@rcsb/rcsb-saguaro-app 3.2.1 → 3.3.0-interfaces

package/CHANGELOG.md

@@ -2,6 +2,16 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [3.3.0] - 2021-11-29
+### Annotations configuration improvements
+- 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
 - Dropdown title configuration is exposed in `InstanceSequenceConfig` attribute `dropdownTitle` 

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

@@ -21,10 +21,11 @@ export declare class RcsbAnnotationConfig {
     uniprotOrder(): Array<string>;
     instanceOrder(): Array<string>;
     entityOrder(): Array<string>;
-    buildAndAddType(d: Feature, targetId?: string): string;
+    buildAndAddType(d: Feature, mainTitle?: string, titleSuffix?: string): string;
     private addNewType;
     sortAndIncludeNewTypes(): void;
     private checkAndIncludeNewType;
+    private cleanAddedTypes;
     isMergedType(type: string): boolean;
     getMergedType(type: string): string;
     annotationMergedPreference(type: string, a: RcsbFvTrackDataElementInterface, b: RcsbFvTrackDataElementInterface): boolean;

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

@@ -20,7 +20,6 @@ export declare class AnnotationCollector implements AnnotationCollectorInterface
     private externalTrackBuilder;
     constructor(acm?: AnnotationConfigInterface);
     collect(requestConfig: AnnotationCollectConfig): Promise<Array<RcsbFvRowConfigInterface>>;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
     setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
     getFeatures(): Promise<Array<Feature>>;

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

@@ -1,6 +1,6 @@
 import { CoreCollectorInterface } from "../CoreCollectorInterface";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
-import { AnnotationFeatures, Feature, QueryAnnotationsArgs, Source } 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";
 export declare type IncreaseAnnotationValueType = (feature: {
@@ -20,8 +20,9 @@ interface CommonAnnotationInterface {
     externalAnnotationTrackBuilder?: ExternalTrackBuilderInterface;
 }
 export interface CollectAnnotationsInterface extends QueryAnnotationsArgs, CommonAnnotationInterface {
-    addTargetInTitle?: Set<Source>;
     collectSwissModel?: boolean;
+    titleSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+    trackTitle?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
 }
 export declare type AnnotationCollectConfig = Partial<CollectAnnotationsInterface>;
 export interface AnnotationCollectorInterface extends CoreCollectorInterface {

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

@@ -8,11 +8,12 @@ export declare class AnnotationTrackManager {
     private readonly annotationTracks;
     private polymerEntityInstanceTranslator;
     constructor(rcsbAnnotationConfig: RcsbAnnotationConfig);
-    processRcsbPdbAnnotations(data: Array<AnnotationFeatures>, requestConfig: AnnotationCollectConfig): void;
+    processRcsbPdbAnnotations(data: Array<AnnotationFeatures>, requestConfig: AnnotationCollectConfig): Promise<void>;
     getAnnotationTracks(): Map<string, AnnotationTrack>;
     private getPolymerEntityInstanceTranslator;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
     private mergeTracks;
     private buildType;
     private addAnnotationToTracks;
+    private addFeature;
 }

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

@@ -5,5 +5,4 @@ export interface CoreCollectorInterface {
     readonly rcsbFvQuery: RcsbClient;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
     setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
 }

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

@@ -30,7 +30,6 @@ export declare class SequenceCollector implements SequenceCollectorInterface {
     getTargets(): Promise<Array<string>>;
     getAlignmentResponse(): Promise<AlignmentResponse>;
     getSequenceLength(): number;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
     setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
     private complete;

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

@@ -0,0 +1,11 @@
+import { QueryInterfacesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+export interface InterfaceInstanceInterface {
+    rcsbId: string;
+    assemblyId: string;
+    interfaceId: string;
+    asymIds: [string, string];
+}
+export declare class InterfaceInstanceCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryInterfacesArgs): Promise<Array<InterfaceInstanceInterface>>;
+}

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

@@ -2,11 +2,13 @@ import { RcsbFv, RcsbFvBoardConfigInterface } from "@rcsb/rcsb-saguaro";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { EntryAssemblyTranslate } from "../../RcsbUtils/EntryAssemblyTranslate";
 import { PolymerEntityChromosomeTranslate } from "../../RcsbUtils/PolymerEntityChromosomeTranslate";
+import { InterfaceInstanceTranslate } from "../../RcsbUtils/InterfaceInstanceTranslate";
 declare class RcsbFvContextManager {
     private rcsbFvManager;
     private rcsbButtonManager;
     private polymerEntityToInstanceMap;
     private entryToAssemblyMap;
+    private interfaceToInstanceMap;
     getFv(elementFvId: string, boardConfig?: Partial<RcsbFvBoardConfigInterface>): RcsbFv;
     hasFv(elementFvId: string): boolean;
     private setFv;
@@ -18,6 +20,7 @@ declare class RcsbFvContextManager {
     getEntityToInstance(entryId: string): Promise<PolymerEntityInstanceTranslate>;
     getEntryToAssembly(entryId: string): Promise<EntryAssemblyTranslate>;
     getEntityToChromosome(entityIds: Array<string>): Promise<PolymerEntityChromosomeTranslate>;
+    getInterfaceToInstance(interfaceId: string): Promise<InterfaceInstanceTranslate>;
 }
 export declare const rcsbFvCtxManager: RcsbFvContextManager;
 export {};

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

@@ -9,6 +9,7 @@ export interface InstanceSequenceOnchangeInterface {
     authId: string;
     asymId: string;
 }
+declare type instanceModule = "interface" | "instance";
 export interface InstanceSequenceConfig {
     dropdownTitle?: string;
     defaultValue?: string | undefined | null;
@@ -16,10 +17,12 @@ export interface InstanceSequenceConfig {
     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, rcsbContext?: PolymerEntityInstanceInterface, module?: instanceModule): Promise<RcsbFvModulePublicInterface>;
 }
+export {};

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

@@ -10,6 +10,7 @@ export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterf
     protected readonly elementId: string;
     protected boardConfigData: RcsbFvBoardConfigInterface;
     protected rowConfigData: Array<RcsbFvRowConfigInterface>;
+    protected polymerEntityInstance: PolymerEntityInstanceTranslate;
     protected readonly sequenceCollector: SequenceCollectorInterface;
     protected readonly annotationCollector: AnnotationCollectorInterface;
     protected alignmentTracks: SequenceCollectorDataInterface;

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

@@ -3,4 +3,5 @@ import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 export declare class RcsbFvEntity extends RcsbFvAbstractModule {
     protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    private titleSuffix;
 }

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

@@ -0,0 +1,10 @@
+import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
+import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
+import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
+export declare class RcsbFvInterface extends RcsbFvAbstractModule {
+    protected readonly annotationCollector: AnnotationCollectorInterface;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    private titleSuffix;
+    private trackTitle;
+}

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

@@ -3,4 +3,5 @@ import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 export declare class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
     protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    private titleSuffix;
 }

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

@@ -1,14 +1,16 @@
 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";
+import { CoreEntry, CoreInterface, CorePolymerEntity, QueryEntriesArgs, QueryEntryArgs, QueryInterfacesArgs, QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 export declare class RcsbClient {
     private rcsbQueryAnnotations;
     private rcsbQueryAlignment;
     private rcsbQueryEntityInstances;
     private rcsbQueryMutipleEntityInstances;
     private rcsbQueryEntryProperties;
+    private rcsbQueryInterfaceInstances;
     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>>;
 }

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/InterfaceInstanceTranslate.d.ts

@@ -0,0 +1,7 @@
+import { InterfaceInstanceInterface } from "../RcsbCollectTools/Translators/InterfaceInstanceCollector";
+export declare class InterfaceInstanceTranslate {
+    private readonly rawData;
+    private readonly instances;
+    constructor(data: Array<InterfaceInstanceInterface>);
+    getInstances(rcsbId: string): [string, string];
+}