@rcsb/rcsb-saguaro-app 2.4.0 → 3.2.1-interfaces

package/CHANGELOG.md

@@ -2,6 +2,29 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [3.2.1] - 2021-11-10
+### Minor configuration
+- Dropdown title configuration is exposed in `InstanceSequenceConfig` attribute `dropdownTitle` 
+
+## [3.1.1] - 2021-11-02
+### Bug fix
+- `RcsbFvAdditionalConfig` missing in `RcsbFvBuilder.buildMultipleInstanceSequenceFv` fixed 
+
+## [3.1.0] - 2021-10-27
+### External track builder improvements
+- `ExternalTrackBuilderInterface` available through `RcsbFvAdditionalConfig` for all `RcsbFvBuilder` types.
+In addition, it includes the query context as additional parameter for processing and addition methods.
+  - `processAlignmentAndFeatures` includes the query context as part of the input parameters
+  - `addTo` includes the query context as part of the input parameters
+  - `filterFeatures` new method for filtering positional features
+  - `filterAlignments` new method for filtering alignment data
+
+## [3.0.0] - 2021-10-15
+### Minor code refactor
+Changed `setTimeout` calls to 'rxjs' `asyncScheduler`
+### Breaking changes
+- rcsb-saguaro update 2.0.0
+
 ## [2.4.0] - 2021-10-08
 ### Minor code refactor and improvements
 - `AnnotationCollectorInterface` new annotation features getter `getAnnotationFeatures`
@@ -11,6 +34,10 @@
 - No more `Map` inheritance in `AnnotationTrack`. Now it delegates `Map` methods 
 - rcsb-saguaro update 1.11.0
 
+## [2.3.6] - 2021-10-04
+### Dependency update
+- Using rcsb-api-tools
+
 ## [2.3.5] - 2021-09-16
 ### Display Improvement
 - Loader spinner added
@@ -72,12 +99,13 @@
 - async/await promise style
 - Recursive waits migrated to rxjx Observables
 - PFV unique building method
-- RcsbFvWebApp.setBoardConfig  and RcsbFvWebApp.getRcsbFv have been removed. 
-  - Custom board config must be defined in RcsbFvAdditionalConfig (Some RcsbFvWebApp methods do not support additional configs yet)
-  - Builder methods return RcsbFvModulePublicInterface
 - Context Manager rcsbFv build new board config param 
 - Select button default value title bug fixed
 - rcsb-saguaro update 1.8.4
+#### Breaking changes
+- RcsbFvWebApp.setBoardConfig  and RcsbFvWebApp.getRcsbFv have been removed. 
+  - Custom board config must be defined in RcsbFvAdditionalConfig (Some RcsbFvWebApp methods do not support additional configs yet)
+  - Builder methods return RcsbFvModulePublicInterface
 
 ## [1.4.8] - 2021-06-15
 ### Optimization

package/LICENSE.md

@@ -0,0 +1,21 @@
+The MIT License
+
+    Copyright (c) 2019 - now, RCSB PDB and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

package/README.md

@@ -8,7 +8,7 @@ Feature Summaries. The package allows access to RCSB Saguaro methods to add or c
 <!---
 <div id="pfvSelect" ></div>  
 <div id="pfv" ></div>
-<script type="text/javascript" src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@2.4.0/build/dist/app.js"></script>
+<script type="text/javascript" src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@3.2.1/build/dist/app.js"></script>
 <script type="text/javascript">
 RcsbFvWebApp.buildInstanceFv("pfv", "4Z35.A", {
     boardConfig:{
@@ -23,7 +23,7 @@ RcsbFvWebApp.buildInstanceFv("pfv", "4Z35.A", {
 `npm install @rcsb/rcsb-saguaro-app`
 
 ### CDN JavaScript
-`<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@2.4.0/build/dist/app.js" type="text/javascript"></script>`
+`<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@3.2.1/build/dist/app.js" type="text/javascript"></script>`
 
 ### JavaScript Examples
 * [PDB Instance Chain View](https://rcsb.github.io/rcsb-saguaro-app/examples/instance.html)

package/build/dist/ExternalResources/NcbiData/NcbiSummary.d.ts

@@ -18,7 +18,7 @@ export interface TaxonomyMetadataInterface {
 export declare class NcbiSummary {
     private static timeout;
     private static httpTimeout;
-    private static jobId;
+    private static jobTask;
     static requestChromosomeData(chrId: string): Promise<ChromosomeMetadataInterface>;
     static requestTaxonomyData(taxId: string): Promise<TaxonomyMetadataInterface>;
 }

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

@@ -4,6 +4,7 @@ import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { AnnotationCollectConfig, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
 import { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
+import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 export declare class AnnotationCollector implements AnnotationCollectorInterface {
     private readonly rcsbAnnotationConfig;
     private readonly annotationsConfigData;
@@ -16,10 +17,11 @@ export declare class AnnotationCollector implements AnnotationCollectorInterface
     private readonly annotationTrackManager;
     private annotationFeatures;
     private readonly annotationFeaturesSubject;
+    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>>;
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
     getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;

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

@@ -8,7 +8,7 @@ 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;

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

@@ -1,7 +1,8 @@
 import { PolymerEntityInstanceTranslate } from "../RcsbUtils/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../RcsbGraphQL/RcsbClient";
+import { ExternalTrackBuilderInterface } from "./FeatureTools/ExternalTrackBuilderInterface";
 export interface CoreCollectorInterface {
     readonly rcsbFvQuery: RcsbClient;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
+    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
 }

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

@@ -1,14 +1,18 @@
 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 "../Translators/PolymerEntityInstancesCollector";
 export interface ExternalTrackBuilderInterface {
-    processAlignmentAndFeatures(data: {
+    processAlignmentAndFeatures?(data: {
         annotations?: Array<AnnotationFeatures>;
         alignments?: AlignmentResponse;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     }): void;
-    filterFeatures(annotations: Array<AnnotationFeatures>): void;
-    addTo(tracks: {
+    filterAlignments?(alignments: AlignmentResponse): AlignmentResponse;
+    filterFeatures?(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+    addTo?(tracks: {
         alignmentTracks?: SequenceCollectorDataInterface;
         annotationTracks?: Array<RcsbFvRowConfigInterface>;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     }): void;
 }

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

@@ -3,6 +3,7 @@ import { CollectAlignmentInterface, SequenceCollectorInterface } from "./Sequenc
 import { SequenceCollectorDataInterface } from "./SequenceCollector";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 export declare class GenomeMapCollector implements SequenceCollectorInterface {
     readonly rcsbFvQuery: RcsbClient;
     collect(requestConfig: CollectAlignmentInterface, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<null>): Promise<SequenceCollectorDataInterface>;
@@ -11,4 +12,5 @@ export declare class GenomeMapCollector implements SequenceCollectorInterface {
     getTargets(): Promise<Array<string>>;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
     getAlignmentResponse(): Promise<AlignmentResponse>;
+    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
 }

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

@@ -3,18 +3,21 @@ import { SequenceCollectorDataInterface } from "./SequenceCollector";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";
+import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 export declare class ObservedSequenceCollector implements SequenceCollectorInterface {
     private entityInstanceMap;
     private unObservedMap;
     private sequenceCollector;
     readonly rcsbFvQuery: RcsbClient;
     private polymerEntityInstanceTranslator;
+    private externalTrackBuilder;
     collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<SequenceCollectorDataInterface>;
     getTargets(): Promise<Array<string>>;
     getAlignmentResponse(): Promise<AlignmentResponse>;
     getSequenceLength(): number;
     getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
+    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
     private loadObservedRegions;
     private addUnmodelled;
     private collectUnmodeledRegions;

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

@@ -3,6 +3,7 @@ import { AlignedRegion, AlignmentResponse } from "@rcsb/rcsb-api-tools/build/Rcs
 import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";
+import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 export interface AlignedObservedRegion extends AlignedRegion {
     unModelled?: boolean;
     openBegin?: boolean;
@@ -23,13 +24,14 @@ export declare class SequenceCollector implements SequenceCollectorInterface {
     private readonly targetsSubject;
     private alignmentResponse;
     private readonly alignmentResponseSubject;
+    private externalTrackBuilder;
     private tagObservedRegions;
     collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<void>, tagObservedRegions?: (region: AlignedRegion, commonContext: TranslateContextInterface) => Array<AlignedObservedRegion>): Promise<SequenceCollectorDataInterface>;
     getTargets(): Promise<Array<string>>;
     getAlignmentResponse(): Promise<AlignmentResponse>;
     getSequenceLength(): number;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
     setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
+    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
     private complete;
     private buildAlignments;
     private buildSequenceTrack;

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

@@ -9,16 +9,20 @@ export interface InstanceSequenceOnchangeInterface {
     authId: string;
     asymId: string;
 }
+declare type instanceModule = "interface" | "instance";
 export interface InstanceSequenceConfig {
+    dropdownTitle?: string;
     defaultValue?: string | undefined | null;
     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): Promise<RcsbFvModulePublicInterface>;
+    static buildInstanceFv(elementId: string, instanceId: string, additionalConfig?: RcsbFvAdditionalConfig, rcsbContext?: PolymerEntityInstanceInterface, module?: instanceModule): Promise<RcsbFvModulePublicInterface>;
 }
+export {};

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

@@ -8,7 +8,7 @@ export declare function buildMultipleAlignmentSequenceFv(elementFvId: string, el
 export declare function buildEntitySummaryFv(elementFvId: string, elementSelectId: string, entityId: string): Promise<RcsbFvModulePublicInterface>;
 export declare function buildSingleEntitySummaryFv(elementId: string, entityId: string): Promise<RcsbFvModulePublicInterface>;
 export declare function buildInstanceSequenceFv(elementFvId: string, elementSelectId: string, entryId: string, config: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildMultipleInstanceSequenceFv(elementFvId: string, elementEntrySelectId: string, elementInstanceSelectId: string, entryIdList: Array<string>, config: InstanceSequenceConfig): Promise<RcsbFvModulePublicInterface>;
+export declare function buildMultipleInstanceSequenceFv(elementFvId: string, elementEntrySelectId: string, elementInstanceSelectId: string, entryIdList: Array<string>, config: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
 export declare function buildAssemblySequenceFv(elementFvId: string, elementSelectAssemblyId: string, elementSelectInstanceId: string, entryId: string, onAsseblyChangeCallback?: (x: string) => void, onInstanceChangeCallback?: (x: InstanceSequenceOnchangeInterface) => void): Promise<RcsbFvModulePublicInterface>;
 export declare function buildUniprotFv(elementId: string, upAcc: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
 export declare function buildEntityFv(elementId: string, entityId: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;

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

@@ -1,4 +1,5 @@
 import { RcsbFv, RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
+import { SequenceCollectorDataInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollector";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
 import { SequenceCollectorInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollectorInterface";
 import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
@@ -9,8 +10,11 @@ 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;
+    protected annotationTracks: Array<RcsbFvRowConfigInterface>;
     private activeDisplayFlag;
     constructor(elementId: string, rcsbFv: RcsbFv);
     setPolymerEntityInstanceTranslator(polymerEntityInstance: PolymerEntityInstanceTranslate): void;
@@ -21,5 +25,9 @@ export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterf
     getFeatures(): Promise<Array<Feature>>;
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
     updateBoardConfig(config: Partial<RcsbFvBoardConfigInterface>): void;
-    abstract build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected abstract protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected abstract concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    private buildExternalTracks;
+    private setExternalTrackBuilder;
 }

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

@@ -44,6 +44,7 @@ export declare class RcsbFvChromosome extends RcsbFvAbstractModule {
     private addSequences;
     private setDisplayView;
     private plot;
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     getTargets(): Promise<Array<string>>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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

@@ -1,5 +1,7 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 export declare class RcsbFvEntity extends RcsbFvAbstractModule {
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    private titleSuffix;
 }

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

@@ -1,5 +1,6 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 export declare class RcsbFvInstance extends RcsbFvAbstractModule {
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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/RcsbFvModuleInterface.d.ts

@@ -16,6 +16,16 @@ export interface RcsbFvAdditionalConfig {
     annotationProcessing?: AnnotationProcessingInterface;
     sequenceCollector?: SequenceCollectorInterface;
     externalTrackBuilder?: ExternalTrackBuilderInterface;
+    rcsbContext?: Partial<{
+        entryId: string;
+        entityId: string;
+        asymId: string;
+        authId: string;
+        upAcc: string;
+        chrId: string;
+        targetId: string;
+        queryId: string;
+    }>;
 }
 export interface RcsbFvModuleBuildInterface {
     queryId?: string;

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

@@ -1,5 +1,6 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 export declare class RcsbFvPairwiseAlignment extends RcsbFvAbstractModule {
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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

@@ -1,5 +1,6 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 export declare class RcsbFvProteinSequence extends RcsbFvAbstractModule {
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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

@@ -5,5 +5,6 @@ import { SequenceCollectorInterface } from "../../RcsbCollectTools/SequenceColle
 export declare class RcsbFvUniprot extends RcsbFvAbstractModule {
     protected readonly sequenceCollector: SequenceCollectorInterface;
     constructor(elementId: string, rcsbFv: RcsbFv);
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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

@@ -1,5 +1,7 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 export declare class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    private titleSuffix;
 }

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

@@ -1,5 +1,6 @@
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 export declare class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
 }

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];
+}