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

package/lib/commonjs/RcsbRequest/RcsbRequestContextManager.d.ts

@@ -1,15 +1,15 @@
 import { PolymerEntityInstanceTranslate } from "../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { EntryAssemblyTranslate } from "../RcsbUtils/Translators/EntryAssemblyTranslate";
 import { GroupPropertiesProvider } from "../RcsbUtils/Groups/GroupPropertiesProvider";
-import { QueryResult } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
+import { QueryResult } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchResultInterface";
 import { InterfaceInstanceTranslate } from "../RcsbUtils/Translators/InterfaceInstanceTranslate";
 import { PolymerEntityChromosomeTranslate } from "../RcsbUtils/Translators/PolymerEntityChromosomeTranslate";
-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 { EntryPropertyInterface } from "../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
 import { FacetType } from "../RcsbSeacrh/FacetStore/FacetMemberInterface";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { RequestConfig as GraphqlRequestInit } from "graphql-request/src/types";
+import { ReturnType } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
+import { ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchQueryInterface";
+import { RequestConfig } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/GraphQLRequest";
 import { PolymerEntityInterface } from "../RcsbCollectTools/DataCollectors/MultiplePolymerEntityCollector";
 import { InstanceSequenceInterface } from "../RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector";
 import { SearchQueryType } from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryInterfaces";
@@ -46,11 +46,11 @@ declare class RcsbRequestContextManager {
     private getAssemblyInterfaces;
     initializeBorregoClient(config: {
         api?: string;
-        requestConfig?: GraphqlRequestInit;
+        requestConfig?: RequestConfig;
     }): void;
     initializeYosemiteClient(config: {
         api?: string;
-        requestConfig?: GraphqlRequestInit;
+        requestConfig?: RequestConfig;
     }): void;
     initializeArchesClient(config: {
         uri?: string;

package/lib/commonjs/RcsbRequest/RcsbRequestContextManager.js

@@ -20,13 +20,13 @@ const InterfaceInstanceCollector_1 = require("../RcsbCollectTools/DataCollectors
 const AssemblyInterfacesCollector_1 = require("../RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector");
 const RcsbRequestTools_1 = require("./RcsbRequestTools");
 const RcsbRequestClient_1 = require("./RcsbRequestClient");
-const GraphQLRequest_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest");
-const SearchRequest_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/SearchRequest");
+const GraphQLRequest_1 = require("@rcsb/rcsb-api-tools/lib/RcsbGraphQL/GraphQLRequest");
+const SearchRequest_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/SearchRequest");
 const Assertions_1 = require("../RcsbUtils/Helpers/Assertions");
 var assertDefined = Assertions_1.Assertions.assertDefined;
 const MultiplePolymerEntityCollector_1 = require("../RcsbCollectTools/DataCollectors/MultiplePolymerEntityCollector");
 const MultipleInstanceSequencesCollector_1 = require("../RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector");
-const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
+const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/lib/RcsbUtils/TagDelimiter");
 class RcsbRequestContextManager {
     constructor() {
         this.polymerEntityToInstanceMap = new Map();

package/lib/commonjs/RcsbRequest/RcsbRequestTools.js

@@ -20,18 +20,20 @@ var RcsbRequestTools;
             if (!Array.isArray(ids))
                 ids = [ids];
             const missing = ids.filter(id => !map.has(id));
-            const collectorPromise = collector.collect({ [collectorKey]: missing });
-            missing.forEach(id => {
-                map.set(id, new Promise((resolve, reject) => {
-                    collectorPromise.then(t => {
-                        const d = t.find(t => propertyKey(t) == id);
-                        if (d)
-                            resolve(d);
-                        else
-                            reject(`${id} not available`);
-                    });
-                }));
-            });
+            if (missing.length > 0) {
+                const collectorPromise = collector.collect({ [collectorKey]: missing });
+                missing.forEach(id => {
+                    map.set(id, new Promise((resolve, reject) => {
+                        collectorPromise.then(t => {
+                            const d = t.find(t => propertyKey(t) == id);
+                            if (d)
+                                resolve(d);
+                            else
+                                reject(`${id} not available`);
+                        });
+                    }));
+                });
+            }
             return Promise.all(ids.map(i => map.get(i)).filter((x) => typeof x !== undefined));
         });
     }

package/lib/commonjs/RcsbSeacrh/FacetStore/DepositionGroupFacetStore.d.ts

@@ -1,4 +1,4 @@
-import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
 import { FacetMemberInterface } from "./FacetMemberInterface";
 import { FacetStoreInterface } from "./FacetStoreInterface";
 declare class DepositionGroupFacetStore implements FacetStoreInterface {

package/lib/commonjs/RcsbSeacrh/FacetStore/DepositionGroupFacetStore.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.depositionGroupFacetStore = void 0;
-const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
-const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata");
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums");
+const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata");
 const SingleFacets_1 = require("./SingleFacets");
 const lodash_1 = require("lodash");
 class DepositionGroupFacetStore {

package/lib/commonjs/RcsbSeacrh/FacetStore/EntityGranularitySearchFacetStore.d.ts

@@ -1,4 +1,4 @@
-import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
 import { FacetMemberInterface } from "./FacetMemberInterface";
 import { FacetStoreInterface } from "./FacetStoreInterface";
 declare class EntityGranularitySearchFacetStore implements FacetStoreInterface {

package/lib/commonjs/RcsbSeacrh/FacetStore/EntityGranularitySearchFacetStore.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.entityGranularityGroupFacetStore = void 0;
-const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
-const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata");
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums");
+const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata");
 const SingleFacets_1 = require("./SingleFacets");
 const lodash_1 = require("lodash");
 class EntityGranularitySearchFacetStore {

package/lib/commonjs/RcsbSeacrh/FacetStore/FacetMemberInterface.d.ts

@@ -1,6 +1,6 @@
 import { ChartConfigInterface, ChartType } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
 import { AttributeFacetType, BucketDataType, FilterFacetType } from "@rcsb/rcsb-search-tools/lib/SearchParseTools/SearchFacetInterface";
-import { RcsbSearchAttributeType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
+import { RcsbSearchAttributeType } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata";
 import { SearchQueryType } from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryInterfaces";
 import { ChartDataColumnInterface, ChartDataValueInterface } from "@rcsb/rcsb-charts/lib/RcsbChartDataProvider/ChartDataProviderInterface";
 import React from "react";

package/lib/commonjs/RcsbSeacrh/FacetStore/FacetStoreInterface.d.ts

@@ -1,5 +1,5 @@
 import { FacetMemberInterface } from "./FacetMemberInterface";
-import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
 export interface FacetStoreInterface {
     getServices(): (Service.Text | Service.TextChem)[];
     getFacetService(service: Service | "all"): FacetMemberInterface[];

package/lib/commonjs/RcsbSeacrh/FacetStore/SequenceGroupFacetStore.d.ts

@@ -1,4 +1,4 @@
-import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
 import { FacetMemberInterface } from "./FacetMemberInterface";
 import { FacetStoreInterface } from "./FacetStoreInterface";
 declare class SequenceGroupFacetStore implements FacetStoreInterface {

package/lib/commonjs/RcsbSeacrh/FacetStore/SequenceGroupFacetStore.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.sequenceGroupFacetStore = void 0;
-const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
-const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata");
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums");
+const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata");
 const SingleFacets_1 = require("./SingleFacets");
 const lodash_1 = require("lodash");
 class SequenceGroupFacetStore {

package/lib/commonjs/RcsbSeacrh/FacetStore/SingleFacets.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SearchFacets = exports.PHENOTYPE_FACET = exports.INTERPRO_FACET = exports.DISEASE_FACET = exports.GO_COMPONENT_FACET = exports.GO_PROCESS_FACET = exports.GO_FUNCTION_FACET = exports.ENZYME_CLASS_FACET = exports.CHEM_COMP_FACET = exports.ENTITY_NAME_FACET = exports.PFAM_FACET = exports.TAXONOMY_FACET = exports.ORGANISM_FACET = exports.LIGAND_OF_INTEREST_FACET = exports.LIGAND_FACET = exports.ECOD_FACET = exports.CATH_FACET = exports.SCOP_FACET = exports.RELEASE_DATE_FACET = exports.CHIMERIC_FACET = exports.TAXONOMY_COUNT_FACET = exports.METHODOLOGY_FACET = exports.RESOLUTION_FACET = exports.EXPERIMENTAL_METHOD_FACET = void 0;
-const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata");
-const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
+const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata");
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums");
 const ChartConfigInterface_1 = require("@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface");
 const SearchQueryTools_1 = require("@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryTools");
 exports.EXPERIMENTAL_METHOD_FACET = {

package/lib/commonjs/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.d.ts

@@ -1,4 +1,4 @@
-import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
 import { FacetMemberInterface } from "./FacetMemberInterface";
 import { FacetStoreInterface } from "./FacetStoreInterface";
 declare class UniprotGroupFacetStore implements FacetStoreInterface {

package/lib/commonjs/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.uniprotGroupFacetStore = void 0;
-const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
-const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata");
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums");
+const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata");
 const SingleFacets_1 = require("./SingleFacets");
 const lodash_1 = require("lodash");
 class UniprotGroupFacetStore {

package/lib/commonjs/RcsbSeacrh/FacetTools.d.ts

@@ -1,9 +1,9 @@
-import { BucketFacet } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
+import { BucketFacet } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchResultInterface";
 import { FacetMemberInterface } from "./FacetStore/FacetMemberInterface";
-import { AttributeTextQueryParameters } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { AttributeTextQueryParameters } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchQueryInterface";
+import { Service } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
 import { ChartDisplayConfigInterface, ChartObjectInterface } from "@rcsb/rcsb-charts/lib/RcsbChartComponent/ChartConfigInterface";
-import { RcsbSearchAttributeType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
+import { RcsbSearchAttributeType } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata";
 export type SearchFilter = {
     attribute: RcsbSearchAttributeType;
     value: AttributeTextQueryParameters['value'];

package/lib/commonjs/RcsbSeacrh/SearchQueryTools.d.ts

@@ -1,8 +1,8 @@
-import { LogicalOperator, ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { RcsbSearchAttributeType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata";
-import { AttributeTextQueryParameters, ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+import { LogicalOperator, ReturnType, Service } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
+import { RcsbSearchAttributeType } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata";
+import { AttributeTextQueryParameters, ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchQueryInterface";
 import { FacetStoreInterface } from "./FacetStore/FacetStoreInterface";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/lib/RcsbDw/Types/DwEnums";
 import { SearchQueryType } from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryInterfaces";
 export declare namespace SearchQueryTools {
     function searchGroupQuery(groupProvenance: GroupProvenanceId, groupId: string, service?: Service.Text | Service.TextChem): SearchQueryType;
@@ -12,6 +12,6 @@ export declare namespace SearchQueryTools {
     function addNewNodeToAttributeSearchQuery(attribute: RcsbSearchAttributeType, value: AttributeTextQueryParameters['value'], operator: AttributeTextQueryParameters["operator"], searchQuery: SearchQueryType, service: Service.Text | Service.TextChem, negation?: boolean): SearchQueryType;
     function searchAttributeQuery(attribute: RcsbSearchAttributeType, value: AttributeTextQueryParameters['value'], operator: AttributeTextQueryParameters["operator"], service: Service.Text | Service.TextChem, negation?: boolean): SearchQueryType;
     function addNodeToSearchQuery(node: SearchQueryType, searchQuery: SearchQueryType, logicalOperator?: LogicalOperator): SearchQueryType;
-    function getFacetStoreFromGroupProvenance(groupProvenanceId: GroupProvenanceId): FacetStoreInterface;
+    function getFacetStoreFromGroupProvenance(groupProvenanceId: GroupProvenanceId): FacetStoreInterface | undefined;
     function searchContentType(searchQuery?: SearchQuery): ResultsContentType;
 }

package/lib/commonjs/RcsbSeacrh/SearchQueryTools.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SearchQueryTools = void 0;
-const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
-const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchMetadata");
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums");
+const SearchMetadata_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata");
 const lodash_1 = require("lodash");
-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 SearchQueryTools_1 = require("@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryTools");
 const DepositionGroupFacetStore_1 = require("./FacetStore/DepositionGroupFacetStore");
 const SequenceGroupFacetStore_1 = require("./FacetStore/SequenceGroupFacetStore");

package/lib/commonjs/RcsbSeacrh/SearchRequestProperty.d.ts

@@ -1,7 +1,7 @@
-import { SearchRequest } from "@rcsb/rcsb-api-tools/build/RcsbSearch/SearchRequest";
-import { QueryResult } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+import { SearchRequest } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/SearchRequest";
+import { QueryResult } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchResultInterface";
+import { ReturnType } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
+import { ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchQueryInterface";
 import { FacetType } from "./FacetStore/FacetMemberInterface";
 import { SearchQueryType } from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryInterfaces";
 declare class SearchRequestProperty {

package/lib/commonjs/RcsbServerConfig/codegen.borrego.json

@@ -1,4 +1,4 @@
 {
-    "schema": "https://1d-coordinates.rcsb.org/graphql",
+    "schema": "https://sequence-coordinates.rcsb.org/graphql",
     "documents": "src/RcsbQueries/Borrego/Query*.graphql"
 }

package/lib/commonjs/RcsbUtils/Groups/GroupGapLessTransformer.d.ts

@@ -1,8 +1,8 @@
-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";
 export declare class GroupGapLessTransformer {
     private readonly gapLessReference;
     private refLength;
     private processAlignments;
-    gapLessAlignments(alignments: AlignmentResponse): void;
-    gapLessFeatures(annotations: Array<AnnotationFeatures>): void;
+    gapLessAlignments(alignments: SequenceAlignments): void;
+    gapLessFeatures(annotations: Array<SequenceAnnotations>): void;
 }

package/lib/commonjs/RcsbUtils/Groups/GroupGapLessTransformer.js

@@ -32,31 +32,20 @@ class GroupGapLessTransformer {
         this.refLength = newIndex - 1;
     }
     gapLessAlignments(alignments) {
-        var _a, _b, _c, _d;
+        var _a, _b;
         this.processAlignments(alignments);
         if (this.gapLessReference.length == 0)
             return;
-        if (alignments.target_alignment)
-            (_a = alignments.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
-                var _a;
-                (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.forEach(region => {
-                    if (region === null || region === void 0 ? void 0 : region.query_begin)
-                        region.query_begin = this.gapLessReference[region.query_begin];
-                    if (region === null || region === void 0 ? void 0 : region.query_end)
-                        region.query_end = this.gapLessReference[region.query_end];
-                });
-            });
-        else
-            (_c = (_b = alignments.target_alignment_subset) === null || _b === void 0 ? void 0 : _b.edges) === null || _c === void 0 ? void 0 : _c.forEach(edge => {
-                var _a, _b;
-                (_b = (_a = edge === null || edge === void 0 ? void 0 : edge.node) === null || _a === void 0 ? void 0 : _a.aligned_regions) === null || _b === void 0 ? void 0 : _b.forEach(region => {
-                    if (region === null || region === void 0 ? void 0 : region.query_begin)
-                        region.query_begin = this.gapLessReference[region.query_begin];
-                    if (region === null || region === void 0 ? void 0 : region.query_end)
-                        region.query_end = this.gapLessReference[region.query_end];
-                });
+        (_a = alignments.target_alignments) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
+            var _a;
+            (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.forEach(region => {
+                if (region === null || region === void 0 ? void 0 : region.query_begin)
+                    region.query_begin = this.gapLessReference[region.query_begin];
+                if (region === null || region === void 0 ? void 0 : region.query_end)
+                    region.query_end = this.gapLessReference[region.query_end];
             });
-        alignments.alignment_logo = (_d = alignments.alignment_logo) === null || _d === void 0 ? void 0 : _d.filter((al, n) => this.gapLessReference[n + 1] != -1);
+        });
+        alignments.alignment_logo = (_b = alignments.alignment_logo) === null || _b === void 0 ? void 0 : _b.filter((al, n) => this.gapLessReference[n + 1] != -1);
         if (alignments.alignment_length)
             alignments.alignment_length = this.refLength;
     }

package/lib/commonjs/RcsbUtils/Groups/GroupProvenanceToAggregationType.d.ts

@@ -1,5 +1,5 @@
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/lib/RcsbDw/Types/DwEnums";
+import { ReturnType } from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
 interface GroupProvenanceToReturnType extends Record<GroupProvenanceId, ReturnType> {
 }
 export declare const groupProvenanceToReturnType: GroupProvenanceToReturnType;

package/lib/commonjs/RcsbUtils/Groups/GroupProvenanceToAggregationType.js

@@ -1,10 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.groupProvenanceToReturnType = void 0;
-const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
-const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
+const DwEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbDw/Types/DwEnums");
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums");
 exports.groupProvenanceToReturnType = {
     [DwEnums_1.GroupProvenanceId.ProvenanceMatchingDepositGroupId]: SearchEnums_1.ReturnType.Entry,
     [DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession]: SearchEnums_1.ReturnType.PolymerEntity,
     [DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity]: SearchEnums_1.ReturnType.PolymerEntity,
+    [DwEnums_1.GroupProvenanceId.ProvenanceMatchingChemicalComponentId]: SearchEnums_1.ReturnType.NonPolymerEntity
 };

package/lib/commonjs/RcsbUtils/PairwiseAlignmentTools/AlignmentReference.d.ts

@@ -1,4 +1,4 @@
-import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
 type AlignmentRefType = (number | undefined)[];
 export declare class AlignmentReference {
     private readonly alignmentRefMap;
@@ -7,7 +7,7 @@ export declare class AlignmentReference {
     private readonly memberRefList;
     constructor(refId: string, targetId: string, alignment: AlignmentRefType, target: AlignmentRefType);
     addAlignment(id: string, alignment: AlignmentRefType, target: AlignmentRefType): void;
-    buildAlignments(): AlignmentResponse;
+    buildAlignments(): SequenceAlignments;
     private addRef;
     private addEnd;
     private addBeg;

package/lib/commonjs/RcsbUtils/PairwiseAlignmentTools/AlignmentReference.js

@@ -96,14 +96,14 @@ class AlignmentReference {
 exports.AlignmentReference = AlignmentReference;
 function buildAlignments(refId, alignmentRefMap, alignmentMembers) {
     const out = {};
-    out.target_alignment = [];
-    out.target_alignment.push({
+    out.target_alignments = [];
+    out.target_alignments.push({
         aligned_regions: buildRegions(alignmentRefMap),
         target_id: refId
     });
     alignmentMembers.forEach(am => {
         var _a;
-        (_a = out.target_alignment) === null || _a === void 0 ? void 0 : _a.push({
+        (_a = out.target_alignments) === null || _a === void 0 ? void 0 : _a.push({
             target_id: am.id,
             aligned_regions: buildRegions(am.map.map((v, n) => typeof v === "number" ? am.target[v] : undefined))
         });

package/lib/commonjs/RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PairwiseAlignmentBuilder = void 0;
 const RcsbAnnotationConstants_1 = require("../../RcsbAnnotationConfig/RcsbAnnotationConstants");
-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 FeatureTools_1 = require("../../RcsbCollectTools/FeatureTools/FeatureTools");
 const TrackUtils_1 = require("../../RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils");
 const gradient = (color1, color2, weight) => {

package/lib/commonjs/RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite.js

@@ -66,35 +66,33 @@ function alignmentGlobalLigandBindingSite() {
                 var _a;
                 if (d)
                     (_a = d.feature_positions) === null || _a === void 0 ? void 0 : _a.forEach(p => {
-                        var _a;
-                        if (p === null || p === void 0 ? void 0 : p.beg_seq_id)
-                            (_a = p.values) === null || _a === void 0 ? void 0 : _a.forEach((v, n) => {
-                                var _a, _b;
-                                const key = (p.beg_seq_id + n).toString();
-                                if (!ligandMap.has(key))
-                                    ligandMap.set(key, new Set());
-                                else if (d.name && !((_a = ligandMap.get(key)) === null || _a === void 0 ? void 0 : _a.has(d.name)))
-                                    (_b = ligandMap.get(key)) === null || _b === void 0 ? void 0 : _b.add(d.name);
-                                else
-                                    return;
-                                const bs = bindingSiteMap.get(key);
-                                if (!bs) {
-                                    bindingSiteMap.set(key, {
-                                        begin: p.beg_seq_id + n,
-                                        type: trackName,
-                                        value: 1
-                                    });
-                                    if (max == 0)
-                                        max = 1;
+                        var _a, _b;
+                        if (p === null || p === void 0 ? void 0 : p.beg_seq_id) {
+                            const key = (p.beg_seq_id).toString();
+                            if (!ligandMap.has(key))
+                                ligandMap.set(key, new Set());
+                            else if (d.name && !((_a = ligandMap.get(key)) === null || _a === void 0 ? void 0 : _a.has(d.name)))
+                                (_b = ligandMap.get(key)) === null || _b === void 0 ? void 0 : _b.add(d.name);
+                            else
+                                return;
+                            const bs = bindingSiteMap.get(key);
+                            if (!bs) {
+                                bindingSiteMap.set(key, {
+                                    begin: p.beg_seq_id,
+                                    type: trackName,
+                                    value: 1
+                                });
+                                if (max == 0)
+                                    max = 1;
+                            }
+                            else {
+                                if (bs) {
+                                    bs.value += 1;
+                                    if (bs.value > max)
+                                        max = bs.value;
                                 }
-                                else {
-                                    if (bs) {
-                                        bs.value += 1;
-                                        if (bs.value > max)
-                                            max = bs.value;
-                                    }
-                                }
-                            });
+                            }
+                        }
                     });
             });
         });

package/lib/commonjs/RcsbUtils/TrackGenerators/BurialFraction.d.ts

@@ -1,3 +1,3 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare function burialFraction(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
-export declare function burialFractionFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare function burialFraction(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
+export declare function burialFractionFilter(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;

package/lib/commonjs/RcsbUtils/TrackGenerators/BurialFraction.js

@@ -2,19 +2,19 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.burialFraction = burialFraction;
 exports.burialFractionFilter = burialFractionFilter;
-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 lodash_1 = require("lodash");
 const FeatureType_1 = require("../../RcsbExport/FeatureType");
 function burialFraction(annotations) {
     const burialFractionOut = new Array();
     const asaUnboundAnn = (0, lodash_1.cloneDeep)(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === GqlTypes_1.Type.AsaUnbound));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.AsaUnbound));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
     const asaBoundAnn = (0, lodash_1.cloneDeep)(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === GqlTypes_1.Type.AsaBound));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.AsaBound));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
     asaUnboundAnn.forEach((asaUnbound) => {
@@ -60,7 +60,7 @@ function burialFraction(annotations) {
 function burialFractionFilter(annotations) {
     return (0, lodash_1.cloneDeep)(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== GqlTypes_1.Source.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.BurialFraction));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== GqlTypes_1.AnnotationReference.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.BurialFraction));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
 }

package/lib/commonjs/RcsbUtils/TrackGenerators/BuriedResidues.d.ts

@@ -1,3 +1,3 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare function buriedResidues(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
-export declare function buriedResiduesFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare function buriedResidues(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
+export declare function buriedResiduesFilter(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;

package/lib/commonjs/RcsbUtils/TrackGenerators/BuriedResidues.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.buriedResidues = buriedResidues;
 exports.buriedResiduesFilter = buriedResiduesFilter;
-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 lodash_1 = require("lodash");
 const FeatureType_1 = require("../../RcsbExport/FeatureType");
 function buriedResidues(annotations) {
@@ -11,11 +11,11 @@ function buriedResidues(annotations) {
     let buriedResidues = {};
     let nBuried = 0;
     mainloop: for (const ann of annotations) {
-        if (ann.source === GqlTypes_1.Source.PdbInstance) {
+        if (ann.source === GqlTypes_1.AnnotationReference.PdbInstance) {
             for (const f of (_a = ann.features) !== null && _a !== void 0 ? _a : []) {
-                if ((f === null || f === void 0 ? void 0 : f.type) === GqlTypes_1.Type.Asa) {
+                if ((f === null || f === void 0 ? void 0 : f.type) === FeatureType_1.FeatureType.Asa) {
                     buriedResidues = (0, lodash_1.cloneDeep)(ann);
-                    buriedResidues.source = GqlTypes_1.Source.PdbInstance;
+                    buriedResidues.source = GqlTypes_1.AnnotationReference.PdbInstance;
                     const feature = (0, lodash_1.cloneDeep)(f);
                     feature.type = FeatureType_1.FeatureType.BuriedResidues;
                     feature.name = "Unbound chain core residues";
@@ -45,7 +45,7 @@ function buriedResidues(annotations) {
 function buriedResiduesFilter(annotations) {
     return (0, lodash_1.cloneDeep)(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== GqlTypes_1.Type.Asa));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== FeatureType_1.FeatureType.Asa));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
 }

package/lib/commonjs/RcsbUtils/TrackGenerators/Logo.d.ts

@@ -1,4 +1,4 @@
-import { AlignmentLogo } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentLogo } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare class Logo<T extends string> {
     private readonly symbols;
     private n;

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

@@ -1,4 +1,4 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 import { RcsbFvTooltipInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvTooltip/RcsbFvTooltipInterface";
 import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
@@ -6,9 +6,9 @@ export declare function addUnmodeledTrackBuilder(unmodeledTrackBuilder: Unmodele
 export declare class UnmodeledTrackBuilder {
     private readonly unmodeledDescription;
     filterFeatures(data: {
-        annotations: Array<AnnotationFeatures>;
+        annotations: Array<SequenceAnnotations>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<Array<AnnotationFeatures>>;
+    }): Promise<Array<SequenceAnnotations>>;
     getTooltip(): RcsbFvTooltipInterface;
     private buildUnobserved;
 }