@rcsb/rcsb-saguaro-app 4.0.7 → 4.1.2

package/build/dist/RcsbSeacrh/FacetStore/EntityGranularitySearchFacetStore.d.ts

@@ -0,0 +1,15 @@
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { FacetMemberInterface } from "./FacetMemberInterface";
+import { FacetStoreInterface } from "./FacetStoreInterface";
+declare class EntityGranularitySearchFacetStore implements FacetStoreInterface {
+    private readonly entryFacet;
+    private readonly instanceFacet;
+    private readonly entityFacet;
+    private readonly nonPolymerFacet;
+    getServices(): Service[];
+    getFacetService(service: Service | "all"): FacetMemberInterface[];
+    readonly facetLayoutGrid: string[];
+    readonly returnType: ReturnType;
+}
+export declare const entityGranularityGroupFacetStore: EntityGranularitySearchFacetStore;
+export {};

package/build/dist/RcsbSeacrh/FacetStore/FacetMemberInterface.d.ts

@@ -0,0 +1,15 @@
+import { CardinalityFacet, DateHistogramFacet, DateRangeFacet, FilterFacet, HistogramFacet, RangeFacet, TermsFacet } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+import { ChartConfigInterface, ChartType } from "../../RcsbChartWeb/RcsbChartComponent/ChartConfigInterface";
+import { BucketFacet } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
+export declare type FacetType = TermsFacet | HistogramFacet | DateHistogramFacet | RangeFacet | DateRangeFacet | CardinalityFacet | FilterFacet;
+export interface FacetMemberInterface {
+    id: string;
+    title: string;
+    attributeName: string;
+    attribute: string;
+    chartType: ChartType;
+    chartConfig?: ChartConfigInterface;
+    facet: FacetType;
+    contentType: "date" | "number" | "string";
+    transformSearchResultFacets?(facets: BucketFacet): BucketFacet;
+}

package/build/dist/RcsbSeacrh/FacetStore/FacetStoreInterface.d.ts

@@ -0,0 +1,8 @@
+import { FacetMemberInterface } from "./FacetMemberInterface";
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+export interface FacetStoreInterface {
+    getServices(): Service[];
+    getFacetService(service: Service | "all"): FacetMemberInterface[];
+    readonly facetLayoutGrid: string[];
+    readonly returnType: ReturnType;
+}

package/build/dist/RcsbSeacrh/FacetStore/SequenceGroupFacetStore.d.ts

@@ -0,0 +1,15 @@
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { FacetMemberInterface } from "./FacetMemberInterface";
+import { FacetStoreInterface } from "./FacetStoreInterface";
+declare class SequenceGroupFacetStore implements FacetStoreInterface {
+    private readonly entryFacet;
+    private readonly instanceFacet;
+    private readonly entityFacet;
+    private readonly nonPolymerFacet;
+    getServices(): Service[];
+    getFacetService(service: Service | "all"): FacetMemberInterface[];
+    readonly facetLayoutGrid: string[];
+    readonly returnType: ReturnType;
+}
+export declare const sequenceGroupFacetStore: SequenceGroupFacetStore;
+export {};

package/build/dist/RcsbSeacrh/FacetStore/SingleFacets.d.ts

@@ -0,0 +1,37 @@
+import { FacetMemberInterface } from "./FacetMemberInterface";
+export declare const EXPERIMENTAL_METHOD_FACET: FacetMemberInterface;
+export declare const RESOLUTION_FACET: FacetMemberInterface;
+export declare const RELEASE_DATE_FACET: FacetMemberInterface;
+export declare const SCOP_FACET: FacetMemberInterface;
+export declare const CATH_FACET: FacetMemberInterface;
+export declare const ECOD_FACET: FacetMemberInterface;
+export declare const LIGAND_FACET: FacetMemberInterface;
+export declare const LIGAND_OF_INTEREST_FACET: FacetMemberInterface;
+export declare const ORGANISM_FACET: FacetMemberInterface;
+export declare const TAXONOMY_FACET: FacetMemberInterface;
+export declare const PFAM_FACET: FacetMemberInterface;
+export declare const ENTITY_NAME_FACET: FacetMemberInterface;
+export declare const CHEM_COMP_FACET: FacetMemberInterface;
+export declare const ENZYME_CLASS_FACET: FacetMemberInterface;
+export declare const GO_FUNCTION_FACET: FacetMemberInterface;
+export declare const GO_PROCESS_FACET: FacetMemberInterface;
+export declare const GO_COMPONENT_FACET: FacetMemberInterface;
+export declare const SearchFacets: {
+    EXPERIMENTAL_METHOD_FACET: FacetMemberInterface;
+    RESOLUTION_FACET: FacetMemberInterface;
+    RELEASE_DATE_FACET: FacetMemberInterface;
+    SCOP_FACET: FacetMemberInterface;
+    LIGAND_FACET: FacetMemberInterface;
+    ORGANISM_FACET: FacetMemberInterface;
+    TAXONOMY_FACET: FacetMemberInterface;
+    PFAM_FACET: FacetMemberInterface;
+    ENTITY_NAME_FACET: FacetMemberInterface;
+    CHEM_COMP_FACET: FacetMemberInterface;
+    ECOD_FACET: FacetMemberInterface;
+    CATH_FACET: FacetMemberInterface;
+    ENZYME_CLASS_FACET: FacetMemberInterface;
+    GO_FUNCTION_FACET: FacetMemberInterface;
+    GO_PROCESS_FACET: FacetMemberInterface;
+    GO_COMPONENT_FACET: FacetMemberInterface;
+    LIGAND_OF_INTEREST_FACET: FacetMemberInterface;
+};

package/build/dist/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.d.ts

@@ -0,0 +1,15 @@
+import { ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { FacetMemberInterface } from "./FacetMemberInterface";
+import { FacetStoreInterface } from "./FacetStoreInterface";
+declare class UniprotGroupFacetStore implements FacetStoreInterface {
+    private readonly entryFacet;
+    private readonly instanceFacet;
+    private readonly entityFacet;
+    private readonly nonPolymerFacet;
+    getServices(): Service[];
+    getFacetService(service: Service | "all"): FacetMemberInterface[];
+    readonly facetLayoutGrid: string[];
+    readonly returnType: ReturnType;
+}
+export declare const uniprotGroupFacetStore: UniprotGroupFacetStore;
+export {};

package/build/dist/RcsbSeacrh/FacetTools.d.ts

@@ -0,0 +1,34 @@
+import { BucketFacet } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
+import { ChartConfigInterface, ChartType } from "../RcsbChartWeb/RcsbChartComponent/ChartConfigInterface";
+import { FacetMemberInterface } from "./FacetStore/FacetMemberInterface";
+import { AttributeTextQueryParameters } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+import { Operator, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+export interface RcsbChartDataInterface {
+    label: string | number;
+    population: number;
+}
+export declare type SearchFilter = {
+    attribute: string;
+    value: AttributeTextQueryParameters['value'];
+    operator: Operator;
+    service: Service.Text | Service.TextChem;
+};
+export interface RcsbChartInterface {
+    chartType: ChartType;
+    labelList?: string[];
+    attribute: string;
+    attributeName: string;
+    chartConfig?: ChartConfigInterface;
+    title: string;
+    data: RcsbChartDataInterface[];
+    filters?: SearchFilter[];
+    contentType: FacetMemberInterface['contentType'];
+}
+export declare class FacetTools {
+    static getResultDrilldowns(facetMembers: FacetMemberInterface[], searchResultFacets: Array<BucketFacet>, labelList?: string[], recursiveOut?: Array<RcsbChartInterface>): Array<RcsbChartInterface>;
+    static subtractDrilldowns(partial: Array<RcsbChartInterface>, full: Array<RcsbChartInterface>): Array<RcsbChartInterface>;
+    static getFacetFromName(facetMembers: FacetMemberInterface[], name: string): FacetMemberInterface;
+    private static includeMissingFacets;
+    private static getFacetChartTypeFromAttribute;
+    private static getFacetFiltersFromName;
+}

package/build/dist/RcsbSeacrh/SearchQueryTools.d.ts

@@ -0,0 +1,16 @@
+import { SearchQueryType } from "./SearchRequestProperty";
+import { LogicalOperator, Operator, ReturnType, Service } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { SearchQuery, AttributeTextQueryParameters } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+import { FacetStoreInterface } from "./FacetStore/FacetStoreInterface";
+import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+export declare namespace SearchQueryTools {
+    function searchGroupQuery(groupProvenance: GroupProvenanceId, groupId: string, service?: Service): SearchQueryType;
+    function addGroupNodeToSearchQuery(groupProvenanceId: GroupProvenanceId, groupId: string, searchQuery: SearchQueryType, service?: Service): SearchQueryType;
+    function buildAttributeSearchQuery(attribute: string, value: AttributeTextQueryParameters['value'], operator: Operator, searchQuery: SearchQueryType, returnType: ReturnType, service: Service.Text | Service.TextChem, negation?: boolean): SearchQuery;
+    function buildNodeSearchQuery(node: SearchQueryType, searchQuery: SearchQueryType, returnType: ReturnType, logicalOperator?: LogicalOperator): SearchQuery;
+    function buildSearchQuery(searchQuery: SearchQueryType, returnType: ReturnType, logicalOperator?: LogicalOperator): SearchQuery;
+    function addNewNodeToAttributeSearchQuery(attribute: string, value: AttributeTextQueryParameters['value'], operator: Operator, searchQuery: SearchQueryType, service: Service.Text | Service.TextChem, negation?: boolean): SearchQueryType;
+    function searchAttributeQuery(attribute: string, value: AttributeTextQueryParameters['value'], operator: Operator, service: Service.Text | Service.TextChem, negation?: boolean): SearchQueryType;
+    function addNodeToSearchQuery(node: SearchQueryType, searchQuery: SearchQueryType, logicalOperator?: LogicalOperator): SearchQueryType;
+    function getFacetStoreFromGroupProvenance(groupProvenanceId: GroupProvenanceId): FacetStoreInterface;
+}

package/build/dist/RcsbSeacrh/SearchRequestProperty.d.ts

@@ -0,0 +1,13 @@
+import { QueryResult } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchResultInterface";
+import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { GroupNode, SearchQuery, TerminalNode } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+import { FacetType } from "./FacetStore/FacetMemberInterface";
+export declare type SearchQueryType = GroupNode | TerminalNode;
+export declare class SearchRequestProperty {
+    private searchRequest;
+    private _requestFacets;
+    requestFacets(query: SearchQueryType, facets: FacetType[], returnType: ReturnType): Promise<QueryResult | null>;
+    requestMembers(query: SearchQuery): Promise<Array<string>>;
+    requestCount(query: SearchQuery): Promise<number>;
+    request(query: SearchQuery): Promise<QueryResult | null>;
+}

package/build/dist/RcsbUtils/AnnotationGenerators/AlignmentGlobalBindingSite.d.ts

@@ -0,0 +1,2 @@
+import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
+export declare function alignmentGlobalLigandBindingSite(): ExternalTrackBuilderInterface;

package/build/dist/RcsbUtils/AnnotationGenerators/AlignmentVariation.d.ts

@@ -0,0 +1,2 @@
+import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
+export declare function alignmentVariation(): ExternalTrackBuilderInterface;

package/build/dist/RcsbUtils/AnnotationGenerators/Logo.d.ts

@@ -0,0 +1,15 @@
+import { AlignmentLogo } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare class Logo<T extends string> {
+    private readonly symbols;
+    private n;
+    constructor(logo: AlignmentLogo[]);
+    private aaTypes;
+    get(aa: T): number;
+    forEach(callback: (aa: T, n: number) => void): void;
+    mode(): T;
+    frequency(): {
+        symbol: T;
+        value: number;
+    }[];
+    entropy(): number;
+}

package/build/dist/RcsbUtils/{GroupPropertiesProvider.d.ts → Groups/GroupPropertiesProvider.d.ts}

@@ -1,4 +1,4 @@
-import { EntryPropertyIntreface } from "../RcsbCollectTools/PropertyCollector/MultipleEntryPropertyCollector";
+import { EntryPropertyIntreface } from "../../RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector";
 export interface GroupPropertiesProviderInterface {
     entryProperties: Array<EntryPropertyIntreface>;
 }

package/build/dist/RcsbUtils/Groups/GroupProvenanceToAggregationType.d.ts

@@ -0,0 +1,6 @@
+import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+interface GroupProvenanceToReturnType extends Record<GroupProvenanceId, ReturnType> {
+}
+export declare const groupProvenanceToReturnType: GroupProvenanceToReturnType;
+export {};

package/build/dist/RcsbUtils/Helpers/UrlTools.d.ts

@@ -0,0 +1,11 @@
+export declare namespace UrlTools {
+    function encodeUrlParameterList(paramList: {
+        key: string;
+        value: any;
+    }[]): void;
+    function encodeUrlParameter(key: string, value: any): void;
+    function decodeUrlParameters(): {
+        key: string;
+        value: any;
+    }[] | undefined;
+}

package/build/dist/RcsbUtils/Translators/AssemblyInterfacesTranslate.d.ts

@@ -1,4 +1,4 @@
-import { AssemblyInterfacesInterface } from "../../RcsbCollectTools/Translators/AssemblyInterfacesCollector";
+import { AssemblyInterfacesInterface } from "../../RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector";
 export declare class AssemblyInterfacesTranslate {
     private readonly rawData;
     private interfaceMap;

package/build/dist/RcsbUtils/Translators/EntryAssemblyTranslate.d.ts

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
+import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 export declare class EntryAssemblyTranslate {
     private readonly rawData;
     constructor(data: Map<string, Array<PolymerEntityInstanceInterface>>);

package/build/dist/RcsbUtils/Translators/InterfaceInstanceTranslate.d.ts

@@ -1,4 +1,4 @@
-import { InterfaceInstanceInterface } from "../../RcsbCollectTools/Translators/InterfaceInstanceCollector";
+import { InterfaceInstanceInterface } from "../../RcsbCollectTools/DataCollectors/InterfaceInstanceCollector";
 export declare class InterfaceInstanceTranslate {
     private readonly rawData;
     private readonly instances;

package/build/dist/RcsbUtils/Translators/MultipleEntityInstanceTranslate.d.ts

@@ -1,5 +1,5 @@
 import { PolymerEntityInstanceTranslate } from "./PolymerEntityInstanceTranslate";
-import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
+import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 export declare class MultipleEntityInstanceTranslate {
     private readonly entityInstanceTranslateMap;
     add(data: Array<PolymerEntityInstanceInterface>): void;

package/build/dist/RcsbUtils/Translators/PolymerEntityInstanceTranslate.d.ts

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
+import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 import { RcsbFvTrackDataElementInterface } from '@rcsb/rcsb-saguaro';
 import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export interface TranslateContextInterface {

package/build/dist/app.d.ts

@@ -1,4 +1,5 @@
-export { buildEntryChromosome, buildFullChromosome, buildEntityChromosome, buildChromosome, buildEntityFv, buildEntitySummaryFv, buildSingleEntitySummaryFv, buildInstanceFv, buildInstanceSequenceFv, buildMultipleInstanceSequenceFv, buildAssemblySequenceFv, buildPairwiseAlignment, buildPfv, buildMultipleAlignmentSequenceFv, buildUniprotEntityFv, buildUniprotEntityInstanceFv, buildUniprotFv, unmount } from "./RcsbFvWeb/RcsbFvBuilder";
-export { RcsbFvContextManager } from "./RcsbExport/RcsbFvContextManager";
+export { buildEntryChromosome, buildFullChromosome, buildEntityChromosome, buildChromosome, buildEntityFv, buildEntitySummaryFv, buildSingleEntitySummaryFv, buildInstanceFv, buildInstanceSequenceFv, buildMultipleInstanceSequenceFv, buildAssemblySequenceFv, buildPairwiseAlignment, buildPfv, buildMultipleAlignmentSequenceFv, buildUniprotEntityFv, buildUniprotEntityInstanceFv, buildUniprotFv, buildGroupFv, unmount } from "./RcsbFvWeb/RcsbFvBuilder";
+import { rcsbRequestCtxManager } from "./RcsbRequest/RcsbRequestContextManager";
+export { rcsbRequestCtxManager as RcsbRequestContextManager };
 export { RcsbFvUI } from "./RcsbExport/RcsbFvUI";
 export { FeatureType } from "./RcsbExport/FeatureType";