@rcsb/rcsb-saguaro-app 4.4.0-models.2 → 4.4.0-models.3

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

@@ -27,7 +27,7 @@ export declare class RcsbAnnotationConfig {
     private checkAndIncludeNewType;
     private cleanAddedTypes;
     isMergedType(type: string): boolean;
-    getMergedType(type: string): string;
+    getMergeConfig(type: string): RcsbMergedTypesInterface;
     annotationMergedPreference(type: string, a: RcsbFvTrackDataElementInterface, b: RcsbFvTrackDataElementInterface): boolean;
     static randomRgba(str?: string): string;
     addProvenance(type: string, provenanceName: string): void;

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory.d.ts

@@ -1,10 +1,10 @@
-import { AlignmentResponse, AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { AlignmentRequestContextType } from "../RcsbFvTrackFactory/AlignmentTrackFactory";
+import { AlignmentResponse, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentRequestContextType } from "../RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
 import { BlockFactoryInterface } from "./BlockFactoryInterface";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { TrackFactoryInterface } from "../RcsbFvTrackFactory/TrackFactoryInterface";
-export declare class AlignmentBlockFactory implements BlockFactoryInterface<[AlignmentRequestContextType, AlignmentResponse, Array<AnnotationFeatures>]> {
-    private readonly alignmentTrackFactory;
-    constructor(alignmentTrackFactory: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment, Array<AnnotationFeatures>]> | TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>);
-    getBlock(alignmentRequestContext: AlignmentRequestContextType, alignmentData: AlignmentResponse, features?: Array<AnnotationFeatures>): Promise<RcsbFvRowConfigInterface[]>;
+export declare class AlignmentBlockFactory implements BlockFactoryInterface<[AlignmentRequestContextType, AlignmentResponse], [AlignmentRequestContextType, TargetAlignment]> {
+    readonly trackFactory: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
+    constructor(alignmentTrackFactory: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>);
+    getBlock(alignmentRequestContext: AlignmentRequestContextType, alignmentData: AlignmentResponse): Promise<RcsbFvRowConfigInterface[]>;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory.d.ts

@@ -5,10 +5,10 @@ import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types
 import { TrackFactoryInterface } from "../RcsbFvTrackFactory/TrackFactoryInterface";
 import { BlockManagerInterface } from "./BlockManager/BlockManagerInterface";
 import { TrackManagerInterface } from "./BlockManager/TrackManagerInterface";
-export declare class AnnotationsBlockFactory implements BlockFactoryInterface<[AnnotationRequestContext, AnnotationFeatures[]]> {
+export declare class AnnotationsBlockFactory implements BlockFactoryInterface<[AnnotationRequestContext, AnnotationFeatures[]], [TrackManagerInterface]> {
     private readonly annotationBlockManager;
     private readonly annotationsBlockData;
-    private readonly annotationTrackFactory;
+    readonly trackFactory: TrackFactoryInterface<[TrackManagerInterface]>;
     constructor(annotationBlockManager: BlockManagerInterface<[AnnotationRequestContext, AnnotationFeatures[]]>, annotationTrackFactory: TrackFactoryInterface<[TrackManagerInterface]>);
     getBlock(annotationsRequestContext: AnnotationRequestContext, annotations: AnnotationFeatures[]): Promise<RcsbFvRowConfigInterface[]>;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockFactoryInterface.d.ts

@@ -1,4 +1,6 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
-export interface BlockFactoryInterface<T extends any[]> {
+import { TrackFactoryInterface } from "../RcsbFvTrackFactory/TrackFactoryInterface";
+export interface BlockFactoryInterface<T extends any[], S extends any[]> {
+    readonly trackFactory: TrackFactoryInterface<S>;
     getBlock(...args: T): Promise<RcsbFvRowConfigInterface[]>;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager.d.ts

@@ -15,7 +15,7 @@ export declare class AnnotationBlockManager implements BlockManagerInterface<[An
     getTracks(): Array<TrackManagerInterface>;
     private has;
     private orderedTypes;
-    private addAnnotationToTracks;
+    private processAnnotations;
     private addFeature;
     private buildType;
     private mergeTracks;

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface.d.ts

@@ -6,7 +6,7 @@ export interface TrackManagerFactoryInterface<T extends any[]> {
     getTrackManager(...args: T): TrackManagerInterface;
 }
 export interface TrackManagerInterface {
-    getTrackId(): string;
+    getId(): string;
     getConfig(): RcsbAnnotationConfigInterface;
     getRange(): {
         min: number;

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/{AlignmentTrackFactory.d.ts → TrackFactoryImpl/AlignmentTrackFactory.d.ts}

@@ -1,19 +1,19 @@
 import { RcsbFvLink, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
 import { AlignedRegion, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "./TrackFactoryInterface";
-import { AlignmentCollectConfig } from "../../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
+import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { TrackFactoryInterface } from "../TrackFactoryInterface";
+import { AlignmentCollectConfig } from "../../../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
 export declare type AlignmentRequestContextType = AlignmentCollectConfig & {
     querySequence?: string;
 };
 export declare class AlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private readonly sequenceTrackFactory;
     private readonly entityInstanceTranslator;
+    private readonly trackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
     getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
-    buildAlignmentRowTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): string | RcsbFvLink;
+    buildAlignmentRowTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
     private getAlignmentTrackConfiguration;
-    private buildInstanceId;
     alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
     addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/{AnnotationsTrackFactory.d.ts → TrackFactoryImpl/AnnotationsTrackFactory.d.ts}

@@ -1,6 +1,6 @@
-import { TrackFactoryInterface } from "./TrackFactoryInterface";
+import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
-import { TrackManagerInterface } from "../RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
+import { TrackManagerInterface } from "../../RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
 export declare class AnnotationsTrackFactory implements TrackFactoryInterface<[TrackManagerInterface]> {
     getTrack(annotations: TrackManagerInterface): Promise<RcsbFvRowConfigInterface>;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/{ObservedAlignmentTrackFactory.d.ts → TrackFactoryImpl/ObservedAlignmentTrackFactory.d.ts}

@@ -1,6 +1,6 @@
 import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "./TrackFactoryInterface";
+import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
 export declare class ObservedAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/{PlainAlignmentTrackFactory.d.ts → TrackFactoryImpl/PlainAlignmentTrackFactory.d.ts}

@@ -1,23 +1,23 @@
 import { RcsbFvColorGradient, RcsbFvLink, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
 import { AlignedRegion, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "./TrackFactoryInterface";
-import { AlignmentCollectConfig } from "../../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
+import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { TrackFactoryInterface } from "../TrackFactoryInterface";
+import { AlignmentCollectConfig } from "../../../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
 export declare type AlignmentRequestContextType = AlignmentCollectConfig & {
     querySequence?: string;
 };
 export declare class PlainAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private readonly sequenceTrackFactory;
     private readonly entityInstanceTranslator;
+    private readonly trackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
     getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>, alignmentColor?: RcsbFvColorGradient): Promise<RcsbFvRowConfigInterface>;
-    buildAlignmentRowTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): string | RcsbFvLink;
+    buildAlignmentRowTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
     getAlignmentTrackConfiguration(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): {
         alignedBlocks: Array<RcsbFvTrackDataElementInterface>;
         mismatchData: Array<RcsbFvTrackDataElementInterface>;
         sequenceData: Array<RcsbFvTrackDataElementInterface>;
     };
-    private buildInstanceId;
     alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
     addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/{PlainObservedAlignmentTrackFactory.d.ts → TrackFactoryImpl/PlainObservedAlignmentTrackFactory.d.ts}

@@ -1,6 +1,6 @@
 import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "./TrackFactoryInterface";
+import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
 export declare class PlainObservedAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/{PositionalScoreAlignmentTrackFactory.d.ts → TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.d.ts}

@@ -1,6 +1,6 @@
 import { AlignedRegion, AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { AlignmentContextInterface, PolymerEntityInstanceTranslate } from "../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "./TrackFactoryInterface";
+import { AlignmentContextInterface, PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
 export declare class PositionalScoreAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/{SequenceTrackFactory.d.ts → TrackFactoryImpl/SequenceTrackFactory.d.ts}

@@ -1,7 +1,7 @@
-import { AlignmentCollectConfig } from "../../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
+import { AlignmentCollectConfig } from "../../../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
 import { RcsbFvLink, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
-import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "./TrackFactoryInterface";
+import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
 interface BuildSequenceDataInterface extends AlignmentContextInterface {
     sequence: string;

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/{UniprotAlignmentTrackFactory.d.ts → TrackFactoryImpl/UniprotAlignmentTrackFactory.d.ts}

@@ -1,8 +1,8 @@
-import { TrackFactoryInterface } from "./TrackFactoryInterface";
+import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
 import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
-import { PolymerEntityInstanceTranslate } from "../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 export declare class UniprotAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private observedAlignmentTrackFactory;
     private positionalScoreAlignmentTrackFactory;

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AlignmentTrackTitleFactory.d.ts

@@ -0,0 +1,11 @@
+import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
+import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
+import { RcsbFvLink } from "@rcsb/rcsb-saguaro";
+import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+export declare class AlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+    private readonly entityInstanceTranslator;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
+    private buildInstanceId;
+}

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryInterface.d.ts

@@ -0,0 +1,4 @@
+import { RcsbFvLink } from "@rcsb/rcsb-saguaro";
+export interface TrackTitleFactoryInterface<T extends any[]> {
+    getTrackTitle(...args: T): Promise<string | RcsbFvLink>;
+}

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

@@ -5,7 +5,7 @@ import { AnnotationRequestContext, AnnotationCollectorInterface } from "../../Rc
 import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface } from "./RcsbFvModuleInterface";
 import { AlignmentResponse, AnnotationFeatures, Feature, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { TrackFactoryInterface } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryInterface";
-import { AlignmentRequestContextType } from "../RcsbFvFactories/RcsbFvTrackFactory/AlignmentTrackFactory";
+import { AlignmentRequestContextType } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
 import { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
 export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterface {
     protected readonly rcsbFv: RcsbFv;