@rcsb/rcsb-saguaro-app 4.0.0-interfaces.8 → 4.0.0-interfaces.9

package/CHANGELOG.md

@@ -12,6 +12,7 @@
     - 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

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, typeSuffix?: string): string;
+    buildAndAddType(d: Feature, trackTitle?: string, titleSuffix?: string, typeSuffix?: string): string;
     private addNewType;
     sortAndIncludeNewTypes(): void;
     private checkAndIncludeNewType;

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

@@ -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/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/RcsbFvWeb/RcsbFvBuilder/RcsbFvContextManager.d.ts

@@ -9,6 +9,7 @@ declare class RcsbFvContextManager {
     private polymerEntityToInstanceMap;
     private entryToAssemblyMap;
     private interfaceToInstanceMap;
+    private assemblyInterfacesMap;
     getFv(elementFvId: string, boardConfig?: Partial<RcsbFvBoardConfigInterface>): RcsbFv;
     hasFv(elementFvId: string): boolean;
     private setFv;
@@ -21,6 +22,7 @@ declare class RcsbFvContextManager {
     getEntryToAssembly(entryId: string): Promise<EntryAssemblyTranslate>;
     getEntityToChromosome(entityIds: Array<string>): Promise<PolymerEntityChromosomeTranslate>;
     getInterfaceToInstance(interfaceId: string): Promise<InterfaceInstanceTranslate>;
+    private getAssemblyInterfaces;
 }
 export declare const rcsbFvCtxManager: RcsbFvContextManager;
 export {};

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

@@ -1,5 +1,5 @@
 import { AlignmentResponse, AnnotationFeatures, QueryAlignmentArgs, QueryAnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { CoreEntry, CoreInterface, CorePolymerEntity, QueryEntriesArgs, QueryEntryArgs, QueryInterfacesArgs, QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/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 rcsbQueryAlignment;
@@ -7,10 +7,12 @@ export declare class RcsbClient {
     private rcsbQueryMutipleEntityInstances;
     private rcsbQueryEntryProperties;
     private rcsbQueryInterfaceInstances;
+    private rcsbQueryAssemblyInterfaces;
     requestRcsbPdbAnnotations(requestConfig: QueryAnnotationsArgs): Promise<Array<AnnotationFeatures>>;
     requestAlignment(requestConfig: QueryAlignmentArgs): Promise<AlignmentResponse>;
     requestEntityInstances(requestConfig: QueryEntryArgs): Promise<CoreEntry>;
     requestMultipleEntityInstances(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<CorePolymerEntity>>;
     requestMultipleEntriesProperties(requestConfig: QueryEntriesArgs): Promise<Array<CoreEntry>>;
     requestInterfaceInstances(requestConfig: QueryInterfacesArgs): Promise<Array<CoreInterface>>;
+    requestAssemblyInterfaces(requestConfig: QueryAssembliesArgs): Promise<Array<CoreAssembly>>;
 }

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/RcsbUtils/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/TagDelimiter.d.ts

@@ -4,4 +4,5 @@ export declare class TagDelimiter {
     static readonly sequenceTitle: string;
     static readonly alignmentTitle: string;
     static readonly operatorComposition: string;
+    static readonly assembly: string;
 }