@rcsb/rcsb-saguaro-app 6.3.7-react-downgrade.1 → 6.3.8

package/lib/commonjs/RcsbAnnotationConfig/RcsbAnnotationConfig.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/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvDisplayTypes } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvDefaultConfigValues";
 import { AnnotationConfigInterface, RcsbAnnotationConfigInterface } from "./AnnotationConfigInterface";
 import { AnnotationRequestContext } from "../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
@@ -19,7 +19,7 @@ export declare class RcsbAnnotationConfig {
     uniprotOrder(): Array<string>;
     instanceOrder(): Array<string>;
     entityOrder(): Array<string>;
-    getAnnotationType(requestConfig: AnnotationRequestContext, ann: AnnotationFeatures, feature: Feature): Promise<string>;
+    getAnnotationType(requestConfig: AnnotationRequestContext, ann: SequenceAnnotations, feature: Features): Promise<string>;
     isMergedType(type: string): boolean;
     getMergeConfig(type: string): RcsbMergedTypesInterface | undefined;
     private addNewType;

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

@@ -1,4 +1,5 @@
 import { AbstractChartComponent } from "./AbsractChartComponent";
+import { ReactNode } from "react";
 export declare class HistogramChartComponent extends AbstractChartComponent {
-    render(): JSX.Element;
+    render(): ReactNode;
 }

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

@@ -1,6 +1,6 @@
 import { AlignmentCollectConfig, AlignmentCollectorInterface } from "./AlignmentCollectorInterface";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare class AlignmentCollector implements AlignmentCollectorInterface {
     private requestStatus;
     readonly rcsbFvQuery: RcsbClient;
@@ -8,10 +8,10 @@ export declare class AlignmentCollector implements AlignmentCollectorInterface {
     private alignmentResponse;
     private readonly alignmentResponseSubject;
     private readonly alignmentLengthSubject;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<SequenceAlignments>;
     getTargets(): Promise<Array<string>>;
-    getAlignment(): Promise<AlignmentResponse>;
+    getAlignment(): Promise<SequenceAlignments>;
     getAlignmentLength(): Promise<number>;
-    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<AlignmentResponse>;
+    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<SequenceAlignments>;
     private complete;
 }

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

@@ -17,15 +17,15 @@ class AlignmentCollector {
     }
     collect(requestConfig, filter) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f;
+            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/lib/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/lib/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

@@ -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/lib/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/AssemblyInterfacesCollector.d.ts

@@ -1,4 +1,4 @@
-import { QueryAssembliesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { QueryAssembliesArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
 export interface AssemblyInterfacesInterface {
     rcsbId: string;
     interfaceIds: Array<string>;

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

@@ -1,4 +1,4 @@
-import { QueryEntryArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { QueryEntryArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
 export declare class EntryAssembliesCollector {
     private readonly rcsbFvQuery;

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

@@ -1,4 +1,4 @@
-import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
 export declare class GroupMemberCollector {
     private readonly rcsbFvQuery;

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

@@ -1,4 +1,4 @@
-import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
 export interface GroupPropertyInterface {
     groupName: string;
     groupDescription: string;

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

@@ -1,4 +1,4 @@
-import { QueryInterfacesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { QueryInterfacesArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
 export interface InterfaceInstanceInterface {
     rcsbId: string;
     assemblyId: string;

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

@@ -1,4 +1,4 @@
-import { QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
 import { MultipleDocumentPropertyCollectorInterface } from "./DataCollectorInterface";
 export declare class MultipleEntityInstancesCollector implements MultipleDocumentPropertyCollectorInterface<"entity_ids", PolymerEntityInstanceInterface> {

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

@@ -1,5 +1,5 @@
-import { QueryEntriesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+import { QueryEntriesArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/lib/RcsbDw/Types/DwEnums";
 export interface EntryPropertyInterface {
     rcsbId: string;
     entryId: string;

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

@@ -1,4 +1,4 @@
-import { QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
 export interface PolymerEntityInterface {
     rcsbId: string;

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

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultiplePolymerEntityCollector = void 0;
 const tslib_1 = require("tslib");
 const MultipleEntityInstancesCollector_1 = require("./MultipleEntityInstancesCollector");
-const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
+const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/lib/RcsbUtils/TagDelimiter");
 class MultiplePolymerEntityCollector {
     constructor() {
         this.multipleEntityInstanceCollector = new MultipleEntityInstancesCollector_1.MultipleEntityInstancesCollector();

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

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PolymerEntityChromosomeCollector = void 0;
 const tslib_1 = require("tslib");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
+const GqlTypes_1 = require("@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes");
 const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
 class PolymerEntityChromosomeCollector {
     constructor() {
@@ -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/DataCollectors/PolymerEntityInstancesCollector.d.ts

@@ -1,5 +1,5 @@
-import { CorePolymerEntityInstance, QueryEntryArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+import { CorePolymerEntityInstance, QueryEntryArgs } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/lib/RcsbDw/Types/DwEnums";
 export interface PolymerEntityInstanceInterface {
     rcsbId: string;
     entityId: string;

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/lib/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/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/lib/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

@@ -1,12 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FeatureType = void 0;
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
+const GqlTypes_1 = require("@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes");
 const BURIAL_FRACTION = "BURIAL_FRACTION";
 const BURIED_RESIDUES = "BURIED_RESIDUES";
 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

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
+const GqlTypes_1 = require("@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes");
 const RcsbFvBuilder_1 = require("../RcsbFvWeb/RcsbFvBuilder");
 const RcsbRequestContextManager_1 = require("../RcsbRequest/RcsbRequestContextManager");
 const Assertions_1 = require("../RcsbUtils/Helpers/Assertions");
@@ -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));
             }));
@@ -888,10 +888,10 @@ function alignmentTransform(alignment) {
         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/GroupHistogram.js

@@ -1,11 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const RcsbGroupBuilder_1 = require("../RcsbGroupWeb/RcsbGroupBuilder");
-const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
+const DwEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbDw/Types/DwEnums");
 const SingleFacets_1 = require("../RcsbSeacrh/FacetStore/SingleFacets");
 const groupId = "P01112";
 // buildGroupContent("select", GroupProvenanceId.ProvenanceSequenceIdentity, groupId);
-// buildGroupMembers("carousel", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, 1, 1)
+(0, RcsbGroupBuilder_1.buildGroupMembers)("carousel", DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity, groupId, 1, 1);
 (0, RcsbGroupBuilder_1.buildGroup)("pfv", DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undefined, [
     SingleFacets_1.TAXONOMY_COUNT_FACET.attributeName,
     SingleFacets_1.DISEASE_FACET.attributeName,

package/lib/commonjs/RcsbFvExamples/InstanceSequenceFv.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
+const GqlTypes_1 = require("@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes");
 const RcsbFvBuilder_1 = require("../RcsbFvWeb/RcsbFvBuilder");
 (0, RcsbFvBuilder_1.buildInstanceSequenceFv)("pfv", "select", "8PDU", {
     module: "interface",
@@ -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

@@ -14,7 +14,7 @@ class UiComponent extends react_1.default.Component {
             }, children: this.props.text }));
     }
 }
-(0, RcsbFvBuilder_1.buildSequenceIdentityAlignmentFv)("pfv", "5_30", undefined, {
+(0, RcsbFvBuilder_1.buildSequenceIdentityAlignmentFv)("pfv", "1_30", undefined, {
     boardConfig: {
         selectionChangeCallback: (selection) => {
             console.log(selection);
@@ -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/SequenceIdentityGroupFv.js

@@ -1,7 +1,7 @@
 "use strict";
 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 DwEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbDw/Types/DwEnums");
 // rcsbRequestCtxManager.initializeBorregoClient({api:"https://clustrelax-dev.rcsb.org/graphql"});
 const query = {
     "query": {

package/lib/commonjs/RcsbFvExamples/UniprotGroupFv.js

@@ -1,8 +1,9 @@
 "use strict";
 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 = {
+const DwEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbDw/Types/DwEnums");
+// import {SearchQuery} from "@rcsb/rcsb-api-tools/lib/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/RcsbFvUI/Components/FilterItemComponent.d.ts

@@ -1,4 +1,5 @@
 import { AbstractMenuItemComponent } from "../AbstractMenuItemComponent";
+import { ReactNode } from "react";
 interface FilterItemProps {
     elements: string[];
     stateChange: (state: FilterPartialState, prevState: FilterPartialState) => void;
@@ -11,6 +12,6 @@ interface FilterItemState extends FilterPartialState {
 }
 export declare class FilterItemComponent extends AbstractMenuItemComponent<FilterItemProps, FilterPartialState, FilterItemState> {
     readonly state: FilterItemState;
-    render(): JSX.Element;
+    render(): ReactNode;
 }
 export {};

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

@@ -1,17 +1,18 @@
 import { AbstractMenuItemComponent } from "../AbstractMenuItemComponent";
+import { ReactNode } from "react";
 export interface PaginationItemState {
     after: number;
     first: number;
 }
 export interface PaginationItemProps {
     count: number;
-    after: string;
+    after: number;
     first: number;
     stateChange(state: PaginationItemState, prevState: PaginationItemState): void;
 }
 export declare class PaginationItemComponent extends AbstractMenuItemComponent<PaginationItemProps, PaginationItemState> {
     readonly state: PaginationItemState;
-    render(): JSX.Element;
+    render(): ReactNode;
     componentDidUpdate(prevProps: Readonly<PaginationItemProps & {
         stateChange(newState: PaginationItemState, oldState: PaginationItemState): void;
     }>, prevState: Readonly<PaginationItemState>, snapshot?: any): 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/RcsbFvChromosomeBuilder.js

@@ -5,7 +5,7 @@ const tslib_1 = require("tslib");
 const RcsbFvChromosome_1 = require("../RcsbFvModule/RcsbFvChromosome");
 const RcsbFvCoreBuilder_1 = require("./RcsbFvCoreBuilder");
 const RcsbRequestContextManager_1 = require("../../RcsbRequest/RcsbRequestContextManager");
-const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
+const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/lib/RcsbUtils/TagDelimiter");
 class RcsbFvChromosomeBuilder {
     static buildFullChromosome(elementFvId, chrId) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {