@rcsb/rcsb-saguaro-app 3.4.0 → 4.0.0-interfaces.4

package/CHANGELOG.md

@@ -2,6 +2,18 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [4.0.0-interfaces] - 2021-12-15
+###  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
+
+## [4.0.0-master] - 2021-12-07
+### Breaking change
+- `ExternalTrackBuilderInterface` methods return a promise and are executed asynchronous
+
 ## [3.4.0] - 2021-12-07
 ### UI improvements
 - Exposed methods for creating dropdown menus. Class `RcsbFvUI` static methods
@@ -14,6 +26,10 @@
 - 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/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, mainTitle?: string, titleSuffix?: string, typeSuffix?: string): string;
     private addNewType;
     sortAndIncludeNewTypes(): void;
     private checkAndIncludeNewType;

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

@@ -3,6 +3,7 @@ import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 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;
@@ -15,14 +16,16 @@ 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 declare type AnnotationCollectConfig = Partial<CollectAnnotationsInterface>;
 export interface AnnotationCollectorInterface extends CoreCollectorInterface {
@@ -31,4 +34,3 @@ export interface AnnotationCollectorInterface extends CoreCollectorInterface {
     getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
     getFeatures(): Promise<Array<Feature>>;
 }
-export {};

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

@@ -7,12 +7,18 @@ export interface ExternalTrackBuilderInterface {
         annotations?: Array<AnnotationFeatures>;
         alignments?: AlignmentResponse;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): void;
-    filterAlignments?(alignments: AlignmentResponse): AlignmentResponse;
-    filterFeatures?(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+    }): Promise<void>;
+    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>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): void;
+    }): Promise<void>;
 }

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

@@ -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

@@ -9,17 +9,21 @@ export interface InstanceSequenceOnchangeInterface {
     authId: string;
     asymId: string;
 }
+declare type instanceModule = "interface" | "instance";
 export interface InstanceSequenceConfig {
     dropdownTitle?: string;
     defaultValue?: string | undefined | null;
+    beforeRenderCallback?: (x: InstanceSequenceOnchangeInterface) => void;
     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, rcsbContext?: PolymerEntityInstanceInterface, module?: instanceModule): Promise<RcsbFvModulePublicInterface>;
 }
+export {};

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/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 +1,9 @@
+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>>];
+}

package/build/dist/app.d.ts

@@ -1,8 +1,12 @@
 import { GroupedOptionsInterface, SelectOptionInterface } from "./RcsbFvWeb/WebTools/SelectButton";
 export { buildEntryChromosome, buildFullChromosome, buildEntityChromosome, buildChromosome, buildEntityFv, buildEntitySummaryFv, buildSingleEntitySummaryFv, buildInstanceFv, buildInstanceSequenceFv, buildMultipleInstanceSequenceFv, buildAssemblySequenceFv, buildPairwiseAlignment, buildPfv, buildMultipleAlignmentSequenceFv, buildUniprotEntityFv, buildUniprotEntityInstanceFv, buildUniprotFv, unmount } from "./RcsbFvWeb/RcsbFvBuilder";
 import { SelectButtonConfigInterface } from "./RcsbFvWeb/WebTools/WebToolsManager";
+import { InterfaceInstanceTranslate } from "./RcsbUtils/InterfaceInstanceTranslate";
 export declare class RcsbFvUI {
     static clearSelectButton(elementFvId: string, selectButtonId: string): void;
     static createSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface> | Array<GroupedOptionsInterface>, config?: SelectButtonConfigInterface): void;
     static addSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface>, config?: SelectButtonConfigInterface): void;
 }
+export declare class RcsbFvContextManager {
+    static getInterfaceToInstance(interfaceId: string): Promise<InterfaceInstanceTranslate>;
+}