@rcsb/rcsb-saguaro-app 2.3.5-groups.9 → 3.0.0

package/CHANGELOG.md

@@ -2,6 +2,25 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [3.0.0] - 2021-10-15
+### Minor code refactor
+Changed `setTimeout` calls to 'rxjs' `asyncScheduler`
+### Breaking changes
+- rcsb-saguaro update 2.0.0
+
+## [2.4.0] - 2021-10-08
+### Minor code refactor and improvements
+- `AnnotationCollectorInterface` new annotation features getter `getAnnotationFeatures`
+- `ExternalTrackBuilderInterface` interface to build tracks from the collected annotations and alignments
+- `SequenceCollectorInterface` new alignment response getter `getAlignmentResponse`
+- `SequenceCollectorInterface` `collect` method accepts a new optional argument `filter?:Array<string>` to filter targets in the alignment
+- No more `Map` inheritance in `AnnotationTrack`. Now it delegates `Map` methods 
+- rcsb-saguaro update 1.11.0
+
+## [2.3.6] - 2021-10-04
+### Dependency update
+- Using rcsb-api-tools
+
 ## [2.3.5] - 2021-09-16
 ### Display Improvement
 - Loader spinner added
@@ -17,7 +36,7 @@
 
 ## [2.3.2] - 2021-08-30
 ### Bug correction
-- `AnnotationTransformer` `annotationConfig` bug fixed
+- `AnnotationTrack` `annotationConfig` bug fixed
 
 ## [2.3.1] - 2021-08-24
 ### Bug correction
@@ -63,12 +82,13 @@
 - async/await promise style
 - Recursive waits migrated to rxjx Observables
 - PFV unique building method
-- RcsbFvWebApp.setBoardConfig  and RcsbFvWebApp.getRcsbFv have been removed. 
-  - Custom board config must be defined in RcsbFvAdditionalConfig (Some RcsbFvWebApp methods do not support additional configs yet)
-  - Builder methods return RcsbFvModulePublicInterface
 - Context Manager rcsbFv build new board config param 
 - Select button default value title bug fixed
 - rcsb-saguaro update 1.8.4
+#### Breaking changes
+- RcsbFvWebApp.setBoardConfig  and RcsbFvWebApp.getRcsbFv have been removed. 
+  - Custom board config must be defined in RcsbFvAdditionalConfig (Some RcsbFvWebApp methods do not support additional configs yet)
+  - Builder methods return RcsbFvModulePublicInterface
 
 ## [1.4.8] - 2021-06-15
 ### Optimization
@@ -106,7 +126,7 @@
 ## [1.4.0] - 2021-06-02
 ### Improvements
 - Typed types 
-- New class AnnotationTransformer transforms Feature into RcsbFvTrackDataElementInterface
+- New class AnnotationTrack transforms Feature into RcsbFvTrackDataElementInterface
 - Added commented code to handle FeaturePositionValue as Arrays
 
 ## [1.3.2] - 2021-05-31

package/README.md

@@ -8,7 +8,7 @@ Feature Summaries. The package allows access to RCSB Saguaro methods to add or c
 <!---
 <div id="pfvSelect" ></div>  
 <div id="pfv" ></div>
-<script type="text/javascript" src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@2.3.4/build/dist/app.js"></script>
+<script type="text/javascript" src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@3.0.0/build/dist/app.js"></script>
 <script type="text/javascript">
 RcsbFvWebApp.buildInstanceFv("pfv", "4Z35.A", {
     boardConfig:{
@@ -23,7 +23,7 @@ RcsbFvWebApp.buildInstanceFv("pfv", "4Z35.A", {
 `npm install @rcsb/rcsb-saguaro-app`
 
 ### CDN JavaScript
-`<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@2.3.4/build/dist/app.js" type="text/javascript"></script>`
+`<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@3.0.0/build/dist/app.js" type="text/javascript"></script>`
 
 ### JavaScript Examples
 * [PDB Instance Chain View](https://rcsb.github.io/rcsb-saguaro-app/examples/instance.html)

package/build/dist/ExternalResources/NcbiData/NcbiSummary.d.ts

@@ -18,7 +18,7 @@ export interface TaxonomyMetadataInterface {
 export declare class NcbiSummary {
     private static timeout;
     private static httpTimeout;
-    private static jobId;
+    private static jobTask;
     static requestChromosomeData(chrId: string): Promise<ChromosomeMetadataInterface>;
     static requestTaxonomyData(taxId: string): Promise<TaxonomyMetadataInterface>;
 }

package/build/dist/ExternalResources/SwissModel/SwissModelQueryAnnotations.d.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare class SwissModelQueryAnnotations {
     private static readonly url;
     private static readonly urlSuffix;

package/build/dist/RcsbAnnotationConfig/RcsbAnnotationConfig.d.ts

@@ -1,4 +1,4 @@
-import { Feature } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvDisplayTypes, RcsbFvTrackDataElementInterface } from '@rcsb/rcsb-saguaro';
 import { AnnotationConfigInterface, RcsbAnnotationConfigInterface } from "./AnnotationConfigInterface";
 export interface RcsbMergedTypesInterface {
@@ -30,6 +30,7 @@ export declare class RcsbAnnotationConfig {
     annotationMergedPreference(type: string, a: RcsbFvTrackDataElementInterface, b: RcsbFvTrackDataElementInterface): boolean;
     static randomRgba(str?: string): string;
     addProvenance(type: string, provenanceName: string): void;
+    addMultipleProvenance(type: string, provenanceList: Array<string>): void;
     getProvenanceList(type: string): Array<string>;
     isTransformedToNumerical(type: string): boolean;
 }

package/build/dist/RcsbCollectTools/AnnotationCollector/AnnotationCollector.d.ts

@@ -1,5 +1,5 @@
 import { RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
-import { AnnotationFeatures, Feature } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { AnnotationCollectConfig, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";

package/build/dist/RcsbCollectTools/AnnotationCollector/AnnotationCollectorHelper.d.ts

@@ -1,8 +1,8 @@
-import { AnnotationTransformer } from "./AnnotationTransformer";
+import { AnnotationTrack } from "./AnnotationTrack";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { RcsbAnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
 export declare class AnnotationCollectorHelper {
-    static buildAnnotationTrack(annotationHandler: AnnotationTransformer, type: string, rcsbAnnotationConfig: RcsbAnnotationConfigInterface, provenanceList: Array<string>): RcsbFvRowConfigInterface;
+    static buildAnnotationTrack(annotationHandler: AnnotationTrack, type: string, rcsbAnnotationConfig: RcsbAnnotationConfigInterface, provenanceList: Array<string>): RcsbFvRowConfigInterface;
     private static buildRcsbFvRowConfigTrack;
     private static buildRcsbFvRowConfigArea;
     private static buildRcsbFvRowConfigBlockArea;

package/build/dist/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.d.ts

@@ -1,7 +1,7 @@
 import { CoreCollectorInterface } from "../CoreCollectorInterface";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
-import { AnnotationFeatures, Feature, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs, Source } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { AnnotationTransformer, FeaturePositionGaps } from "./AnnotationTransformer";
+import { AnnotationFeatures, Feature, QueryAnnotationsArgs, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationTrack, FeaturePositionGaps } from "./AnnotationTrack";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 export declare type IncreaseAnnotationValueType = (feature: {
     type: string;
@@ -11,8 +11,9 @@ export declare type IncreaseAnnotationValueType = (feature: {
     p: FeaturePositionGaps;
 }) => number;
 export interface AnnotationProcessingInterface {
-    increaseAnnotationValue?: IncreaseAnnotationValueType;
-    computeAnnotationValue?: (annotationTracks: Map<string, AnnotationTransformer>) => void;
+    getAnnotationValue?: IncreaseAnnotationValueType;
+    computeAnnotationValue?: (annotationTracks: Map<string, AnnotationTrack>) => void;
+    addTrackElementCallback?: IncreaseAnnotationValueType;
 }
 interface CommonAnnotationInterface {
     annotationProcessing?: AnnotationProcessingInterface;
@@ -22,11 +23,9 @@ export interface CollectAnnotationsInterface extends QueryAnnotationsArgs, Commo
     addTargetInTitle?: Set<Source>;
     collectSwissModel?: boolean;
 }
-export interface CollectGroupAnnotationsInterface extends QueryGroup_AnnotationsArgs, CommonAnnotationInterface {
-}
-export declare type AnnotationCollectConfig = Partial<CollectAnnotationsInterface & CollectGroupAnnotationsInterface>;
+export declare type AnnotationCollectConfig = Partial<CollectAnnotationsInterface>;
 export interface AnnotationCollectorInterface extends CoreCollectorInterface {
-    collect(requestConfig: CollectAnnotationsInterface | CollectGroupAnnotationsInterface): Promise<Array<RcsbFvRowConfigInterface>>;
+    collect(requestConfig: CollectAnnotationsInterface): Promise<Array<RcsbFvRowConfigInterface>>;
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
     getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
     getFeatures(): Promise<Array<Feature>>;

package/build/dist/RcsbCollectTools/AnnotationCollector/{AnnotationTransformer.d.ts → AnnotationTrack.d.ts}

@@ -1,23 +1,38 @@
 import { RcsbFvTrackDataElementGapInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
-import { Feature, FeaturePosition, SequenceReference, Source } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Feature, FeaturePosition, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { RcsbAnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
-import { IncreaseAnnotationValueType } from "./AnnotationCollectorInterface";
+import { AnnotationProcessingInterface } from "./AnnotationCollectorInterface";
 export interface FeaturePositionGaps extends FeaturePosition {
     gaps?: Array<RcsbFvTrackDataElementGapInterface>;
 }
-export declare class AnnotationTransformer extends Map<string, RcsbFvTrackDataElementInterface> {
+export declare class AnnotationTrack {
     private valueRange;
     private readonly entityInstanceTranslator;
     private readonly type;
     private readonly annotationConfig;
+    private readonly trackElementMap;
     constructor(type: string, annotationConfig: RcsbAnnotationConfigInterface, entityInstanceTranslator: PolymerEntityInstanceTranslate);
     getRange(): {
         min: number;
         max: number;
     };
-    addElement(reference: SequenceReference | undefined, queryId: string, source: Source, targetId: string, d: Feature, increaseValue?: IncreaseAnnotationValueType): void;
+    addFeature(ann: {
+        reference: SequenceReference | undefined;
+        queryId: string;
+        source: Source;
+        targetId: string;
+        feature: Feature;
+    }, annotationProcessing?: AnnotationProcessingInterface): void;
+    size(): number;
+    forEach(f: (ann: RcsbFvTrackDataElementInterface, loc: string) => void): void;
+    addAll(trackElementsMap: AnnotationTrack, color?: string): void;
+    getTrackProvenance(): Set<string>;
+    set(loc: string, ann: RcsbFvTrackDataElementInterface): void;
+    values(): Array<RcsbFvTrackDataElementInterface>;
     private buildRcsbFvTrackDataElement;
+    private addRange;
+    private transformToNumerical;
     private expandValues;
     private addAuthorResIds;
     private isNumericalDisplay;

package/build/dist/RcsbCollectTools/AnnotationCollector/AnnotationTrackManager.d.ts

@@ -1,5 +1,5 @@
-import { AnnotationTransformer } from "./AnnotationTransformer";
-import { AnnotationFeatures } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationTrack } from "./AnnotationTrack";
+import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbAnnotationConfig } from "../../RcsbAnnotationConfig/RcsbAnnotationConfig";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { AnnotationCollectConfig } from "./AnnotationCollectorInterface";
@@ -9,7 +9,7 @@ export declare class AnnotationTrackManager {
     private polymerEntityInstanceTranslator;
     constructor(rcsbAnnotationConfig: RcsbAnnotationConfig);
     processRcsbPdbAnnotations(data: Array<AnnotationFeatures>, requestConfig: AnnotationCollectConfig): void;
-    getAnnotationTracks(): Map<string, AnnotationTransformer>;
+    getAnnotationTracks(): Map<string, AnnotationTrack>;
     private getPolymerEntityInstanceTranslator;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
     private mergeTracks;

package/build/dist/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.d.ts

@@ -1,5 +1,5 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
-import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { SequenceCollectorDataInterface } from "../SequenceCollector/SequenceCollector";
 export interface ExternalTrackBuilderInterface {
     processAlignmentAndFeatures(data: {

package/build/dist/RcsbCollectTools/PropertyCollector/MultipleEntryPropertyCollector.d.ts

@@ -1,4 +1,4 @@
-import { QueryEntriesArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { QueryEntriesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 export interface EntryPropertyIntreface {
     rcsbId: string;
     entryId: string;

package/build/dist/RcsbCollectTools/SequenceCollector/GenomeMapCollector.d.ts

@@ -2,10 +2,10 @@ import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { CollectAlignmentInterface, SequenceCollectorInterface } from "./SequenceCollectorInterface";
 import { SequenceCollectorDataInterface } from "./SequenceCollector";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
-import { AlignmentResponse } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare class GenomeMapCollector implements SequenceCollectorInterface {
     readonly rcsbFvQuery: RcsbClient;
-    collect(requestConfig: CollectAlignmentInterface, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<void>): Promise<SequenceCollectorDataInterface>;
+    collect(requestConfig: CollectAlignmentInterface, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<null>): Promise<SequenceCollectorDataInterface>;
     getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
     getSequenceLength(): number;
     getTargets(): Promise<Array<string>>;

package/build/dist/RcsbCollectTools/SequenceCollector/ObservedSequenceCollector.d.ts

@@ -1,4 +1,4 @@
-import { AlignmentResponse } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { SequenceCollectorDataInterface } from "./SequenceCollector";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";

package/build/dist/RcsbCollectTools/SequenceCollector/SequenceCollector.d.ts

@@ -1,5 +1,5 @@
 import { RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
-import { AlignedRegion, AlignmentResponse } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignedRegion, AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";

package/build/dist/RcsbCollectTools/SequenceCollector/SequenceCollectorHelper.d.ts

@@ -1,5 +1,5 @@
 import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
-import { AlignedRegion, SequenceReference, TargetAlignment } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignedRegion, SequenceReference, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvLink, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
 import { AlignedObservedRegion } from "./SequenceCollector";
 import { AlignmentCollectConfig } from "./SequenceCollectorInterface";
@@ -21,7 +21,7 @@ interface BuildSequenceDataInterface extends TranslateContextInterface {
 }
 export declare class SequenceCollectorHelper {
     private entityInstanceTranslator;
-    buildAlignments(alignmentData: BuildAlignementsInterface, dynamicDisplayFlag: boolean, tagObservedRegions: (region: AlignedRegion, commonContext: TranslateContextInterface, noQuerySequenceFlag?: boolean) => Array<AlignedObservedRegion>): {
+    buildAlignments(alignmentData: BuildAlignementsInterface, dynamicDisplayFlag: boolean, tagObservedRegions: (region: AlignedRegion, commonContext: TranslateContextInterface) => Array<AlignedObservedRegion>): {
         alignments: Array<RcsbFvRowConfigInterface>;
         targets: Array<string>;
     };

package/build/dist/RcsbCollectTools/SequenceCollector/SequenceCollectorInterface.d.ts

@@ -1,7 +1,6 @@
 import { CoreCollectorInterface } from "../CoreCollectorInterface";
 import { SequenceCollectorDataInterface } from "./SequenceCollector";
-import { AlignmentResponse, QueryAlignmentArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbQueryGroupAlignmentArguments } from "../../RcsbGraphQL/RcsbQueryAlignment";
+import { AlignmentResponse, QueryAlignmentArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 interface CommonAlignmentInterface {
     filterByTargetContains?: string;
     dynamicDisplay?: boolean;
@@ -11,14 +10,11 @@ interface CommonAlignmentInterface {
 }
 export interface CollectAlignmentInterface extends QueryAlignmentArgs, CommonAlignmentInterface {
 }
-export interface CollectGroupAlignmentInterface extends RcsbQueryGroupAlignmentArguments, CommonAlignmentInterface {
-    sequencePrefix: string;
-}
-export declare type AlignmentCollectConfig = Partial<CollectAlignmentInterface & CollectGroupAlignmentInterface>;
+export declare type AlignmentCollectConfig = Partial<CollectAlignmentInterface>;
 export interface SequenceCollectorInterface extends CoreCollectorInterface {
     getTargets(): Promise<Array<string>>;
     getAlignmentResponse(): Promise<AlignmentResponse>;
     getSequenceLength(): number;
-    collect(requestConfig: CollectAlignmentInterface | CollectGroupAlignmentInterface, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<void>): Promise<SequenceCollectorDataInterface>;
+    collect(requestConfig: CollectAlignmentInterface, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<void>): Promise<SequenceCollectorDataInterface>;
 }
 export {};

package/build/dist/RcsbCollectTools/Translators/EntryAssembliesCollector.d.ts

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

package/build/dist/RcsbCollectTools/Translators/MultipleEntityInstancesCollector.d.ts

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

package/build/dist/RcsbCollectTools/Translators/PolymerEntityInstancesCollector.d.ts

@@ -1,4 +1,4 @@
-import { CorePolymerEntityInstance, QueryEntryArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { CorePolymerEntityInstance, QueryEntryArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 export interface PolymerEntityInstanceInterface {
     rcsbId: string;
     entityId: string;

package/build/dist/RcsbFvWeb/RcsbFvBuilder/RcsbFvContextManager.d.ts

@@ -2,19 +2,11 @@ import { RcsbFv, RcsbFvBoardConfigInterface } from "@rcsb/rcsb-saguaro";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { EntryAssemblyTranslate } from "../../RcsbUtils/EntryAssemblyTranslate";
 import { PolymerEntityChromosomeTranslate } from "../../RcsbUtils/PolymerEntityChromosomeTranslate";
-import { GroupPropertiesProvider } from "../../RcsbUtils/GroupPropertiesProvider";
-import { QueryResult } from "@rcsb/rcsb-saguaro-api/build/RcsbSearch/Types/SearchResultInterface";
-import { SearchQueryType } from "../../RcsbSeacrh/SearchRequestProperty";
-import { GroupPropertyInterface } from "../../RcsbCollectTools/PropertyCollector/GroupPropertyCollector";
-import { QueryGroupArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { FacetType } from "../../RcsbSeacrh/FacetStore/FacetMemberInterface";
-import { ReturnType } from "@rcsb/rcsb-saguaro-api/build/RcsbSearch/Types/SearchEnums";
 declare class RcsbFvContextManager {
     private rcsbFvManager;
     private rcsbButtonManager;
     private polymerEntityToInstanceMap;
     private entryToAssemblyMap;
-    private groupPropertyMap;
     getFv(elementFvId: string, boardConfig?: Partial<RcsbFvBoardConfigInterface>): RcsbFv;
     hasFv(elementFvId: string): boolean;
     private setFv;
@@ -23,13 +15,9 @@ declare class RcsbFvContextManager {
     removeFv(elementFvId: string): void;
     private setEntityToInstance;
     private setEntryToAssembly;
-    private setGroupProperties;
     getEntityToInstance(entryId: string): Promise<PolymerEntityInstanceTranslate>;
     getEntryToAssembly(entryId: string): Promise<EntryAssemblyTranslate>;
     getEntityToChromosome(entityIds: Array<string>): Promise<PolymerEntityChromosomeTranslate>;
-    getGroupMemberProperties(groupQuery: QueryGroupArgs): Promise<GroupPropertiesProvider>;
-    getSearchQueryResult(query: SearchQueryType, facets: FacetType[], returnType: ReturnType): Promise<QueryResult>;
-    getGroupProperties(groupQuery: QueryGroupArgs): Promise<GroupPropertyInterface>;
 }
 export declare const rcsbFvCtxManager: RcsbFvContextManager;
 export {};

package/build/dist/RcsbFvWeb/RcsbFvBuilder/RcsbFvCoreBuilder.d.ts

@@ -3,8 +3,6 @@ import { RcsbFv } from "@rcsb/rcsb-saguaro";
 import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface, RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
 import { SelectButtonConfigInterface } from "../WebTools/WebToolsManager";
 import { GroupedOptionsInterface, SelectOptionInterface } from "../WebTools/SelectButton";
-import { SearchQuery } from "@rcsb/rcsb-saguaro-api/build/RcsbSearch/Types/SearchQueryInterface";
-import { GroupReference } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export interface CreateFvInterface {
     elementId: string;
     fvModuleI: new (elementId: string, rcsbFv: RcsbFv) => RcsbFvModuleInterface;
@@ -34,5 +32,4 @@ export declare class RcsbFvCoreBuilder {
     static clearAdditionalSelectButton(elementFvId: string, selectButtonId: string): void;
     static addSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface>, config?: SelectButtonConfigInterface): void;
     static showMessage(elementId: string, message: string): void;
-    static buildGroupTabs(elementId: string, group: GroupReference, groupId: string, query?: SearchQuery): void;
 }

package/build/dist/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.d.ts

@@ -1,4 +1,4 @@
-import { SequenceReference } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
 export interface PfvBuilderInterface {
     queryId: string;

package/build/dist/RcsbFvWeb/RcsbFvBuilder.d.ts

@@ -1,9 +1,8 @@
-import { RcsbFvAdditionalConfig, RcsbFvModulePublicInterface } from "./RcsbFvModule/RcsbFvModuleInterface";
+import { RcsbFvAdditionalConfig } from "./RcsbFvModule/RcsbFvModuleInterface";
 import { PairwiseAlignmentInterface } from "./PairwiseAlignmentTools/PairwiseAlignmentBuilder";
 import { InstanceSequenceConfig, InstanceSequenceOnchangeInterface } from "./RcsbFvBuilder/RcsbFvInstanceBuilder";
 import { PfvBuilderInterface } from "./RcsbFvBuilder/RcsbFvProteinSequenceBuilder";
-import { GroupReference } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { SearchQuery } from "@rcsb/rcsb-saguaro-api/build/RcsbSearch/Types/SearchQueryInterface";
+import { RcsbFvModulePublicInterface } from "./RcsbFvModule/RcsbFvModuleInterface";
 export declare function unmount(elementId: string): void;
 export declare function buildMultipleAlignmentSequenceFv(elementFvId: string, elementSelectId: string, upAcc: string): Promise<RcsbFvModulePublicInterface>;
 export declare function buildEntitySummaryFv(elementFvId: string, elementSelectId: string, entityId: string): Promise<RcsbFvModulePublicInterface>;
@@ -22,4 +21,3 @@ export declare function buildFullChromosome(elementFvId: string, chrId: string):
 export declare function buildEntryChromosome(elementFvId: string, entitySelectId: string, chromosomeSelectId: string, entryId: string): Promise<RcsbFvModulePublicInterface>;
 export declare function buildEntityChromosome(elementFvId: string, elementSelectId: string, entityId: string): Promise<RcsbFvModulePublicInterface>;
 export declare function buildChromosome(elementFvId: string, entityId: string, chrId: string, elementSelectId?: string): Promise<RcsbFvModulePublicInterface>;
-export declare function buildGroupFv(elementId: string, group: GroupReference, groupId: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig): void;

package/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.d.ts

@@ -3,7 +3,7 @@ import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityIns
 import { SequenceCollectorInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollectorInterface";
 import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface } from "./RcsbFvModuleInterface";
-import { Feature } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterface {
     protected readonly rcsbFv: RcsbFv;
     protected readonly elementId: string;

package/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.d.ts

@@ -1,4 +1,4 @@
-import { Feature, FilterInput, GroupReference, SequenceReference, Source } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Feature, FilterInput, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { RcsbFv, RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { PairwiseAlignmentInterface } from "../PairwiseAlignmentTools/PairwiseAlignmentBuilder";
@@ -8,7 +8,6 @@ import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureToo
 export interface RcsbFvAdditionalConfig {
     sources?: Array<Source>;
     filters?: Array<FilterInput>;
-    batchFilters?: Array<FilterInput>;
     alignmentFilter?: Array<string>;
     hideAlignments?: boolean;
     bottomAlignments?: boolean;
@@ -17,14 +16,8 @@ export interface RcsbFvAdditionalConfig {
     annotationProcessing?: AnnotationProcessingInterface;
     sequenceCollector?: SequenceCollectorInterface;
     externalTrackBuilder?: ExternalTrackBuilderInterface;
-    page?: {
-        first: number;
-        after: string;
-    };
 }
 export interface RcsbFvModuleBuildInterface {
-    group?: GroupReference;
-    groupId?: string;
     queryId?: string;
     from?: SequenceReference;
     to?: SequenceReference;

package/build/dist/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.d.ts

@@ -1,4 +1,4 @@
-import { QueryAlignmentArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { QueryAlignmentArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare class RcsbFvAlignmentCollectorQueue {
     private readonly nWorkers;
     private readonly workerList;

package/build/dist/RcsbFvWeb/WebTools/WebToolsManager.d.ts

@@ -1,8 +1,6 @@
 /// <reference types="react" />
 import { GroupedOptionsInterface, OptionPropsInterface, SelectOptionInterface } from "./SelectButton";
 import { OptionProps } from "react-select/src/components/Option";
-import { SearchQuery } from "@rcsb/rcsb-saguaro-api/build/RcsbSearch/Types/SearchQueryInterface";
-import { GroupReference } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export interface SelectButtonConfigInterface {
     addTitle?: boolean;
     defaultValue?: string | undefined | null;
@@ -21,7 +19,8 @@ export declare class WebToolsManager {
     static clearSelectButton(elementId: string): void;
     static clearAdditionalSelectButton(elementId: string): void;
     static innerClearSelectButton(elementId: string, suffix: string): void;
-    static buildGroupTabs(elementId: string, group: GroupReference, groupId: string, query?: SearchQuery): void;
     static buildLoaderSpinner(elementId: string): void;
     static unmountLoaderSpinner(elementId: string): void;
+    private static hideElement;
+    private static showElement;
 }

package/build/dist/RcsbGraphQL/RcsbClient.d.ts

@@ -1,20 +1,14 @@
-import { RcsbQueryGroupAlignmentArguments } from "./RcsbQueryAlignment";
-import { AlignmentResponse, AnnotationFeatures, QueryAlignmentArgs, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { CoreEntry, CoreGroup, CorePolymerEntity, QueryEntriesArgs, QueryEntryArgs, QueryPolymer_EntitiesArgs, QueryGroupArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { AlignmentResponse, AnnotationFeatures, QueryAlignmentArgs, QueryAnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { CoreEntry, CorePolymerEntity, QueryEntriesArgs, QueryEntryArgs, QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 export declare class RcsbClient {
     private rcsbQueryAnnotations;
-    private rcsbQueryGroupAnnotations;
     private rcsbQueryAlignment;
-    private rcsbQueryGroupAlignment;
     private rcsbQueryEntityInstances;
     private rcsbQueryMutipleEntityInstances;
     private rcsbQueryEntryProperties;
     requestRcsbPdbAnnotations(requestConfig: QueryAnnotationsArgs): Promise<Array<AnnotationFeatures>>;
-    requestRcsbPdbGroupAnnotations(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<AnnotationFeatures>>;
     requestAlignment(requestConfig: QueryAlignmentArgs): Promise<AlignmentResponse>;
-    requestGroupAlignment(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<AlignmentResponse>;
     requestEntityInstances(requestConfig: QueryEntryArgs): Promise<CoreEntry>;
     requestMultipleEntityInstances(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<CorePolymerEntity>>;
-    requestGroupInfo(requestConfig: QueryGroupArgs): Promise<CoreGroup>;
     requestMultipleEntriesProperties(requestConfig: QueryEntriesArgs): Promise<Array<CoreEntry>>;
 }

package/build/dist/RcsbGraphQL/RcsbCoreQueryInterface.d.ts

@@ -1,4 +1,4 @@
-import { GraphQLRequest } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/GraphQLRequest";
+import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
 export interface RcsbCoreQueryInterface<Q, R> {
     readonly client: GraphQLRequest;
     request(requestConfig: Q): Promise<R>;

package/build/dist/RcsbGraphQL/RcsbQueryAlignment.d.ts

@@ -1,17 +1,7 @@
-import { AlignmentResponse, QueryAlignmentArgs, QueryGroup_AlignmentArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse, QueryAlignmentArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
-import { GraphQLRequest } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/GraphQLRequest";
+import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
 export declare class RcsbQueryAlignment implements RcsbCoreQueryInterface<QueryAlignmentArgs, AlignmentResponse> {
     readonly client: GraphQLRequest;
     request(requestConfig: QueryAlignmentArgs): Promise<AlignmentResponse>;
 }
-export declare type RcsbQueryGroupAlignmentArguments = QueryGroup_AlignmentArgs & {
-    page: {
-        first: number;
-        after: string;
-    };
-};
-export declare class RcsbQueryGroupAlignment implements RcsbCoreQueryInterface<RcsbQueryGroupAlignmentArguments, AlignmentResponse> {
-    readonly client: GraphQLRequest;
-    request(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<AlignmentResponse>;
-}

package/build/dist/RcsbGraphQL/RcsbQueryAnnotations.d.ts

@@ -1,11 +1,7 @@
-import { AnnotationFeatures, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures, QueryAnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
-import { GraphQLRequest } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/GraphQLRequest";
+import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
 export declare class RcsbQueryAnnotations implements RcsbCoreQueryInterface<QueryAnnotationsArgs, Array<AnnotationFeatures>> {
     readonly client: GraphQLRequest;
     request(requestConfig: QueryAnnotationsArgs): Promise<Array<AnnotationFeatures>>;
 }
-export declare class RcsbQueryGroupAnnotations implements RcsbCoreQueryInterface<QueryGroup_AnnotationsArgs, Array<AnnotationFeatures>> {
-    readonly client: GraphQLRequest;
-    request(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<AnnotationFeatures>>;
-}

package/build/dist/RcsbGraphQL/RcsbQueryEntryInstances.d.ts

@@ -1,6 +1,6 @@
-import { CoreEntry, QueryEntryArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { CoreEntry, QueryEntryArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
-import { GraphQLRequest } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/GraphQLRequest";
+import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
 export declare class RcsbQueryEntryInstances implements RcsbCoreQueryInterface<QueryEntryArgs, CoreEntry> {
     readonly client: GraphQLRequest;
     request(requestConfig: QueryEntryArgs): Promise<CoreEntry>;

package/build/dist/RcsbGraphQL/RcsbQueryMultipleEntityInstances.d.ts

@@ -1,6 +1,6 @@
-import { CorePolymerEntity, QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { CorePolymerEntity, QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
-import { GraphQLRequest } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/GraphQLRequest";
+import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
 export declare class RcsbQueryMultipleEntityInstances implements RcsbCoreQueryInterface<QueryPolymer_EntitiesArgs, Array<CorePolymerEntity>> {
     readonly client: GraphQLRequest;
     request(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<CorePolymerEntity>>;

package/build/dist/RcsbGraphQL/RcsbQueryMultipleEntriesProperties.d.ts

@@ -1,6 +1,6 @@
 import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
-import { CoreEntry, QueryEntriesArgs } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { GraphQLRequest } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/GraphQLRequest";
+import { CoreEntry, QueryEntriesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
 export declare class RcsbQueryMultipleEntriesProperties implements RcsbCoreQueryInterface<QueryEntriesArgs, Array<CoreEntry>> {
     readonly client: GraphQLRequest;
     request(requestConfig: QueryEntriesArgs): Promise<Array<CoreEntry>>;

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

@@ -1,6 +1,6 @@
 import { PolymerEntityInstanceInterface } from "../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
 import { RcsbFvTrackDataElementInterface } from '@rcsb/rcsb-saguaro';
-import { SequenceReference, Source } from "@rcsb/rcsb-saguaro-api/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export interface TranslateContextInterface {
     queryId: string;
     targetId: string;

package/build/dist/app.d.ts

@@ -1 +1 @@
-export { buildEntryChromosome, buildFullChromosome, buildEntityChromosome, buildChromosome, buildEntityFv, buildEntitySummaryFv, buildSingleEntitySummaryFv, buildInstanceFv, buildInstanceSequenceFv, buildMultipleInstanceSequenceFv, buildAssemblySequenceFv, buildPairwiseAlignment, buildPfv, buildMultipleAlignmentSequenceFv, buildUniprotEntityFv, buildUniprotEntityInstanceFv, buildUniprotFv, buildGroupFv, unmount } from "./RcsbFvWeb/RcsbFvBuilder";
+export { buildEntryChromosome, buildFullChromosome, buildEntityChromosome, buildChromosome, buildEntityFv, buildEntitySummaryFv, buildSingleEntitySummaryFv, buildInstanceFv, buildInstanceSequenceFv, buildMultipleInstanceSequenceFv, buildAssemblySequenceFv, buildPairwiseAlignment, buildPfv, buildMultipleAlignmentSequenceFv, buildUniprotEntityFv, buildUniprotEntityInstanceFv, buildUniprotFv, unmount } from "./RcsbFvWeb/RcsbFvBuilder";