ alignmentFilter: [entityId] }, additionalConfig({
                                         field: GqlTypes_1.FieldName.TargetId,
                                         operation: GqlTypes_1.OperationType.Contains,
-                                        source: GqlTypes_1.Source.PdbInstance,
+                                        source: GqlTypes_1.AnnotationReference.PdbInstance,
                                         values: [pdbId + TagDelimiter_1.TagDelimiter.instance]
                                     })));
                                 }
@@ -80,13 +80,13 @@ function additionalConfig(f) {
     const filters = [{
             field: GqlTypes_1.FieldName.Type,
             operation: GqlTypes_1.OperationType.Equals,
-            source: GqlTypes_1.Source.PdbInstance,
-            values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.UnobservedAtomXyz, GqlTypes_1.Type.MaQaMetricLocalTypeOther, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
+            source: GqlTypes_1.AnnotationReference.PdbInstance,
+            values: [GqlTypes_1.FeaturesType.UnobservedResidueXyz, GqlTypes_1.FeaturesType.UnobservedAtomXyz, GqlTypes_1.FeaturesType.MaQaMetricLocalTypeOther, GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt]
         }];
     if (f)
         filters.push(f);
     return {
-        sources: [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance],
+        sources: [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.PdbInstance],
         filters: filters
     };
 }

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupAlignmentBuilder.js

@@ -26,8 +26,8 @@ class RcsbFvGroupAlignmentBuilder {
         });
     }
     static buildGroupAlignmentFv(elementId, groupProvenance, groupId, query, additionalConfig) {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         return tslib_1.__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) {
@@ -37,7 +37,7 @@ class RcsbFvGroupAlignmentBuilder {
             else {
                 entityCount = yield SearchRequestProperty_1.searchRequestProperty.requestCount({ query: SearchQueryTools_1.SearchQueryTools.searchGroupQuery(groupProvenance, groupId), return_type: SearchEnums_1.ReturnType.PolymerEntity });
             }
-            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { page: Object.assign({ first: 50, after: "0" }, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page), alignmentFilter: filterEntities, externalTrackBuilder: FeatureTools_1.FeatureTools.mergeTrackBuilders((0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)(), additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalTrackBuilder) });
+            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { page: Object.assign({ first: 50, after: 0 }, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page), alignmentFilter: filterEntities, externalTrackBuilder: FeatureTools_1.FeatureTools.mergeTrackBuilders((0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)(), additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalTrackBuilder) });
             // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
             const pfvArgs = [
                 (0, GroupPfvApp_1.getReferenceFromGroupProvenance)(groupProvenance),
@@ -60,20 +60,20 @@ class RcsbFvGroupAlignmentBuilder {
                 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",
+                    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) => {
                         switch (groupProvenance) {
                             case DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity:
                                 sequenceIdentityCallback(elementId, pfv, RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
                                         first: state.first,
-                                        after: state.after.toString()
+                                        after: state.after
                                     }, excludeLogo: true }));
                                 break;
                             case DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession:
                                 uniprotCallback(elementId, pfv, RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotAlignmentFv, [groupId], Object.assign(Object.assign({}, additionalConfig), { page: {
                                         first: state.first,
-                                        after: state.after.toString()
+                                        after: state.after
                                     } }));
                                 break;
                         }

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

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

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.js

@@ -9,8 +9,8 @@ const RcsbRequestContextManager_1 = require("../../RcsbRequest/RcsbRequestContex
 const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
 //TODO Find a better structure for change callbacks
 class RcsbFvInstanceBuilder {
-    static buildMultipleInstanceSequenceFv(elementFvId, elementEntrySelectId, elementInstanceSelectId, entryIdList, config = {}, additionalConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+    static buildMultipleInstanceSequenceFv(elementFvId_1, elementEntrySelectId_1, elementInstanceSelectId_1, entryIdList_1) {
+        return tslib_1.__awaiter(this, arguments, void 0, function* (elementFvId, elementEntrySelectId, elementInstanceSelectId, entryIdList, config = {}, additionalConfig) {
             RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.buildSelectButton(elementFvId, elementEntrySelectId, entryIdList.map(entryId => {
                 return {
                     label: entryId,
@@ -38,8 +38,8 @@ class RcsbFvInstanceBuilder {
         });
     }
     static buildSelectorInstanceFv(instanceList, elementFvId, elementSelectId, entryId, config, additionalConfig) {
-        var _a;
         return tslib_1.__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/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.js

@@ -7,14 +7,14 @@ const RcsbFvProteinSequence_1 = require("../RcsbFvModule/RcsbFvProteinSequence")
 const RcsbFvCoreBuilder_1 = require("./RcsbFvCoreBuilder");
 class RcsbFvProteinSequenceBuilder {
     static buildPfv(elementId, config) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a;
             const alignmentSource = (_a = config.alignmentSource) !== null && _a !== void 0 ? _a : config.reference;
-            const sources = [GqlTypes_1.Source.Uniprot];
+            const sources = [GqlTypes_1.AnnotationReference.Uniprot];
             if (config.reference == GqlTypes_1.SequenceReference.PdbEntity)
-                sources.unshift(GqlTypes_1.Source.PdbEntity);
+                sources.unshift(GqlTypes_1.AnnotationReference.PdbEntity);
             if (config.reference == GqlTypes_1.SequenceReference.PdbInstance)
-                sources.unshift(GqlTypes_1.Source.PdbInstance);
+                sources.unshift(GqlTypes_1.AnnotationReference.PdbInstance);
             return new Promise((resolve, reject) => {
                 try {
                     RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.createFv({

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvUniprotBuilder.js

@@ -12,8 +12,8 @@ const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimite
 const ALL = "ALL";
 //TODO Find a better structure for change callbacks
 class RcsbFvUniprotBuilder {
-    static buildUniprotMultipleEntitySequenceFv(elementFvId, elementSelectId, upAcc, config = {}, additionalConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+    static buildUniprotMultipleEntitySequenceFv(elementFvId_1, elementSelectId_1, upAcc_1) {
+        return tslib_1.__awaiter(this, arguments, void 0, function* (elementFvId, elementSelectId, upAcc, config = {}, additionalConfig) {
             return new Promise((resolve, reject) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 let externalContext;
                 if (typeof config.beforeChangeCallback === "function")