@rcsb/rcsb-saguaro-app 4.0.0-groups.13 → 4.0.0-interfaces.10

package/CHANGELOG.md

@@ -2,6 +2,18 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [4.0.0-interfaces] - 2022-01-24
+###  Annotation collector improvements 
+-  Added interface `CollectAnnotationsInterface` for generating new annotations internally (not exposed)
+    - `annotationGenerator?(annotations: Array<AnnotationFeatures>)` generates new annotations from the collected ones
+    - `annotationFilter?(annotations: Array<AnnotationFeatures>)` filter the collected annotations
+    - Both methods are called before annotations processing and thus, they should be configured in `RcsbAnnotationConfig.ac.json` or equivalent config file
+    - Checking content before adding generated features
+    - New callback attribute `InstanceSequenceConfig` > `beforeChangeCallback`. This function is called when instance 
+    dropdown menu changes and before rendering the new 1D RcsbFv. 
+    The callback may return a `RcsbContextType` object that will be included in the `additionalConfig`
+- Added two new classes (`AssemblyInterfacesCollector` and `AssemblyInterfacesTranslate`) to collect and handle assembly and interface id relationships
+
 ## [4.0.0-master] - 2021-12-07
 ### Breaking change
 - `ExternalTrackBuilderInterface` methods return a promise and are executed asynchronous
@@ -18,6 +30,10 @@
 - Removed interface `CollectAnnotationsInterface` attribute `addTargetInTitle`
 - Added `titleSuffix` and `trackTitle` attributes to `CollectAnnotationsInterface`
      - These new attributes are defined as async functions (ann: AnnotationFeatures, d: Feature) => Promise<string|undefined> to provide or modify track titles based on the features content
+- New `RcsbFvInterface` module
+     - Interface `InstanceSequenceConfig` provides a new attribute `module` to choose between the `RcsbFvInstance` or RcsbFvInterface` modules
+- New classes to collect and translate instance/interface ids relationships from data api
+    - `RcsbQueryInterfaceInstances`, `InterfaceInstanceCollector` and  `InterfaceInstanceTranslate`
 
 ## [3.2.1] - 2021-11-10
 ### Minor configuration

package/README.md

@@ -49,7 +49,7 @@ click events.
 - **RcsbFvWebApp.setBoardConfig**(boardConfigData: [RcsbFvBoardConfigInterface](https://rcsb.github.io/rcsb-saguaro/interfaces/rcsbfvboardconfiginterface.html))
 - **RcsbFvWebApp.getRcsbFv**(elementId: string)
 
-###GraphQL configuration
+### GraphQL configuration
 ##### Building TypeScript interfaces
 - Files ["src/RcsbServerConfig/codegen.borrego.json", "src/RcsbServerConfig/codegen.yosemite.json"]
 - Borrego Interfaces: graphql-codegen --config src/RcsbServerConfig/codegen.borrego.json
@@ -59,6 +59,20 @@ click events.
 - Config Files: ["src/RcsbGraphQL/Queries/Borrego/.graphqlconfig", "src/RcsbGraphQL/Queries/Yosemite/.graphqlconfig"]
 - Generated Schemas: ["src/RcsbGraphQL/Queries/Borrego/schema.graphql", "src/RcsbGraphQL/Queries/Yosemite/schema.graphql"]
 
+### New RCSB data-api request method
+- A new graphql query defined in `src/RcsbGraphQL/Queries/Yosemite` (e.g. `QueryAssemblyInterfaces.graphql`)
+- A new request class using `rcsb-api-tools` defined in `src/RcsbGraphQL` (e.g. `RcsbQueryAssemblyInterfaces.ts`)
+- A new method in the `RcsbClient` class defined in `src/RcsbGraphQL/RcsbClient.ts` (e.g. `requestAssemblyInterfaces`)
+    - This method must used the request class defined above
+- A new collector class based on the request class in `src/RcsbCollectTools/Translators` (e.g. `AssemblyInterfacesCollector`)
+    - This class must call the method defined above
+    - This class may transform the RCSB data-api schema into a more convenient interface
+- A new translator class defined in `src/RcsbUtils` (e.g. `AssemblyInterfacesTranslate`)
+    - The constructor gets the data collected by the above class
+    - The class exposes the methods needs to provide the relationships between RCSB objects of different granularity
+- A new method in the `RcsbFvContextManager` defined in `src/RcsbFvWeb/RcsbFvBuilder`
+    - This method must avoid duplicate requests
+
 Contributing
 ---
 All contributions are welcome. Please, make a pull request or open an issue.

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

@@ -21,7 +21,7 @@ export declare class RcsbAnnotationConfig {
     uniprotOrder(): Array<string>;
     instanceOrder(): Array<string>;
     entityOrder(): Array<string>;
-    buildAndAddType(d: Feature, mainTitle?: string, titleSuffix?: string): string;
+    buildAndAddType(d: Feature, trackTitle?: string, titleSuffix?: string, typeSuffix?: string): string;
     private addNewType;
     sortAndIncludeNewTypes(): void;
     private checkAndIncludeNewType;

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

@@ -1,7 +1,7 @@
 import { RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
 import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AnnotationCollectConfig, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
 import { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";

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

@@ -1,8 +1,9 @@
 import { CoreCollectorInterface } from "../CoreCollectorInterface";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
-import { AnnotationFeatures, Feature, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures, Feature, QueryAnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AnnotationTrack, FeaturePositionGaps } from "./AnnotationTrack";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
+import { PolymerEntityInstanceInterface } from "../Translators/PolymerEntityInstancesCollector";
 export declare type IncreaseAnnotationValueType = (feature: {
     type: string;
     targetId: string;
@@ -15,22 +16,21 @@ export interface AnnotationProcessingInterface {
     computeAnnotationValue?: (annotationTracks: Map<string, AnnotationTrack>) => void;
     addTrackElementCallback?: IncreaseAnnotationValueType;
 }
-interface CommonAnnotationInterface {
+export interface CollectAnnotationsInterface extends QueryAnnotationsArgs {
+    collectSwissModel?: boolean;
+    rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     annotationProcessing?: AnnotationProcessingInterface;
     externalAnnotationTrackBuilder?: ExternalTrackBuilderInterface;
-}
-export interface CollectAnnotationsInterface extends QueryAnnotationsArgs, CommonAnnotationInterface {
-    collectSwissModel?: boolean;
+    annotationGenerator?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+    annotationFilter?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
     titleSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
     trackTitle?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+    typeSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
 }
-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>>;
 }
-export {};

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

@@ -1,6 +1,6 @@
 import { RcsbFvTrackDataElementGapInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
 import { Feature, FeaturePosition, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbAnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
 import { AnnotationProcessingInterface } from "./AnnotationCollectorInterface";
 export interface FeaturePositionGaps extends FeaturePosition {

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

@@ -1,7 +1,7 @@
 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 { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AnnotationCollectConfig } from "./AnnotationCollectorInterface";
 export declare class AnnotationTrackManager {
     private readonly rcsbAnnotationConfig;
@@ -12,8 +12,8 @@ export declare class AnnotationTrackManager {
     getAnnotationTracks(): Map<string, AnnotationTrack>;
     private getPolymerEntityInstanceTranslator;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-    private mergeTracks;
-    private buildType;
     private addAnnotationToTracks;
     private addFeature;
+    private buildType;
+    private mergeTracks;
 }

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

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceTranslate } from "../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../RcsbGraphQL/RcsbClient";
 import { ExternalTrackBuilderInterface } from "./FeatureTools/ExternalTrackBuilderInterface";
 export interface CoreCollectorInterface {

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

@@ -8,8 +8,14 @@ export interface ExternalTrackBuilderInterface {
         alignments?: AlignmentResponse;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     }): Promise<void>;
-    filterAlignments?(alignments: AlignmentResponse): Promise<AlignmentResponse>;
-    filterFeatures?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+    filterAlignments?(data: {
+        alignments: AlignmentResponse;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    }): Promise<AlignmentResponse>;
+    filterFeatures?(data: {
+        annotations: Array<AnnotationFeatures>;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    }): Promise<Array<AnnotationFeatures>>;
     addTo?(tracks: {
         alignmentTracks?: SequenceCollectorDataInterface;
         annotationTracks?: Array<RcsbFvRowConfigInterface>;

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

@@ -1,7 +1,7 @@
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { CollectAlignmentInterface, SequenceCollectorInterface } from "./SequenceCollectorInterface";
 import { SequenceCollectorDataInterface } from "./SequenceCollector";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 export declare class GenomeMapCollector implements SequenceCollectorInterface {

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

@@ -1,6 +1,6 @@
 import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { SequenceCollectorDataInterface } from "./SequenceCollector";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";

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

@@ -1,6 +1,6 @@
 import { RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
 import { AlignedRegion, AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";

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

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 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";
@@ -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-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbQueryGroupAlignmentArguments } from "../../RcsbGraphQL/RcsbQueryAlignment";
 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/AssemblyInterfacesCollector.d.ts

@@ -0,0 +1,9 @@
+import { QueryAssembliesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+export interface AssemblyInterfacesInterface {
+    rcsbId: string;
+    interfaceIds: Array<string>;
+}
+export declare class AssemblyInterfacesCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryAssembliesArgs): Promise<Array<AssemblyInterfacesInterface>>;
+}

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

@@ -0,0 +1,12 @@
+import { QueryInterfacesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+export interface InterfaceInstanceInterface {
+    rcsbId: string;
+    assemblyId: string;
+    interfaceId: string;
+    asymIds: [string, string];
+    operatorIds: [Array<Array<string>>, Array<Array<string>>];
+}
+export declare class InterfaceInstanceCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryInterfacesArgs): Promise<Array<InterfaceInstanceInterface>>;
+}

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

@@ -1,20 +1,15 @@
 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-api-tools/build/RcsbSearch/Types/SearchResultInterface";
-import { SearchQueryType } from "../../RcsbSeacrh/SearchRequestProperty";
-import { GroupPropertyInterface } from "../../RcsbCollectTools/PropertyCollector/GroupPropertyCollector";
-import { QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { FacetType } from "../../RcsbSeacrh/FacetStore/FacetMemberInterface";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { EntryAssemblyTranslate } from "../../RcsbUtils/Translators/EntryAssemblyTranslate";
+import { PolymerEntityChromosomeTranslate } from "../../RcsbUtils/Translators/PolymerEntityChromosomeTranslate";
+import { InterfaceInstanceTranslate } from "../../RcsbUtils/Translators/InterfaceInstanceTranslate";
 declare class RcsbFvContextManager {
     private rcsbFvManager;
     private rcsbButtonManager;
     private polymerEntityToInstanceMap;
     private entryToAssemblyMap;
-    private groupPropertyMap;
+    private interfaceToInstanceMap;
+    private assemblyInterfacesMap;
     getFv(elementFvId: string, boardConfig?: Partial<RcsbFvBoardConfigInterface>): RcsbFv;
     hasFv(elementFvId: string): boolean;
     private setFv;
@@ -23,13 +18,11 @@ 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: QueryPolymer_Entity_GroupArgs): Promise<GroupPropertiesProvider>;
-    getSearchQueryResult(query: SearchQueryType, facets: FacetType[], returnType: ReturnType): Promise<QueryResult | null>;
-    getGroupProperties(groupQuery: QueryPolymer_Entity_GroupArgs): Promise<GroupPropertyInterface>;
+    getInterfaceToInstance(interfaceId: string): Promise<InterfaceInstanceTranslate>;
+    private getAssemblyInterfaces;
 }
 export declare const rcsbFvCtxManager: RcsbFvContextManager;
 export {};

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

@@ -1,10 +1,8 @@
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 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-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { GroupReference } from "@rcsb/rcsb-api-tools/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/RcsbFvInstanceBuilder.d.ts

@@ -1,5 +1,5 @@
 /// <reference types="react" />
-import { RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
+import { RcsbContextType, RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
 import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
 import { OptionPropsInterface } from "../WebTools/SelectButton";
 import { RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
@@ -9,17 +9,21 @@ export interface InstanceSequenceOnchangeInterface {
     authId: string;
     asymId: string;
 }
+declare type instanceModule = "interface" | "instance";
 export interface InstanceSequenceConfig {
     dropdownTitle?: string;
     defaultValue?: string | undefined | null;
+    beforeChangeCallback?: (x: InstanceSequenceOnchangeInterface) => undefined | RcsbContextType;
     onChangeCallback?: (x: InstanceSequenceOnchangeInterface) => void;
     filterInstances?: Set<string>;
     displayAuthId?: boolean;
     selectButtonOptionProps?: (props: OptionProps<OptionPropsInterface>) => JSX.Element;
+    module?: instanceModule;
 }
 export declare class RcsbFvInstanceBuilder {
     static buildMultipleInstanceSequenceFv(elementFvId: string, elementEntrySelectId: string, elementInstanceSelectId: string, entryIdList: Array<string>, config: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
     static buildInstanceSequenceFv(elementFvId: string, elementSelectId: string, entryId: string, config: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
     static buildSelectorInstanceFv(instanceList: Array<PolymerEntityInstanceInterface>, elementFvId: string, elementSelectId: string, entryId: string, config: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-    static buildInstanceFv(elementId: string, instanceId: string, additionalConfig?: RcsbFvAdditionalConfig, rcsbContext?: PolymerEntityInstanceInterface): Promise<RcsbFvModulePublicInterface>;
+    static buildInstanceFv(elementId: string, instanceId: string, additionalConfig?: RcsbFvAdditionalConfig, module?: instanceModule): Promise<RcsbFvModulePublicInterface>;
 }
+export {};

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-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { SearchQuery } from "@rcsb/rcsb-api-tools/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

@@ -1,6 +1,6 @@
 import { RcsbFv, RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
 import { SequenceCollectorDataInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollector";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { SequenceCollectorInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollectorInterface";
 import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface } from "./RcsbFvModuleInterface";

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

@@ -0,0 +1,12 @@
+import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
+import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
+import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
+export declare class RcsbFvInterface extends RcsbFvAbstractModule {
+    protected readonly annotationCollector: AnnotationCollectorInterface;
+    private instanceId;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    private typeSuffix;
+    private titleSuffix;
+    private trackTitle;
+}

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

@@ -1,10 +1,21 @@
-import { Feature, FilterInput, GroupReference, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { Feature, FilterInput, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbFv, RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { PairwiseAlignmentInterface } from "../PairwiseAlignmentTools/PairwiseAlignmentBuilder";
 import { AnnotationProcessingInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { SequenceCollectorInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollectorInterface";
 import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
+export declare type RcsbContextType = Partial<{
+    entryId: string;
+    entityId: string;
+    asymId: string;
+    authId: string;
+    upAcc: string;
+    chrId: string;
+    targetId: string;
+    queryId: string;
+    operatorIds: Array<string>;
+}>;
 export interface RcsbFvAdditionalConfig {
     sources?: Array<Source>;
     filters?: Array<FilterInput>;
@@ -16,24 +27,9 @@ export interface RcsbFvAdditionalConfig {
     annotationProcessing?: AnnotationProcessingInterface;
     sequenceCollector?: SequenceCollectorInterface;
     externalTrackBuilder?: ExternalTrackBuilderInterface;
-    page?: {
-        first: number;
-        after: string;
-    };
-    rcsbContext?: Partial<{
-        entryId: string;
-        entityId: string;
-        asymId: string;
-        authId: string;
-        upAcc: string;
-        chrId: string;
-        targetId: string;
-        queryId: string;
-    }>;
+    rcsbContext?: RcsbContextType;
 }
 export interface RcsbFvModuleBuildInterface {
-    group?: GroupReference;
-    groupId?: string;
     queryId?: string;
     from?: SequenceReference;
     to?: SequenceReference;

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-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { GroupGranularityType } from "../../RcsbSeacrh/QueryStore/SearchGroupQuery";
 export interface SelectButtonConfigInterface {
     addTitle?: boolean;
     defaultValue?: string | undefined | null;
@@ -22,7 +20,6 @@ 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, groupGranularity: GroupGranularityType, groupId: string, query?: SearchQuery): void;
     static buildLoaderSpinner(elementId: string): void;
     static unmountLoaderSpinner(elementId: string): void;
     private static hideElement;

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

@@ -1,20 +1,18 @@
-import { RcsbQueryGroupAlignmentArguments } from "./RcsbQueryAlignment";
-import { AlignmentResponse, AnnotationFeatures, QueryAlignmentArgs, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { CoreEntry, GroupPolymerEntity, CorePolymerEntity, QueryEntriesArgs, QueryEntryArgs, QueryPolymer_EntitiesArgs, QueryPolymer_Entity_GroupArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { AlignmentResponse, AnnotationFeatures, QueryAlignmentArgs, QueryAnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { CoreAssembly, CoreEntry, CoreInterface, CorePolymerEntity, QueryAssembliesArgs, QueryEntriesArgs, QueryEntryArgs, QueryInterfacesArgs, 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;
+    private rcsbQueryInterfaceInstances;
+    private rcsbQueryAssemblyInterfaces;
     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: QueryPolymer_Entity_GroupArgs): Promise<GroupPolymerEntity>;
     requestMultipleEntriesProperties(requestConfig: QueryEntriesArgs): Promise<Array<CoreEntry>>;
+    requestInterfaceInstances(requestConfig: QueryInterfacesArgs): Promise<Array<CoreInterface>>;
+    requestAssemblyInterfaces(requestConfig: QueryAssembliesArgs): Promise<Array<CoreAssembly>>;
 }

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

@@ -1,17 +1,7 @@
-import { AlignmentResponse, QueryAlignmentArgs, QueryGroup_AlignmentArgs } from "@rcsb/rcsb-api-tools/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-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-api-tools/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-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/RcsbQueryAssemblyInterfaces.d.ts

@@ -0,0 +1,7 @@
+import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
+import { CoreAssembly, QueryAssembliesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
+export declare class RcsbQueryAssemblyInterfaces implements RcsbCoreQueryInterface<QueryAssembliesArgs, Array<CoreAssembly>> {
+    readonly client: GraphQLRequest;
+    request(requestConfig: QueryAssembliesArgs): Promise<Array<CoreAssembly>>;
+}

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

@@ -0,0 +1,7 @@
+import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
+import { CoreInterface, QueryInterfacesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
+export declare class RcsbQueryInterfaceInstances implements RcsbCoreQueryInterface<QueryInterfacesArgs, Array<CoreInterface>> {
+    readonly client: GraphQLRequest;
+    request(requestConfig: QueryInterfacesArgs): Promise<Array<CoreInterface>>;
+}

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

@@ -0,0 +1,4 @@
+import { AnnotationFeatures, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare const BURIAL_FRACTION: Type;
+export declare function burialFraction(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+export declare function burialFractionFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;

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

@@ -0,0 +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>;

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

@@ -3,4 +3,6 @@ export declare class TagDelimiter {
     static readonly instance: string;
     static readonly sequenceTitle: string;
     static readonly alignmentTitle: string;
+    static readonly operatorComposition: string;
+    static readonly assembly: string;
 }

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

@@ -0,0 +1,7 @@
+import { AssemblyInterfacesInterface } from "../../RcsbCollectTools/Translators/AssemblyInterfacesCollector";
+export declare class AssemblyInterfacesTranslate {
+    private readonly rawData;
+    private interfaceMap;
+    constructor(data: Array<AssemblyInterfacesInterface>);
+    getInterfaces(assemblyId: string): Array<string>;
+}

package/build/dist/RcsbUtils/{EntryAssemblyTranslate.d.ts → Translators/EntryAssemblyTranslate.d.ts}

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

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

@@ -0,0 +1,9 @@
+import { InterfaceInstanceInterface } from "../../RcsbCollectTools/Translators/InterfaceInstanceCollector";
+export declare class InterfaceInstanceTranslate {
+    private readonly rawData;
+    private readonly instances;
+    private readonly operatorsIds;
+    constructor(data: Array<InterfaceInstanceInterface>);
+    getInstances(rcsbId: string): [string, string];
+    getOperatorIds(rcsbId: string): [Array<Array<string>>, Array<Array<string>>];
+}