@rcsb/rcsb-saguaro-app 4.3.6 → 4.4.0-models.2

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

@@ -0,0 +1,19 @@
+import { AlignmentCollectConfig, AlignmentCollectorInterface } from "./AlignmentCollectorInterface";
+import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare class AlignmentCollector implements AlignmentCollectorInterface {
+    private sequenceLength;
+    private requestStatus;
+    private dynamicDisplay;
+    readonly rcsbFvQuery: RcsbClient;
+    private readonly targetsSubject;
+    private alignmentResponse;
+    private readonly alignmentResponseSubject;
+    private readonly alignmentLengthSubject;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
+    getTargets(): Promise<Array<string>>;
+    getAlignment(): Promise<AlignmentResponse>;
+    getAlignmentLength(): Promise<number>;
+    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<AlignmentResponse>;
+    private complete;
+}

package/build/dist/RcsbCollectTools/{SequenceCollector/SequenceCollectorInterface.d.ts → AlignmentCollector/AlignmentCollectorInterface.d.ts}

@@ -1,5 +1,3 @@
-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 {
@@ -15,10 +13,10 @@ export interface CollectGroupAlignmentInterface extends RcsbQueryGroupAlignmentA
     sequencePrefix: string;
 }
 export declare type AlignmentCollectConfig = Partial<CollectAlignmentInterface & CollectGroupAlignmentInterface>;
-export interface SequenceCollectorInterface extends CoreCollectorInterface {
+export interface AlignmentCollectorInterface {
     getTargets(): Promise<Array<string>>;
-    getAlignmentResponse(): Promise<AlignmentResponse>;
-    getSequenceLength(): number;
-    collect(requestConfig: CollectAlignmentInterface | CollectGroupAlignmentInterface, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<void>): Promise<SequenceCollectorDataInterface>;
+    getAlignment(): Promise<AlignmentResponse>;
+    getAlignmentLength(): Promise<number>;
+    collect(requestConfig: CollectAlignmentInterface | CollectGroupAlignmentInterface, filter?: Array<string>): Promise<AlignmentResponse>;
 }
 export {};

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

@@ -1,31 +1,16 @@
-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/Translators/PolymerEntityInstanceTranslate";
-import { AnnotationCollectConfig, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
-import { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
-import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
+import { AnnotationRequestContext, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
 export declare class AnnotationCollector implements AnnotationCollectorInterface {
-    private readonly rcsbAnnotationConfig;
-    private readonly annotationsConfigData;
     readonly rcsbFvQuery: RcsbClient;
-    private polymerEntityInstanceTranslator;
     private requestStatus;
     private rawFeatures;
-    private readonly rawFeaturesSubject;
-    private readonly annotationsConfigDataSubject;
-    private readonly annotationTrackManager;
     private annotationFeatures;
+    private readonly rawFeaturesSubject;
     private readonly annotationFeaturesSubject;
-    private externalTrackBuilder;
-    constructor(acm?: AnnotationConfigInterface);
-    collect(requestConfig: AnnotationCollectConfig): Promise<Array<RcsbFvRowConfigInterface>>;
-    setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
+    collect(requestConfig: AnnotationRequestContext): Promise<Array<AnnotationFeatures>>;
     getFeatures(): Promise<Array<Feature>>;
-    getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
     getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
-    private processRcsbPdbAnnotations;
     private requestAnnotations;
     private complete;
 }

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

@@ -1,9 +1,8 @@
-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 { AnnotationTrack, FeaturePositionGaps } from "./AnnotationTrack";
+import { FeaturePositionGaps } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
+import { TrackManagerInterface } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
 export declare type IncreaseAnnotationValueType = (feature: {
     type: string;
     targetId: string;
@@ -13,7 +12,7 @@ export declare type IncreaseAnnotationValueType = (feature: {
 }) => number;
 export interface AnnotationProcessingInterface {
     getAnnotationValue?: IncreaseAnnotationValueType;
-    computeAnnotationValue?: (annotationTracks: Map<string, AnnotationTrack>) => void;
+    computeAnnotationValue?: (annotationTracks: Map<string, TrackManagerInterface>) => void;
     addTrackElementCallback?: IncreaseAnnotationValueType;
 }
 export interface CommonAnnotationInterface {
@@ -31,10 +30,9 @@ export interface CollectAnnotationsInterface extends QueryAnnotationsArgs, Commo
 }
 export interface CollectGroupAnnotationsInterface extends QueryGroup_AnnotationsArgs, CommonAnnotationInterface {
 }
-export declare type AnnotationCollectConfig = Partial<CollectAnnotationsInterface & CollectGroupAnnotationsInterface>;
-export interface AnnotationCollectorInterface extends CoreCollectorInterface {
-    collect(requestConfig: CollectAnnotationsInterface | CollectGroupAnnotationsInterface): Promise<Array<RcsbFvRowConfigInterface>>;
-    getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
+export declare type AnnotationRequestContext = Partial<CollectAnnotationsInterface & CollectGroupAnnotationsInterface>;
+export interface AnnotationCollectorInterface {
+    collect(requestConfig: CollectAnnotationsInterface | CollectGroupAnnotationsInterface): Promise<Array<AnnotationFeatures>>;
     getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
     getFeatures(): Promise<Array<Feature>>;
 }

package/build/dist/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.d.ts

@@ -8,6 +8,7 @@ export interface EntryPropertyIntreface {
     taxNames: Array<string>;
     entryMolecularWeight: number;
     description: Array<string>;
+    entityToInstance: Map<string, Array<string>>;
 }
 export declare class MultipleEntryPropertyCollector {
     private readonly rcsbFvQuery;

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

@@ -1,6 +1,5 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { SequenceCollectorDataInterface } from "../SequenceCollector/SequenceCollector";
 import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
 export interface ExternalTrackBuilderInterface {
     processAlignmentAndFeatures?(data: {
@@ -17,7 +16,7 @@ export interface ExternalTrackBuilderInterface {
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     }): Promise<Array<AnnotationFeatures>>;
     addTo?(tracks: {
-        alignmentTracks?: SequenceCollectorDataInterface;
+        alignmentTracks?: Array<RcsbFvRowConfigInterface>;
         annotationTracks?: Array<RcsbFvRowConfigInterface>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     }): Promise<void>;

package/build/dist/RcsbFvExamples/SequenceIdentityGroupFv.d.ts

@@ -0,0 +1 @@
+export {};

package/build/dist/RcsbFvExamples/UniprotGroupFv.d.ts

@@ -0,0 +1 @@
+export {};

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

@@ -0,0 +1,10 @@
+import { AlignmentResponse, AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentRequestContextType } from "../RcsbFvTrackFactory/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[]>;
+}

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

@@ -0,0 +1,14 @@
+import { AnnotationRequestContext } from "../../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
+import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
+import { BlockFactoryInterface } from "./BlockFactoryInterface";
+import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { TrackFactoryInterface } from "../RcsbFvTrackFactory/TrackFactoryInterface";
+import { BlockManagerInterface } from "./BlockManager/BlockManagerInterface";
+import { TrackManagerInterface } from "./BlockManager/TrackManagerInterface";
+export declare class AnnotationsBlockFactory implements BlockFactoryInterface<[AnnotationRequestContext, AnnotationFeatures[]]> {
+    private readonly annotationBlockManager;
+    private readonly annotationsBlockData;
+    private readonly annotationTrackFactory;
+    constructor(annotationBlockManager: BlockManagerInterface<[AnnotationRequestContext, AnnotationFeatures[]]>, annotationTrackFactory: TrackFactoryInterface<[TrackManagerInterface]>);
+    getBlock(annotationsRequestContext: AnnotationRequestContext, annotations: AnnotationFeatures[]): Promise<RcsbFvRowConfigInterface[]>;
+}

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

@@ -0,0 +1,4 @@
+import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
+export interface BlockFactoryInterface<T extends any[]> {
+    getBlock(...args: T): Promise<RcsbFvRowConfigInterface[]>;
+}

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

@@ -0,0 +1,22 @@
+import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { RcsbAnnotationConfig } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConfig";
+import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { AnnotationRequestContext } from "../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
+import { BlockManagerInterface } from "./BlockManagerInterface";
+import { TrackManagerFactoryInterface, TrackManagerInterface } from "./TrackManagerInterface";
+import { RcsbAnnotationConfigInterface } from "../../../../RcsbAnnotationConfig/AnnotationConfigInterface";
+export declare class AnnotationBlockManager implements BlockManagerInterface<[AnnotationRequestContext, AnnotationFeatures[]]> {
+    private readonly rcsbAnnotationConfig;
+    private readonly annotationTracks;
+    private readonly polymerEntityInstanceTranslator;
+    private readonly trackManagerFactory;
+    constructor(trackManagerFactory: TrackManagerFactoryInterface<[string, RcsbAnnotationConfigInterface, PolymerEntityInstanceTranslate]>, rcsbAnnotationConfig: RcsbAnnotationConfig, polymerEntityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    setData(requestConfig: AnnotationRequestContext, data: Array<AnnotationFeatures>): Promise<void>;
+    getTracks(): Array<TrackManagerInterface>;
+    private has;
+    private orderedTypes;
+    private addAnnotationToTracks;
+    private addFeature;
+    private buildType;
+    private mergeTracks;
+}

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

@@ -0,0 +1,11 @@
+import { RcsbFvTrackDataElementGapInterface } from "@rcsb/rcsb-saguaro";
+import { FeaturePosition } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { RcsbAnnotationConfigInterface } from "../../../../RcsbAnnotationConfig/AnnotationConfigInterface";
+import { TrackManagerFactoryInterface, TrackManagerInterface } from "./TrackManagerInterface";
+export interface FeaturePositionGaps extends FeaturePosition {
+    gaps?: Array<RcsbFvTrackDataElementGapInterface>;
+}
+export declare class AnnotationTrackManagerFactory implements TrackManagerFactoryInterface<[string, RcsbAnnotationConfigInterface, PolymerEntityInstanceTranslate]> {
+    getTrackManager(trackId: string, annotationConfig: RcsbAnnotationConfigInterface, entityInstanceTranslator: PolymerEntityInstanceTranslate): TrackManagerInterface;
+}

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

@@ -0,0 +1,5 @@
+import { TrackManagerInterface } from "./TrackManagerInterface";
+export interface BlockManagerInterface<T extends any[]> {
+    setData(...args: T): Promise<void>;
+    getTracks(): TrackManagerInterface[];
+}

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

@@ -0,0 +1,27 @@
+import { RcsbAnnotationConfigInterface } from "../../../../RcsbAnnotationConfig/AnnotationConfigInterface";
+import { Feature, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationProcessingInterface } from "../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
+import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
+export interface TrackManagerFactoryInterface<T extends any[]> {
+    getTrackManager(...args: T): TrackManagerInterface;
+}
+export interface TrackManagerInterface {
+    getTrackId(): string;
+    getConfig(): RcsbAnnotationConfigInterface;
+    getRange(): {
+        min: number;
+        max: number;
+    };
+    addFeature(ann: {
+        reference: SequenceReference | undefined;
+        queryId: string;
+        source: Source;
+        targetId: string;
+        feature: Feature;
+    }, annotationProcessing?: AnnotationProcessingInterface): void;
+    size(): number;
+    forEach(f: (ann: RcsbFvTrackDataElementInterface, loc: string) => void): void;
+    addAll(trackElementsMap: TrackManagerInterface, color?: string): void;
+    getTrackProvenance(): Set<string>;
+    values(): Array<RcsbFvTrackDataElementInterface>;
+}

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

@@ -0,0 +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";
+export declare type AlignmentRequestContextType = AlignmentCollectConfig & {
+    querySequence?: string;
+};
+export declare class AlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+    private readonly sequenceTrackFactory;
+    private readonly entityInstanceTranslator;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
+    buildAlignmentRowTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): 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

@@ -0,0 +1,6 @@
+import { TrackFactoryInterface } from "./TrackFactoryInterface";
+import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
+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

@@ -0,0 +1,17 @@
+import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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]> {
+    private alignmentTrackFactory;
+    private unObservedResidues;
+    private readonly instanceEntityMap;
+    private readonly entityInstanceNumberMap;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrack(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(unObservedRegions: Array<AnnotationFeatures>): Promise<void>;
+    private collectFeatureEntryProperties;
+    private prepareFeaturesAlignmentMap;
+    private alignedRegionToTrackElementList;
+}

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

@@ -0,0 +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";
+export declare type AlignmentRequestContextType = AlignmentCollectConfig & {
+    querySequence?: string;
+};
+export declare class PlainAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+    private readonly sequenceTrackFactory;
+    private readonly entityInstanceTranslator;
+    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;
+    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

@@ -0,0 +1,17 @@
+import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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]> {
+    private alignmentTrackFactory;
+    private unObservedResidues;
+    private readonly instanceEntityMap;
+    private readonly entityInstanceNumberMap;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(unObservedRegions: Array<AnnotationFeatures>): Promise<void>;
+    private collectFeatureEntryProperties;
+    private prepareFeaturesAlignmentMap;
+    private alignedRegionToTrackElementList;
+}

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

@@ -0,0 +1,16 @@
+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 { RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
+import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
+export declare class PositionalScoreAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+    private alignmentTrackFactory;
+    private positionalScores;
+    private readonly instanceEntityMap;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(positionalScores: Array<AnnotationFeatures>): Promise<void>;
+    private collectFeatureEntryProperties;
+    private prepareFeaturesAlignmentMap;
+    private alignedRegionToTrackElementList;
+}

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

@@ -0,0 +1,20 @@
+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 { AlignmentRequestContextType } from "./AlignmentTrackFactory";
+interface BuildSequenceDataInterface extends AlignmentContextInterface {
+    sequence: string;
+    begin: number;
+    oriBegin: number;
+}
+export declare class SequenceTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, string]> {
+    private readonly entityInstanceTranslator;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrack(alignmentQueryContext: AlignmentRequestContextType, querySequence: string): Promise<RcsbFvRowConfigInterface>;
+    buildSequenceData(config: BuildSequenceDataInterface, source: "from" | "to"): Array<RcsbFvTrackDataElementInterface>;
+    addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
+    buildSequenceRowTitle(requestConfig: AlignmentCollectConfig): string | RcsbFvLink;
+    private buildInstanceId;
+}
+export {};

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

@@ -0,0 +1,4 @@
+import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
+export interface TrackFactoryInterface<T extends any[]> {
+    getTrack(...args: T): Promise<RcsbFvRowConfigInterface>;
+}

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

@@ -0,0 +1,12 @@
+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";
+export declare class UniprotAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+    private observedAlignmentTrackFactory;
+    private positionalScoreAlignmentTrackFactory;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrack(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(unObservedRegions: Array<AnnotationFeatures>, positionalScores: Array<AnnotationFeatures>): Promise<void>;
+}

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

@@ -1,23 +1,28 @@
 import { RcsbFv, RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
-import { SequenceCollectorDataInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollector";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { SequenceCollectorInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollectorInterface";
-import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
+import { AlignmentCollectorInterface } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
+import { AnnotationRequestContext, AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface } from "./RcsbFvModuleInterface";
-import { AlignmentResponse, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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 { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
 export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterface {
     protected readonly rcsbFv: RcsbFv;
     protected readonly elementId: string;
     protected boardConfigData: RcsbFvBoardConfigInterface;
     protected rowConfigData: Array<RcsbFvRowConfigInterface>;
     protected polymerEntityInstance: PolymerEntityInstanceTranslate;
-    protected readonly sequenceCollector: SequenceCollectorInterface;
+    protected readonly alignmentCollector: AlignmentCollectorInterface;
     protected readonly annotationCollector: AnnotationCollectorInterface;
-    protected alignmentTracks: SequenceCollectorDataInterface;
+    protected referenceTrack: RcsbFvRowConfigInterface;
+    protected alignmentTracks: Array<RcsbFvRowConfigInterface>;
     protected annotationTracks: Array<RcsbFvRowConfigInterface>;
+    private rcsbFvRowUpdatePromise;
     private activeDisplayFlag;
     constructor(elementId: string, rcsbFv: RcsbFv);
     setPolymerEntityInstanceTranslator(polymerEntityInstance: PolymerEntityInstanceTranslate): void;
+    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
     display(): Promise<void>;
     activeDisplay(): boolean;
     getFv(): RcsbFv;
@@ -25,10 +30,11 @@ export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterf
     getAlignmentResponse(): Promise<AlignmentResponse>;
     getFeatures(): Promise<Array<Feature>>;
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
-    updateBoardConfig(config: Partial<RcsbFvBoardConfigInterface>): void;
     build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    wait(): Promise<void>;
     protected abstract protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     protected abstract concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    protected buildAlignmentTracks(alignmentRequestContext: AlignmentRequestContextType, alignmentResponse: AlignmentResponse, trackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>): Promise<void>;
+    protected buildAnnotationsTrack(annotationsRequestContext: AnnotationRequestContext, annotationsFeatures: AnnotationFeatures[], annotationConfigMap?: AnnotationConfigInterface): Promise<void>;
     private buildExternalTracks;
-    private setExternalTrackBuilder;
 }

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

@@ -1,8 +1,6 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
-import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 export declare class RcsbFvGroupAlignment extends RcsbFvAbstractModule {
-    protected readonly annotationCollector: AnnotationCollectorInterface;
     protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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

@@ -1,8 +1,6 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
-import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 export declare class RcsbFvGroupAnnotation extends RcsbFvAbstractModule {
-    protected readonly annotationCollector: AnnotationCollectorInterface;
     protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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

@@ -1,8 +1,6 @@
 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;

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

@@ -53,7 +53,7 @@ export interface RcsbFvModuleInterface extends RcsbFvModulePublicInterface {
     display(): void;
     build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     setPolymerEntityInstanceTranslator(polymerEntityInstance: PolymerEntityInstanceTranslate): void;
-    updateBoardConfig(config: Partial<RcsbFvBoardConfigInterface>): void;
+    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
 }
 export interface RcsbFvModulePublicInterface {
     getTargets(): Promise<Array<string>>;
@@ -61,4 +61,5 @@ export interface RcsbFvModulePublicInterface {
     getFeatures(): Promise<Array<Feature>>;
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
     getFv(): RcsbFv;
+    wait(): Promise<void>;
 }

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

@@ -1,8 +1,6 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
-import { SequenceCollectorInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollectorInterface";
 export declare class RcsbFvUniprot extends RcsbFvAbstractModule {
-    protected readonly sequenceCollector: SequenceCollectorInterface;
     protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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

@@ -5,4 +5,12 @@ export declare class TagDelimiter {
     static readonly alignmentTitle: string;
     static readonly operatorComposition: string;
     static readonly assembly: string;
+    static parseEntity(rcsbId: string): {
+        entryId: string;
+        entityId: string;
+    };
+    static parseInstance(rcsbId: string): {
+        instanceId: string;
+        entryId: string;
+    };
 }

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

@@ -1,12 +1,13 @@
 import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 import { RcsbFvTrackDataElementInterface } from '@rcsb/rcsb-saguaro';
 import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export interface TranslateContextInterface {
+export interface AlignmentContextInterface {
     queryId: string;
     targetId: string;
     from: SequenceReference | undefined;
     to: SequenceReference | Source;
     targetSequenceLength?: number;
+    querySequenceLength?: number;
 }
 export declare class PolymerEntityInstanceTranslate {
     private readonly rawData;
@@ -23,6 +24,6 @@ export declare class PolymerEntityInstanceTranslate {
     translateAsymToAuth(id: string): string;
     translateAuthToAsym(id: string): string;
     translateAuthResId(asymId: string, index: number): string;
-    addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: TranslateContextInterface): RcsbFvTrackDataElementInterface;
+    addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
     private helperAddAuthorResIds;
 }