external alignment providers

CHANGELOG.md

@@ -2,6 +2,15 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [2.4.0] - 2023-02-03
+### Improvements
+- New entry method `RcsbFv3DDataProviderInterface` that ingests and displays external alignments
+- New interface `ComponentActionInterface` used to define what actions are triggered after a new structure is loaded
+- Interface `LoadMolstarInterface<P,L>` requires two generics: `P` load argument type and `L` load return type
+- Interface `ViewerModelMapManagerInterface<R,L>` needs a new generic that defines the type returned by the loading method in `LoadMolstarInterface`.
+  - It defines a new method `getModelIdFromTrajectory(trajectory: L): string|undefined` 
+that is used to map loaded structure ids with user provided ids in `LoadParams`
+
 ## [2.3.7] - 2022-12-12
 ### Bug fix
 - `assemblyId` parameter has been removed from `AlignmentTrajectoryPresetProvider`

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rcsb/rcsb-saguaro-3d",
-  "version": "2.3.7",
+  "version": "2.4.0-data-provider.1",
   "description": "RCSB Molstar/Saguaro Web App",
   "main": "build/dist/app.js",
   "files": [
@@ -48,6 +48,7 @@
     "@babel/preset-env": "^7.18.10",
     "@types/d3-selection": "^3.0.3",
     "@types/d3-zoom": "^3.0.1",
+    "@types/lodash": "^4.14.191",
     "@types/react": "^18.0.15",
     "@types/react-dom": "^18.0.6",
     "@types/uniqid": "^5.3.2",
@@ -59,6 +60,7 @@
     "del-cli": "^5.0.0",
     "file-loader": "^6.2.0",
     "html-webpack-plugin": "^5.5.0",
+    "lodash": "^4.17.21",
     "mini-css-extract-plugin": "^2.6.1",
     "ncp": "^2.0.0",
     "path-browserify": "^1.0.1",
@@ -82,11 +84,11 @@
   },
   "dependencies": {
     "@rcsb/rcsb-api-tools": "^4.1.1",
-    "@rcsb/rcsb-molstar": "^2.5.5",
+    "@rcsb/rcsb-molstar": "^2.5.11",
     "@rcsb/rcsb-saguaro": "^2.5.5",
-    "@rcsb/rcsb-saguaro-app": "^4.5.8",
+    "@rcsb/rcsb-saguaro-app": "^4.6.0-data-provider.7",
     "http-server": "^14.1.1",
-    "molstar": "^3.13.0"
+    "molstar": "^3.29.0"
   },
   "bugs": {
     "url": "https://github.com/rcsb/rcsb-saguaro-3d/issues"

src/RcsbFv3D/RcsbFv3DAbstract.tsx

@@ -8,25 +8,27 @@ import {PluginContext} from "molstar/lib/mol-plugin/context";
 import {CSSProperties} from "react";
 import {StructureViewerInterface} from "../RcsbFvStructure/StructureViewerInterface";
 import {StructureViewerBehaviourObserverInterface} from "../RcsbFvStructure/StructureViewerBehaviourInterface";
+import {RcsbFvStateManager} from "../RcsbFvState/RcsbFvStateManager";
+import {RcsbFvStateInterface} from "../RcsbFvState/RcsbFvStateInterface";
 
-export interface RcsbFv3DAbstractInterface<T,R,S,U> {
+export interface RcsbFv3DAbstractInterface<T,R,L,S,U> {
     elementId: string;
     cssConfig?: RcsbFv3DCssConfig;
-    sequenceConfig: RcsbFvSequenceInterface<T,R,U>;
+    sequenceConfig: RcsbFvSequenceInterface<T,R,L,U>;
     structureConfig: RcsbFvStructureConfigInterface<R,S>;
-    structureViewer: StructureViewerInterface<R,S>;
-    structureViewerBehaviourObserver: StructureViewerBehaviourObserverInterface<R>;
+    structureViewer: StructureViewerInterface<R,L,S>;
+    structureViewerBehaviourObserver: StructureViewerBehaviourObserverInterface<R,L>;
 }
 
-export abstract class RcsbFv3DAbstract<T,R,S,U> {
+export abstract class RcsbFv3DAbstract<T,R,L,S,U> {
 
     private readonly elementId: string;
     private reactRoot: Root;
     private readonly structureConfig: RcsbFvStructureConfigInterface<R,S>;
-    private readonly structureViewer: StructureViewerInterface<R,S>;
-    private readonly structureViewerBehaviourObserver: StructureViewerBehaviourObserverInterface<R>;
-    private readonly sequenceConfig: RcsbFvSequenceInterface<T,R,U>;
-    private readonly ctxManager: RcsbFvContextManager<T,R,S,U> = new RcsbFvContextManager<T,R,S,U>();
+    private readonly structureViewer: StructureViewerInterface<R,L,S>;
+    private readonly structureViewerBehaviourObserver: StructureViewerBehaviourObserverInterface<R,L>;
+    private readonly sequenceConfig: RcsbFvSequenceInterface<T,R,L,U>;
+    private readonly ctxManager: RcsbFvContextManager<T,R,L,S,U> = new RcsbFvContextManager<T,R,L,S,U>();
     private fullScreenFlag: boolean = false;
     private overflowStyle: string = "";
     private readonly cssConfig:{
@@ -35,7 +37,7 @@ export abstract class RcsbFv3DAbstract<T,R,S,U> {
         sequencePanel?: CSSProperties
     } | undefined;
 
-    protected constructor(config: RcsbFv3DAbstractInterface<T,R,S,U>) {
+    protected constructor(config: RcsbFv3DAbstractInterface<T,R,L,S,U>) {
        this.elementId = config.elementId;
        if(config.cssConfig) this.cssConfig = config.cssConfig;
        this.sequenceConfig = config.sequenceConfig;
@@ -55,7 +57,7 @@ export abstract class RcsbFv3DAbstract<T,R,S,U> {
         }
         this.reactRoot = createRoot(element);
         this.reactRoot.render(
-            <RcsbFv3DComponent<T,R,S,U>
+            <RcsbFv3DComponent<T,R,L,S,U>
                 structurePanelConfig={this.structureConfig}
                 sequencePanelConfig={this.sequenceConfig}
                 id={this.elementId}
@@ -81,7 +83,7 @@ export abstract class RcsbFv3DAbstract<T,R,S,U> {
         }
     }
 
-    public updateConfig(config: {structurePanelConfig?: Partial<RcsbFvStructureConfigInterface<R,S>>; sequencePanelConfig?: Partial<RcsbFvSequenceInterface<T,R,U>>;}){
+    public updateConfig(config: {structurePanelConfig?: Partial<RcsbFvStructureConfigInterface<R,S>>; sequencePanelConfig?: Partial<RcsbFvSequenceInterface<T,R,L,U>>;}){
         this.ctxManager.next({eventType: EventType.UPDATE_CONFIG, eventData:config});
     }
 

src/RcsbFv3D/RcsbFv3DAlignmentProvider.tsx

@@ -0,0 +1,128 @@
+import * as React from "react";
+import {RcsbFv3DAbstract} from "./RcsbFv3DAbstract";
+import {
+    RcsbFvAdditionalConfig,
+    RcsbFvModulePublicInterface, RcsbModuleDataProviderInterface
+} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface";
+import uniqid from "uniqid";
+
+import {
+    LoadMethod,
+    LoadMolstarInterface,
+    LoadMolstarReturnType
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
+import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
+
+import {StructureViewer} from "../RcsbFvStructure/StructureViewers/StructureViewer";
+import {MolstarManagerFactory} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarManagerFactory";
+import {
+    MsaCallbackManagerFactory
+} from "../RcsbFvSequence/SequenceViews/RcsbView/CallbackManagerFactoryImplementation/MsaCallbackManager";
+import {RcsbFvStructure} from "../RcsbFvStructure/RcsbFvStructure";
+import {RcsbFv3DCssConfig} from "./RcsbFv3DComponent";
+import {MolstarAlignmentLoader} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarAlignmentLoader";
+import {MsaBehaviourObserver} from "../RcsbFvStructure/StructureViewerBehaviour/MsaBehaviour";
+import {
+    PolymerEntityInstanceInterface
+} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
+import {HelpLinkComponent} from "../RcsbFvSequence/SequenceViews/RcsbView/Components/HelpLinkComponent";
+import {AlignmentResponse} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import {DataContainer} from "../Utils/DataContainer";
+import {
+    MsaPfvManagerFactory, MsaPfvManagerInterface
+} from "../RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/MsaPfvManagerFactory";
+import {buildDataProviderFv} from "@rcsb/rcsb-saguaro-app";
+import {
+    LocationProviderInterface,
+    TransformProviderInterface
+} from "../RcsbFvStructure/StructureUtils/StructureLoaderInterface";
+
+import {
+    AlignmentTrajectoryParamsType
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/AlignmentTrajectoryPresetProvider";
+import {
+    MolstarComponentActionFactory
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarComponentAction";
+import {MolstarTools} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarTools";
+import getModelIdFromTrajectory = MolstarTools.getModelIdFromTrajectory;
+
+export interface RcsbFv3DDataProviderInterface  {
+    elementId?: string;
+    config: {
+        dataProvider: RcsbModuleDataProviderInterface;
+        transformProvider?: TransformProviderInterface;
+        structureLocationProvider?: LocationProviderInterface;
+        title?: string;
+        subtitle?: string;
+    };
+    additionalConfig?:RcsbFvAdditionalConfig;
+    molstarProps?: Partial<ViewerProps>;
+    cssConfig?: RcsbFv3DCssConfig;
+}
+
+type AlignmentLoadMolstarType = LoadMolstarInterface<AlignmentTrajectoryParamsType,LoadMolstarReturnType>;
+export class RcsbFv3DAlignmentProvider extends RcsbFv3DAbstract<
+        MsaPfvManagerInterface<[RcsbModuleDataProviderInterface]>,
+        AlignmentLoadMolstarType|undefined,
+        LoadMolstarReturnType,
+        {viewerElement:string|HTMLElement; viewerProps:Partial<ViewerProps>;},
+        {context:{id:string}; module:RcsbFvModulePublicInterface;}
+    > {
+
+    constructor(params:RcsbFv3DDataProviderInterface){
+        const elementId: string = params.elementId ?? uniqid("RcsbFv3D_");
+        const alignmentResponseContainer:DataContainer<AlignmentResponse> = new DataContainer<AlignmentResponse>();
+        super({
+            elementId,
+            sequenceConfig:{
+                type: "rcsb",
+                title: params.config.title,
+                subtitle: params.config.subtitle,
+                config:{
+                    rcsbId: "external-data",
+                    additionalConfig: params.additionalConfig,
+                    pfvParams:{
+                        id: "external-data",
+                        buildMsaAlignmentFv: buildDataProviderFv,
+                        pfvArgs:[params.config.dataProvider],
+                        alignmentResponseContainer
+                    },
+                    buildPfvOnMount: true,
+                    pfvManagerFactory: new MsaPfvManagerFactory<[RcsbModuleDataProviderInterface],AlignmentLoadMolstarType,LoadMolstarReturnType>(),
+                    callbackManagerFactory: new MsaCallbackManagerFactory<AlignmentLoadMolstarType|undefined, LoadMolstarReturnType, {context:{id:string} & Partial<PolymerEntityInstanceInterface>}>({
+                        pluginLoadParamsDefinition,
+                        alignmentResponseContainer
+                    }),
+                    additionalContent:(props)=>(<HelpLinkComponent {...props} helpHref={"/docs/grouping-structures/groups-1d-3d-alignment"}/>)
+                }
+            },
+            structureConfig: {
+                loadConfig: undefined,
+                structureViewerConfig: {
+                    viewerElement:RcsbFvStructure.componentId(elementId),
+                    viewerProps: params.molstarProps ?? {}
+                }
+            },
+            structureViewer: new StructureViewer<
+                AlignmentLoadMolstarType,
+                LoadMolstarReturnType,
+                {viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}
+            >( new MolstarManagerFactory(getModelIdFromTrajectory) ),
+            structureViewerBehaviourObserver: new MsaBehaviourObserver<AlignmentLoadMolstarType,LoadMolstarReturnType>(
+                new MolstarAlignmentLoader({
+                    transformProvider: params.config.transformProvider,
+                    structureLocationProvider: params.config.structureLocationProvider
+                }),
+                new MolstarComponentActionFactory()
+            )
+        });
+    }
+
+}
+
+const pluginLoadParamsDefinition = (entryId:string)=>({
+    loadMethod: LoadMethod.loadPdbId,
+    loadParams:{
+        entryId
+    }
+})

src/RcsbFv3D/RcsbFv3DAssembly.tsx

@@ -1,10 +1,17 @@
 import * as React from "react";
 import {RcsbFv3DAbstract} from "./RcsbFv3DAbstract";
-import {RcsbRepresentationPreset} from "../RcsbFvStructure/StructureViewers/MolstarViewer/StructureRepresentation";
+import {
+    AssemblyTrajectoryParamsType,
+    AssemblyTrajectoryPresetProvider
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/AssemblyTrajectoryPresetProvider";
 import {RcsbFvAdditionalConfig} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface";
 import {InstanceSequenceConfig} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder";
 import {OperatorInfo} from "../RcsbFvStructure/StructureViewerInterface";
-import {LoadMethod, LoadMolstarInterface} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
+import {
+    LoadMethod,
+    LoadMolstarInterface,
+    LoadMolstarReturnType
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {StructureViewer} from "../RcsbFvStructure/StructureViewers/StructureViewer";
 import {MolstarManagerFactory} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarManagerFactory";
@@ -19,6 +26,8 @@ import {
 } from "../RcsbFvSequence/SequenceViews/RcsbView/CallbackManagerFactoryImplementation/AssemblyCallbackManager";
 import {AssemblyBehaviourObserver} from "../RcsbFvStructure/StructureViewerBehaviour/AssemblyBehaviour";
 import {HelpLinkComponent} from "../RcsbFvSequence/SequenceViews/RcsbView/Components/HelpLinkComponent";
+import {MolstarTools} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarTools";
+import getModelIdFromTrajectory = MolstarTools.getModelIdFromTrajectory;
 
 type RcsbFv3DAssemblyAdditionalConfig = RcsbFvAdditionalConfig & {operatorChangeCallback?:(operatorInfo: OperatorInfo)=>void};
 
@@ -37,7 +46,14 @@ export interface RcsbFv3DAssemblyInterface {
     cssConfig?: RcsbFv3DCssConfig;
 }
 
-export class RcsbFv3DAssembly extends RcsbFv3DAbstract<{instanceSequenceConfig?:InstanceSequenceConfig},LoadMolstarInterface,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>},undefined>{
+type AssemblyLoadMolstarType = LoadMolstarInterface<AssemblyTrajectoryParamsType,LoadMolstarReturnType>;
+export class RcsbFv3DAssembly extends RcsbFv3DAbstract<
+    {instanceSequenceConfig?:InstanceSequenceConfig},
+    AssemblyLoadMolstarType,
+    LoadMolstarReturnType,
+    {viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>},
+    undefined
+>{
 
     constructor(params: RcsbFv3DAssemblyInterface) {
         const elementId: string = params.elementId ?? uniqid("RcsbFv3D_");
@@ -55,31 +71,33 @@ export class RcsbFv3DAssembly extends RcsbFv3DAbstract<{instanceSequenceConfig?:
                         instanceSequenceConfig:params.instanceSequenceConfig
                     },
                     pfvManagerFactory: new AssemblyPfvManagerFactory(),
-                    callbackManagerFactory: new AssemblyCallbackManagerFactory<LoadMolstarInterface>(),
+                    callbackManagerFactory: new AssemblyCallbackManagerFactory<AssemblyLoadMolstarType,LoadMolstarReturnType>(),
                     additionalContent:(props)=>(<HelpLinkComponent {...props} helpHref={"/docs/sequence-viewers/3d-protein-feature-view"}/>)
                 }
             },
             structureConfig: {
-                loadConfig: {
-                    loadMethod: LoadMethod.loadPdbId,
-                    loadParams: {
-                        entryId: params.config.entryId,
-                        id: params.config.entryId,
-                        reprProvider: RcsbRepresentationPreset,
-                        params: {
-                            preset: {
-                                assemblyId: typeof (params.config.assemblyId) === "string" && params.config.assemblyId?.length > 0 ? params.config.assemblyId : '1'
-                            }
-                        }
-                    }
-                },
                 structureViewerConfig: {
                     viewerElement: RcsbFvStructure.componentId(elementId),
                     viewerProps:params.molstarProps ?? {}
                 }
             },
-            structureViewer: new StructureViewer<LoadMolstarInterface,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}>(new MolstarManagerFactory()),
-            structureViewerBehaviourObserver: new AssemblyBehaviourObserver<LoadMolstarInterface>(),
+            structureViewer: new StructureViewer<
+                AssemblyLoadMolstarType,
+                LoadMolstarReturnType,
+                {viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}
+            >(new MolstarManagerFactory(getModelIdFromTrajectory)),
+            structureViewerBehaviourObserver: new AssemblyBehaviourObserver<AssemblyLoadMolstarType,LoadMolstarReturnType>({
+                loadMethod: LoadMethod.loadPdbId,
+                loadParams: {
+                    entryId: params.config.entryId,
+                    id: params.config.entryId,
+                    reprProvider: AssemblyTrajectoryPresetProvider,
+                    params: {
+                        assemblyId: typeof (params.config.assemblyId) === "string" && params.config.assemblyId?.length > 0 ? params.config.assemblyId : '1',
+                        modelIndex: 0
+                    }
+                }
+            }),
             cssConfig: params.cssConfig
         });
     }

src/RcsbFv3D/RcsbFv3DComponent.tsx

@@ -1,7 +1,6 @@
 import * as React from "react";
 import classes from '../styles/RcsbFvStyle.module.scss';
 
-import {StructureViewer} from '../RcsbFvStructure/StructureViewers/StructureViewer';
 import {StructureViewerInterface} from '../RcsbFvStructure/StructureViewerInterface';
 
 import '../styles/RcsbFvMolstarStyle.module.scss';
@@ -15,10 +14,10 @@ import {
 } from "../RcsbFvContextManager/RcsbFvContextManager";
 import {Subscription} from "rxjs";
 import {PluginContext} from "molstar/lib/mol-plugin/context";
-import {RcsbFvSelectorManager} from "../RcsbFvState/RcsbFvSelectorManager";
 import {CSSProperties, MouseEvent} from "react";
-import {RcsbFvStateManager} from "../RcsbFvState/RcsbFvStateManager";
 import {StructureViewerBehaviourObserverInterface} from "../RcsbFvStructure/StructureViewerBehaviourInterface";
+import {RcsbFvStateInterface} from "../RcsbFvState/RcsbFvStateInterface";
+import {RcsbFvStateManager} from "../RcsbFvState/RcsbFvStateManager";
 
 export interface RcsbFv3DCssConfig {
     overwriteCss?: boolean;
@@ -27,31 +26,31 @@ export interface RcsbFv3DCssConfig {
     sequencePanel?: CSSProperties;
 }
 
-export interface RcsbFv3DComponentInterface<T,R,S,U> {
+export interface RcsbFv3DComponentInterface<T,R,L,S,U> {
     structurePanelConfig:RcsbFvStructureConfigInterface<R,S>;
-    sequencePanelConfig: RcsbFvSequenceInterface<T,R,U>;
+    sequencePanelConfig: RcsbFvSequenceInterface<T,R,L,U>;
     id: string;
-    ctxManager: RcsbFvContextManager<T,R,S,U>;
+    ctxManager: RcsbFvContextManager<T,R,L,S,U>;
     cssConfig?:RcsbFv3DCssConfig;
     unmount:(flag:boolean)=>void;
     fullScreen: boolean;
-    structureViewer: StructureViewerInterface<R,S>;
-    structureViewerBehaviourObserver: StructureViewerBehaviourObserverInterface<R>;
+    structureViewer: StructureViewerInterface<R,L,S>;
+    structureViewerBehaviourObserver: StructureViewerBehaviourObserverInterface<R,L>;
 }
 
-interface RcsbFv3DComponentState<T,R,S,U> {
+interface RcsbFv3DComponentState<T,R,L,S,U> {
     structurePanelConfig:RcsbFvStructureConfigInterface<R,S>;
-    sequencePanelConfig:RcsbFvSequenceInterface<T,R,U>;
+    sequencePanelConfig:RcsbFvSequenceInterface<T,R,L,U>;
     pfvScreenFraction: number;
 }
 
-export class RcsbFv3DComponent<T,R,S,U> extends React.Component <RcsbFv3DComponentInterface<T,R,S,U>, RcsbFv3DComponentState<T,R,S,U>> {
+export class RcsbFv3DComponent<T,R,L,S,U> extends React.Component <RcsbFv3DComponentInterface<T,R,L,S,U>, RcsbFv3DComponentState<T,R,L,S,U>> {
 
-    private readonly stateManager: RcsbFvStateManager = new RcsbFvStateManager();
+    private readonly stateManager: RcsbFvStateInterface = new RcsbFvStateManager();
     private subscription: Subscription;
     private readonly ROOT_DIV_ID: string = "rootPanelDiv";
 
-    readonly state: RcsbFv3DComponentState<T,R,S,U> = {
+    readonly state: RcsbFv3DComponentState<T,R,L,S,U> = {
         structurePanelConfig: this.props.structurePanelConfig,
         sequencePanelConfig: this.props.sequencePanelConfig,
         pfvScreenFraction: 0.55
@@ -68,7 +67,7 @@ export class RcsbFv3DComponent<T,R,S,U> extends React.Component <RcsbFv3DCompone
                     onMouseUp={ (e)=>{this.splitPanelMouseUp()} }
                 >
                     <div style={this.structureCssConfig(this.props.cssConfig?.structurePanel)} >
-                        <RcsbFvStructure<R,S>
+                        <RcsbFvStructure<R,L,S>
                             {...this.state.structurePanelConfig}
                             componentId={this.props.id}
                             structureViewer={this.props.structureViewer}
@@ -77,7 +76,7 @@ export class RcsbFv3DComponent<T,R,S,U> extends React.Component <RcsbFv3DCompone
                         />
                     </div>
                     <div style={this.sequenceCssConfig(this.props.cssConfig?.sequencePanel)}  >
-                        <RcsbFvSequence<T,R,U>
+                        <RcsbFvSequence<T,R,L,U>
                             type={this.state.sequencePanelConfig.type}
                             config={this.state.sequencePanelConfig.config}
                             componentId={this.props.id}
@@ -139,9 +138,9 @@ export class RcsbFv3DComponent<T,R,S,U> extends React.Component <RcsbFv3DCompone
     }
 
     private subscribe(): Subscription{
-        return this.props.ctxManager.subscribe((obj:RcsbFvContextManagerInterface<T,R,S,U>)=>{
+        return this.props.ctxManager.subscribe((obj:RcsbFvContextManagerInterface<T,R,L,S,U>)=>{
             if(obj.eventType == EventType.UPDATE_CONFIG){
-                this.updateConfig(obj.eventData as UpdateConfigInterface<T,R,S,U>)
+                this.updateConfig(obj.eventData as UpdateConfigInterface<T,R,L,S,U>)
             }else if(obj.eventType == EventType.PLUGIN_CALL){
                 this.props.structureViewer.pluginCall(obj.eventData as ((f:PluginContext)=>void));
             }
@@ -153,9 +152,9 @@ export class RcsbFv3DComponent<T,R,S,U> extends React.Component <RcsbFv3DCompone
         this.subscription.unsubscribe();
     }
 
-    private updateConfig(config:UpdateConfigInterface<T,R,S,U>){
+    private updateConfig(config:UpdateConfigInterface<T,R,L,S,U>){
         const structureConfig: Partial<RcsbFvStructureConfigInterface<R,S>> | undefined = config.structurePanelConfig;
-        const sequenceConfig: Partial<RcsbFvSequenceInterface<T,R,U>> | undefined = config.sequencePanelConfig;
+        const sequenceConfig: Partial<RcsbFvSequenceInterface<T,R,L,U>> | undefined = config.sequencePanelConfig;
         if(structureConfig != null && sequenceConfig != null){
             this.setState({structurePanelConfig:{...this.state.structurePanelConfig, ...structureConfig}, sequencePanelConfig:{...this.state.sequencePanelConfig, ...sequenceConfig}});
         }else if(structureConfig != null){

src/RcsbFv3D/RcsbFv3DCustom.tsx

@@ -3,18 +3,23 @@ import {RcsbFvStructure, RcsbFvStructureConfigInterface} from "../RcsbFvStructur
 import {CustomViewInterface} from "../RcsbFvSequence/SequenceViews/CustomView/CustomView";
 import {RcsbFv3DAbstract} from "./RcsbFv3DAbstract";
 import uniqid from "uniqid";
-import {LoadMolstarInterface} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
+import {
+    LoadMolstarInterface,
+    LoadMolstarReturnType
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {StructureViewer} from "../RcsbFvStructure/StructureViewers/StructureViewer";
 import {MolstarManagerFactory} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarManagerFactory";
 import {RcsbFv3DCssConfig} from "./RcsbFv3DComponent";
 import {NullBehaviourObserver} from "../RcsbFvStructure/StructureViewerBehaviour/NullBehaviour";
+import {MolstarTools} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarTools";
+import getModelIdFromTrajectory = MolstarTools.getModelIdFromTrajectory;
 
 export interface RcsbFv3DCustomInterface  {
     elementId?: string;
-    structurePanelConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface,{viewerProps:Partial<ViewerProps>}>;
+    structurePanelConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface<undefined,undefined>,{viewerProps:Partial<ViewerProps>}>;
     sequencePanelConfig: {
-        config: CustomViewInterface<LoadMolstarInterface>;
+        config: CustomViewInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>;
         title?: string;
         subtitle?: string;
     }
@@ -22,7 +27,7 @@ export interface RcsbFv3DCustomInterface  {
 
 }
 
-export class RcsbFv3DCustom extends RcsbFv3DAbstract<{},LoadMolstarInterface,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>},undefined> {
+export class RcsbFv3DCustom extends RcsbFv3DAbstract<{},LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>},undefined> {
 
     constructor(params: RcsbFv3DCustomInterface) {
         const elementId: string = params.elementId ?? uniqid("RcsbFv3D_");
@@ -39,8 +44,12 @@ export class RcsbFv3DCustom extends RcsbFv3DAbstract<{},LoadMolstarInterface,{vi
                 ...params.sequencePanelConfig,
                 type:"custom",
             },
-            structureViewer:new StructureViewer<LoadMolstarInterface,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}>( new MolstarManagerFactory() ),
-            structureViewerBehaviourObserver: new NullBehaviourObserver<LoadMolstarInterface>(),
+            structureViewer:new StructureViewer<
+                LoadMolstarInterface<undefined,undefined>,
+                LoadMolstarReturnType,
+                {viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}
+            >( new MolstarManagerFactory(()=>undefined) ),
+            structureViewerBehaviourObserver: new NullBehaviourObserver<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>(),
             cssConfig: params.cssConfig
         });
     }

src/RcsbFv3D/RcsbFv3DSequenceIdentity.tsx

@@ -6,7 +6,11 @@ import {
 } from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface";
 import uniqid from "uniqid";
 
-import {LoadMethod, LoadMolstarInterface} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
+import {
+    LoadMethod,
+    LoadMolstarInterface,
+    LoadMolstarReturnType
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 
 import {StructureViewer} from "../RcsbFvStructure/StructureViewers/StructureViewer";
@@ -16,7 +20,7 @@ import {
 } from "../RcsbFvSequence/SequenceViews/RcsbView/CallbackManagerFactoryImplementation/MsaCallbackManager";
 import {RcsbFvStructure} from "../RcsbFvStructure/RcsbFvStructure";
 import {RcsbFv3DCssConfig} from "./RcsbFv3DComponent";
-import {MolstarAlignmentLoader} from "../RcsbFvStructure/StructureUtils/MolstarAlignmentLoader";
+import {MolstarAlignmentLoader} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarAlignmentLoader";
 import {MsaBehaviourObserver} from "../RcsbFvStructure/StructureViewerBehaviour/MsaBehaviour";
 import {
     PolymerEntityInstanceInterface
@@ -29,6 +33,14 @@ import {
     MsaPfvManagerFactory, MsaPfvManagerInterface
 } from "../RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/MsaPfvManagerFactory";
 import {buildSequenceIdentityAlignmentFv} from "@rcsb/rcsb-saguaro-app";
+import {
+    AlignmentTrajectoryParamsType
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/AlignmentTrajectoryPresetProvider";
+import {
+    MolstarComponentActionFactory
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarComponentAction";
+import {MolstarTools} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarTools";
+import getModelIdFromTrajectory = MolstarTools.getModelIdFromTrajectory;
 
 export interface RcsbFv3DSequenceIdentityInterface  {
     elementId?: string;
@@ -43,9 +55,11 @@ export interface RcsbFv3DSequenceIdentityInterface  {
     cssConfig?: RcsbFv3DCssConfig;
 }
 
+type AlignmentLoadMolstarType = LoadMolstarInterface<AlignmentTrajectoryParamsType,LoadMolstarReturnType>;
 export class RcsbFv3DSequenceIdentity extends RcsbFv3DAbstract<
-        MsaPfvManagerInterface,
-        LoadMolstarInterface|undefined,
+        MsaPfvManagerInterface<[string,SearchQuery|undefined]>,
+        AlignmentLoadMolstarType,
+        LoadMolstarReturnType,
         {viewerElement:string|HTMLElement; viewerProps:Partial<ViewerProps>;},
         {context:{id:string}; module:RcsbFvModulePublicInterface;}
     > {
@@ -63,13 +77,13 @@ export class RcsbFv3DSequenceIdentity extends RcsbFv3DAbstract<
                     additionalConfig: params.additionalConfig,
                     pfvParams:{
                         id: params.config.groupId,
-                        query: params.config.query,
+                        pfvArgs:[params.config.groupId,params.config.query],
                         buildMsaAlignmentFv: buildSequenceIdentityAlignmentFv,
                         alignmentResponseContainer
                     },
                     buildPfvOnMount: true,
-                    pfvManagerFactory: new MsaPfvManagerFactory<LoadMolstarInterface>(),
-                    callbackManagerFactory: new MsaCallbackManagerFactory<LoadMolstarInterface, {context:{id:string} & Partial<PolymerEntityInstanceInterface>}>({
+                    pfvManagerFactory: new MsaPfvManagerFactory<[string,SearchQuery?],AlignmentLoadMolstarType,LoadMolstarReturnType>(),
+                    callbackManagerFactory: new MsaCallbackManagerFactory<AlignmentLoadMolstarType,LoadMolstarReturnType, {context:{id:string} & Partial<PolymerEntityInstanceInterface>}>({
                         pluginLoadParamsDefinition,
                         alignmentResponseContainer
                     }),
@@ -77,14 +91,20 @@ export class RcsbFv3DSequenceIdentity extends RcsbFv3DAbstract<
                 }
             },
             structureConfig: {
-                loadConfig: undefined,
                 structureViewerConfig: {
                     viewerElement:RcsbFvStructure.componentId(elementId),
                     viewerProps: params.molstarProps ?? {}
                 }
             },
-            structureViewer: new StructureViewer<LoadMolstarInterface,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}>( new MolstarManagerFactory() ),
-            structureViewerBehaviourObserver: new MsaBehaviourObserver<LoadMolstarInterface>(new MolstarAlignmentLoader())
+            structureViewer: new StructureViewer<
+                AlignmentLoadMolstarType,
+                LoadMolstarReturnType,
+                {viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}
+            >( new MolstarManagerFactory(getModelIdFromTrajectory) ),
+            structureViewerBehaviourObserver: new MsaBehaviourObserver<AlignmentLoadMolstarType,LoadMolstarReturnType>(
+                new MolstarAlignmentLoader(),
+                new MolstarComponentActionFactory()
+            )
         });
     }
 

src/RcsbFv3D/RcsbFv3DUniprot.tsx

@@ -6,12 +6,13 @@ import {
 } from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface";
 import uniqid from "uniqid";
 
-import {LoadMethod, LoadMolstarInterface} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
+import {
+    LoadMethod,
+    LoadMolstarInterface,
+    LoadMolstarReturnType
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 
-import {
-    UniprotSequenceOnchangeInterface
-} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvBuilder/RcsbFvUniprotBuilder";
 import {StructureViewer} from "../RcsbFvStructure/StructureViewers/StructureViewer";
 import {MolstarManagerFactory} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarManagerFactory";
 import {
@@ -19,7 +20,7 @@ import {
 } from "../RcsbFvSequence/SequenceViews/RcsbView/CallbackManagerFactoryImplementation/MsaCallbackManager";
 import {RcsbFvStructure} from "../RcsbFvStructure/RcsbFvStructure";
 import {RcsbFv3DCssConfig} from "./RcsbFv3DComponent";
-import {MolstarAlignmentLoader} from "../RcsbFvStructure/StructureUtils/MolstarAlignmentLoader";
+import {MolstarAlignmentLoader} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarAlignmentLoader";
 import {MsaBehaviourObserver} from "../RcsbFvStructure/StructureViewerBehaviour/MsaBehaviour";
 import {SearchQuery} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
 import {HelpLinkComponent} from "../RcsbFvSequence/SequenceViews/RcsbView/Components/HelpLinkComponent";
@@ -30,6 +31,14 @@ import {
     MsaPfvManagerInterface
 } from "../RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/MsaPfvManagerFactory";
 import {buildUniprotAlignmentFv} from "@rcsb/rcsb-saguaro-app";
+import {
+    AlignmentTrajectoryParamsType
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/AlignmentTrajectoryPresetProvider";
+import {
+    MolstarComponentActionFactory
+} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarComponentAction";
+import {MolstarTools} from "../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarTools";
+import getModelIdFromTrajectory = MolstarTools.getModelIdFromTrajectory;
 
 export interface RcsbFv3DUniprotInterface  {
     elementId?: string;
@@ -44,9 +53,12 @@ export interface RcsbFv3DUniprotInterface  {
     cssConfig?: RcsbFv3DCssConfig;
 }
 
+
+type AlignmentLoadMolstarType = LoadMolstarInterface<AlignmentTrajectoryParamsType,LoadMolstarReturnType>;
 export class RcsbFv3DUniprot extends RcsbFv3DAbstract<
-        MsaPfvManagerInterface,
-        LoadMolstarInterface|undefined,
+        MsaPfvManagerInterface<[string,SearchQuery?]>,
+        AlignmentLoadMolstarType,
+        LoadMolstarReturnType,
         {viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>},
         {context:{id:string},module:RcsbFvModulePublicInterface}
     > {
@@ -64,13 +76,13 @@ export class RcsbFv3DUniprot extends RcsbFv3DAbstract<
                     additionalConfig: params.additionalConfig,
                     pfvParams:{
                         id:params.config.upAcc,
-                        query:params.config.query,
+                        pfvArgs:[params.config.upAcc,params.config.query],
                         buildMsaAlignmentFv:buildUniprotAlignmentFv,
                         alignmentResponseContainer
                     },
                     buildPfvOnMount: true,
-                    pfvManagerFactory: new MsaPfvManagerFactory<LoadMolstarInterface>(),
-                    callbackManagerFactory: new MsaCallbackManagerFactory<LoadMolstarInterface, {context: {id:string};}>({
+                    pfvManagerFactory: new MsaPfvManagerFactory<[string,SearchQuery?],AlignmentLoadMolstarType, LoadMolstarReturnType>(),
+                    callbackManagerFactory: new MsaCallbackManagerFactory<AlignmentLoadMolstarType, LoadMolstarReturnType, {context: {id:string};}>({
                         pluginLoadParamsDefinition,
                         alignmentResponseContainer
                     }),
@@ -78,14 +90,20 @@ export class RcsbFv3DUniprot extends RcsbFv3DAbstract<
                 }
             },
             structureConfig: {
-                loadConfig: undefined,
                 structureViewerConfig: {
                     viewerElement:RcsbFvStructure.componentId(elementId),
                     viewerProps: params.molstarProps ?? {}
                 }
             },
-            structureViewer: new StructureViewer<LoadMolstarInterface,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}>( new MolstarManagerFactory() ),
-            structureViewerBehaviourObserver: new MsaBehaviourObserver<LoadMolstarInterface>(new MolstarAlignmentLoader())
+            structureViewer: new StructureViewer<
+                AlignmentLoadMolstarType,
+                LoadMolstarReturnType,
+                {viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}
+            >( new MolstarManagerFactory(getModelIdFromTrajectory) ),
+            structureViewerBehaviourObserver: new MsaBehaviourObserver<AlignmentLoadMolstarType,LoadMolstarReturnType>(
+                new MolstarAlignmentLoader(),
+                new MolstarComponentActionFactory()
+            )
         });
     }
 

src/RcsbFvContextManager/RcsbFvContextManager.ts

@@ -4,9 +4,9 @@ import {RcsbFvSequenceInterface} from "../RcsbFvSequence/RcsbFvSequence";
 import {PluginContext} from "molstar/lib/mol-plugin/context";
 
 /**Main Event Data Object Interface*/
-export interface RcsbFvContextManagerInterface<T,R,S,U> {
+export interface RcsbFvContextManagerInterface<T,R,L,S,U> {
     eventType: EventType;
-    eventData: string | UpdateConfigInterface<T,R,S,U> | ((plugin: PluginContext) => void);
+    eventData: string | UpdateConfigInterface<T,R,L,S,U> | ((plugin: PluginContext) => void);
 }
 
 /**Event types*/
@@ -15,24 +15,24 @@ export enum EventType {
     PLUGIN_CALL = "pluginCall"
 }
 
-export interface UpdateConfigInterface<T,R,S,U> {
+export interface UpdateConfigInterface<T,R,L,S,U> {
     structurePanelConfig?:Partial<RcsbFvStructureConfigInterface<R,S>>;
-    sequencePanelConfig?:Partial<RcsbFvSequenceInterface<T,R,U>>;
+    sequencePanelConfig?:Partial<RcsbFvSequenceInterface<T,R,L,U>>;
 }
 
 /**rxjs Event Handler Object. It allows objects to subscribe methods and then, get(send) events to(from) other objects*/
-export class RcsbFvContextManager<T,R,S,U> {
-    private readonly subject: Subject<RcsbFvContextManagerInterface<T,R,S,U>> = new Subject<RcsbFvContextManagerInterface<T,R,S,U>>();
+export class RcsbFvContextManager<T,R,L,S,U> {
+    private readonly subject: Subject<RcsbFvContextManagerInterface<T,R,L,S,U>> = new Subject<RcsbFvContextManagerInterface<T,R,L,S,U>>();
     /**Call other subscribed methods
      * @param obj Event Data Structure Interface
      * */
-    public next( obj: RcsbFvContextManagerInterface<T,R,S,U> ):void {
+    public next( obj: RcsbFvContextManagerInterface<T,R,L,S,U> ):void {
         this.subject.next(obj);
     }
     /**Subscribe loadMethod
      * @return Subscription
      * */
-    public subscribe(f:(x:RcsbFvContextManagerInterface<T,R,S,U>)=>void):Subscription {
+    public subscribe(f:(x:RcsbFvContextManagerInterface<T,R,L,S,U>)=>void):Subscription {
         return this.subject.asObservable().subscribe(f);
     }
     /**Unsubscribe all methods*/

src/RcsbFvSequence/RcsbFvSequence.tsx

@@ -7,11 +7,11 @@ import {
 import {PluginContext} from "molstar/lib/mol-plugin/context";
 import {RcsbFv, RcsbFvTrackDataElementInterface} from "@rcsb/rcsb-saguaro";
 import {RcsbView, RcsbViewInterface} from "./SequenceViews/RcsbView/RcsbView";
-import {RcsbFvStateManager} from "../RcsbFvState/RcsbFvStateManager";
+import {RcsbFvStateInterface} from "../RcsbFvState/RcsbFvStateInterface";
 
-export interface RcsbFvSequenceInterface<T,R,U>{
+export interface RcsbFvSequenceInterface<T,R,L,U>{
     type: "custom" | "rcsb";
-    config: RcsbViewInterface<T,R,U> | CustomViewInterface<R>;
+    config: RcsbViewInterface<T,R,L,U> | CustomViewInterface<R,L>;
     title?: string;
     subtitle?: string;
 }
@@ -21,13 +21,13 @@ interface CallbackConfig {
     sequenceCallback?: (rcsbFv: RcsbFv)=>void;
 }
 
-type StructureViewerType<R> = ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>;
-export class RcsbFvSequence<T,R,U> extends React.Component <RcsbFvSequenceInterface<T,R,U> & CallbackConfig & {unmount:(flag:boolean)=>void, structureViewer: StructureViewerType<R>,  stateManager: RcsbFvStateManager, componentId:string}, RcsbFvSequenceInterface<T,R,U> > {
+type StructureViewerType<R,L> = ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>;
+export class RcsbFvSequence<T,R,L,U> extends React.Component <RcsbFvSequenceInterface<T,R,L,U> & CallbackConfig & {unmount:(flag:boolean)=>void, structureViewer: StructureViewerType<R,L>,  stateManager: RcsbFvStateInterface, componentId:string}, RcsbFvSequenceInterface<T,R,L,U> > {
 
     render() {
         if(this.props.type == "custom"){
-            const config: CustomViewInterface<R> = this.props.config as CustomViewInterface<R>;
-            return (<CustomView<R>
+            const config: CustomViewInterface<R,L> = this.props.config as CustomViewInterface<R,L>;
+            return (<CustomView<R,L>
                 {...config}
                 componentId={this.props.componentId}
                 structureViewer={this.props.structureViewer}
@@ -37,8 +37,8 @@ export class RcsbFvSequence<T,R,U> extends React.Component <RcsbFvSequenceInterf
                 unmount={this.props.unmount}
             />)
         }else if(this.props.type == "rcsb"){
-            const config: RcsbViewInterface<T,R,U> = this.props.config as unknown as RcsbViewInterface<T,R,U>;
-            return (<RcsbView<T,R,U>
+            const config: RcsbViewInterface<T,R,L,U> = this.props.config as unknown as RcsbViewInterface<T,R,L,U>;
+            return (<RcsbView<T,R,L,U>
                 {...config}
                 componentId={this.props.componentId}
                 structureViewer={this.props.structureViewer}

src/RcsbFvSequence/SequenceViews/AbstractView.tsx

@@ -7,24 +7,24 @@ import {
     ViewerCallbackManagerInterface, ViewerActionManagerInterface
 } from "../../RcsbFvStructure/StructureViewerInterface";
 import {SequenceViewInterface} from "./SequenceViewInterface";
-import {RcsbFvStateManager} from "../../RcsbFvState/RcsbFvStateManager";
+import {RcsbFvStateInterface} from "../../RcsbFvState/RcsbFvStateInterface";
 
-export interface AbstractViewInterface<R> {
+export interface AbstractViewInterface<R,L> {
     componentId: string;
     title?: string;
     subtitle?: string;
-    structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>;
-    stateManager: RcsbFvStateManager;
+    structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>;
+    stateManager: RcsbFvStateInterface;
     unmount:(flag:boolean,callback:()=>void)=>void;
 }
 
-export abstract class AbstractView<P,S,R> extends React.Component <P & AbstractViewInterface<R>, S> implements SequenceViewInterface {
+export abstract class AbstractView<P,S,R,L> extends React.Component <P & AbstractViewInterface<R,L>, S> implements SequenceViewInterface {
 
     protected readonly componentDivId: string;
     protected readonly rcsbFvDivId: string;
     private updateDimTask: Subscription | null = null;
 
-    protected constructor(props:P & AbstractViewInterface<R>) {
+    protected constructor(props:P & AbstractViewInterface<R,L>) {
         super(props);
         this.componentDivId = props.componentId+"_"+RcsbFvDOMConstants.PFV_DIV;
         this.rcsbFvDivId = props.componentId+"_"+RcsbFvDOMConstants.PFV_APP_ID;

src/RcsbFvSequence/SequenceViews/CustomView/CustomView.tsx

@@ -8,39 +8,37 @@ import {
     RcsbFvTrackDataElementInterface
 } from "@rcsb/rcsb-saguaro";
 import * as React from "react";
-import {RcsbFvSelectorManager} from "../../../RcsbFvState/RcsbFvSelectorManager";
 import {
-    SaguaroPluginModelMapType,
     StructureViewerPublicInterface
 } from "../../../RcsbFvStructure/StructureViewerInterface";
-import {RcsbFvStateManager} from "../../../RcsbFvState/RcsbFvStateManager";
 import uniqid from "uniqid";
+import {RcsbFvStateInterface} from "../../../RcsbFvState/RcsbFvStateInterface";
 
-export type CustomViewStateInterface<R> = Omit<CustomViewInterface<R>, "modelChangeCallback">;
+export type CustomViewStateInterface<R,L> = Omit<CustomViewInterface<R,L>, "modelChangeCallback">;
 
-export interface CustomViewInterface<R> {
-    blockConfig: FeatureBlockInterface<R> | Array<FeatureBlockInterface<R>>;
+export interface CustomViewInterface<R,L> {
+    blockConfig: FeatureBlockInterface<R,L> | Array<FeatureBlockInterface<R,L>>;
     blockSelectorElement?: (blockSelector: BlockSelectorManager) => JSX.Element;
-    modelChangeCallback?: () => CustomViewStateInterface<R>;
-    blockChangeCallback?: (plugin: StructureViewerPublicInterface<R>, pfvList: Array<RcsbFv>, stateManager: RcsbFvStateManager) => void;
+    modelChangeCallback?: () => CustomViewStateInterface<R,L>;
+    blockChangeCallback?: (plugin: StructureViewerPublicInterface<R,L>, pfvList: Array<RcsbFv>, stateManager: RcsbFvStateInterface) => void;
 }
 
-export interface FeatureBlockInterface<R> {
+export interface FeatureBlockInterface<R,L> {
     blockId:string;
     blockTitle?: string;
     blockShortName?: string;
-    featureViewConfig: Array<FeatureViewInterface<R>> | FeatureViewInterface<R>;
+    featureViewConfig: Array<FeatureViewInterface<R,L>> | FeatureViewInterface<R,L>;
 }
 
-export interface FeatureViewInterface<R> {
+export interface FeatureViewInterface<R,L> {
     boardId?:string;
     boardConfig: RcsbFvBoardConfigInterface;
     rowConfig: Array<RcsbFvRowConfigInterface>;
-    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<R>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => void;
-    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface<R>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => void;
-    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<R>, stateManager: RcsbFvStateManager, hoverRegion: Array<RcsbFvTrackDataElementInterface>) => void;
-    structureSelectionCallback: (plugin: StructureViewerPublicInterface<R>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => void;
-    structureHoverCallback: (plugin: StructureViewerPublicInterface<R>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => void;
+    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<R,L>, stateManager: RcsbFvStateInterface, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => void;
+    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface<R,L>, stateManager: RcsbFvStateInterface, d: RcsbFvTrackDataElementInterface) => void;
+    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<R,L>, stateManager: RcsbFvStateInterface, hoverRegion: Array<RcsbFvTrackDataElementInterface>) => void;
+    structureSelectionCallback: (plugin: StructureViewerPublicInterface<R,L>, pfv: RcsbFv, stateManager: RcsbFvStateInterface) => void;
+    structureHoverCallback: (plugin: StructureViewerPublicInterface<R,L>, pfv: RcsbFv, stateManager: RcsbFvStateInterface) => void;
 }
 
 export class BlockSelectorManager {
@@ -63,23 +61,23 @@ export class BlockSelectorManager {
     }
 }
 
-export class CustomView<R> extends AbstractView<CustomViewInterface<R>, CustomViewStateInterface<R>,R> {
+export class CustomView<R,L> extends AbstractView<CustomViewInterface<R,L>, CustomViewStateInterface<R,L>,R,L> {
 
     private blockViewSelector: BlockSelectorManager = new BlockSelectorManager( this.blockChange.bind(this) );
-    private boardMap: Map<string, FeatureViewInterface<R>> = new Map<string, FeatureViewInterface<R>>();
+    private boardMap: Map<string, FeatureViewInterface<R,L>> = new Map<string, FeatureViewInterface<R,L>>();
     private blockMap: Map<string, Array<string>> = new Map<string, Array<string>>();
     private rcsbFvMap: Map<string, RcsbFv> = new Map<string, RcsbFv>();
     private firstModelLoad: boolean = true;
     private innerSelectionFlag: boolean = false;
     private updateContext:"state-change"|null = null;
 
-    readonly state: CustomViewStateInterface<R> = {
+    readonly state: CustomViewStateInterface<R,L> = {
         blockConfig: this.props.blockConfig,
         blockSelectorElement: this.props.blockSelectorElement,
         blockChangeCallback: this.props.blockChangeCallback
     };
 
-    constructor(props: CustomViewInterface<R> & AbstractViewInterface<R>) {
+    constructor(props: CustomViewInterface<R,L> & AbstractViewInterface<R,L>) {
         super(props);
         this.mapBlocks(props.blockConfig);
     }
@@ -96,7 +94,7 @@ export class CustomView<R> extends AbstractView<CustomViewInterface<R>, CustomVi
         });
     }
 
-    componentDidUpdate(prevProps: Readonly<CustomViewInterface<R> & AbstractViewInterface<R>>, prevState: Readonly<CustomViewStateInterface<R>>, snapshot?: any) {
+    componentDidUpdate(prevProps: Readonly<CustomViewInterface<R,L> & AbstractViewInterface<R,L>>, prevState: Readonly<CustomViewStateInterface<R,L>>, snapshot?: any) {
         if(this.updateContext != "state-change") {
             this.updateContext = "state-change";
             this.mapBlocks(this.props.blockConfig);
@@ -108,7 +106,7 @@ export class CustomView<R> extends AbstractView<CustomViewInterface<R>, CustomVi
         }
     }
 
-    private mapBlocks(config: FeatureBlockInterface<R> | Array<FeatureBlockInterface<R>>){
+    private mapBlocks(config: FeatureBlockInterface<R,L> | Array<FeatureBlockInterface<R,L>>){
         this.rcsbFvMap.forEach((pfv, id) => {
             pfv.unmount();
         });
@@ -219,7 +217,7 @@ export class CustomView<R> extends AbstractView<CustomViewInterface<R>, CustomVi
             return;
         }
         if(typeof this.props.modelChangeCallback === "function") {
-            let newConfig: CustomViewStateInterface<R> = this.props.modelChangeCallback();
+            let newConfig: CustomViewStateInterface<R,L> = this.props.modelChangeCallback();
             if(newConfig != null ){
                 this.updateContext = "state-change";
                 if(newConfig.blockConfig != null && newConfig.blockSelectorElement != null){
@@ -235,7 +233,12 @@ export class CustomView<R> extends AbstractView<CustomViewInterface<R>, CustomVi
         }
     }
 
-    setState<K extends keyof CustomViewStateInterface<R>>(state: ((prevState: Readonly<CustomViewStateInterface<R>>, props: Readonly<CustomViewInterface<R> & AbstractViewInterface<R>>) => (Pick<CustomViewStateInterface<R>, K> | CustomViewStateInterface<R> | null)) | Pick<CustomViewStateInterface<R>, K> | CustomViewStateInterface<R> | null, callback?: () => void) {
+    setState<K extends keyof CustomViewStateInterface<R,L>>(
+        state: ((
+            prevState: Readonly<CustomViewStateInterface<R,L>>,
+            props: Readonly<CustomViewInterface<R,L> & AbstractViewInterface<R,L>>
+        ) => (Pick<CustomViewStateInterface<R,L>, K> | CustomViewStateInterface<R,L> | null)) | Pick<CustomViewStateInterface<R,L>, K> | CustomViewStateInterface<R,L> | null, callback?: () => void
+    ) {
         super.setState(state, ()=>{
             this.blockViewSelector.setActiveBlock( (this.state.blockConfig instanceof Array ? this.state.blockConfig : [this.state.blockConfig])[0].blockId! )
             if(typeof callback === "function") callback();

src/RcsbFvSequence/SequenceViews/RcsbView/CallbackManagerFactoryImplementation/AssemblyCallbackManager.ts

@@ -13,13 +13,13 @@ import {
 import {RegionSelectionInterface} from "../../../../RcsbFvState/RcsbFvSelectorManager";
 import {DataContainer} from "../../../../Utils/DataContainer";
 
-export class AssemblyCallbackManagerFactory<R> implements CallbackManagerFactoryInterface<R,undefined> {
-    getCallbackManager(config: CallbackConfigInterface<R>): CallbackManagerInterface<undefined> {
-        return new AssemblyCallbackManager<R>(config);
+export class AssemblyCallbackManagerFactory<R,L> implements CallbackManagerFactoryInterface<R,L,undefined> {
+    getCallbackManager(config: CallbackConfigInterface<R,L>): CallbackManagerInterface<undefined> {
+        return new AssemblyCallbackManager<R,L>(config);
     }
 }
 
-class AssemblyCallbackManager<R> extends AbstractCallbackManager<R,undefined> {
+class AssemblyCallbackManager<R,L> extends AbstractCallbackManager<R,L,undefined> {
 
     public featureClickCallback(e:RcsbFvTrackDataElementInterface): void {
         if(e == null){

src/RcsbFvSequence/SequenceViews/RcsbView/CallbackManagerFactoryImplementation/MsaCallbackManager.ts

@@ -14,7 +14,7 @@ import {TagDelimiter} from "@rcsb/rcsb-saguaro-app";
 import {AlignmentMapper as AM} from "../../../../Utils/AlignmentMapper";
 import {DataContainer} from "../../../../Utils/DataContainer";
 
-export class MsaCallbackManagerFactory<R,U> implements CallbackManagerFactoryInterface<R,U> {
+export class MsaCallbackManagerFactory<R,L,U> implements CallbackManagerFactoryInterface<R,L,U> {
 
     private readonly pluginLoadParamsDefinition:(id: string)=>R;
     private readonly alignmentResponseContainer: DataContainer<AlignmentResponse>;
@@ -27,7 +27,7 @@ export class MsaCallbackManagerFactory<R,U> implements CallbackManagerFactoryInt
         this.alignmentResponseContainer = config.alignmentResponseContainer;
     }
 
-    getCallbackManager(config: CallbackConfigInterface<R>): CallbackManagerInterface<U> {
+    getCallbackManager(config: CallbackConfigInterface<R,L>): CallbackManagerInterface<U> {
         return new MsaCallbackManager( {
             ...config,
             loadParamRequest:this.pluginLoadParamsDefinition,
@@ -38,13 +38,13 @@ export class MsaCallbackManagerFactory<R,U> implements CallbackManagerFactoryInt
 }
 
 type SelectedRegion = {modelId: string, labelAsymId: string, region: RegionSelectionInterface, operatorName?: string};
-class MsaCallbackManager<R,U>  extends AbstractCallbackManager<R,U>{
+class MsaCallbackManager<R,L,U>  extends AbstractCallbackManager<R,L,U>{
 
     private readonly loadParamRequest:(id: string)=>R;
     private readonly targetIds: {[key:string]:boolean} = {};
     private readonly alignmentResponseContainer: DataContainer<AlignmentResponse>;
 
-    constructor(config: CallbackConfigInterface<R> & {loadParamRequest:(id: string)=>R;alignmentResponseContainer: DataContainer<AlignmentResponse>;}) {
+    constructor(config: CallbackConfigInterface<R,L> & {loadParamRequest:(id: string)=>R;alignmentResponseContainer: DataContainer<AlignmentResponse>;}) {
         super(config);
         this.loadParamRequest = config.loadParamRequest;
         this.alignmentResponseContainer = config.alignmentResponseContainer;
@@ -96,7 +96,9 @@ class MsaCallbackManager<R,U>  extends AbstractCallbackManager<R,U>{
         let regions: SelectedRegion[] = [];
         if(alignment) {
             allSel.forEach(sel => {
-                const chain: ChainInfo | undefined = this.stateManager.assemblyModelSate.getModelChainInfo(sel.modelId)?.chains.find(ch => ch.entityId == TagDelimiter.parseEntity(sel.modelId).entityId && ch.label == sel.labelAsymId);
+                const chain: ChainInfo | undefined = this.stateManager.assemblyModelSate.getModelChainInfo(sel.modelId)?.chains.find(
+                    ch => (ch.entityId == TagDelimiter.parseRcsbId(sel.modelId).entityId || ch.label == TagDelimiter.parseRcsbId(sel.modelId).instanceId) && ch.label == sel.labelAsymId
+                );
                 if (chain) {
                     regions = regions.concat(this.getModelRegions(sel.regions.map(r => ({
                         begin: r.begin,
@@ -127,7 +129,9 @@ class MsaCallbackManager<R,U>  extends AbstractCallbackManager<R,U>{
     private getModelRegions(selection: Array<RcsbFvTrackDataElementInterface>, alignment: AlignmentResponse, modelList: string[], pointer:"query"|"target"): SelectedRegion[] {
         const regions: SelectedRegion[] = [];
         modelList.forEach(modelId=>{
-            const chain: ChainInfo|undefined = this.stateManager.assemblyModelSate.getModelChainInfo(modelId)?.chains.find(ch=>ch.entityId==TagDelimiter.parseEntity(modelId).entityId);
+            const chain: ChainInfo|undefined = this.stateManager.assemblyModelSate.getModelChainInfo(modelId)?.chains.find(
+                ch=>ch.entityId==TagDelimiter.parseRcsbId(modelId).entityId || ch.label==TagDelimiter.parseRcsbId(modelId).instanceId
+            );
             if(!chain)
                 return;
             const labelAsymId: string | undefined = chain.label;

src/RcsbFvSequence/SequenceViews/RcsbView/CallbackManagerFactoryInterface.ts

@@ -7,7 +7,7 @@ import {
     RcsbFvModulePublicInterface
 } from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface";
 import {PfvManagerInterface} from "./PfvManagerFactoryInterface";
-import {RcsbFvStateManager} from "../../../RcsbFvState/RcsbFvStateManager";
+import {RcsbFvStateInterface} from "../../../RcsbFvState/RcsbFvStateInterface";
 
 export interface CallbackManagerInterface<U> {
     structureViewerSelectionCallback(mode:'select'|'hover'): Promise<void>;
@@ -18,25 +18,25 @@ export interface CallbackManagerInterface<U> {
     pfvChangeCallback(args:U): Promise<void>;
 }
 
-export interface CallbackManagerFactoryInterface<R,U> {
-    getCallbackManager(config: CallbackConfigInterface<R>): CallbackManagerInterface<U>;
+export interface CallbackManagerFactoryInterface<R,L,U> {
+    getCallbackManager(config: CallbackConfigInterface<R,L>): CallbackManagerInterface<U>;
 }
 
-export interface CallbackConfigInterface<R> {
+export interface CallbackConfigInterface<R,L> {
     rcsbFvContainer: DataContainer<RcsbFvModulePublicInterface>;
-    stateManager: RcsbFvStateManager;
-    structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>;
+    stateManager: RcsbFvStateInterface;
+    structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>;
     pfvFactory: PfvManagerInterface;
 }
 
-export abstract class AbstractCallbackManager<R,U> implements CallbackManagerInterface<U> {
+export abstract class AbstractCallbackManager<R,L,U> implements CallbackManagerInterface<U> {
     protected readonly rcsbFvContainer: DataContainer<RcsbFvModulePublicInterface>;
-    protected readonly stateManager: RcsbFvStateManager;
-    protected readonly structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>;
+    protected readonly stateManager: RcsbFvStateInterface;
+    protected readonly structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>;
     protected pfvFactory: PfvManagerInterface;
     private readonly isInnerSelection: DataContainer<boolean> = new DataContainer<boolean>();
 
-    constructor(config: CallbackConfigInterface<R>) {
+    constructor(config: CallbackConfigInterface<R,L>) {
         this.rcsbFvContainer = config.rcsbFvContainer;
         this.stateManager = config.stateManager;
         this.structureViewer = config.structureViewer;

src/RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/AssemblyPfvComponents/ChainDisplayComponent.tsx

@@ -3,7 +3,7 @@ import {
     StructureViewerInterface
 } from "../../../../../RcsbFvStructure/StructureViewerInterface";
 
-type DisplayComponentMethod = (StructureViewerInterface<undefined,[]>)["displayComponent"]
+type DisplayComponentMethod = (StructureViewerInterface<undefined,undefined,[]>)["displayComponent"]
 interface ChainDisplayInterface {
     structureViewer: {
         displayComponent:DisplayComponentMethod

src/RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/AssemblyPfvManagerFactory.tsx

@@ -32,25 +32,25 @@ import {
 import {ColorTheme} from "molstar/lib/mol-theme/color";
 import {PLDDTConfidenceColorThemeProvider} from "molstar/lib/extensions/model-archive/quality-assessment/color/plddt";
 
-interface AssemblyPfvManagerInterface<R> extends PfvManagerFactoryConfigInterface<R,undefined>{
-    useOperatorsFlag: boolean | undefined;
-    instanceSequenceConfig: InstanceSequenceConfig | undefined;
+interface AssemblyPfvManagerInterface<R,L> extends PfvManagerFactoryConfigInterface<R,L,undefined>{
+    useOperatorsFlag?: boolean;
+    instanceSequenceConfig?: InstanceSequenceConfig;
 }
 
-export class AssemblyPfvManagerFactory<R> implements PfvManagerFactoryInterface<{instanceSequenceConfig: InstanceSequenceConfig|undefined;useOperatorsFlag: boolean | undefined;},R,undefined> {
-    public getPfvManager(config:  AssemblyPfvManagerInterface<R>): PfvManagerInterface {
-        return new AssemblyPfvManager<R>(config);
+export class AssemblyPfvManagerFactory<R,L> implements PfvManagerFactoryInterface<{instanceSequenceConfig: InstanceSequenceConfig|undefined;useOperatorsFlag: boolean | undefined;},R,L,undefined> {
+    public getPfvManager(config:  AssemblyPfvManagerInterface<R,L>): PfvManagerInterface {
+        return new AssemblyPfvManager<R,L>(config);
     }
 }
 
-class AssemblyPfvManager<R> extends AbstractPfvManager<{instanceSequenceConfig: InstanceSequenceConfig|undefined;useOperatorsFlag: boolean | undefined;},R,undefined> {
+class AssemblyPfvManager<R,L> extends AbstractPfvManager<{instanceSequenceConfig?: InstanceSequenceConfig;useOperatorsFlag?: boolean;},R,L,undefined> {
 
     private readonly instanceSequenceConfig: InstanceSequenceConfig|undefined;
     private readonly useOperatorsFlag:boolean | undefined;
     private readonly OPERATOR_DROPDOWN_TITLE: string = "Symmetry Partner";
     private module: RcsbFvModulePublicInterface | undefined = undefined;
 
-    constructor(config: AssemblyPfvManagerInterface<R>) {
+    constructor(config: AssemblyPfvManagerInterface<R,L>) {
         super(config);
         this.instanceSequenceConfig = config.instanceSequenceConfig;
         this.useOperatorsFlag = config.useOperatorsFlag;
@@ -113,7 +113,7 @@ class AssemblyPfvManager<R> extends AbstractPfvManager<{instanceSequenceConfig:
             );
         }
         if(!config.defaultAuthId)
-            await createComponents<R>(this.structureViewer, this.stateManager.assemblyModelSate.getMap());
+            await createComponents<R,L>(this.structureViewer, this.stateManager.assemblyModelSate.getMap());
         return this.module;
     }
 
@@ -153,8 +153,8 @@ class AssemblyPfvManager<R> extends AbstractPfvManager<{instanceSequenceConfig:
                 if(ann.source == Source.PdbInterface && ann.target_id && data.rcsbContext?.asymId) {
                     const interfaceToInstance: InterfaceInstanceTranslate = await RcsbRequestContextManager.getInterfaceToInstance(ann.target_id);
                     if(typeof ann.target_identifiers?.interface_partner_index === "number" && ann.target_identifiers.assembly_id === this.stateManager.assemblyModelSate.getString("assemblyId") && Array.isArray(interfaceToInstance.getOperatorIds(ann.target_id))) {
-                        const operatorIds:string[][] = interfaceToInstance.getOperatorIds(ann.target_id)[ann.target_identifiers.interface_partner_index];
-                        if(ann.features && this.stateManager.assemblyModelSate.getOperator() && operatorIds.map(o=>o.join("|")).includes( this.stateManager.assemblyModelSate.getOperator()!.ids.join("|") )){
+                        const operatorIds:string[][]|undefined = interfaceToInstance.getOperatorIds(ann.target_id)?.[ann.target_identifiers.interface_partner_index];
+                        if(ann.features && this.stateManager.assemblyModelSate.getOperator() && operatorIds?.map(o=>o.join("|")).includes( this.stateManager.assemblyModelSate.getOperator()!.ids.join("|") )){
                             ann.features = ann.features.filter(f=>(f && f.type == FeatureType.BurialFraction));
                             if(ann.features.length > 0)
                                 return ann;
@@ -176,7 +176,7 @@ class AssemblyPfvManager<R> extends AbstractPfvManager<{instanceSequenceConfig:
 
 }
 
-async function createComponents<R>(plugin: ViewerActionManagerInterface<R>, modelMap:SaguaroPluginModelMapType): Promise<void> {
+async function createComponents<R,L>(plugin: ViewerActionManagerInterface<R,L>, modelMap:SaguaroPluginModelMapType): Promise<void> {
     plugin.displayComponent("Water", false);
     await plugin.colorComponent("Polymer", 'chain-id');
     const chains: Array<{modelId: string; auth: string; label: string;}> = new Array<{modelId: string; auth: string; label: string;}>();

src/RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/MsaPfvComponents/MsaRowMarkComponent.tsx

@@ -7,15 +7,15 @@ import React from "react";
 import classes from '../../../../../styles/MsaPfvStyle.module.scss';
 import {Property} from "csstype";
 import {asyncScheduler, Subscription} from "rxjs";
-import {RcsbFvStateManager} from "../../../../../RcsbFvState/RcsbFvStateManager";
 import {TagDelimiter} from "@rcsb/rcsb-saguaro-app";
+import {RcsbFvStateInterface} from "../../../../../RcsbFvState/RcsbFvStateInterface";
 
 interface MsaRowMarkInterface  {
     isGlowing:boolean;
     clickCallback?:()=>void;
     hoverCallback?:()=>void;
-    rowRef:{entryId:string;entityId:string;};
-    stateManager: RcsbFvStateManager;
+    rowRef:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;};
+    stateManager: RcsbFvStateInterface;
 }
 
 interface MsaRowMarkState {
@@ -67,7 +67,9 @@ export class MsaRowMarkComponent extends React.Component <MsaRowMarkInterface,Ms
     }
 
     private modelChange(): void {
-       if(Array.from(this.props.stateManager.assemblyModelSate.getMap()?.keys() ?? []).includes(`${this.props.rowRef.entryId}${TagDelimiter.entity}${this.props.rowRef.entityId}`))
+       if(Array.from(this.props.stateManager.assemblyModelSate.getMap()?.keys() ?? []).includes(
+           "entityId" in this.props.rowRef ? `${this.props.rowRef.entryId}${TagDelimiter.entity}${this.props.rowRef.entityId}` : `${this.props.rowRef.entryId}${TagDelimiter.instance}${this.props.rowRef.instanceId}`
+       ))
            this.setState({visibility: "visible", borderLeftColor: this.ACTIVE_COLOR});
        else if(this.state.visibility == "visible")
            this.setState({visibility: undefined, borderLeftColor: undefined});

src/RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/MsaPfvComponents/MsaRowTitleCheckboxComponent.tsx

@@ -4,18 +4,19 @@
 */
 
 import * as React from "react";
-import {RcsbFvStateManager} from "../../../../../RcsbFvState/RcsbFvStateManager";
 import {TagDelimiter} from "@rcsb/rcsb-saguaro-app";
 import {Subscription} from "rxjs";
+import {RcsbFvStateInterface} from "../../../../../RcsbFvState/RcsbFvStateInterface";
 
 interface MsaRowTitleCheckboxInterface {
     disabled:boolean;
     entryId: string;
-    entityId: string;
     tag:"aligned"|"polymer"|"non-polymer";
-    stateManager:RcsbFvStateManager
+    stateManager:RcsbFvStateInterface
 }
 
+type MsaRowTitleCheckboxType = MsaRowTitleCheckboxInterface & {entityId:string} | MsaRowTitleCheckboxInterface & {instanceId:string;}
+
 interface MsaRowTitleCheckboxState {
     checked:boolean;
     disabled:boolean;
@@ -24,16 +25,16 @@ interface MsaRowTitleCheckboxState {
 //TODO keeps a global state of the (checkboxes <=> mol-star components) This needs further review!!!
 const globalState: {[key:string]: "active"|"inactive"|"disabled"|undefined;} = {};
 
-export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCheckboxInterface,MsaRowTitleCheckboxState> {
+export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCheckboxType,MsaRowTitleCheckboxState> {
 
     readonly state: MsaRowTitleCheckboxState = {
-        checked: globalState[this.entityId() + this.props.tag] == "active" || this.props.tag == "aligned",
-        disabled: globalState[this.entityId() + this.props.tag] == "disabled"
+        checked: globalState[this.compId() + this.props.tag] == "active" || this.props.tag == "aligned",
+        disabled: globalState[this.compId() + this.props.tag] == "disabled"
     };
 
     private subscription: Subscription;
 
-    constructor(props: MsaRowTitleCheckboxInterface) {
+    constructor(props: MsaRowTitleCheckboxType) {
         super(props);
     }
 
@@ -52,7 +53,7 @@ export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCh
 
     public componentDidUpdate(prevProps: Readonly<MsaRowTitleCheckboxInterface>, prevState: Readonly<MsaRowTitleCheckboxState>, snapshot?: any) {
         if(prevProps.disabled != this.props.disabled && !this.props.disabled ) {
-            switch (globalState[ this.entityId()+this.props.tag ]){
+            switch (globalState[ this.compId()+this.props.tag ]){
                 case "active":
                     this.setState({checked: true, disabled:false});
                     break;
@@ -67,7 +68,7 @@ export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCh
             }
         }else if(prevProps.disabled != this.props.disabled) {
             this.setState({checked: this.props.tag == "aligned"},()=>{
-                globalState[ this.entityId()+this.props.tag ]  = this.state.checked ? "active" : "inactive";
+                globalState[ this.compId()+this.props.tag ]  = this.state.checked ? "active" : "inactive";
             });
         }
     }
@@ -79,7 +80,7 @@ export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCh
     private subscribe(): void{
         this.subscription = this.props.stateManager.subscribe<
             "representation-change"|"missing-component",
-            {label:string;isHidden:boolean;} & {tag:MsaRowTitleCheckboxInterface["tag"];isHidden:boolean;pdb:{entryId:string;entityId:string;};}
+            {label:string;isHidden:boolean;} & {tag:MsaRowTitleCheckboxInterface["tag"];isHidden:boolean;pdb:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;};}
         >((o)=>{
             if(o.type == "representation-change" && o.view == "3d-view" && o.data)
                 this.structureViewerRepresentationChange(o.data);
@@ -89,10 +90,10 @@ export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCh
     }
 
     private missingComponent(pdb:{entryId:string;entityId:string;tag:string;}): void{
-       if(this.entityId() == `${pdb.entryId}${TagDelimiter.entity}${pdb.entityId}` && this.props.tag == pdb.tag){
-           globalState[this.entityId()+this.props.tag] = "disabled"
-           this.setState({disabled:true});
-       }
+        if(this.compId() == this.getRcsbId(pdb) && this.props.tag == pdb.tag){
+            globalState[this.compId()+this.props.tag] = "disabled"
+            this.setState({disabled:true});
+        }
 
     }
 
@@ -101,7 +102,7 @@ export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCh
         const suffix: string = row.pop()!;
         const entryId: string = row.join(TagDelimiter.entity);
         const entityId: string = suffix.substring(0,1);
-        if( this.entityId() == `${entryId}${TagDelimiter.entity}${entityId}` ){
+        if( this.compId() == `${entryId}${TagDelimiter.entity}${entityId}` ){
             //TODO this is a one to many relationship
             /*if( d.label.includes("polymer") && this.props.tag == "polymer" && d.isHidden == this.state.checked){
                 this.setState({checked:!this.state.checked});
@@ -117,14 +118,17 @@ export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCh
         if(this.props.disabled || this.state.disabled)
             return;
         this.setState({checked:!this.state.checked},()=>{
-            globalState[this.entityId()+this.props.tag] = this.state.checked ? "active" : "inactive";
-            this.props.stateManager.next<"representation-change",{tag:MsaRowTitleCheckboxInterface["tag"];isHidden:boolean;pdb:{entryId:string;entityId:string;};}>({
+            globalState[this.compId()+this.props.tag] = this.state.checked ? "active" : "inactive";
+            this.props.stateManager.next<"representation-change",{tag:MsaRowTitleCheckboxInterface["tag"];isHidden:boolean;pdb:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;};}>({
                 view:"1d-view",
                 type: "representation-change",
                 data:{
-                    pdb:{
+                    pdb: "entityId" in this.props ? {
+                        entryId: this.props.entryId,
+                        entityId: this.props.entityId,
+                    } :  {
                         entryId: this.props.entryId,
-                        entityId: this.props.entityId
+                        instanceId: this.props.instanceId
                     },
                     isHidden:!this.state.checked,
                     tag:this.props.tag
@@ -153,8 +157,11 @@ export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCh
         };
     }
 
-    private entityId(): string {
-        return `${this.props.entryId}${TagDelimiter.entity}${this.props.entityId}`;
+    private compId(): string {
+        if("entityId" in this.props)
+            return `${this.props.entryId}${TagDelimiter.entity}${this.props.entityId}`;
+        else
+            return `${this.props.entryId}${TagDelimiter.instance}${this.props.instanceId}`;
     };
 
     private title(): string | undefined{
@@ -169,4 +176,12 @@ export class MsaRowTitleCheckboxComponent extends React.Component <MsaRowTitleCh
                 return `${this.state.checked ? "Hide" : "Show"} Non-polymer Chains`;
         }
     }
+
+    private getRcsbId(pdb:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;}): string {
+        if("instanceId" in pdb)
+            return `${pdb.entryId}${TagDelimiter.instance}${pdb.instanceId}`;
+        else
+            return `${pdb.entryId}${TagDelimiter.entity}${pdb.entityId}`;
+    }
+
 }

src/RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/MsaPfvComponents/MsaRowTitleComponent.tsx

@@ -10,17 +10,17 @@ import {
     AlignmentRequestContextType
 } from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
 import {TargetAlignment} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import {RcsbFvStateManager} from "../../../../../RcsbFvState/RcsbFvStateManager";
 import {Subscription} from "rxjs";
 import {TagDelimiter} from "@rcsb/rcsb-saguaro-app";
 import {MsaRowTitleCheckboxComponent} from "./MsaRowTitleCheckboxComponent";
 import {MouseEvent} from "react";
 import {Property} from "csstype";
+import {RcsbFvStateInterface} from "../../../../../RcsbFvState/RcsbFvStateInterface";
 
 interface MsaRowTitleInterface extends RcsbFvRowTitleInterface {
     alignmentContext: AlignmentRequestContextType;
     targetAlignment: TargetAlignment;
-    stateManager:RcsbFvStateManager;
+    stateManager:RcsbFvStateInterface;
     titleClick: ()=>void;
 }
 
@@ -75,9 +75,9 @@ export class MsaRowTitleComponent extends React.Component <MsaRowTitleInterface,
                    </div>
                </div>
                <div  style={{cursor: this.cursor()}} onClick={(e: MouseEvent)=>this.altClick(e)} >
-                   <MsaRowTitleCheckboxComponent disabled={this.state.disabled} {...TagDelimiter.parseEntity(this.props.targetAlignment.target_id!)} tag={"aligned"} stateManager={this.props.stateManager}/>
-                   <MsaRowTitleCheckboxComponent disabled={this.state.disabled} {...TagDelimiter.parseEntity(this.props.targetAlignment.target_id!)} tag={"polymer"} stateManager={this.props.stateManager}/>
-                   <MsaRowTitleCheckboxComponent disabled={this.state.disabled} {...TagDelimiter.parseEntity(this.props.targetAlignment.target_id!)} tag={"non-polymer"} stateManager={this.props.stateManager}/>
+                   <MsaRowTitleCheckboxComponent disabled={this.state.disabled} {...TagDelimiter.parseEntityOrInstance(this.props.targetAlignment.target_id!)} tag={"aligned"} stateManager={this.props.stateManager}/>
+                   <MsaRowTitleCheckboxComponent disabled={this.state.disabled} {...TagDelimiter.parseEntityOrInstance(this.props.targetAlignment.target_id!)} tag={"polymer"} stateManager={this.props.stateManager}/>
+                   <MsaRowTitleCheckboxComponent disabled={this.state.disabled} {...TagDelimiter.parseEntityOrInstance(this.props.targetAlignment.target_id!)} tag={"non-polymer"} stateManager={this.props.stateManager}/>
                </div>
            </div>
        );
@@ -126,17 +126,19 @@ export class MsaRowTitleComponent extends React.Component <MsaRowTitleInterface,
     }
 
     private click(e: MouseEvent): void{
+        const rcsbId = TagDelimiter.parseEntityOrInstance(this.props.targetAlignment.target_id!);
+        const entityTag = "entityId" in rcsbId ? `#entity-${rcsbId.entityId}` : "";
         if(e.shiftKey) {
             const newWin: Window|null = window.open(
-                `/structure/${TagDelimiter.parseEntity(this.props.targetAlignment.target_id!).entryId}#entity-${TagDelimiter.parseEntity(this.props.targetAlignment.target_id!).entityId}`,
+                `/structure/${rcsbId.entryId}${entityTag}`,
                 "_blank"
             );
             if(!newWin || newWin.closed || typeof newWin.closed === 'undefined')
-                document.location.href = `/structure/${TagDelimiter.parseEntity(this.props.targetAlignment.target_id!).entryId}#entity-${TagDelimiter.parseEntity(this.props.targetAlignment.target_id!).entityId}`;
+                document.location.href = `/structure/${rcsbId.entryId}${entityTag}`;
         } else {
             if(this.state.blocked)
                 return;
-            this.setState({blocked:true});
+            this.block();
             this.props.titleClick();
         }
     }

src/RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/MsaPfvComponents/MsaUiSortComponent.tsx

@@ -4,12 +4,12 @@ import {DataContainer} from "../../../../../Utils/DataContainer";
 import {
     RcsbFvModulePublicInterface
 } from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface";
-import {RcsbFvStateManager} from "../../../../../RcsbFvState/RcsbFvStateManager";
 import {RcsbFvRowConfigInterface} from "@rcsb/rcsb-saguaro";
+import {RcsbFvStateInterface} from "../../../../../RcsbFvState/RcsbFvStateInterface";
 
 export interface MsaUiSortInterface {
     rcsbFvContainer: DataContainer<RcsbFvModulePublicInterface>;
-    stateManager: RcsbFvStateManager;
+    stateManager: RcsbFvStateInterface;
 }
 export class MsaUiSortComponent extends React.Component<MsaUiSortInterface, {}>{
 

src/RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryImplementation/MsaPfvManagerFactory.ts

@@ -24,101 +24,94 @@ import {DataContainer} from "../../../../Utils/DataContainer";
 import {MsaUiSortComponent} from "./MsaPfvComponents/MsaUiSortComponent";
 import {ActionMethods} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvUI/Helper/ActionMethods";
 
-export interface MsaPfvManagerInterface {
+export interface MsaPfvManagerInterface<T extends any[]> {
     id:string;
     alignmentResponseContainer: DataContainer<AlignmentResponse>;
-    buildMsaAlignmentFv(elementId: string, upAcc: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig & ActionMethods.FvChangeConfigInterface): Promise<RcsbFvModulePublicInterface>;
-    query?: SearchQuery;
+    pfvArgs: T;
+    buildMsaAlignmentFv(...args:[string, ...T, RcsbFvAdditionalConfig & ActionMethods.FvChangeConfigInterface]): Promise<RcsbFvModulePublicInterface>;
 }
 
-type MsaPfvManagerInterType<R> = MsaPfvManagerInterface & PfvManagerFactoryConfigInterface<R,{context: {id:string};}>
+type MsaPfvManagerInterType<T extends any[], R,L> = MsaPfvManagerInterface<T> & PfvManagerFactoryConfigInterface<R,L,{context: {id:string};}>
 
-export class MsaPfvManagerFactory<R> implements PfvManagerFactoryInterface<{id:string},R,{context: {id:string};}> {
+export class MsaPfvManagerFactory<T extends any[], R,L> implements PfvManagerFactoryInterface<{id:string},R,L,{context: {id:string};}> {
 
-    getPfvManager(config: MsaPfvManagerInterType<R>): PfvManagerInterface {
+    getPfvManager(config: MsaPfvManagerInterType<T,R,L>): PfvManagerInterface {
         return new MsaPfvManager(config);
     }
 
 }
 
 type AlignmentDataType = {
-    pdb:{
-        entryId:string;
-        entityId:string;
-    },
+    pdb:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;},
     targetAlignment: TargetAlignment;
 };
 
-class MsaPfvManager<R> extends AbstractPfvManager<{id:string},R,{context: {id:string} &  Partial<PolymerEntityInstanceInterface>;}>{
+class MsaPfvManager<T extends any[],R,L> extends AbstractPfvManager<{id:string},R,L,{context: {id:string} &  Partial<PolymerEntityInstanceInterface>;}>{
 
-    private readonly config:MsaPfvManagerInterType<R>;
+    private readonly config:MsaPfvManagerInterType<T,R,L>;
     private module:RcsbFvModulePublicInterface;
 
-    constructor(config:MsaPfvManagerInterType<R>) {
+    constructor(config:MsaPfvManagerInterType<T,R,L>) {
         super(config);
         this.config = config;
     }
 
     async create(): Promise<RcsbFvModulePublicInterface | undefined> {
-        const module:RcsbFvModulePublicInterface = await this.config.buildMsaAlignmentFv(
-            this.rcsbFvDivId,
-            this.config.id,
-            this.config.query,
-            {
-                ... this.additionalConfig,
-                boardConfig: this.boardConfigContainer.get(),
-                externalTrackBuilder:{
-                    filterAlignments: (data: { alignments: AlignmentResponse; rcsbContext?: Partial<PolymerEntityInstanceInterface> }) => {
-                        const visAlignment = this.config.alignmentResponseContainer?.get()?.target_alignment
-                                ?.filter(ta=>ta?.target_id && this.config.stateManager.assemblyModelSate.getMap()?.has(ta.target_id));
-                        const otherAlignment = data.alignments.target_alignment
-                            ?.filter(ta=>ta?.target_id && !this.config.stateManager.assemblyModelSate.getMap()?.has(ta.target_id));
-                        return new Promise(resolve => resolve({
-                            ...data.alignments,
-                            target_alignment: (visAlignment ?? []).concat(otherAlignment ?? [])
-                        }));
-                    }
-                },
-                trackConfigModifier: {
-                    alignment: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignment) => new Promise((resolve)=>{
-                        resolve({
-                            rowMark:{
-                                externalRowMark: {
-                                    component:MsaRowMarkComponent,
-                                    props:{
-                                        rowRef:TagDelimiter.parseEntity(targetAlignment.target_id!),
-                                        stateManager: this.stateManager
-                                    }
-                                },
-                                clickCallback:() => this.loadAlignment(alignmentContext,targetAlignment)
-                            },
-                            externalRowTitle: {
-                                rowTitleComponent:MsaRowTitleComponent,
-                                rowTitleAdditionalProps:{
-                                    alignmentContext,
-                                    targetAlignment,
-                                    stateManager: this.stateManager,
-                                    titleClick: ()=> this.loadAlignment(alignmentContext,targetAlignment)
+        const args: [string, ...T, RcsbFvAdditionalConfig & ActionMethods.FvChangeConfigInterface] = [this.rcsbFvDivId, ...this.config.pfvArgs, {
+            ... this.additionalConfig,
+            boardConfig: this.boardConfigContainer.get(),
+            externalTrackBuilder:{
+                filterAlignments: (data: { alignments: AlignmentResponse; rcsbContext?: Partial<PolymerEntityInstanceInterface> }) => {
+                    const visAlignment = this.config.alignmentResponseContainer?.get()?.target_alignment
+                        ?.filter(ta=>ta?.target_id && this.config.stateManager.assemblyModelSate.getMap()?.has(ta.target_id));
+                    const otherAlignment = data.alignments.target_alignment
+                        ?.filter(ta=>ta?.target_id && !this.config.stateManager.assemblyModelSate.getMap()?.has(ta.target_id));
+                    return new Promise(resolve => resolve({
+                        ...data.alignments,
+                        target_alignment: (visAlignment ?? []).concat(otherAlignment ?? [])
+                    }));
+                }
+            },
+            trackConfigModifier: {
+                alignment: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignment) => new Promise((resolve)=>{
+                    resolve({
+                        rowMark:{
+                            externalRowMark: {
+                                component:MsaRowMarkComponent,
+                                props:{
+                                    rowRef:TagDelimiter.parseEntityOrInstance(targetAlignment.target_id!),
+                                    stateManager: this.stateManager
                                 }
                             },
-                            metadata:{
-                                targetId:targetAlignment.target_id
+                            clickCallback:() => this.loadAlignment(alignmentContext,targetAlignment)
+                        },
+                        externalRowTitle: {
+                            rowTitleComponent:MsaRowTitleComponent,
+                            rowTitleAdditionalProps:{
+                                alignmentContext,
+                                targetAlignment,
+                                stateManager: this.stateManager,
+                                titleClick: ()=> this.loadAlignment(alignmentContext,targetAlignment)
                             }
-                        });
-                    })
-                },
-                beforeChangeCallback: (module) => {
-                    this.config.pfvChangeCallback({context:{id:this.config.id}});
-                },
-                externalUiComponents:[{
-                    component:MsaUiSortComponent,
-                    props: {
-                        rcsbFvContainer: this.rcsbFvContainer,
-                        stateManager: this.stateManager
-                    }
-                }]
-            }
-        );
+                        },
+                        metadata:{
+                            targetId:targetAlignment.target_id
+                        }
+                    });
+                })
+            },
+            beforeChangeCallback: () => {
+                this.config.pfvChangeCallback({context:{id:this.config.id}});
+            },
+            externalUiComponents:[{
+                component:MsaUiSortComponent,
+                props: {
+                    rcsbFvContainer: this.rcsbFvContainer,
+                    stateManager: this.stateManager
+                }
+            }]
+        }];
+        const module:RcsbFvModulePublicInterface = await this.config.buildMsaAlignmentFv(...args);
         this.rcsbFvContainer.set(module);
         await this.readyStateLoad();
         return module;
@@ -137,7 +130,7 @@ class MsaPfvManager<R> extends AbstractPfvManager<{id:string},R,{context: {id:st
                 type:"model-change",
                 view:"1d-view",
                 data:{
-                    pdb:TagDelimiter.parseEntity(targetAlignment.target_id),
+                    pdb:TagDelimiter.parseEntityOrInstance(targetAlignment.target_id),
                     targetAlignment
                 }
             });

src/RcsbFvSequence/SequenceViews/RcsbView/PfvManagerFactoryInterface.ts

@@ -8,20 +8,20 @@ import {
     ViewerCallbackManagerInterface, ViewerActionManagerInterface
 } from "../../../RcsbFvStructure/StructureViewerInterface";
 import {RcsbFvBoardConfigInterface} from "@rcsb/rcsb-saguaro";
-import {RcsbFvStateManager} from "../../../RcsbFvState/RcsbFvStateManager";
+import {RcsbFvStateInterface} from "../../../RcsbFvState/RcsbFvStateInterface";
 
-export interface PfvManagerFactoryConfigInterface<R,U> {
+export interface PfvManagerFactoryConfigInterface<R,L,U> {
     rcsbFvDivId: string;
     rcsbFvContainer: DataContainer<RcsbFvModulePublicInterface>;
-    stateManager: RcsbFvStateManager;
-    structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface <R>;
+    stateManager: RcsbFvStateInterface;
+    structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface <R,L>;
     boardConfigContainer: DataContainer<Partial<RcsbFvBoardConfigInterface>>;
     pfvChangeCallback(context: U): Promise<void>;
     additionalConfig: RcsbFvAdditionalConfig & {operatorChangeCallback?:(operatorInfo: OperatorInfo)=>void} | undefined;
 }
 
-export interface PfvManagerFactoryInterface<T,R,U> {
-    getPfvManager(config:T & PfvManagerFactoryConfigInterface<R,U>): PfvManagerInterface;
+export interface PfvManagerFactoryInterface<T,R,L,U> {
+    getPfvManager(config:T & PfvManagerFactoryConfigInterface<R,L,U>): PfvManagerInterface;
 }
 
 export interface BuildPfvInterface {
@@ -33,17 +33,17 @@ export interface PfvManagerInterface {
     create(config?: BuildPfvInterface): Promise<RcsbFvModulePublicInterface | undefined>;
 }
 
-export abstract class AbstractPfvManager<T,R,U> implements PfvManagerInterface {
+export abstract class AbstractPfvManager<T,R,L,U> implements PfvManagerInterface {
 
     protected readonly rcsbFvDivId: string;
     protected readonly rcsbFvContainer: DataContainer<RcsbFvModulePublicInterface>;
-    protected readonly stateManager: RcsbFvStateManager;
-    protected readonly structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface <R>;
+    protected readonly stateManager: RcsbFvStateInterface;
+    protected readonly structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface <R,L>;
     protected readonly boardConfigContainer: DataContainer<Partial<RcsbFvBoardConfigInterface>>;
     protected readonly pfvChangeCallback: (context: U)=>Promise<void>;
     protected readonly additionalConfig: RcsbFvAdditionalConfig & {operatorChangeCallback?:(operatorInfo: OperatorInfo)=>void} | undefined;
 
-    protected constructor(config:T & PfvManagerFactoryConfigInterface<R,U>){
+    protected constructor(config:T & PfvManagerFactoryConfigInterface<R,L,U>){
         this.rcsbFvDivId = config.rcsbFvDivId;
         this.rcsbFvContainer = config.rcsbFvContainer;
         this.stateManager = config.stateManager;

src/RcsbFvSequence/SequenceViews/RcsbView/RcsbView.tsx

@@ -15,25 +15,25 @@ import {
     CallbackManagerInterface
 } from "./CallbackManagerFactoryInterface";
 
-export interface RcsbViewInterface<T,R,U> {
+export interface RcsbViewInterface<T,R,L,U> {
     rcsbId: string;
     additionalConfig?: RcsbFvAdditionalConfig & {operatorChangeCallback?:(operatorInfo: OperatorInfo)=>void};
     useOperatorsFlag?:boolean;
     pfvParams:T;
-    pfvManagerFactory: PfvManagerFactoryInterface<T,R,U>;
-    callbackManagerFactory: CallbackManagerFactoryInterface<R,U>;
-    additionalContent?(props:RcsbViewInterface<T,R,U> & AbstractViewInterface<R>): JSX.Element;
+    pfvManagerFactory: PfvManagerFactoryInterface<T,R,L,U>;
+    callbackManagerFactory: CallbackManagerFactoryInterface<R,L,U>;
+    additionalContent?(props:RcsbViewInterface<T,R,L,U> & AbstractViewInterface<R,L>): JSX.Element;
     buildPfvOnMount?: boolean;
 }
 
-export class RcsbView<T,R,U> extends AbstractView<RcsbViewInterface<T,R,U>, {}, R>{
+export class RcsbView<T,R,L,U> extends AbstractView<RcsbViewInterface<T,R,L,U>, {}, R,L>{
 
     private boardConfigContainer: DataContainer<Partial<RcsbFvBoardConfigInterface>> = new DataContainer();
     private rcsbFvContainer: DataContainer<RcsbFvModulePublicInterface> = new DataContainer<RcsbFvModulePublicInterface>();
     private readonly callbackManager: CallbackManagerInterface<U>;
     private readonly pfvFactory: PfvManagerInterface;
 
-    constructor(props:RcsbViewInterface<T,R,U> & AbstractViewInterface<R>) {
+    constructor(props:RcsbViewInterface<T,R,L,U> & AbstractViewInterface<R,L>) {
         super(props);
         this.pfvFactory = this.props.pfvManagerFactory.getPfvManager({
             ...this.props.pfvParams,

src/RcsbFvState/RcsbFvStateInterface.ts

@@ -6,7 +6,7 @@
 
 import {RcsbFvSelectorManager} from "./RcsbFvSelectorManager";
 import {AssemblyModelSate} from "./AssemblyModelSate";
-import {Subscription} from "rxjs";
+import {Subject, Subscription} from "rxjs";
 
 export type RcsbFvStateType<T="feature-click",D=undefined> = {
     type: "feature-click"|"selection-change"|"hover-change"|"model-change"|"representation-change"|"pfv-change"|T;
@@ -18,6 +18,7 @@ export interface RcsbFvStateInterface {
 
     readonly selectionState: RcsbFvSelectorManager;
     readonly assemblyModelSate: AssemblyModelSate;
+    readonly subject: Subject<RcsbFvStateType<any,any>>
 
 
     subscribe<T,D>(o:(state:RcsbFvStateType<T,D>)=>void): Subscription;

src/RcsbFvState/RcsbFvStateManager.ts

@@ -13,7 +13,7 @@ export class RcsbFvStateManager implements RcsbFvStateInterface {
     readonly assemblyModelSate: AssemblyModelSate = new AssemblyModelSate();
     readonly selectionState: RcsbFvSelectorManager = new RcsbFvSelectorManager();
 
-    private readonly subject: Subject<RcsbFvStateType<any,any>> = new Subject<RcsbFvStateType>();
+    readonly subject: Subject<RcsbFvStateType<any,any>> = new Subject<RcsbFvStateType>();
 
     next<T,D>(state: RcsbFvStateType<T,D>): void {
         this.subject.next(state);

src/RcsbFvStructure/RcsbFvStructure.tsx

@@ -1,23 +1,22 @@
 import * as React from "react";
 import {StructureViewerInterface} from "./StructureViewerInterface";
 import {RcsbFvDOMConstants} from "../RcsbFvConstants/RcsbFvConstants";
-import {RcsbFvSelectorManager} from "../RcsbFvState/RcsbFvSelectorManager";
-import {RcsbFvStateManager} from "../RcsbFvState/RcsbFvStateManager";
 import {StructureViewerBehaviourObserverInterface} from "./StructureViewerBehaviourInterface";
+import {RcsbFvStateInterface} from "../RcsbFvState/RcsbFvStateInterface";
 
 export interface RcsbFvStructureConfigInterface<R,S> {
-    loadConfig: R | Array<R>;
+    loadConfig?: R | R[];
     structureViewerConfig: S;
 }
 
-interface RcsbFvStructureAdditionalInterface<R,S>{
+interface RcsbFvStructureAdditionalInterface<R,L,S>{
     componentId: string;
-    structureViewer: StructureViewerInterface<R,S>;
-    stateManager: RcsbFvStateManager;
-    structureViewerBehaviourObserver: StructureViewerBehaviourObserverInterface<R>;
+    structureViewer: StructureViewerInterface<R,L,S>;
+    stateManager: RcsbFvStateInterface;
+    structureViewerBehaviourObserver: StructureViewerBehaviourObserverInterface<R,L>;
 }
 
-export class RcsbFvStructure<R,S> extends React.Component <RcsbFvStructureConfigInterface<R,S> & RcsbFvStructureAdditionalInterface<R,S>, RcsbFvStructureConfigInterface<R,S> > {
+export class RcsbFvStructure<R,L,S> extends React.Component <RcsbFvStructureConfigInterface<R,S> & RcsbFvStructureAdditionalInterface<R,L,S>, RcsbFvStructureConfigInterface<R,S> > {
 
     render():JSX.Element {
         return (

src/RcsbFvStructure/StructureUtils/ComponentActionInterface.ts

@@ -0,0 +1,11 @@
+import {RcsbFvStateInterface} from "../../RcsbFvState/RcsbFvStateInterface";
+
+export interface ComponentActionFactoryInterface<L> {
+    getComponentAction(config: {stateManager: RcsbFvStateInterface}): ComponentActionInterface<L>;
+}
+
+export interface ComponentActionInterface<L> {
+
+    accept(x: L, context?:{ entryId:string; entityId:string; } | { entryId:string; instanceId:string; }): void;
+
+}

src/RcsbFvStructure/StructureUtils/MolstarAlignmentLoader.ts

@@ -1,62 +0,0 @@
-/*
-* Copyright (c) 2021 RCSB PDB and contributors, licensed under MIT, See LICENSE file for more info.
-* @author Joan Segura Mora <joan.segura@rcsb.org>
-*/
-
-import {StructureLoaderInterface} from "./StructureLoaderInterface";
-import {ViewerActionManagerInterface, ViewerCallbackManagerInterface} from "../StructureViewerInterface";
-import {LoadMethod, LoadMolstarInterface} from "../StructureViewers/MolstarViewer/MolstarActionManager";
-import {TagDelimiter} from "@rcsb/rcsb-saguaro-app";
-import {
-    AlignmentTrajectoryPresetProvider, TrajectoryParamsType
-} from "../StructureViewers/MolstarViewer/TrajectoryPresetProvider/AlignmentTrajectoryPresetProvider";
-import {TargetAlignment} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import {RcsbFvStateInterface} from "../../RcsbFvState/RcsbFvStateInterface";
-
-export class MolstarAlignmentLoader implements StructureLoaderInterface<[
-        ViewerCallbackManagerInterface & ViewerActionManagerInterface <LoadMolstarInterface<TrajectoryParamsType>>,
-        {entryId:string;entityId:string;},
-        TargetAlignment,
-        RcsbFvStateInterface
-    ]> {
-
-    private readonly structureMap: Set<string> = new Set<string>();
-
-    async load(
-        structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface <LoadMolstarInterface<TrajectoryParamsType>>,
-        pdb:{entryId:string;entityId:string;},
-        targetAlignment: TargetAlignment,
-        stateManager: RcsbFvStateInterface
-    ): Promise<void> {
-        const structureId: string = `${pdb.entryId}${TagDelimiter.entity}${pdb.entityId}`;
-        if(!this.structureMap.has(structureId)){
-            await structureViewer.load({
-                loadMethod: LoadMethod.loadPdbId,
-                loadParams:{
-                    id: structureId,
-                    entryId:pdb.entryId,
-                    reprProvider: AlignmentTrajectoryPresetProvider,
-                    params:{
-                        modelIndex: 0,
-                        pdb,
-                        targetAlignment,
-                        stateManager
-                    }
-                }
-            });
-            this.structureMap.add(
-                structureId
-            );
-        } else {
-            await structureViewer.removeStructure({
-                loadMethod: LoadMethod.loadPdbId,
-                loadParams:{
-                    id: structureId
-                }
-            });
-            this.structureMap.delete(structureId);
-            return;
-        }
-    }
-
-}

src/RcsbFvStructure/StructureUtils/StructureLoaderInterface.ts

@@ -3,6 +3,19 @@
 * @author Joan Segura Mora <joan.segura@rcsb.org>
 */
 
-export interface StructureLoaderInterface<X extends any[]> {
-    load(...args:X): Promise<void>;
+export interface StructureLoaderInterface<X extends any[], L=undefined> {
+    load(...args:X): Promise<undefined|L>;
+}
+
+export type TransformMatrixType = [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number];
+export type RigidTransformType =  {
+    transform: TransformMatrixType,
+    regions?: [number,number][]
+};
+export interface TransformProviderInterface {
+    get(entryId:string, asymId?:string): RigidTransformType[] | undefined;
+}
+
+export interface LocationProviderInterface {
+    get(entryId:string): string | undefined;
 }

src/RcsbFvStructure/StructureViewerBehaviour/AssemblyBehaviour.ts

@@ -16,11 +16,20 @@ import {
 import {RcsbFvStateInterface} from "../../RcsbFvState/RcsbFvStateInterface";
 import {asyncScheduler, Subscription} from "rxjs";
 
-export class AssemblyBehaviourObserver<R> implements StructureViewerBehaviourObserverInterface<R> {
+export class AssemblyBehaviourObserver<R,L> implements StructureViewerBehaviourObserverInterface<R,L> {
 
     private structureBehaviour: StructureViewerBehaviourInterface;
-    public observe(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>, stateManager: RcsbFvStateInterface): void {
+    private readonly assemblyLoadConfig: R;
+
+    constructor(assemblyLoadConfig: R) {
+        this.assemblyLoadConfig = assemblyLoadConfig;
+    }
+
+    public observe(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>, stateManager: RcsbFvStateInterface): void {
         this.structureBehaviour = new AssemblyBehaviour(structureViewer, stateManager);
+        structureViewer.load(this.assemblyLoadConfig).then(()=>{
+            console.info("Assembly load complete");
+        })
     }
 
     public unsubscribe(): void {
@@ -29,15 +38,15 @@ export class AssemblyBehaviourObserver<R> implements StructureViewerBehaviourObs
 
 }
 
-class AssemblyBehaviour<R> implements StructureViewerBehaviourInterface {
+class AssemblyBehaviour<R,L> implements StructureViewerBehaviourInterface {
 
-    private readonly structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>;
+    private readonly structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>;
     private readonly stateManager: RcsbFvStateInterface;
     private readonly subscription: Subscription;
     private selectedComponentId: string|undefined;
     private readonly CREATE_COMPONENT_THR: number = 3;
 
-    constructor(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>, stateManager: RcsbFvStateInterface) {
+    constructor(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>, stateManager: RcsbFvStateInterface) {
         this.structureViewer = structureViewer;
         this.stateManager = stateManager;
         this.subscription = this.subscribe();

src/RcsbFvStructure/StructureViewerBehaviour/MsaBehaviour.ts

@@ -23,27 +23,29 @@ import {RegionSelectionInterface} from "../../RcsbFvState/RcsbFvSelectorManager"
 import {TargetAlignment} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import {FunctionCall} from "../../Utils/FunctionCall";
 import onetimeCall = FunctionCall.onetimeCall;
+import {ComponentActionFactoryInterface, ComponentActionInterface} from "../StructureUtils/ComponentActionInterface";
 
-type MsaBehaviourType<R> = StructureLoaderInterface<[
-        ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>,
-    {entryId:string;entityId:string;},
-    TargetAlignment,
-    RcsbFvStateInterface
-]>;
+type MsaBehaviourType<R,L> = StructureLoaderInterface<[
+    ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>,
+    { entryId:string; entityId:string; } | { entryId:string; instanceId:string; },
+    TargetAlignment
+],L>;
 
-export class MsaBehaviourObserver<R> implements StructureViewerBehaviourObserverInterface<R> {
+export class MsaBehaviourObserver<R,L> implements StructureViewerBehaviourObserverInterface<R,L> {
 
     private structureBehaviour: StructureViewerBehaviourInterface;
-    private readonly structureLoader: MsaBehaviourType<R>;
+    private readonly structureLoader: MsaBehaviourType<R,L>;
+    private readonly componentActionFactory: ComponentActionFactoryInterface<L>;
 
-    constructor(structureLoader: MsaBehaviourType<R>) {
-        this.structureLoader = structureLoader
+    constructor(structureLoader: MsaBehaviourType<R,L>, componentActionFactory: ComponentActionFactoryInterface<L>) {
+        this.structureLoader = structureLoader;
+        this.componentActionFactory = componentActionFactory;
     }
     public observe(
-        structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>,
+        structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>,
         stateManager: RcsbFvStateInterface
     ): void {
-        this.structureBehaviour = new MsaBehaviour(structureViewer, stateManager, this.structureLoader);
+        this.structureBehaviour = new MsaBehaviour(structureViewer, stateManager, this.structureLoader, this.componentActionFactory.getComponentAction({stateManager}));
     }
 
     public unsubscribe(): void {
@@ -54,30 +56,30 @@ export class MsaBehaviourObserver<R> implements StructureViewerBehaviourObserver
 
 type SelectedRegion = {modelId: string, labelAsymId: string, region: RegionSelectionInterface, operatorName?: string};
 type AlignmentDataType = {
-    pdb:{
-        entryId:string;
-        entityId:string;
-    },
+    pdb:{ entryId:string; entityId:string; } | { entryId:string; instanceId:string; },
     targetAlignment: TargetAlignment;
 };
-class MsaBehaviour<R> implements StructureViewerBehaviourInterface {
+class MsaBehaviour<R,L> implements StructureViewerBehaviourInterface {
 
-    private readonly structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>;
+    private readonly structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>;
     private readonly stateManager: RcsbFvStateInterface;
     private readonly subscription: Subscription;
-    private readonly structureLoader: MsaBehaviourType<R>;
+    private readonly structureLoader: MsaBehaviourType<R,L>;
+    private readonly componentAction: ComponentActionInterface<L>;
     private readonly componentList: string[] = [];
 
     private readonly CREATE_COMPONENT_THR: number = 5;
 
     constructor(
-        structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>,
+        structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>,
         stateManager: RcsbFvStateInterface,
-        structureLoader: MsaBehaviourType<R>
+        structureLoader: MsaBehaviourType<R,L>,
+        componentAction: ComponentActionInterface<L>
     ) {
         this.structureViewer = structureViewer;
         this.stateManager = stateManager;
         this.structureLoader = structureLoader;
+        this.componentAction = componentAction;
         this.subscription = this.subscribe();
     }
 
@@ -157,26 +159,28 @@ class MsaBehaviour<R> implements StructureViewerBehaviourInterface {
     unsubscribe(): void {
     }
 
-    reprChange(data?:{pdb:{entryId:string;entityId:string;}} & {tag:"aligned"|"polymer"|"non-polymer";isHidden:boolean;}): void {
+    reprChange(data?:{pdb:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;}} & {tag:"aligned"|"polymer"|"non-polymer";isHidden:boolean;}): void {
         if(data){
+            const chainInfo: ChainInfo|undefined = this.stateManager.assemblyModelSate.getModelChainInfo(this.getRcsbId(data.pdb))?.chains.find(
+                ch=>(("entityId" in data.pdb && ch.entityId==data.pdb.entityId) || ("instanceId" in data.pdb && ch.label==data.pdb.instanceId))
+            );
+            if(!chainInfo)
+                return;
             switch (data.tag){
                 case "aligned":
-                    const chain: ChainInfo|undefined = this.stateManager.assemblyModelSate.getModelChainInfo(`${data.pdb.entryId}${TagDelimiter.entity}${data.pdb.entityId}`)?.chains.find(ch=>ch.entityId==data.pdb.entityId);
-                    if(chain){
-                        const asymId: string|undefined = chain.label;
-                        const operatorInfo: OperatorInfo[] = chain.operators ?? [];
-                        const componentId: string = `${data.pdb.entryId}${TagDelimiter.entity}${data.pdb.entityId}${TagDelimiter.instance}${asymId}${TagDelimiter.assembly}${operatorInfo[0].ids.join(",")}${TagDelimiter.assembly}${"polymer"}`;
-                        this.structureViewer.displayComponent(componentId, !data.isHidden);
-                    }
+                    const asymId: string|undefined = chainInfo.label;
+                    const operatorInfo: OperatorInfo[] = chainInfo.operators ?? [];
+                    const alignedCompId: string = `${data.pdb.entryId}${TagDelimiter.entity}${chainInfo.entityId}${TagDelimiter.instance}${asymId}${TagDelimiter.assembly}${operatorInfo[0].ids.join(",")}${TagDelimiter.assembly}${"polymer"}`;
+                    this.structureViewer.displayComponent(alignedCompId, !data.isHidden);
                     break;
                 case "polymer":
-                    const componentId: string = `${data.pdb.entryId}${TagDelimiter.entity}${data.pdb.entityId}${TagDelimiter.assembly}${data.tag}`;
-                    this.structureViewer.displayComponent(componentId, !data.isHidden);
+                    const polymerCompId: string = `${data.pdb.entryId}${TagDelimiter.entity}${chainInfo.entityId}${TagDelimiter.assembly}${data.tag}`;
+                    this.structureViewer.displayComponent(polymerCompId, !data.isHidden);
                     break;
                 case "non-polymer":
                     createSelectionExpressions(data.pdb.entryId).map(expression=>expression.tag).filter(tag=>(tag!="water" && tag != "polymer")).forEach(tag=>{
-                        const componentId: string = `${data.pdb.entryId}${TagDelimiter.entity}${data.pdb.entityId}${TagDelimiter.assembly}${tag}`;
-                        this.structureViewer.displayComponent(componentId, !data.isHidden);
+                        const nonPolymerCompId: string = `${data.pdb.entryId}${TagDelimiter.entity}${chainInfo.entityId}${TagDelimiter.assembly}${tag}`;
+                        this.structureViewer.displayComponent(nonPolymerCompId, !data.isHidden);
                     });
                     break;
             }
@@ -184,8 +188,12 @@ class MsaBehaviour<R> implements StructureViewerBehaviourInterface {
     }
 
     async modelChange(data?:AlignmentDataType): Promise<void> {
-        if(data)
-            await this.structureLoader.load(this.structureViewer, data.pdb, data.targetAlignment, this.stateManager);
+        if(data) {
+            const trajectory = await this.structureLoader.load(this.structureViewer, data.pdb, data.targetAlignment);
+            if(trajectory){
+                this.componentAction.accept(trajectory, data.pdb);
+            }
+        }
     }
 
     private select(mode:"select"|"hover"): void{
@@ -224,4 +232,11 @@ class MsaBehaviour<R> implements StructureViewerBehaviourInterface {
         }));
     }
 
+    private getRcsbId(pdb:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;}): string {
+        if("instanceId" in pdb)
+            return `${pdb.entryId}${TagDelimiter.instance}${pdb.instanceId}`;
+        else
+           return `${pdb.entryId}${TagDelimiter.entity}${pdb.entityId}`;
+    }
+
 }

src/RcsbFvStructure/StructureViewerBehaviour/NullBehaviour.ts

@@ -7,9 +7,9 @@ import {StructureViewerBehaviourObserverInterface} from "../StructureViewerBehav
 import {ViewerActionManagerInterface, ViewerCallbackManagerInterface} from "../StructureViewerInterface";
 import {RcsbFvStateInterface} from "../../RcsbFvState/RcsbFvStateInterface";
 
-export class NullBehaviourObserver<R> implements StructureViewerBehaviourObserverInterface<R> {
+export class NullBehaviourObserver<R,L> implements StructureViewerBehaviourObserverInterface<R,L> {
 
-    observe(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>, stateManager: RcsbFvStateInterface): void {
+    observe(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>, stateManager: RcsbFvStateInterface): void {
     }
 
     unsubscribe(): void {

src/RcsbFvStructure/StructureViewerBehaviourInterface.ts

@@ -6,8 +6,8 @@
 import {ViewerActionManagerInterface, ViewerCallbackManagerInterface} from "./StructureViewerInterface";
 import {RcsbFvStateInterface} from "../RcsbFvState/RcsbFvStateInterface";
 
-export interface StructureViewerBehaviourObserverInterface<R> {
-    observe(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R>, stateManager: RcsbFvStateInterface): void;
+export interface StructureViewerBehaviourObserverInterface<R,L> {
+    observe(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<R,L>, stateManager: RcsbFvStateInterface): void;
     unsubscribe(): void;
 }
 

src/RcsbFvStructure/StructureViewerInterface.ts

@@ -2,8 +2,8 @@ import {PluginContext} from "molstar/lib/mol-plugin/context";
 import {StructureRepresentationRegistry} from "molstar/lib/mol-repr/structure/registry";
 import {ColorTheme} from "molstar/lib/mol-theme/color";
 import {RegionSelectionInterface} from "../RcsbFvState/RcsbFvSelectorManager";
-import {RcsbFvStateManager} from "../RcsbFvState/RcsbFvStateManager";
 import {Subscription} from "rxjs";
+import {RcsbFvStateInterface} from "../RcsbFvState/RcsbFvStateInterface";
 
 export type ChainType = "polymer"|"water"|"branched"|"non-polymer"|"macrolide";
 export type OperatorInfo = {ids:string[], name: string};
@@ -33,14 +33,14 @@ export interface SaguaroRegionList extends SaguaroChain{
     regions: Array<RegionSelectionInterface>;
 }
 
-export interface StructureViewerInterface<R,S> extends StructureViewerPublicInterface<R>,ViewerCallbackManagerInterface {
-    init: (stateManager: RcsbFvStateManager, args:S) => void;
+export interface StructureViewerInterface<R,L,S> extends StructureViewerPublicInterface<R,L>,ViewerCallbackManagerInterface {
+    init: (stateManager: RcsbFvStateInterface, args:S) => void;
 }
 
-export interface StructureViewerPublicInterface<R> extends ViewerActionManagerInterface<R>{}
+export interface StructureViewerPublicInterface<R,L> extends ViewerActionManagerInterface<R,L>{}
 
-export interface ViewerManagerFactoryInterface<R,S extends {}> {
-    getViewerManagerFactory(stateManager: RcsbFvStateManager, args: S): {callbackManager:ViewerCallbackManagerInterface;actionManager:ViewerActionManagerInterface<R>};
+export interface ViewerManagerFactoryInterface<R,L,S extends {}> {
+    getViewerManagerFactory(stateManager: RcsbFvStateInterface, args: S): {callbackManager:ViewerCallbackManagerInterface;actionManager:ViewerActionManagerInterface<R,L>};
 }
 
 export interface ViewerCallbackManagerInterface {
@@ -53,8 +53,8 @@ export interface ViewerCallbackManagerInterface {
     pluginCall(f: (plugin: PluginContext) => void): void;
 }
 
-export interface ViewerActionManagerInterface<R> {
-    load(loadConfig: R|Array<R>): Promise<void>;
+export interface ViewerActionManagerInterface<R,L> {
+    load<Z extends R|R[]>(loadConfig: Z): Z extends R ? Promise<L|undefined> : Promise<(L|undefined)[]>;
     removeStructure(removeConfig: R|Array<R>): Promise<void>;
     select(modelId:string, labelAsymId: string, begin: number, end: number, mode: 'select'|'hover', operation:'add'|'set', operatorName?:string): void;
     select(selection: Array<SaguaroPosition>, mode: 'select'|'hover', operation:'add'|'set'): void;
@@ -78,8 +78,9 @@ export interface ViewerActionManagerInterface<R> {
     resetCamera(): void;
 }
 
-export interface ViewerModelMapManagerInterface<R> {
-    add(lC: R): void;
+export interface ViewerModelMapManagerInterface<R,L> {
+    add(lC: R, trajectory: L): void;
+    getModelIdFromTrajectory(trajectory: L): string|undefined;
     delete(lC: R): void;
     getChains(): SaguaroPluginModelMapType;
     getModelId(id: string): string;

src/RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager.ts

@@ -21,6 +21,12 @@ import {Mat4} from "molstar/lib/mol-math/linear-algebra";
 import {BuiltInTrajectoryFormat} from "molstar/lib/mol-plugin-state/formats/trajectory";
 import {PluginState} from "molstar/lib/mol-plugin/state";
 import {TrajectoryHierarchyPresetProvider} from "molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset";
+import {StateObject, StateObjectSelector} from "molstar/lib/mol-state";
+import {PluginStateObject} from "molstar/lib/mol-plugin-state/objects";
+import {StateTransformer} from "molstar/lib/mol-state/transformer";
+import {
+    StructureRepresentationPresetProvider
+} from "molstar/lib/mol-plugin-state/builder/structure/representation-preset";
 
 export enum LoadMethod {
     loadPdbId = "loadPdbId",
@@ -29,12 +35,20 @@ export enum LoadMethod {
     loadStructureFromData = "loadStructureFromData"
 }
 
-export interface LoadMolstarInterface<P=any> {
+export interface LoadMolstarInterface<P,L> {
     loadMethod: LoadMethod;
-    loadParams: LoadParams<P>;
+    loadParams: LoadParams<P,L>;
 }
 
-interface LoadParams<P=any,S={}> {
+export type LoadMolstarReturnType = {
+    model?: StateObjectSelector<PluginStateObject.Molecule.Model, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>,
+    modelProperties?: StateObjectSelector<PluginStateObject.Molecule.Model, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>,
+    structure?: StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>,
+    structureProperties?: StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>,
+    representation?: StructureRepresentationPresetProvider.Result
+};
+
+interface LoadParams<P,L> {
     entryId?: string;
     props?: PresetProps;
     matrix?: Mat4;
@@ -44,21 +58,21 @@ interface LoadParams<P=any,S={}> {
     type?: PluginState.SnapshotType,
     data?: string | number[]
     id?:string;
-    reprProvider?: TrajectoryHierarchyPresetProvider<P,S>;
+    reprProvider?: TrajectoryHierarchyPresetProvider<P,L>;
     params?:P;
 }
 
-export class MolstarActionManager implements ViewerActionManagerInterface<LoadMolstarInterface>{
+export class MolstarActionManager<P,L> implements ViewerActionManagerInterface<LoadMolstarInterface<P,L>,L>{
 
     private readonly viewer: Viewer;
 
     private readonly innerSelectionFlag: DataContainer<boolean>;
     private readonly innerReprChangeFlag: DataContainer<boolean>;
-    private readonly modelMapManager: ViewerModelMapManagerInterface<LoadMolstarInterface>;
+    private readonly modelMapManager: ViewerModelMapManagerInterface<LoadMolstarInterface<P,L>,L>;
     private readonly componentMap: Map<string, StructureComponentRef> = new Map<string, StructureComponentRef>();
     private readonly loadingFlag: DataContainer<boolean>;
 
-    constructor(config:{viewer: Viewer;modelMapManager: ViewerModelMapManagerInterface<LoadMolstarInterface>;innerSelectionFlag: DataContainer<boolean>;  innerReprChangeFlag: DataContainer<boolean>; loadingFlag: DataContainer<boolean>;}) {
+    constructor(config:{viewer: Viewer;modelMapManager: ViewerModelMapManagerInterface<LoadMolstarInterface<P,L>,L>;innerSelectionFlag: DataContainer<boolean>;  innerReprChangeFlag: DataContainer<boolean>; loadingFlag: DataContainer<boolean>;}) {
         this.viewer = config.viewer;
         this.modelMapManager = config.modelMapManager;
         this.innerSelectionFlag = config.innerSelectionFlag;
@@ -66,30 +80,36 @@ export class MolstarActionManager implements ViewerActionManagerInterface<LoadMo
         this.loadingFlag = config.loadingFlag;
     }
 
-    async load(loadConfig: LoadMolstarInterface|Array<LoadMolstarInterface>): Promise<void>{
+    async load(loadConfig: LoadMolstarInterface<P,L>): Promise<L|undefined>;
+    async load(loadConfig: LoadMolstarInterface<P,L>[]): Promise<(L|undefined)[]>;
+    async load(loadConfig: LoadMolstarInterface<P,L>|LoadMolstarInterface<P,L>[]): Promise<L|undefined|(L|undefined)[]>{
         this.loadingFlag.set(true);
+        const out: (L|undefined)[] = [];
         for (const lC of (Array.isArray(loadConfig) ? loadConfig : [loadConfig])) {
             if(checkLoadData(lC)) {
                 if (lC.loadMethod == LoadMethod.loadPdbId) {
-                    const config: LoadParams = lC.loadParams as LoadParams;
-                    await this.viewer.loadPdbId(config.entryId!, {props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params});
+                    const config: LoadParams<P,L> = lC.loadParams as LoadParams<P,L>;
+                    out.push(await this.viewer.loadPdbId(config.entryId!, {props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params}) as L|undefined);
                 } else if (lC.loadMethod == LoadMethod.loadStructureFromUrl) {
-                    const config: LoadParams = lC.loadParams as LoadParams;
-                    await this.viewer.loadStructureFromUrl(config.url!, config.format!, config.isBinary!,{props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params});
+                    const config: LoadParams<P,L> = lC.loadParams as LoadParams<P,L>;
+                    out.push(await this.viewer.loadStructureFromUrl(config.url!, config.format!, config.isBinary!,{props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params}) as L|undefined);
                 } else if (lC.loadMethod == LoadMethod.loadSnapshotFromUrl) {
-                    const config: LoadParams = lC.loadParams as LoadParams;
-                    await this.viewer.loadSnapshotFromUrl(config.url!, config.type!);
+                    const config: LoadParams<P,L> = lC.loadParams as LoadParams<P,L>;
+                   await this.viewer.loadSnapshotFromUrl(config.url!, config.type!);
                 } else if (lC.loadMethod == LoadMethod.loadStructureFromData) {
-                    const config: LoadParams = lC.loadParams as LoadParams;
-                    await this.viewer.loadStructureFromData(config.data!, config.format!, config.isBinary!, {props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params});
+                    const config: LoadParams<P,L> = lC.loadParams as LoadParams<P,L>;
+                    out.push(await this.viewer.loadStructureFromData(config.data!, config.format!, config.isBinary!, {props: config.props, matrix: config.matrix, reprProvider: config.reprProvider, params: config.params}) as L|undefined);
                 }
-                this.modelMapManager.add(lC);
+                const trajectory = out[out.length-1];
+                if(trajectory)
+                    this.modelMapManager.add(lC,trajectory);
             }
         }
         this.loadingFlag.set(false);
+        return out.length == 1 ? out[0] : out;
     }
 
-    async removeStructure(loadConfig: LoadMolstarInterface|Array<LoadMolstarInterface>): Promise<void>{
+    async removeStructure(loadConfig: LoadMolstarInterface<P,L>|Array<LoadMolstarInterface<P,L>>): Promise<void>{
         loadConfig = Array.isArray(loadConfig) ? loadConfig : [loadConfig];
         loadConfig.forEach(lC=>{
             (Array.isArray(lC.loadParams) ? lC.loadParams : [lC.loadParams]).forEach(loadParams=>{
@@ -317,10 +337,9 @@ function getStructureWithModelId(structures: StructureRef[], modelId: string): S
     }
 }
 
-
-function checkLoadData(loadConfig: LoadMolstarInterface): boolean{
+function checkLoadData<P,S>(loadConfig: LoadMolstarInterface<P,S>): boolean{
     const method: LoadMethod = loadConfig.loadMethod;
-    const params: LoadParams | Array<LoadParams> = loadConfig.loadParams;
+    const params: LoadParams<P,S> | Array<LoadParams<P,S>> = loadConfig.loadParams;
     if( method == LoadMethod.loadPdbId ){
         if(params instanceof Array || params.entryId == null)
             throw loadConfig.loadMethod+": missing pdbId";

src/RcsbFvStructure/StructureViewers/MolstarViewer/MolstarCallbackManager.ts

@@ -1,5 +1,4 @@
 import {
-    SaguaroPluginModelMapType,
     SaguaroSet,
     ViewerCallbackManagerInterface,
     ViewerModelMapManagerInterface
@@ -15,18 +14,16 @@ import {
 import {OrderedSet} from "molstar/lib/mol-data/int";
 import {Queries as Q} from "molstar/lib/mol-model/structure/query";
 import {PluginContext} from "molstar/lib/mol-plugin/context";
-import {StateObject} from "molstar/lib/mol-state";
 import {Viewer} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {Subscription} from "rxjs";
-import {RcsbFvSelectorManager} from "../../../RcsbFvState/RcsbFvSelectorManager";
 import {DataContainer, DataContainerReader} from "../../../Utils/DataContainer";
-import {RcsbFvStateManager} from "../../../RcsbFvState/RcsbFvStateManager";
+import {RcsbFvStateInterface} from "../../../RcsbFvState/RcsbFvStateInterface";
 
-type ModelMapType = Omit<ViewerModelMapManagerInterface<null>,'add'|'delete'>;
+type ModelMapType = Omit<ViewerModelMapManagerInterface<unknown,unknown>,'add'|'delete'>;
 export class MolstarCallbackManager implements ViewerCallbackManagerInterface{
 
     private readonly viewer: Viewer;
-    private readonly  stateManager: RcsbFvStateManager;
+    private readonly  stateManager: RcsbFvStateInterface;
     private readonly loadingFlag: DataContainerReader<boolean>;
     private readonly modelMapManager: ModelMapType;
     private readonly innerSelectionFlag: DataContainer<boolean>;
@@ -37,7 +34,7 @@ export class MolstarCallbackManager implements ViewerCallbackManagerInterface{
     private modelChangeSubs: Subscription;
     private reprChangeSubs: Subscription;
 
-    constructor(config:{viewer: Viewer; stateManager: RcsbFvStateManager;loadingFlag: DataContainerReader<boolean>;modelMapManager: ModelMapType;innerSelectionFlag: DataContainer<boolean>; innerReprChangeFlag: DataContainer<boolean>;}) {
+    constructor(config:{viewer: Viewer; stateManager: RcsbFvStateInterface;loadingFlag: DataContainerReader<boolean>;modelMapManager: ModelMapType;innerSelectionFlag: DataContainer<boolean>; innerReprChangeFlag: DataContainer<boolean>;}) {
         this.viewer = config.viewer;
         this.stateManager = config.stateManager;
         this.loadingFlag = config.loadingFlag;

src/RcsbFvStructure/StructureViewers/MolstarViewer/MolstarManagerFactory.ts

@@ -4,12 +4,17 @@ import {Viewer, ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {MolstarModelMapManager} from "./MolstarModelMapManager";
 import {MolstarCallbackManager} from "./MolstarCallbackManager";
 import {DataContainer} from "../../../Utils/DataContainer";
-import {RcsbFvSelectorManager} from "../../../RcsbFvState/RcsbFvSelectorManager";
-import {RcsbFvStateManager} from "../../../RcsbFvState/RcsbFvStateManager";
+import {RcsbFvStateInterface} from "../../../RcsbFvState/RcsbFvStateInterface";
 
-export class MolstarManagerFactory implements ViewerManagerFactoryInterface<LoadMolstarInterface,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}> {
+export class MolstarManagerFactory<P,L> implements ViewerManagerFactoryInterface<LoadMolstarInterface<P,L>,L,{viewerElement:string|HTMLElement,viewerProps:Partial<ViewerProps>}> {
 
-    public getViewerManagerFactory(stateManager: RcsbFvStateManager, viewerParams: {viewerElement: string | HTMLElement, viewerProps: Partial<ViewerProps>}) {
+    private readonly getModelIdFromTrajectory: (trajectory: L) => string|undefined;
+
+    constructor(getModelIdFromTrajectory: (trajectory: L) => string|undefined) {
+        this.getModelIdFromTrajectory = getModelIdFromTrajectory;
+    }
+
+    public getViewerManagerFactory(stateManager: RcsbFvStateInterface, viewerParams: {viewerElement: string | HTMLElement, viewerProps: Partial<ViewerProps>}) {
         const loadingFlag: DataContainer<boolean> = new DataContainer(false);
         const innerSelectionFlag: DataContainer<boolean> = new DataContainer(false);
         const innerReprChangeFlag: DataContainer<boolean> = new DataContainer(false);
@@ -24,7 +29,7 @@ export class MolstarManagerFactory implements ViewerManagerFactoryInterface<Load
             }
         });
         viewer.plugin.selectionMode = true;
-        const modelMapManager:MolstarModelMapManager = new MolstarModelMapManager(viewer);
+        const modelMapManager:MolstarModelMapManager<L> = new MolstarModelMapManager(viewer, this.getModelIdFromTrajectory);
         const callbackManager: MolstarCallbackManager =  new MolstarCallbackManager({
             viewer: viewer,
             stateManager: stateManager,
@@ -33,7 +38,7 @@ export class MolstarManagerFactory implements ViewerManagerFactoryInterface<Load
             innerSelectionFlag: innerSelectionFlag,
             innerReprChangeFlag: innerReprChangeFlag
         });
-        const actionManager = new MolstarActionManager({
+        const actionManager = new MolstarActionManager<P,L>({
             viewer: viewer,
             modelMapManager: modelMapManager,
             innerSelectionFlag: innerSelectionFlag,

src/RcsbFvStructure/StructureViewers/MolstarViewer/MolstarModelMapManager.ts

@@ -6,39 +6,28 @@ import {
 } from "../../StructureViewerInterface";
 import {PluginContext} from "molstar/lib/mol-plugin/context";
 import {Structure, StructureElement, StructureProperties as SP} from "molstar/lib/mol-model/structure";
-import {StructureRef} from "molstar/lib/mol-plugin-state/manager/structure/hierarchy-state";
 import {State} from "molstar/lib/mol-state";
 import {PluginStateObject as PSO} from "molstar/lib/mol-plugin-state/objects";
 import {Viewer} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {LoadMethod} from "./MolstarActionManager";
 
-interface LoadParams<P=any,S={}> {
-    id?:string;
-    params?:P;
+interface LoadParams {
+    id:string;
 }
 
-export class MolstarModelMapManager implements ViewerModelMapManagerInterface<{loadMethod: LoadMethod; loadParams: LoadParams;}> {
+export class MolstarModelMapManager<L> implements ViewerModelMapManagerInterface<{loadMethod: LoadMethod; loadParams: LoadParams;},L> {
 
     private readonly viewer: Viewer;
     private readonly modelMap: Map<string,string|undefined> = new Map<string, string>();
+    private readonly delegateModelIdFromTrajectory: (trajectory:L)=>string|undefined;
 
-    constructor(viewer: Viewer) {
+    constructor(viewer: Viewer, delegateModelIdFromTrajectory: (trajectory:L)=>string|undefined) {
         this.viewer = viewer;
+        this.delegateModelIdFromTrajectory = delegateModelIdFromTrajectory;
     }
 
-    public add(lC: {loadMethod: LoadMethod; loadParams: LoadParams;}){
-        //TODO get rid of the getMap mechanics
-        if(typeof lC.loadParams.params?.getMap === "function") {
-            const map: Map<string,string> = lC.loadParams.params.getMap();
-            if(typeof map?.forEach === "function")
-                map.forEach((modelId: string, key: string) => {
-                    if (typeof modelId === "string" && typeof key === "string") {
-                        this.modelMap.set(key, modelId);
-                        this.modelMap.set(modelId, key);
-                    }
-                })
-        }
-        this.map(lC.loadParams);
+    public add(lC: {loadMethod: LoadMethod; loadParams: LoadParams;}, trajectory: L){
+        this.map(lC.loadParams, trajectory);
     }
 
     public delete(lC: {loadMethod: LoadMethod; loadParams: LoadParams;}) {
@@ -65,18 +54,17 @@ export class MolstarModelMapManager implements ViewerModelMapManagerInterface<{l
         return this.modelMap.get(id) ?? id;
     }
 
-    private map(loadParams: LoadParams): void{
-        const structureRefList = getStructureOptions(this.viewer.plugin);
-        if(structureRefList.length > 0) {
-            const structureRef = structureRefList[structureRefList.length - 1];
-            const structure = getStructure(structureRef[0], this.viewer.plugin.state.data);
-            let modelEntityId = getModelEntityOptions(structure)[0][0];
-            const chains: [{ modelId: string, entryId: string }, ChainInfo[]] = getChainValues(structure, modelEntityId);
-            if (!this.modelMap.has(chains[0].modelId)) {
-                this.modelMap.set(chains[0].modelId, loadParams.id);
-                if (loadParams.id != null)
-                    this.modelMap.set(loadParams.id!, chains[0].modelId);
-            }
+    public getModelIdFromTrajectory(trajectory: L): string|undefined {
+        return this.delegateModelIdFromTrajectory(trajectory);
+    }
+
+    private map(loadParams: LoadParams, trajectory: L): void{
+        const modelId = this.getModelIdFromTrajectory(trajectory);
+        if(!modelId || !loadParams.id)
+            throw new Error("modelId not found");
+        if(!this.modelMap.has(modelId)){
+            this.modelMap.set(modelId,loadParams.id);
+            this.modelMap.set(loadParams.id,modelId)
         }
     }
 }
@@ -109,17 +97,6 @@ function getChainValues(structure: Structure, modelEntityId: string): [{modelId:
     return [id,Array.from(chains.values())];
 }
 
-function getStructureWithModelId(structures: StructureRef[], modelId: string): Structure|undefined{
-    for(const structure of structures){
-        if(!structure.cell?.obj?.data?.units)
-            continue;
-        const unit =  structure.cell.obj.data.units[0];
-        const id:string = unit.model.id;
-        if(id === modelId)
-            return structure.cell.obj.data
-    }
-}
-
 function getStructure(ref: string, state: State) {
     const cell = state.select(ref)[0];
     if (!ref || !cell || !cell.obj) return Structure.Empty;
@@ -159,9 +136,6 @@ function splitModelEntityId(modelEntityId: string) {
 
 function opKey(l: StructureElement.Location): OperatorInfo {
     const ids = SP.unit.pdbx_struct_oper_list_ids(l);
-    const ncs = SP.unit.struct_ncs_oper_id(l);
-    const hkl = SP.unit.hkl(l);
-    const spgrOp = SP.unit.spgrOp(l);
     const name = SP.unit.operator_name(l);
     return {ids:ids,name:name};
 }

src/RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarAlignmentLoader.ts

@@ -0,0 +1,97 @@
+/*
+* Copyright (c) 2021 RCSB PDB and contributors, licensed under MIT, See LICENSE file for more info.
+* @author Joan Segura Mora <joan.segura@rcsb.org>
+*/
+
+import {
+    LocationProviderInterface,
+    StructureLoaderInterface,
+    TransformProviderInterface
+} from "../../../StructureUtils/StructureLoaderInterface";
+import {ViewerActionManagerInterface, ViewerCallbackManagerInterface} from "../../../StructureViewerInterface";
+import {
+    LoadMethod,
+    LoadMolstarInterface,
+    LoadMolstarReturnType
+} from "../MolstarActionManager";
+import {TagDelimiter} from "@rcsb/rcsb-saguaro-app";
+import {
+    AlignmentTrajectoryPresetProvider,
+    AlignmentTrajectoryParamsType
+} from "../TrajectoryPresetProvider/AlignmentTrajectoryPresetProvider";
+import {TargetAlignment} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import {RcsbFvStateInterface} from "../../../../RcsbFvState/RcsbFvStateInterface";
+import {Mat4} from "molstar/lib/mol-math/linear-algebra";
+import {
+    FelxibleAlignmentTrajectoryParamsType,
+    FlexibleAlignmentTrajectoryPresetProvider
+} from "../TrajectoryPresetProvider/FlexibleAlignmentTrajectoryPresetProvider";
+
+export class MolstarAlignmentLoader implements StructureLoaderInterface<[
+        ViewerCallbackManagerInterface & ViewerActionManagerInterface<LoadMolstarInterface<AlignmentTrajectoryParamsType|FelxibleAlignmentTrajectoryParamsType,LoadMolstarReturnType>,LoadMolstarReturnType>,
+        {entryId:string;entityId:string;}|{entryId:string;instanceId:string;},
+        TargetAlignment
+    ], LoadMolstarReturnType> {
+
+    private readonly transformProvider?: TransformProviderInterface;
+    private readonly structureLocationProvider?: LocationProviderInterface;
+    constructor(loadConfig?:{transformProvider?: TransformProviderInterface; structureLocationProvider?: LocationProviderInterface}) {
+        this.transformProvider = loadConfig?.transformProvider;
+        this.structureLocationProvider = loadConfig?.structureLocationProvider;
+    }
+    private readonly structureMap: Set<string> = new Set<string>();
+
+    async load(
+        structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface<LoadMolstarInterface<AlignmentTrajectoryParamsType|FelxibleAlignmentTrajectoryParamsType,LoadMolstarReturnType>,LoadMolstarReturnType>,
+        pdb:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;},
+        targetAlignment: TargetAlignment
+    ): Promise<undefined|LoadMolstarReturnType> {
+        const structureId: string = `${pdb.entryId}${"entityId" in pdb ? TagDelimiter.entity : TagDelimiter.instance}${"entityId" in pdb ? pdb.entityId : pdb.instanceId}`;
+        if(!this.structureMap.has(structureId)){
+            const url: string|undefined = this.structureLocationProvider?.get(pdb.entryId);
+            const transform = ("instanceId" in pdb ? this.transformProvider?.get(pdb.entryId, pdb.instanceId) : undefined) ?? undefined;
+            const provider = !transform?.length || transform.length == 1 ? {
+                reprProvider: AlignmentTrajectoryPresetProvider,
+                params:{
+                    modelIndex: 0,
+                    pdb,
+                    targetAlignment,
+                    matrix: transform?.[0].transform
+                }
+            } : {
+                reprProvider: FlexibleAlignmentTrajectoryPresetProvider,
+                params:{
+                    modelIndex: 0,
+                    pdb,
+                    targetAlignment,
+                    transform: transform
+                }
+            };
+            const trajectory = await structureViewer.load({
+                loadMethod: url ? LoadMethod.loadStructureFromUrl : LoadMethod.loadPdbId,
+                loadParams: {
+                    url,
+                    format: url ? "mmcif" : undefined,
+                    isBinary: url ? false : undefined,
+                    id: structureId,
+                    entryId:pdb.entryId,
+                    ...provider
+                }
+            });
+            this.structureMap.add(
+                structureId
+            );
+            return trajectory;
+        } else {
+            await structureViewer.removeStructure({
+                loadMethod: LoadMethod.loadPdbId,
+                loadParams:{
+                    id: structureId
+                }
+            });
+            this.structureMap.delete(structureId);
+            return;
+        }
+    }
+
+}

src/RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarComponentAction.ts

@@ -0,0 +1,55 @@
+import {
+    ComponentActionFactoryInterface,
+    ComponentActionInterface
+} from "../../../StructureUtils/ComponentActionInterface";
+import {LoadMolstarReturnType} from "../MolstarActionManager";
+import {RcsbFvStateInterface} from "../../../../RcsbFvState/RcsbFvStateInterface";
+import {createSelectionExpressions} from "@rcsb/rcsb-molstar/build/src/viewer/helpers/selection";
+
+export class MolstarComponentActionFactory implements ComponentActionFactoryInterface<LoadMolstarReturnType> {
+    getComponentAction(config: { stateManager: RcsbFvStateInterface }): ComponentActionInterface<LoadMolstarReturnType> {
+        return new MolstarComponentAction(config.stateManager);
+    }
+}
+class MolstarComponentAction implements ComponentActionInterface<LoadMolstarReturnType> {
+
+    private readonly stateManager: RcsbFvStateInterface;
+    constructor(stateManager: RcsbFvStateInterface) {
+        this.stateManager =stateManager;
+    }
+
+    accept(trajectory: LoadMolstarReturnType, context: { entryId:string; entityId:string; } | { entryId:string; instanceId:string; }): void {
+        const components = trajectory.representation?.components;
+        if(!components)
+            return;
+        if(!components["polymer"]){
+            this.stateManager.next<
+                "missing-component",
+                {tag:"aligned"|"polymer"|"non-polymer";entryId:string;entityId:string;}|{tag:"aligned"|"polymer"|"non-polymer";entryId:string;instanceId:string;}
+            >({
+                type:"missing-component",
+                view: "3d-view",
+                data: {
+                    tag:"polymer",
+                    ...context
+                }
+            });
+        }
+        for(const expression of createSelectionExpressions(context.entryId)) {
+            if(components[expression.tag] && expression.tag != "polymer" && expression.tag != "water")
+                return;
+        }
+        this.stateManager.next<
+            "missing-component",
+            {tag:"aligned"|"polymer"|"non-polymer";entryId:string;entityId:string;}|{tag:"aligned"|"polymer"|"non-polymer";entryId:string;instanceId:string;}
+        >({
+            type:"missing-component",
+            view: "3d-view",
+            data: {
+                tag:"non-polymer",
+               ...context
+            }
+        });
+    }
+
+}

src/RcsbFvStructure/StructureViewers/MolstarViewer/MolstarUtils/MolstarTools.ts

@@ -0,0 +1,9 @@
+import {LoadMolstarReturnType} from "../MolstarActionManager";
+
+export namespace MolstarTools {
+
+    export function getModelIdFromTrajectory(trajectory:LoadMolstarReturnType): string|undefined {
+        return trajectory.structure?.obj?.data.units[0].model.id;
+    }
+
+}

src/RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/AlignmentRepresentationPresetProvider.ts

@@ -39,181 +39,203 @@ import {
 } from "molstar/lib/extensions/model-archive/quality-assessment/prop";
 import {MmcifFormat} from "molstar/lib/mol-model-formats/structure/mmcif";
 import {CustomProperty} from "molstar/lib/mol-model-props/common/custom-property";
-import {RcsbFvStateInterface} from "../../../../RcsbFvState/RcsbFvStateInterface";
+import {StructureBuilder} from "molstar/lib/mol-plugin-state/builder/structure";
+import {StructureRepresentationBuilder} from "molstar/lib/mol-plugin-state/builder/structure/representation";
+import {RigidTransformType, TransformMatrixType} from "../../../StructureUtils/StructureLoaderInterface";
 
 type RepresentationParamsType = {
-    pdb?:{entryId:string;entityId:string;};
+    pdb?:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;};
+    matrix?: TransformMatrixType;
     targetAlignment?:TargetAlignment;
-    stateManagerContainer?:{
-        data:RcsbFvStateInterface;
-    };
 }
 
 let refData: Structure|undefined = undefined;
 let refParams: StructureAlignmentParamsType|undefined = undefined;
-export const AlignmentRepresentationPresetProvider = StructureRepresentationPresetProvider<RepresentationParamsType,any>({
-        id: 'alignment-to-reference',
-        display: {
-            name: 'Alignemnt to Reference'
-        },
-        isApplicable: (structureRef: PluginStateObject.Molecule.Structure, plugin: PluginContext): boolean => true,
-        params: (structureRef: PluginStateObject.Molecule.Structure | undefined, plugin: PluginContext) => ({
-            pdb: PD.Value<{entryId:string;entityId:string;}|undefined>(undefined),
-            targetAlignment: PD.Value<TargetAlignment|undefined>(undefined),
-            stateManagerContainer: PD.Value<{data:RcsbFvStateInterface}|undefined>(undefined)
-        }),
-        apply: async (structureRef: StateObjectRef<PluginStateObject.Molecule.Structure>, params: RepresentationParamsType, plugin: PluginContext) => {
-            const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, structureRef);
-            if(!structureCell) return;
-            const structure = structureCell.obj!.data;
-
-
-            const entryId = params.pdb?.entryId!;
-            const entityId = params.pdb?.entityId!;
-            const l = StructureElement.Location.create(structure);
-            let alignedAsymId;
-            let alignedOperatorName;
-            let alignedType;
-            for(const unit of structure.units) {
-                StructureElement.Location.set(l, structure, unit, unit.elements[0]);
-                const alignedEntityId = SP.chain.label_entity_id(l);
-                if(alignedEntityId == params.pdb?.entityId){
-                    alignedAsymId = SP.chain.label_asym_id(l);
-                    alignedOperatorName = SP.unit.operator_name(l);
-                    alignedType = SP.entity.type(l);
-                    const alignedOperators = SP.unit.pdbx_struct_oper_list_ids(l);
-                    if(alignedType != "polymer")
-                        return;
-                    if(plugin.managers.structure.hierarchy.current.structures.length == 1){
-                        refParams = {
-                            entryId: entryId,
-                            labelAsymId: alignedAsymId,
-                            operatorName:alignedOperatorName,
-                            targetAlignment:params.targetAlignment!
-                        };
-                    }
-                    if(refParams && params.pdb){
-                        await structuralAlignment(plugin, refParams, {
-                            entryId: entryId,
-                            labelAsymId: alignedAsymId,
-                            operatorName:alignedOperatorName,
-                            targetAlignment:params.targetAlignment!
-                        }, structure);
-                    }
-                    const comp = await plugin.builders.structure.tryCreateComponentFromExpression(
-                        structureCell,
-                        MS.struct.generator.atomGroups({
-                            'chain-test': MS.core.logic.and([
-                                MS.core.rel.eq([MS.ammp('label_asym_id'), alignedAsymId]),
-                                MS.core.rel.eq([MS.acp('operatorName'), alignedOperatorName])
-                            ])
-                        }),
-                        uniqid(`${entryId}${TagDelimiter.entity}${entityId}${TagDelimiter.instance}${alignedAsymId}${TagDelimiter.entity}${alignedOperators.join(",")}`),
-                        {
-                            label: `${entryId}${TagDelimiter.entity}${entityId}${TagDelimiter.instance}${alignedAsymId}${TagDelimiter.assembly}${alignedOperators.join(",")}${TagDelimiter.assembly}${alignedType}`
-                        }
-                    );
-                    //TODO This needs to be called after tryCreateComponentFromExpression
-                    const {update, builder} = reprBuilder(plugin, {
-                        ignoreHydrogens: true,
-                        ignoreLight: false,
-                        quality: "auto"
-                    });
-                    builder.buildRepresentation(update, comp, {
-                        color: PLDDTConfidenceColorThemeProvider.isApplicable({ structure }) ? PLDDTConfidenceColorThemeProvider.name as ColorTheme.BuiltIn : "chain-id",
-                        type: "cartoon"
-                    });
-                    await update.commit({ revertOnError: false });
-                    break;
+
+type ComponentType = Awaited<ReturnType<InstanceType<typeof StructureBuilder>["tryCreateComponentFromExpression"]>>;
+type RepresentationType = ReturnType<InstanceType<typeof StructureRepresentationBuilder>["buildRepresentation"]>;
+type ComponentMapType = Record<string,ComponentType>;
+type RepresentationMapType = Record<string,RepresentationType>;
+
+export const AlignmentRepresentationPresetProvider = StructureRepresentationPresetProvider({
+    id: 'alignment-to-reference',
+    display: {
+        name: 'Alignment to Reference'
+    },
+    isApplicable: (structureRef: PluginStateObject.Molecule.Structure, plugin: PluginContext): boolean => true,
+    params: (structureRef: PluginStateObject.Molecule.Structure | undefined, plugin: PluginContext) => ({
+        pdb: PD.Value<{entryId:string;entityId:string;}|{entryId:string;instanceId:string;}|undefined>(undefined),
+        targetAlignment: PD.Value<TargetAlignment|undefined>(undefined),
+        matrix:PD.Value<TransformMatrixType|undefined>(undefined)
+    }),
+    apply: async (structureRef: StateObjectRef<PluginStateObject.Molecule.Structure>, params: RepresentationParamsType, plugin: PluginContext) => {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, structureRef);
+        if(!structureCell)
+            return {};
+        const structure = structureCell.obj!.data;
+
+
+        const entryId = params.pdb?.entryId!;
+        const entityId = params.pdb && "entityId" in params.pdb ? params.pdb?.entityId : undefined;
+        const instanceId = params.pdb && "instanceId" in params.pdb ?  params.pdb?.instanceId : undefined;
+        const l = StructureElement.Location.create(structure);
+        let alignedEntityId;
+        let alignedAsymId;
+        let alignedOperatorName;
+        let alignedType;
+
+        const componentMap :  ComponentMapType = {}
+        const representationMap :  RepresentationMapType = {}
+
+        for(const unit of structure.units) {
+            StructureElement.Location.set(l, structure, unit, unit.elements[0]);
+            if(SP.chain.label_entity_id(l) == entityId || SP.chain.label_asym_id(l) == instanceId){
+                alignedEntityId = SP.chain.label_entity_id(l);
+                alignedAsymId = SP.chain.label_asym_id(l);
+                alignedOperatorName = SP.unit.operator_name(l);
+                alignedType = SP.entity.type(l);
+                const alignedOperators: string[] = SP.unit.pdbx_struct_oper_list_ids(l);
+                if(alignedOperators.length == 0) alignedOperators.push("0")
+                if(alignedType != "polymer")
+                    return {};
+                if(plugin.managers.structure.hierarchy.current.structures.length == 1){
+                    refParams = {
+                        entryId: entryId,
+                        labelAsymId: alignedAsymId,
+                        operatorName:alignedOperatorName,
+                        targetAlignment:params.targetAlignment!
+                    };
+                }
+                if(refParams && params.pdb && !params.matrix){
+                    await structuralAlignment(plugin, refParams, {
+                        entryId: entryId,
+                        labelAsymId: alignedAsymId,
+                        operatorName:alignedOperatorName,
+                        targetAlignment:params.targetAlignment!
+                    }, structure);
+                }else if(params.matrix){
+                    await matrixAlign(plugin, structureRef, params.matrix);
                 }
+                const comp = await plugin.builders.structure.tryCreateComponentFromExpression(
+                    structureCell,
+                    MS.struct.generator.atomGroups({
+                        'chain-test': MS.core.logic.and([
+                            MS.core.rel.eq([MS.ammp('label_asym_id'), alignedAsymId]),
+                            MS.core.rel.eq([MS.acp('operatorName'), alignedOperatorName])
+                        ])
+                    }),
+                    uniqid(`${entryId}${TagDelimiter.entity}${alignedEntityId}${TagDelimiter.instance}${alignedAsymId}${TagDelimiter.entity}${alignedOperators.join(",")}`),
+                    {
+                        label: `${entryId}${TagDelimiter.entity}${alignedEntityId}${TagDelimiter.instance}${alignedAsymId}${TagDelimiter.assembly}${alignedOperators.join(",")}${TagDelimiter.assembly}${alignedType}`
+                    }
+                );
+                componentMap["aligned"] = comp;
+
+                //TODO This needs to be called after tryCreateComponentFromExpression
+                const {update, builder} = reprBuilder(plugin, {
+                    ignoreHydrogens: true,
+                    ignoreLight: false,
+                    quality: "auto"
+                });
+                representationMap["aligned"] = builder.buildRepresentation(update, comp, {
+                    color: PLDDTConfidenceColorThemeProvider.isApplicable({ structure }) ? PLDDTConfidenceColorThemeProvider.name as ColorTheme.BuiltIn : "chain-id",
+                    type: "cartoon"
+                });
+
+                await update.commit({ revertOnError: false });
+                break;
             }
+        }
+        const expressions = []
+        const asymObserved: {[key:string]:boolean} = {};
+        for(const unit of structure.units){
+            StructureElement.Location.set(l, structure, unit, unit.elements[0]);
+            const asymId = SP.chain.label_asym_id(l);
+            const operatorName = SP.unit.operator_name(l);
+            if(asymId == alignedAsymId && operatorName == alignedOperatorName)
+                continue;
+            if(asymObserved[`${asymId}${TagDelimiter.assembly}${operatorName}`])
+                continue;
+            asymObserved[`${asymId}${TagDelimiter.assembly}${operatorName}`] = true;
+            const type = SP.entity.type(l);
+            if (type == "polymer") {
+                expressions.push(MS.core.logic.and([
+                    MS.core.rel.eq([MS.ammp('label_asym_id'), asymId]),
+                    MS.core.rel.eq([MS.acp('operatorName'), operatorName])
+                ]))
+            }
+        }
+        const compId = `${entryId}${TagDelimiter.entity}${alignedEntityId}${TagDelimiter.assembly}${alignedType}`;
+        const comp = await plugin.builders.structure.tryCreateComponentFromExpression(
+            structureCell,
+            MS.struct.generator.atomGroups({
+                'chain-test': MS.core.logic.or(expressions)
+            }),
+            uniqid(compId),
+            {
+                label: compId
+            }
+        );
+        componentMap["polymer"] = comp;
 
-            const expressions = []
-            const asymObserved: {[key:string]:boolean} = {};
-            for(const unit of structure.units){
-                StructureElement.Location.set(l, structure, unit, unit.elements[0]);
-                const asymId = SP.chain.label_asym_id(l);
-                const operatorName = SP.unit.operator_name(l);
-                if(asymId == alignedAsymId && operatorName == alignedOperatorName)
-                    continue;
-                if(asymObserved[`${asymId}${TagDelimiter.assembly}${operatorName}`])
-                    continue;
-                asymObserved[`${asymId}${TagDelimiter.assembly}${operatorName}`] = true;
-                const type = SP.entity.type(l);
-                if (type == "polymer") {
-                    expressions.push(MS.core.logic.and([
-                        MS.core.rel.eq([MS.ammp('label_asym_id'), asymId]),
-                        MS.core.rel.eq([MS.acp('operatorName'), operatorName])
-                    ]))
-                }
+        const {update, builder} = reprBuilder(plugin, {
+            ignoreHydrogens: true,
+            ignoreLight: false,
+            quality: "auto"
+        });
+        representationMap["polymer"] = builder.buildRepresentation(update, comp, {
+            color: PLDDTConfidenceColorThemeProvider.isApplicable({ structure }) ? PLDDTConfidenceColorThemeProvider.name as ColorTheme.BuiltIn : "chain-id",
+            type: "cartoon"
+        }, {
+            initialState:{
+                isHidden:true
             }
+        });
+
+        await update.commit({ revertOnError: false });
+
+        let anyLigComp;
+        for(const expression of createSelectionExpressions(entryId)){
+            if(expression.tag == "polymer")
+                continue;
             const comp = await plugin.builders.structure.tryCreateComponentFromExpression(
                 structureCell,
-                MS.struct.generator.atomGroups({
-                    'chain-test': MS.core.logic.or(expressions)
-                }),
-                uniqid(`${entryId}${TagDelimiter.entity}${entityId}${TagDelimiter.assembly}${alignedType}`),
+                expression.expression,
+                uniqid(`${entryId}${TagDelimiter.entity}${alignedEntityId}${TagDelimiter.assembly}${expression.tag}`),
                 {
-                    label: `${entryId}${TagDelimiter.entity}${entityId}${TagDelimiter.assembly}${alignedType}`
-                }
-            );
-            const {update, builder} = reprBuilder(plugin, {
+                    label: `${entryId}${TagDelimiter.entity}${alignedEntityId}${TagDelimiter.assembly}${expression.tag}`
+                });
+            componentMap[expression.tag] = comp;
+            //TODO This needs to be called after tryCreateComponentFromExpression
+            const { update, builder } = reprBuilder(plugin, {
                 ignoreHydrogens: true,
                 ignoreLight: false,
                 quality: "auto"
             });
-            builder.buildRepresentation(update, comp, {
-                color: PLDDTConfidenceColorThemeProvider.isApplicable({ structure }) ? PLDDTConfidenceColorThemeProvider.name as ColorTheme.BuiltIn : "chain-id",
-                type: "cartoon"
-            }, {
+            representationMap[expression.tag] = builder.buildRepresentation(update, comp, {
+                type: expression.type
+            },{
                 initialState:{
                     isHidden:true
                 }
             });
+
             await update.commit({ revertOnError: false });
-            if(!comp && params.stateManagerContainer?.data){
-                params.stateManagerContainer.data.next<"missing-component", {tag:"aligned"|"polymer"|"non-polymer";entryId:string;entityId:string;}>({type:"missing-component", view: "3d-view", data:{tag:"polymer", entryId, entityId}})
-            }
+            if(comp && expression.tag != "water") anyLigComp = comp;
+        }
 
-            let anyLigComp;
-            for(const expression of createSelectionExpressions(entryId)){
-                if(expression.tag == "polymer")
-                    continue;
-                const comp = await plugin.builders.structure.tryCreateComponentFromExpression(
-                    structureCell,
-                    expression.expression,
-                    uniqid(`${entryId}${TagDelimiter.entity}${entityId}${TagDelimiter.assembly}${expression.tag}`),
-                    {
-                        label: `${entryId}${TagDelimiter.entity}${entityId}${TagDelimiter.assembly}${expression.tag}`
-                    });
-                //TODO This needs to be called after tryCreateComponentFromExpression
-                const { update, builder } = reprBuilder(plugin, {
-                    ignoreHydrogens: true,
-                    ignoreLight: false,
-                    quality: "auto"
-                });
-                builder.buildRepresentation(update, comp, {
-                    type: expression.type
-                },{
-                    initialState:{
-                        isHidden:true
-                    }
-                });
-                await update.commit({ revertOnError: false });
-                if(comp && expression.tag != "water") anyLigComp = comp;
-            }
-            if(!anyLigComp && params.stateManagerContainer?.data){
-                params.stateManagerContainer.data.next<"missing-component", {tag:"polymer"|"non-polymer";entryId:string;entityId:string;}>({type:"missing-component", view: "3d-view", data:{tag:"non-polymer", entryId, entityId}})
-            }
-            for (const c of plugin.managers.structure.hierarchy.currentComponentGroups){
-                for (const comp of c) {
-                    if(typeof comp.cell.state.isHidden === "undefined" && comp.representations[0].cell.state.isHidden)
-                        plugin.managers.structure.component.toggleVisibility(c);
-                }
+        for (const c of plugin.managers.structure.hierarchy.currentComponentGroups){
+            for (const comp of c) {
+                if(typeof comp.cell.state.isHidden === "undefined" && comp.representations[0].cell.state.isHidden)
+                    plugin.managers.structure.component.toggleVisibility(c);
             }
         }
-    });
-
+        return {
+            components: componentMap,
+            representations: representationMap
+        };
+    }
+});
 
 type StructureAlignmentParamsType = {
     entryId:string;
@@ -221,6 +243,19 @@ type StructureAlignmentParamsType = {
     operatorName:string;
     targetAlignment:TargetAlignment;
 };
+
+async function matrixAlign(plugin: PluginContext,  structureRef: StateObjectRef<PluginStateObject.Molecule.Structure>, matrix: TransformMatrixType): Promise<void> {
+    const trans = {
+        transform: {
+            name: 'matrix' as const,
+            params: {data: matrix, transpose: false}
+        }
+    };
+    const b = plugin.state.data.build().to(structureRef)
+        .insert(StateTransforms.Model.TransformStructureConformation,trans);
+    await plugin.runTask(plugin.state.data.updateTree(b));
+}
+
 async function structuralAlignment(plugin: PluginContext, ref:StructureAlignmentParamsType, pdb:StructureAlignmentParamsType, structure: Structure): Promise<void> {
     if(ref.entryId == pdb.entryId){
         refData = structure;

src/RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/AlignmentTrajectoryPresetProvider.ts

@@ -17,85 +17,85 @@ import {
 import {PLDDTConfidenceColorThemeProvider} from "molstar/lib/extensions/model-archive/quality-assessment/color/plddt";
 import {AlignmentRepresentationPresetProvider} from "./AlignmentRepresentationPresetProvider";
 import {TargetAlignment} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import {RcsbFvStateInterface} from "../../../../RcsbFvState/RcsbFvStateInterface";
 import {Structure, StructureElement, StructureProperties as SP} from "molstar/lib/mol-model/structure";
+import {RigidTransformType, TransformMatrixType} from "../../../StructureUtils/StructureLoaderInterface";
 
-export type TrajectoryParamsType = {
-    pdb?: {entryId:string;entityId:string;};
+
+export type AlignmentTrajectoryParamsType = {
+    pdb?:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;};
+    matrix?: TransformMatrixType;
     targetAlignment?: TargetAlignment;
-    stateManager?:RcsbFvStateInterface;
     modelIndex?: number;
     plddt?: 'off' | 'single-chain' | 'on';
 }
 
 type StructureObject = StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>
 
-export const AlignmentTrajectoryPresetProvider = TrajectoryHierarchyPresetProvider<TrajectoryParamsType,any>({
+export const AlignmentTrajectoryPresetProvider = TrajectoryHierarchyPresetProvider({
     id: 'alignment-to-reference',
     display: {
-        name: 'Alignemnt to Reference'
+        name: 'Alignment to Reference'
     },
     isApplicable: (trajectory: PluginStateObject.Molecule.Trajectory, plugin: PluginContext): boolean => true,
-    params: (trajectory: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext):ParamDefinition.For<TrajectoryParamsType> => ({
-        pdb:PD.Value<{entryId:string;entityId:string;}|undefined>(undefined),
+    params: (trajectory: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext): ParamDefinition.For<AlignmentTrajectoryParamsType> => ({
+        pdb:PD.Value<{entryId:string;entityId:string;}|{entryId:string;instanceId:string;}|undefined>(undefined),
         targetAlignment: PD.Value<TargetAlignment|undefined>(undefined),
-        stateManager: PD.Value<RcsbFvStateInterface|undefined>(undefined),
         modelIndex:PD.Value<number|undefined>(undefined),
-        plddt:PD.Value<'off' | 'single-chain' | 'on' | undefined>(undefined)
+        plddt:PD.Value<'off' | 'single-chain' | 'on' | undefined>(undefined),
+        matrix:PD.Value<TransformMatrixType|undefined>(undefined)
     }),
-    apply: async (trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>, params: TrajectoryParamsType, plugin: PluginContext) => {
+    apply: async (trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>, params: AlignmentTrajectoryParamsType, plugin: PluginContext) => {
+        if(!params.pdb)
+            return {};
         const modelParams = { modelIndex: params.modelIndex || 0 };
-        const structureParams: RootStructureDefinition.Params = { name: 'model', params: {} };
         const builder = plugin.builders.structure;
+
+        const model = await builder.createModel(trajectory, modelParams);
+        const modelProperties = await builder.insertModelProperties(model);
         let structure;
-        let model;
-        let modelProperties;
-        let unitcell: StateObjectSelector | undefined = undefined;
         let assemblyId: number =  1;
-        let  entityCheck: boolean = false;
+        let entityCheck: boolean = false;
+
         do{
-            Object.assign(structureParams, {
+            const structureParams: RootStructureDefinition.Params = {
                 name: 'assembly',
                 params: { id:  (assemblyId++).toString()}
-            } as RootStructureDefinition.Params);
-
-            model = await builder.createModel(trajectory, modelParams);
-            modelProperties = await builder.insertModelProperties(model);
+            };
             structure = await builder.createStructure(modelProperties || model, structureParams);
-            if(structure.state?.cells)
-                for(const cell of structure.state?.cells.values()){
-                    const strData: Structure = (cell.obj as StateObject<Structure>).data;
-                    if(cell.obj?.type.name == "Structure" && strData.model.entryId == params.pdb?.entryId){
-                        const l = StructureElement.Location.create(strData);
-                        for(const unit of strData.units){
-                            StructureElement.Location.set(l, strData, unit, unit.elements[0]);
-                            entityCheck = SP.chain.label_entity_id(l) == params.pdb.entityId;
-                            if(entityCheck)
-                                break;
-                        }
-                        break;
+            const cell = structure.cell;
+            if(cell) {
+                const units = structure.cell?.obj?.data.units;
+                const strData: Structure = (cell.obj as StateObject<Structure>).data;
+                if (units){
+                    const l = StructureElement.Location.create(strData);
+                    for(const unit of units){
+                        StructureElement.Location.set(l, strData, unit, unit.elements[0]);
+                        entityCheck = (SP.chain.label_entity_id(l) == ("entityId" in params.pdb ? params.pdb.entityId : undefined) || SP.chain.label_asym_id(l) == ("instanceId" in params.pdb ? params.pdb.instanceId : undefined));
+                        if(entityCheck)
+                            break;
                     }
                 }
+            }
             if(!entityCheck)
                 plugin.managers.structure.hierarchy.remove([
                     plugin.managers.structure.hierarchy.current.structures[plugin.managers.structure.hierarchy.current.structures.length-1]
                 ]);
         }while(!entityCheck);
+
         const structureProperties = await builder.insertStructureProperties(structure);
-        const representation: StructureRepresentationPresetProvider.Result | undefined = await plugin.builders.structure.representation.applyPreset(
+        const representation = await plugin.builders.structure.representation.applyPreset(
             structureProperties,
             AlignmentRepresentationPresetProvider,
             {
                 pdb:params.pdb,
                 targetAlignment:params.targetAlignment,
-                stateManagerContainer: params.stateManager ? {data:params.stateManager} : undefined
+                matrix: params.matrix
             }
         );
         //TODO what is the purpose of this return?
         return {
             model,
             modelProperties,
-            unitcell,
             structure,
             structureProperties,
             representation

src/RcsbFvStructure/StructureViewers/MolstarViewer/StructureRepresentation.ts → src/RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/AssemblyTrajectoryPresetProvider.ts

@@ -2,30 +2,38 @@ import {
     PresetStructureRepresentations,
     StructureRepresentationPresetProvider
 } from "molstar/lib/mol-plugin-state/builder/structure/representation-preset";
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import {ParamDefinition, ParamDefinition as PD} from 'molstar/lib/mol-util/param-definition';
 import {TrajectoryHierarchyPresetProvider} from "molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset";
 import {StateObjectSelector} from "molstar/lib/mol-state";
 import {PluginStateObject} from "molstar/lib/mol-plugin-state/objects";
 import {StateObject} from "molstar/lib/mol-state/object";
 import {StateTransformer} from "molstar/lib/mol-state/transformer";
+import {PluginContext} from "molstar/lib/mol-plugin/context";
+import {AlignmentTrajectoryParamsType} from "./AlignmentTrajectoryPresetProvider";
 
 type StructureObject = StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>
 
-const RcsbParams = () => ({
-    preset: PD.Value<{assemblyId:string;modelIndex:number;}>({ assemblyId: '1' , modelIndex:0})
-});
 
-export const RcsbRepresentationPreset: TrajectoryHierarchyPresetProvider = TrajectoryHierarchyPresetProvider({
+
+export type AssemblyTrajectoryParamsType = {
+    assemblyId:string;
+    modelIndex:number;
+}
+
+export const AssemblyTrajectoryPresetProvider = TrajectoryHierarchyPresetProvider({
     id: "rcsb-saguaro-3d",
     display: {
         name: 'Feature View 3D'
     },
-    params: RcsbParams,
+    params: (trajectory: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext): ParamDefinition.For<AssemblyTrajectoryParamsType> => ({
+        assemblyId: PD.Value<string>("1"),
+        modelIndex: PD.Value<number>(0)
+    }),
     async apply(trajectory, params, plugin) {
         const builder = plugin.builders.structure;
-        const model = await builder.createModel(trajectory, {modelIndex: params.preset.modelIndex});
+        const model = await builder.createModel(trajectory, {modelIndex: params.modelIndex});
         const modelProperties = await builder.insertModelProperties(model);
-        const assemblyId: string = params.preset.assemblyId;
+        const assemblyId: string = params.assemblyId;
         const structure: StructureObject = await builder.createStructure(
             modelProperties,
             (assemblyId != "" && assemblyId != "0") ? {name: 'assembly', params:{id:assemblyId}} : {name:"model", params:{}}

src/RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/FlexibleAlignmentBuiltIn.ts

@@ -0,0 +1,89 @@
+import {PluginStateObject as PSO, PluginStateTransform} from "molstar/lib/mol-plugin-state/objects";
+import {ParamDefinition as PD} from "molstar/lib/mol-util/param-definition";
+import {RigidTransformType} from "../../../StructureUtils/StructureLoaderInterface";
+import {
+    Structure,
+    StructureElement,
+    StructureProperties as SP,
+    StructureSelection
+} from "molstar/lib/mol-model/structure";
+import {MolScriptBuilder as MS} from "molstar/lib/mol-script/language/builder";
+import {StructureQueryHelper} from "molstar/lib/mol-plugin-state/helpers/structure-query";
+import {Mat4} from "molstar/lib/mol-math/linear-algebra";
+import {RootStructureDefinition} from "molstar/lib/mol-plugin-state/helpers/root-structure";
+import {Task} from "molstar/lib/mol-task";
+import {PluginContext} from "molstar/lib/mol-plugin/context";
+
+export const FlexibleAlignmentBuiltIn = PluginStateTransform.BuiltIn({
+    name: "Flexible Alignment",
+    display: "Flexible Alignment",
+    from: PSO.Molecule.Model,
+    to: PSO.Molecule.Structure,
+    params:{
+        pdb:PD.Value<{entryId:string;entityId:string;}|{entryId:string;instanceId:string;}|undefined>(undefined),
+        transform:PD.Value<RigidTransformType[]|undefined>(undefined)
+    }
+})({
+    apply({a, params}, plugin: PluginContext){
+        return Task.create('Build Flexible Chain' , async (ctx)=>{
+            const base = await RootStructureDefinition.create(plugin, ctx, a.data);
+            const structure = base.data;
+            const entityId = params.pdb && "entityId" in params.pdb ? params.pdb?.entityId : undefined;
+            const instanceId = params.pdb && "instanceId" in params.pdb ?  params.pdb?.instanceId : undefined;
+            const l = StructureElement.Location.create(structure);
+            let alignedEntityId;
+            let alignedAsymId;
+            let alignedOperatorName;
+            let alignedType;
+
+            for(const unit of structure.units) {
+                StructureElement.Location.set(l, structure, unit, unit.elements[0]);
+                if(SP.chain.label_entity_id(l) == entityId || SP.chain.label_asym_id(l) == instanceId){
+                    alignedEntityId = SP.chain.label_entity_id(l);
+                    alignedAsymId = SP.chain.label_asym_id(l);
+                    alignedOperatorName = SP.unit.operator_name(l);
+                    alignedType = SP.entity.type(l);
+                    const alignedOperators: string[] = SP.unit.pdbx_struct_oper_list_ids(l);
+                    if(alignedOperators.length == 0) alignedOperators.push("0")
+                    if(alignedType != "polymer")
+                        throw new Error("");
+
+                    const builder = Structure.Builder({ label: structure.label });
+                    builder.beginChainGroup();
+                    for(const trans of params.transform ?? []){
+                        const residues = [];
+                        for(const r of trans.regions ?? []) {
+                            residues.push(toRange(r[0], r[1]));
+                        }
+                        const expression = MS.struct.generator.atomGroups({
+                            'chain-test': MS.core.logic.and([
+                                MS.core.rel.eq([MS.ammp('label_asym_id'), alignedAsymId]),
+                                MS.core.rel.eq([MS.acp('operatorName'), alignedOperatorName])
+                            ]),
+                            'residue-test': MS.core.set.has([MS.set(...residues.flat()), MS.ammp('label_seq_id')])
+                        });
+                        const { selection } = StructureQueryHelper.createAndRun(structure, expression);
+                        const s = StructureSelection.unionStructure(selection);
+                        const ts: Structure = Structure.transform(s, trans.transform as unknown as Mat4);
+                        const u = ts.units[0];
+                        builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, u.traits, u.invariantId);
+                    }
+                    builder.endChainGroup();
+                    const blockStructure = builder.getStructure();
+                    return new PSO.Molecule.Structure(blockStructure, { label: structure.label });
+                }
+            }
+            throw new Error("");
+        });
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});
+
+function toRange(start: number, end?: number): number[] {
+    if (!end) return [start];
+    const b = start < end ? start : end;
+    const e = start < end ? end : start;
+    return [...Array(e - b + 1)].map((_, i) => b + i);
+}

src/RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/FlexibleAlignmentRepresentationPresetProvider.ts

@@ -0,0 +1,126 @@
+/*
+* Copyright (c) 2021 RCSB PDB and contributors, licensed under MIT, See LICENSE file for more info.
+* @author Joan Segura Mora <joan.segura@rcsb.org>
+*/
+
+import {
+    StructureRepresentationPresetProvider
+} from "molstar/lib/mol-plugin-state/builder/structure/representation-preset";
+import {PluginContext} from "molstar/lib/mol-plugin/context";
+import {PluginStateObject} from "molstar/lib/mol-plugin-state/objects";
+import {StateObjectRef} from "molstar/lib/mol-state";
+import {
+    Model,
+    QueryContext, ResidueIndex,
+    Structure,
+    StructureElement,
+    StructureProperties as SP,
+    StructureSelection,
+    Unit
+} from "molstar/lib/mol-model/structure";
+import {MolScriptBuilder as MS} from "molstar/lib/mol-script/language/builder";
+import uniqid from "uniqid";
+import {PLDDTConfidenceColorThemeProvider} from "molstar/lib/extensions/model-archive/quality-assessment/color/plddt";
+import {ColorTheme} from "molstar/lib/mol-theme/color";
+import {createSelectionExpressions} from "@rcsb/rcsb-molstar/build/src/viewer/helpers/selection";
+import {ParamDefinition as PD} from "molstar/lib/mol-util/param-definition";
+import {Loci} from "molstar/lib/mol-model/loci";
+import {superpose} from "molstar/lib/mol-model/structure/structure/util/superposition";
+import {Mat4} from "molstar/lib/mol-math/linear-algebra";
+import {SymmetryOperator} from "molstar/lib/mol-math/geometry/symmetry-operator";
+import {StateTransforms} from "molstar/lib/mol-plugin-state/transforms";
+import {TagDelimiter} from "@rcsb/rcsb-saguaro-app";
+import {AlignedRegion, TargetAlignment} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import {AlignmentMapper as AM} from "../../../../Utils/AlignmentMapper";
+import {compile} from 'molstar/lib/mol-script/runtime/query/compiler';
+import reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
+import {
+    QualityAssessment,
+} from "molstar/lib/extensions/model-archive/quality-assessment/prop";
+import {MmcifFormat} from "molstar/lib/mol-model-formats/structure/mmcif";
+import {CustomProperty} from "molstar/lib/mol-model-props/common/custom-property";
+import {RcsbFvStateInterface} from "../../../../RcsbFvState/RcsbFvStateInterface";
+import {StructureBuilder} from "molstar/lib/mol-plugin-state/builder/structure";
+import {StructureRepresentationBuilder} from "molstar/lib/mol-plugin-state/builder/structure/representation";
+import {RigidTransformType} from "../../../StructureUtils/StructureLoaderInterface";
+import {StructureQueryHelper} from "molstar/lib/mol-plugin-state/helpers/structure-query";
+import {RootStructureDefinition} from "molstar/lib/mol-plugin-state/helpers/root-structure";
+import {RuntimeContext} from "molstar/lib/mol-task";
+import {
+    createStructureRepresentationParams
+} from "molstar/lib/mol-plugin-state/helpers/structure-representation-params";
+
+type ComponentType = Awaited<ReturnType<InstanceType<typeof StructureBuilder>["tryCreateComponentFromExpression"]>>;
+type RepresentationType = ReturnType<InstanceType<typeof StructureRepresentationBuilder>["buildRepresentation"]>;
+type ComponentMapType = Record<string,ComponentType>;
+type RepresentationMapType = Record<string,RepresentationType>;
+
+export const FlexibleAlignmentRepresentationPresetProvider = StructureRepresentationPresetProvider({
+    id: 'alignment-to-reference',
+    display: {
+        name: 'Alignment to Reference'
+    },
+    isApplicable: (structureRef: PluginStateObject.Molecule.Structure, plugin: PluginContext): boolean => true,
+    params: (structureRef: PluginStateObject.Molecule.Structure | undefined, plugin: PluginContext) => undefined,
+    apply: async (structureRef: StateObjectRef<PluginStateObject.Molecule.Structure>, params: undefined, plugin: PluginContext) => {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, structureRef);
+        if(!structureCell)
+            return {};
+
+        const componentMap :  ComponentMapType = {}
+        const representationMap :  RepresentationMapType = {}
+
+        if(structureCell.obj) structureCell.obj.label = "Adios :("
+        const structure = structureCell.obj!.data;
+        const l = StructureElement.Location.create(structure);
+        const  unit = structure.units[0];
+        StructureElement.Location.set(l, structure, unit, unit.elements[0]);
+        const entryId = SP.unit.model_entry_id(l);
+        const alignedEntityId = SP.chain.label_entity_id(l);
+        const alignedAsymId = SP.chain.label_asym_id(l);
+        const alignedOperatorName = SP.unit.operator_name(l);
+        const alignedOperators: string[] = SP.unit.pdbx_struct_oper_list_ids(l);
+        if(alignedOperators.length == 0) alignedOperators.push("0")
+        const alignedType = SP.entity.type(l);
+
+        const comp = await plugin.builders.structure.tryCreateComponentFromExpression(
+            structureCell,
+            MS.struct.generator.atomGroups({
+                'chain-test': MS.core.logic.and([
+                    MS.core.rel.eq([MS.ammp('label_asym_id'), alignedAsymId]),
+                    MS.core.rel.eq([MS.acp('operatorName'), alignedOperatorName])
+                ])
+            }),
+            uniqid(`${entryId}${TagDelimiter.entity}${alignedEntityId}${TagDelimiter.instance}${alignedAsymId}${TagDelimiter.assembly}${alignedOperators.join(",")}${TagDelimiter.assembly}${alignedType}`),
+            {
+                label: `${entryId}${TagDelimiter.entity}${alignedEntityId}${TagDelimiter.instance}${alignedAsymId}${TagDelimiter.assembly}${alignedOperators.join(",")}${TagDelimiter.assembly}${alignedType}`
+            }
+        );
+        componentMap["aligned"] = comp;
+
+        //TODO This needs to be called after tryCreateComponentFromExpression
+        const {update, builder} = reprBuilder(plugin, {
+            ignoreHydrogens: true,
+            ignoreLight: false,
+            quality: "auto"
+        });
+        representationMap["aligned"] = builder.buildRepresentation(update, comp, {
+            color: PLDDTConfidenceColorThemeProvider.isApplicable({ structure }) ? PLDDTConfidenceColorThemeProvider.name as ColorTheme.BuiltIn : "chain-id",
+            type: "cartoon"
+        });
+        await update.commit({ revertOnError: false });
+
+        return {
+            components: componentMap,
+            representations: representationMap
+        };
+    }
+});
+
+
+function toRange(start: number, end?: number): number[] {
+    if (!end) return [start];
+    const b = start < end ? start : end;
+    const e = start < end ? end : start;
+    return [...Array(e - b + 1)].map((_, i) => b + i);
+};

src/RcsbFvStructure/StructureViewers/MolstarViewer/TrajectoryPresetProvider/FlexibleAlignmentTrajectoryPresetProvider.ts

@@ -0,0 +1,113 @@
+/*
+* Copyright (c) 2021 RCSB PDB and contributors, licensed under MIT, See LICENSE file for more info.
+* @author Joan Segura Mora <joan.segura@rcsb.org>
+*/
+
+import {TrajectoryHierarchyPresetProvider} from "molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset";
+import {PluginContext} from "molstar/lib/mol-plugin/context";
+import {PluginStateObject} from "molstar/lib/mol-plugin-state/objects";
+import {ParamDefinition, ParamDefinition as PD} from "molstar/lib/mol-util/param-definition";
+import {StateObjectRef, StateObjectSelector} from "molstar/lib/mol-state";
+import {RootStructureDefinition} from "molstar/lib/mol-plugin-state/helpers/root-structure";
+import {StateTransformer} from "molstar/lib/mol-state/transformer";
+import {StateObject} from "molstar/lib/mol-state/object";
+import {
+    StructureRepresentationPresetProvider
+} from "molstar/lib/mol-plugin-state/builder/structure/representation-preset";
+import {PLDDTConfidenceColorThemeProvider} from "molstar/lib/extensions/model-archive/quality-assessment/color/plddt";
+import {AlignmentRepresentationPresetProvider} from "./AlignmentRepresentationPresetProvider";
+import {TargetAlignment} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import {Structure, StructureElement, StructureProperties as SP} from "molstar/lib/mol-model/structure";
+import {RigidTransformType, TransformMatrixType} from "../../../StructureUtils/StructureLoaderInterface";
+import {FlexibleAlignmentRepresentationPresetProvider} from "./FlexibleAlignmentRepresentationPresetProvider";
+import {FlexibleAlignmentBuiltIn} from "./FlexibleAlignmentBuiltIn";
+import {CustomStructureProperties} from "molstar/lib/mol-plugin-state/transforms/model";
+
+export type FelxibleAlignmentTrajectoryParamsType = {
+    pdb?:{entryId:string;entityId:string;}|{entryId:string;instanceId:string;};
+    transform?: RigidTransformType[];
+    modelIndex?: number;
+    plddt?: 'off' | 'single-chain' | 'on';
+}
+
+type StructureObject = StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>
+
+export const FlexibleAlignmentTrajectoryPresetProvider = TrajectoryHierarchyPresetProvider({
+    id: 'alignment-to-reference',
+    display: {
+        name: 'Alignment to Reference'
+    },
+    isApplicable: (trajectory: PluginStateObject.Molecule.Trajectory, plugin: PluginContext): boolean => true,
+    params: (trajectory: PluginStateObject.Molecule.Trajectory | undefined, plugin: PluginContext): ParamDefinition.For<FelxibleAlignmentTrajectoryParamsType> => ({
+        pdb:PD.Value<{entryId:string;entityId:string;}|{entryId:string;instanceId:string;}|undefined>(undefined),
+        modelIndex:PD.Value<number|undefined>(undefined),
+        plddt:PD.Value<'off' | 'single-chain' | 'on' | undefined>(undefined),
+        transform:PD.Value<RigidTransformType[]|undefined>(undefined)
+    }),
+    apply: async (trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>, params: FelxibleAlignmentTrajectoryParamsType, plugin: PluginContext) => {
+        if(!params.pdb)
+            return {};
+        const modelParams = { modelIndex: params.modelIndex || 0 };
+        const builder = plugin.builders.structure;
+
+        const model = await builder.createModel(trajectory, modelParams);
+        const modelProperties = await builder.insertModelProperties(model);
+        let structure;
+        let assemblyId: number =  1;
+        let entityCheck: boolean = false;
+
+        do{
+            const structureParams: RootStructureDefinition.Params = {
+                name: 'assembly',
+                params: { id:  (assemblyId++).toString()}
+            };
+            structure = await builder.createStructure(modelProperties || model, structureParams);
+            const cell = structure.cell;
+            if(cell) {
+                const units = structure.cell?.obj?.data.units;
+                const strData: Structure = (cell.obj as StateObject<Structure>).data;
+                if (units){
+                    const l = StructureElement.Location.create(strData);
+                    for(const unit of units){
+                        StructureElement.Location.set(l, strData, unit, unit.elements[0]);
+                        entityCheck = (SP.chain.label_entity_id(l) == ("entityId" in params.pdb ? params.pdb.entityId : undefined) || SP.chain.label_asym_id(l) == ("instanceId" in params.pdb ? params.pdb.instanceId : undefined));
+                        if(entityCheck)
+                            break;
+                    }
+                }
+            }
+            if(!entityCheck)
+                plugin.managers.structure.hierarchy.remove([
+                    plugin.managers.structure.hierarchy.current.structures[plugin.managers.structure.hierarchy.current.structures.length-1]
+                ]);
+        }while(!entityCheck);
+        plugin.managers.structure.hierarchy.remove([
+            plugin.managers.structure.hierarchy.current.structures[plugin.managers.structure.hierarchy.current.structures.length-1]
+        ]);
+        structure = await plugin.state.data.build().to(modelProperties).apply(FlexibleAlignmentBuiltIn, {
+            pdb: params.pdb,
+            transform: params.transform
+        }).commit();
+
+        const structureProperties = await builder.insertStructureProperties(structure);
+        const representation = await plugin.builders.structure.representation.applyPreset(
+            structure,
+            FlexibleAlignmentRepresentationPresetProvider
+        );
+        //TODO what is the purpose of this return?
+        return {
+            model,
+            modelProperties,
+            structure,
+            structureProperties,
+            representation
+        };
+    }
+});
+
+function checkPlddtColorTheme(structure: StructureObject | undefined, plddt: 'on' | 'single-chain' | 'off') {
+    if (!structure?.data) return false;
+    if (plddt === 'off') return false;
+    if (plddt === 'single-chain' && structure.data?.polymerUnitCount !== 1) return false;
+    return PLDDTConfidenceColorThemeProvider.isApplicable({ structure: structure.data });
+}

src/RcsbFvStructure/StructureViewers/StructureViewer.ts

@@ -1,7 +1,6 @@
 import {
     SaguaroChain,
     StructureViewerInterface,
-    SaguaroPluginModelMapType,
     SaguaroPosition,
     SaguaroRange,
     ViewerCallbackManagerInterface,
@@ -11,21 +10,19 @@ import {
 import {PluginContext} from "molstar/lib/mol-plugin/context";
 import {StructureRepresentationRegistry} from "molstar/lib/mol-repr/structure/registry";
 import {ColorTheme} from "molstar/lib/mol-theme/color";
-import {RcsbFvStateManager} from "../../RcsbFvState/RcsbFvStateManager";
 import {Subscription} from "rxjs";
+import {RcsbFvStateInterface} from "../../RcsbFvState/RcsbFvStateInterface";
 
-
-
-export class StructureViewer<R,S> implements StructureViewerInterface<R,S> {
-    private readonly structureViewerManagerFactory:  ViewerManagerFactoryInterface<R,S>;
+export class StructureViewer<R,L,S> implements StructureViewerInterface<R,L,S> {
+    private readonly structureViewerManagerFactory:  ViewerManagerFactoryInterface<R,L,S>;
     private callbackManager: ViewerCallbackManagerInterface;
-    private actionManager: ViewerActionManagerInterface<R>;
+    private actionManager: ViewerActionManagerInterface<R,L>;
 
-    constructor(structureViewerManagerFactory:  ViewerManagerFactoryInterface<R,S>) {
+    constructor(structureViewerManagerFactory:  ViewerManagerFactoryInterface<R,L,S>) {
         this.structureViewerManagerFactory = structureViewerManagerFactory;
     }
 
-    public init( stateManager: RcsbFvStateManager, args:S): void {
+    public init( stateManager: RcsbFvStateInterface, args:S): void {
         const {actionManager,callbackManager} = this.structureViewerManagerFactory.getViewerManagerFactory(stateManager, args);
         this.actionManager = actionManager;
         this.callbackManager = callbackManager;
@@ -40,12 +37,15 @@ export class StructureViewer<R,S> implements StructureViewerInterface<R,S> {
         await this.actionManager.clear();
     }
 
-    async load(loadConfig: R|Array<R>): Promise<void>{
-      await this.actionManager.load(loadConfig);
+    async load(loadConfig: R): Promise<L|undefined>;
+    async load(loadConfig: R[]): Promise<(L|undefined)[]>;
+    async load(loadConfig: R|R[]): Promise<(L|undefined)|(L|undefined)[]>{
+      const out = await this.actionManager.load(Array.isArray(loadConfig) ? loadConfig: [loadConfig]);
       this.modelChange();
+      return out;
     }
 
-    async removeStructure(loadConfig: R|Array<R>): Promise<void>{
+    async removeStructure(loadConfig: R|R[]): Promise<void>{
         await this.actionManager.removeStructure(loadConfig);
         this.modelChange();
     }

src/examples/alignment-provider/index.ts

@@ -0,0 +1,17 @@
+import {RcsbFv3DAlignmentProvider} from "../../RcsbFv3D/RcsbFv3DAlignmentProvider";
+import {dataProvider, structureLocationProvider, transformProvider} from "./providers/ExternalAlignmentProvider";
+
+document.addEventListener("DOMContentLoaded", function(event) {
+
+    const panel3D = new RcsbFv3DAlignmentProvider({
+        config:{
+            dataProvider: dataProvider,
+            transformProvider: transformProvider,
+            structureLocationProvider: structureLocationProvider,
+            title: "Title >> Alignment Provider",
+            subtitle: "Subtitle >> Alignment Provider"
+        }
+    });
+    panel3D.render();
+
+});

src/examples/alignment-provider/providers/AlignmentReference.ts

@@ -0,0 +1,181 @@
+import {cloneDeep} from "lodash";
+import {
+    AlignedRegion,
+    AlignmentResponse,
+} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+
+type AlignmentRefType = (number|undefined)[];
+type AlignmentMemberType = {
+    id:string;
+    map: AlignmentRefType;
+    ref: AlignmentRefType;
+    target: AlignmentRefType;
+};
+export class AlignmentReference {
+    private readonly alignmentRefMap: AlignmentRefType;
+    private readonly refId:string;
+    private readonly alignmentRefGaps: Record<number, number>;
+    private readonly memberRefList: AlignmentMemberType[] = [];
+
+    constructor(refId: string, length: number) {
+        this.alignmentRefMap = Array(length).fill(0).map((v,n)=>n+1);
+        this.alignmentRefGaps = {};
+        this.refId = refId;
+    }
+
+    public addAlignment(id:string, alignment: AlignmentRefType, target: AlignmentRefType): void {
+        const gaps = findGaps(alignment);
+        for (const gapBeg in gaps) {
+            if(this.alignmentRefGaps[gapBeg])
+                this.extendGap(parseInt(gapBeg), gaps[gapBeg])
+            else
+                this.addGap(parseInt(gapBeg), gaps[gapBeg])
+        }
+        const beg = alignment.filter(a=>(a && this.alignmentRefMap[0] && a<this.alignmentRefMap[0])) as number[];
+        if(beg.length > 0)
+            this.addBeg(beg);
+        const n = this.alignmentRefMap[this.alignmentRefMap.length-1] as number;
+        const end = alignment.filter(a=>(a && n && a>n)) as number[];
+        if(end.length > 0)
+            this.addEnd(end);
+        this.addRef(id,alignment,target);
+    }
+
+    public buildAlignments(): AlignmentResponse {
+        return buildAlignments(this.refId, this.alignmentRefMap, this.memberRefList);
+    }
+
+    private addRef(id: string, alignment: AlignmentRefType, target: AlignmentRefType): void {
+        const map: AlignmentRefType = Array(this.alignmentRefMap.length).fill(undefined);
+        alignment.forEach((v,n)=>{
+            if(typeof v === "undefined")
+                return;
+            const index = this.alignmentRefMap.findIndex(e=>e===v);
+            if(index>=0)
+                map[index] = n;
+        });
+        const gaps = findGaps(alignment);
+        for (const gapBeg in gaps) {
+            const index = this.alignmentRefMap.findIndex(v=>v===parseInt(gapBeg));
+            for(let i = 1;i<=gaps[gapBeg];i++){
+                map[index+i] = (map[index] as number)+i;
+            }
+        }
+        this.memberRefList.push({
+            id,
+            map,
+            ref: cloneDeep(alignment),
+            target: cloneDeep(target)
+        });
+    }
+
+    private addEnd(indexList: number[]): void {
+        const last = this.alignmentRefMap.length;
+        this.alignmentRefMap.splice(last, 0, ...indexList);
+        this.memberRefList.forEach(mr=>{
+            mr.map.splice(last,0, ...Array(indexList.length).fill(undefined));
+        });
+    }
+
+    private addBeg(indexList: number[]): void {
+        this.alignmentRefMap.splice(0, 0, ...indexList);
+        this.memberRefList.forEach(mr=>{
+            mr.map.splice(0,0, ...Array(indexList.length).fill(undefined));
+        });
+    }
+
+    private addGap(gapBeg: number, gapLength: number): void {
+        this.alignmentRefGaps[gapBeg] = gapLength;
+        const i = this.alignmentRefMap.findIndex((v)=>v===gapBeg)+1;
+        this.alignmentRefMap.splice(i,0, ...Array(gapLength).fill(undefined));
+        this.memberRefList.forEach(mr=>{
+            mr.map.splice(i,0, ...Array(gapLength).fill(undefined));
+        });
+    }
+
+    private extendGap(gapBeg: number, gapLength: number): void {
+        if(!this.alignmentRefGaps[gapBeg] || this.alignmentRefGaps[gapBeg] >= gapLength)
+            return;
+        const delta = gapLength - this.alignmentRefGaps[gapBeg];
+        this.alignmentRefGaps[gapBeg] += delta;
+        const i = this.alignmentRefMap.findIndex((v)=>v===gapBeg)+1;
+        this.alignmentRefMap.splice(i,0, ...Array(delta).fill(undefined));
+        this.memberRefList.forEach(mr=>{
+            mr.map.splice(i,0, ...Array(delta).fill(undefined));
+        });
+    }
+
+}
+
+function buildAlignments(refId:string, alignmentRefMap: AlignmentRefType, alignmentMembers: AlignmentMemberType[]): AlignmentResponse {
+    const out: AlignmentResponse = {};
+    out.target_alignment = [];
+    out.target_alignment.push({
+        aligned_regions: buildRegions(alignmentRefMap),
+        target_id: refId
+    });
+    alignmentMembers.forEach(am=>{
+        out.target_alignment?.push({
+            target_id: am.id,
+            aligned_regions: buildRegions(am.map.map((v,n)=> typeof v === "number" ? am.target[v] : undefined))
+        });
+    })
+    return out;
+}
+
+function buildRegions(alignment:AlignmentRefType): AlignedRegion[] {
+    const out: AlignedRegion[] = [];
+    let begIndex = 0;
+    let begPos = 0;
+    alignment.forEach((v,n)=>{
+        if(!v){
+            if(begIndex>0){
+                out.push({
+                    query_begin: begIndex,
+                    target_begin: begPos,
+                    query_end: n,
+                    target_end: alignment[n-1] as number
+                });
+                begIndex = 0;
+                begPos = 0;
+            }
+        }else{
+            if(begIndex == 0){
+                begIndex = n+1;
+                begPos = v;
+            }
+        }
+    });
+    if(begPos>0){
+        const n = alignment.length;
+        out.push({
+            query_begin: begIndex,
+            target_begin: begPos,
+            query_end: n,
+            target_end: alignment[n-1] as number
+        });
+    }
+    return out;
+}
+
+function findGaps(alignment: AlignmentRefType): Record<number,number> {
+    const out: Record<number, number> = {};
+    let gapBeg = 0;
+    let gapLength = 0;
+    alignment.forEach((v,n)=>{
+        if(!v){
+            if(gapBeg == 0)
+                gapBeg = alignment[n-1] as number;
+            gapLength++;
+        }else{
+            if(gapLength > 0){
+                out[gapBeg]=gapLength;
+                gapBeg = 0;
+                gapLength = 0;
+            }
+        }
+    })
+    if(gapLength > 0)
+        out[gapBeg]=gapLength;
+    return out;
+}

src/examples/alignment-provider/providers/ExternalAlignmentProvider.ts

@@ -0,0 +1,1824 @@
+import {
+    AlignmentResponse,
+    SequenceReference,
+} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import {
+    AlignmentCollectConfig,
+    AlignmentCollectorInterface
+} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
+import {RcsbRequestContextManager} from "@rcsb/rcsb-saguaro-app";
+
+import {
+    RcsbModuleDataProviderInterface
+} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface";
+import {AlignmentReference} from "./AlignmentReference";
+import {
+    LocationProviderInterface,
+    RigidTransformType, TransformMatrixType,
+    TransformProviderInterface
+} from "../../../RcsbFvStructure/StructureUtils/StructureLoaderInterface";
+import {
+    InstanceSequenceInterface
+} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector";
+import {Alignment, AlignmentRegion, StructureAlignmentResponse} from "./alignment-response";
+
+const alignment = {
+    "info": {
+        "uuid": "e6e216de-c650-4ad5-bd81-45e75dfbe180",
+        "status": "COMPLETE"
+    },
+    "meta": {
+        "alignment_mode": "pairwise",
+        "alignment_method": "fatcat-rigid"
+    },
+    "results": [
+        {
+            "structures": [
+                {
+                    "entry_id": "101M",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                },
+                {
+                    "entry_id": "1ASH",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                }
+            ],
+            "structure_alignment": [
+                {
+                    "regions": [
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 4,
+                                "beg_index": 0,
+                                "length": 47
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 52,
+                                "beg_index": 52,
+                                "length": 70
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 124,
+                                "beg_index": 128,
+                                "length": 22
+                            }
+                        ],
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 1,
+                                "beg_index": 0,
+                                "length": 17
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 22,
+                                "beg_index": 21,
+                                "length": 61
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 86,
+                                "beg_index": 86,
+                                "length": 14
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 101,
+                                "beg_index": 101,
+                                "length": 47
+                            }
+                        ]
+                    ],
+                    "transformations": [
+                        [
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1
+                        ],
+                        [
+                            -0.7671995717115603,
+                            -0.5623954843039239,
+                            0.30840904072376607,
+                            0,
+                            -0.6011420900233072,
+                            0.4627787494512096,
+                            -0.6515090303739346,
+                            0,
+                            0.2236805864799372,
+                            -0.6852351043918645,
+                            -0.6931232552303105,
+                            0,
+                            37.48154540719762,
+                            28.2044983569036,
+                            -7.345065372687518,
+                            1
+                        ]
+                    ],
+                    "summary": {
+                        "scores": [
+                            {
+                                "value": 1.95,
+                                "type": "RMSD"
+                            },
+                            {
+                                "value": 330.13,
+                                "type": "similarity-score"
+                            }
+                        ],
+                        "n_aln_residue_pairs": 139
+                    }
+                }
+            ],
+            "sequence_alignment": [
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 4,
+                            "beg_index": 0,
+                            "length": 17
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 21,
+                            "beg_index": 21,
+                            "length": 62
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 83,
+                            "beg_index": 86,
+                            "length": 14
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 97,
+                            "beg_index": 101,
+                            "length": 49
+                        }
+                    ],
+                    "gaps": [
+                        {
+                            "beg_index": 17,
+                            "length": 4
+                        },
+                        {
+                            "beg_index": 83,
+                            "length": 3
+                        },
+                        {
+                            "beg_index": 100,
+                            "length": 1
+                        }
+                    ]
+                },
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 1,
+                            "beg_index": 0,
+                            "length": 51
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 52,
+                            "beg_index": 52,
+                            "length": 74
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 126,
+                            "beg_index": 128,
+                            "length": 22
+                        }
+                    ],
+                    "gaps": [
+                        {
+                            "beg_index": 51,
+                            "length": 1
+                        },
+                        {
+                            "beg_index": 126,
+                            "length": 2
+                        }
+                    ]
+                }
+            ],
+            "summary": {
+                "scores": [
+                    {
+                        "value": 0.15,
+                        "type": "sequence-identity"
+                    },
+                    {
+                        "value": 1.94,
+                        "type": "RMSD"
+                    },
+                    {
+                        "value": 0.79,
+                        "type": "TM-score"
+                    },
+                    {
+                        "value": 330.13,
+                        "type": "similarity-score"
+                    },
+                    {
+                        "value": 0.34,
+                        "type": "sequence-similarity"
+                    }
+                ],
+                "n_aln_residue_pairs": 139,
+                "n_modeled_residues": [
+                    154,
+                    147
+                ],
+                "seq_aln_len": 150,
+                "aln_coverage": [
+                    90,
+                    95
+                ]
+            }
+        },
+        {
+            "structures": [
+                {
+                    "entry_id": "101M",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                },
+                {
+                    "entry_id": "4HHB",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                }
+            ],
+            "structure_alignment": [
+                {
+                    "regions": [
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 2,
+                                "beg_index": 0,
+                                "length": 48
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 56,
+                                "beg_index": 54,
+                                "length": 93
+                            }
+                        ],
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 1,
+                                "beg_index": 0,
+                                "length": 141
+                            }
+                        ]
+                    ],
+                    "transformations": [
+                        [
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1
+                        ],
+                        [
+                            0.5659010881349978,
+                            0.8158255303919226,
+                            0.11909938038614465,
+                            0,
+                            0.49060456462775587,
+                            -0.21711201635870375,
+                            -0.8439013766543271,
+                            0,
+                            -0.6626183815847819,
+                            0.5359954069890864,
+                            -0.5231116554547112,
+                            0,
+                            16.44633740010974,
+                            7.329736404913569,
+                            7.069768946221407,
+                            1
+                        ]
+                    ],
+                    "summary": {
+                        "scores": [
+                            {
+                                "value": 1.41,
+                                "type": "RMSD"
+                            },
+                            {
+                                "value": 360.42,
+                                "type": "similarity-score"
+                            }
+                        ],
+                        "n_aln_residue_pairs": 141
+                    }
+                }
+            ],
+            "sequence_alignment": [
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 2,
+                            "beg_index": 0,
+                            "length": 147
+                        }
+                    ]
+                },
+                {
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 1,
+                            "beg_index": 0,
+                            "length": 48
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 49,
+                            "beg_index": 54,
+                            "length": 93
+                        }
+                    ],
+                    "gaps": [
+                        {
+                            "beg_index": 48,
+                            "length": 6
+                        }
+                    ]
+                }
+            ],
+            "summary": {
+                "scores": [
+                    {
+                        "value": 1.63,
+                        "type": "RMSD"
+                    },
+                    {
+                        "value": 360.42,
+                        "type": "similarity-score"
+                    },
+                    {
+                        "value": 0.26,
+                        "type": "sequence-identity"
+                    },
+                    {
+                        "value": 0.83,
+                        "type": "TM-score"
+                    },
+                    {
+                        "value": 0.4,
+                        "type": "sequence-similarity"
+                    }
+                ],
+                "n_aln_residue_pairs": 141,
+                "n_modeled_residues": [
+                    154,
+                    141
+                ],
+                "seq_aln_len": 147,
+                "aln_coverage": [
+                    92,
+                    100
+                ]
+            }
+        },
+        {
+            "structures": [
+                {
+                    "entry_id": "101M",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                },
+                {
+                    "entry_id": "3IA3",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                }
+            ],
+            "structure_alignment": [
+                {
+                    "regions": [
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 6,
+                                "beg_index": 0,
+                                "length": 2
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 9,
+                                "beg_index": 3,
+                                "length": 10
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 70,
+                                "beg_index": 64,
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+const flexAlignment = {
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+        "status": "COMPLETE"
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+const alignmentExample = {
+    "info": {
+        "uuid": "538d54e2-039c-44c8-bd5f-bb26af9c45bb",
+        "status": "COMPLETE"
+    },
+    "meta": {
+        "alignment_mode": "pairwise",
+        "alignment_method": "fatcat-rigid"
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+    "results": [
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+                    "url": "https://alphafold.ebi.ac.uk/files/AF-P41235-F1-model_v2.cif",
+                    "format": "mmcif",
+                    "is_binary": false,
+                    "name": "AF-P41235-F1",
+                    "selection": {
+                        "asym_id": "A"
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+                {
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+                    "selection": {
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+            "structure_alignment": [
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+                            0.3849529305900804,
+                            0,
+                            -0.6205267418674186,
+                            -0.18505769796524382,
+                            0.7620368829992492,
+                            0,
+                            -0.4173004513190375,
+                            -0.7448149455737514,
+                            -0.5206832340097945,
+                            0,
+                            2.241812113864647,
+                            17.198483576583477,
+                            -52.357664887014344,
+                            1
+                        ]
+                    ],
+                    "summary": {
+                        "scores": [
+                            {
+                                "value": 214.71,
+                                "type": "similarity-score"
+                            },
+                            {
+                                "value": 0.47,
+                                "type": "RMSD"
+                            }
+                        ],
+                        "n_aln_residue_pairs": 76
+                    }
+                }
+            ],
+            "sequence_alignment": [
+                {
+                    "sequence": "MRLSKTLVDMDMADYSAALDPAYTTLEFENVQVLTMGNDTSPSEGTNLNAPNSLGVSALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGGSPSDAPHAHHPLHPHLMQEHMGTNVIVANTMPTHLSNGQMCEWPRPRGQAATPETPQPSPPGGSGSEPYKLLPGAVATIVKPLSAIPQPTITKQEVI",
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 58,
+                            "beg_index": 0,
+                            "length": 76
+                        }
+                    ]
+                },
+                {
+                    "sequence": "ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD",
+                    "regions": [
+                        {
+                            "asym_id": "C",
+                            "beg_seq_id": 1,
+                            "beg_index": 0,
+                            "length": 76
+                        }
+                    ]
+                }
+            ],
+            "summary": {
+                "scores": [
+                    {
+                        "value": 1,
+                        "type": "sequence-identity"
+                    },
+                    {
+                        "value": 214.71,
+                        "type": "similarity-score"
+                    },
+                    {
+                        "value": 1,
+                        "type": "sequence-similarity"
+                    },
+                    {
+                        "value": 0.49,
+                        "type": "RMSD"
+                    },
+                    {
+                        "value": 0.16,
+                        "type": "TM-score"
+                    }
+                ],
+                "n_aln_residue_pairs": 76,
+                "n_modeled_residues": [
+                    474,
+                    76
+                ],
+                "seq_aln_len": 76,
+                "aln_coverage": [
+                    16,
+                    100
+                ]
+            }
+        },
+        {
+            "structures": [
+                {
+                    "url": "https://alphafold.ebi.ac.uk/files/AF-P41235-F1-model_v2.cif",
+                    "format": "mmcif",
+                    "is_binary": false,
+                    "name": "AF-P41235-F1",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                },
+                {
+                    "entry_id": "1PZL",
+                    "selection": {
+                        "asym_id": "A"
+                    }
+                }
+            ],
+            "structure_alignment": [
+                {
+                    "regions": [
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 146,
+                                "beg_index": 0,
+                                "length": 21
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 173,
+                                "beg_index": 27,
+                                "length": 206
+                            }
+                        ],
+                        [
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 5,
+                                "beg_index": 0,
+                                "length": 21
+                            },
+                            {
+                                "asym_id": "A",
+                                "beg_seq_id": 32,
+                                "beg_index": 27,
+                                "length": 206
+                            }
+                        ]
+                    ],
+                    "transformations": [
+                        [
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1,
+                            0,
+                            0,
+                            0,
+                            0,
+                            1
+                        ],
+                        [
+                            -0.010053370832324049,
+                            -0.2331468555903751,
+                            -0.9723895687754106,
+                            0,
+                            -0.5818706004499447,
+                            -0.7894818469306177,
+                            0.19530749524542618,
+                            0,
+                            -0.813219241082581,
+                            0.5677684009306454,
+                            -0.12772434708280683,
+                            0,
+                            26.741147368855113,
+                            9.829205405298664,
+                            85.1383381307709,
+                            1
+                        ]
+                    ],
+                    "summary": {
+                        "scores": [
+                            {
+                                "value": 0.85,
+                                "type": "RMSD"
+                            },
+                            {
+                                "value": 638.55,
+                                "type": "similarity-score"
+                            }
+                        ],
+                        "n_aln_residue_pairs": 227
+                    }
+                }
+            ],
+            "sequence_alignment": [
+                {
+                    "sequence": "MRLSKTLVDMDMADYSAALDPAYTTLEFENVQVLTMGNDTSPSEGTNLNAPNSLGVSALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGGSPSDAPHAHHPLHPHLMQEHMGTNVIVANTMPTHLSNGQMCEWPRPRGQAATPETPQPSPPGGSGSEPYKLLPGAVATIVKPLSAIPQPTITKQEVI",
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 146,
+                            "beg_index": 0,
+                            "length": 233
+                        }
+                    ]
+                },
+                {
+                    "sequence": "SSYELASLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGGS",
+                    "regions": [
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 5,
+                            "beg_index": 0,
+                            "length": 21
+                        },
+                        {
+                            "asym_id": "A",
+                            "beg_seq_id": 32,
+                            "beg_index": 27,
+                            "length": 206
+                        }
+                    ],
+                    "gaps": [
+                        {
+                            "beg_index": 21,
+                            "length": 6
+                        }
+                    ]
+                }
+            ],
+            "summary": {
+                "scores": [
+                    {
+                        "value": 1.1,
+                        "type": "RMSD"
+                    },
+                    {
+                        "value": 0.47,
+                        "type": "TM-score"
+                    },
+                    {
+                        "value": 638.55,
+                        "type": "similarity-score"
+                    },
+                    {
+                        "value": 1,
+                        "type": "sequence-similarity"
+                    },
+                    {
+                        "value": 0.99,
+                        "type": "sequence-identity"
+                    }
+                ],
+                "n_aln_residue_pairs": 227,
+                "n_modeled_residues": [
+                    474,
+                    227
+                ],
+                "seq_aln_len": 233,
+                "aln_coverage": [
+                    48,
+                    100
+                ]
+            }
+        }
+    ]
+};
+
+class RcsbStructuralAlignmentProvider implements AlignmentCollectorInterface {
+
+    private alignmentResponse: AlignmentResponse | undefined = undefined;
+    private readonly alignment: StructureAlignmentResponse;
+    constructor(alignment: StructureAlignmentResponse) {
+        this.alignment = alignment;
+    }
+
+    async collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse> {
+        return new Promise(async (resolve)=>{
+            resolve(await this.data());
+        });
+    }
+    async getTargets(): Promise<string[]> {
+        return new Promise(async (resolve)=>{
+            resolve((await this.data()).target_alignment?.map(ta=>ta?.target_id ?? "NA") ?? [])
+        })
+    }
+    async getAlignmentLength(): Promise<number> {
+        return new Promise(async (resolve)=>{
+            const ends = (await this.data() ).target_alignment?.map(ta=>ta?.aligned_regions?.[ta?.aligned_regions?.length-1]?.query_end);
+            resolve(Math.max(...(ends as number[])))
+        })
+    }
+    async getAlignment(): Promise<AlignmentResponse> {
+        return new Promise(async (resolve)=>{
+            resolve(this.data());
+        });
+    }
+    private async data(): Promise<AlignmentResponse> {
+        if(this.alignmentResponse)
+            return this.alignmentResponse;
+        return new Promise((resolve)=>{
+            alignmentTransform(this.alignment).then(ar=>{
+                this.alignmentResponse = ar;
+                resolve(ar);
+            })
+        });
+    }
+
+}
+
+class RcsbStructuralTransformProvider implements TransformProviderInterface {
+
+    private readonly alignment: StructureAlignmentResponse;
+    constructor(alignment: StructureAlignmentResponse) {
+        this.alignment = alignment;
+    }
+
+    get(entryId: string, asymId?: string): RigidTransformType[] {
+        const res = this.alignment.results?.find(res=>{
+            const r = res.structures[1];
+            return ("entry_id" in r && r.entry_id == entryId && r.selection && "asym_id" in r.selection && r.selection.asym_id == asymId)
+        });
+        if(res?.structure_alignment.length == 1) {
+            return [{
+                transform: res.structure_alignment[0].transformations[1] as TransformMatrixType
+            }];
+        }else if(res?.structure_alignment.length && res?.structure_alignment.length > 1){
+            return res.structure_alignment.map(sa=>({
+                transform: sa.transformations[1] as TransformMatrixType,
+                regions: sa.regions?.[1].map(r=>[r.beg_seq_id,r.beg_seq_id+r.length-1])
+            }));
+        }else{
+            return [{
+                transform: [1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1]
+            }];
+        }
+    }
+
+}
+
+class RcsbStructureLocationProvider implements LocationProviderInterface {
+
+    private readonly alignment: StructureAlignmentResponse;
+    constructor(alignment: StructureAlignmentResponse) {
+        this.alignment = alignment;
+    }
+
+    get(entryId:string): string|undefined {
+        for(const res of this.alignment.results ?? []){
+            if("url" in res.structures[0] && res.structures[0].url && res.structures[0].name == entryId ){
+                return res.structures[0].url;
+            }
+            if("url" in res.structures[1] && res.structures[1].url && res.structures[1].name == entryId ){
+                return res.structures[1].url;
+            }
+        }
+        return undefined;
+    }
+
+}
+
+async function alignmentTransform(alignment: StructureAlignmentResponse): Promise<AlignmentResponse> {
+    if(!alignment.results)
+        return {};
+    const alignmentRef = await mergeAlignments(alignment.results);
+    const out: AlignmentResponse = alignmentRef.buildAlignments();
+    const seqs = await getSequences(alignment.results);
+    out.target_alignment?.forEach(ta=>{
+        const seq = seqs.find(s=>s.rcsbId===ta?.target_id)?.sequence
+        if(seq && ta)
+            ta.target_sequence = seq;
+    });
+    return out;
+}
+
+async function mergeAlignments(results: Alignment[]): Promise<AlignmentReference> {
+    const result = results[0];
+    if(!result)
+        throw "Results not available";
+    const seqs = await getSequences([result]);
+    const alignmentRef = new AlignmentReference( getInstanceId(result, 0), seqs[0].sequence.length)
+    results.forEach(result=>{
+        if(result.sequence_alignment)
+            alignmentRef.addAlignment(getInstanceId(result), transformToGapedDomain(result.sequence_alignment[0].regions), transformToGapedDomain(result.sequence_alignment[1].regions));
+        else if(result.structure_alignment && result.structure_alignment[0].regions && result.structure_alignment[1].regions)
+            alignmentRef.addAlignment(getInstanceId(result), transformToGapedDomain(result.structure_alignment[0].regions.flat()), transformToGapedDomain(result.structure_alignment[1].regions.flat()));
+    });
+    return alignmentRef;
+}
+
+function getInstanceId(result: Alignment, index: 0|1 = 1): string {
+    const res = result.structures[index];
+    if("entry_id" in res && res.entry_id && res.selection && "asym_id" in res.selection)
+        return`${res.entry_id}.${res.selection.asym_id}`;
+    else if("name" in res && res.selection &&"asym_id" in res.selection)
+        return `${res.name}.${res.selection.asym_id}`;
+    throw new Error("Missing entry_id and name from result");
+}
+
+function transformToGapedDomain(regions: AlignmentRegion[]): (number|undefined)[] {
+    const out: (number|undefined)[]  = [];
+    let prevRegionEnd = 0;
+    regions.forEach(region=>{
+        const beg = region.beg_index+1;
+        const end = region.beg_index+region.length;
+        if(beg > (prevRegionEnd+1)){
+            const nGaps = beg - (prevRegionEnd+1);
+            out.push(...Array(nGaps).fill(undefined));
+        }
+        prevRegionEnd = end;
+        const seqBeg = region.beg_seq_id;
+        const seqEnd = region.beg_seq_id+region.length-1;
+        for(let i=seqBeg;i<=seqEnd;i++){
+            out.push(i);
+        }
+    });
+    return out;
+}
+
+async function getSequences(results: Alignment[]): Promise<InstanceSequenceInterface[]> {
+    const out: InstanceSequenceInterface[] = [];
+    const missingIds: string[] = [];
+    const res = results[0];
+    if(res.sequence_alignment?.[0].sequence) {
+        out.push( {
+            rcsbId: getInstanceId(res,0),
+            sequence: res.sequence_alignment[0].sequence
+        })
+    }else{
+        missingIds.push( getInstanceId(res, 0) )
+    }
+    results.forEach(res=>{
+        if(res.sequence_alignment?.[1].sequence) {
+            out.push( {
+                rcsbId: getInstanceId(res,1),
+                sequence: res.sequence_alignment[1].sequence
+            })
+        }else{
+            missingIds.push( getInstanceId(res) )
+        }
+    });
+    return  out.concat(await RcsbRequestContextManager.getInstanceSequences(missingIds));
+}
+
+const structuralAlignment: StructureAlignmentResponse = flexAlignment as StructureAlignmentResponse;
+
+export const dataProvider: RcsbModuleDataProviderInterface = {
+    alignments: {
+        collector: new RcsbStructuralAlignmentProvider(structuralAlignment),
+        context:{
+            queryId: "structural-alignment",
+            to: SequenceReference.PdbInstance
+        }
+    }
+};
+
+export const transformProvider = new RcsbStructuralTransformProvider(structuralAlignment);
+
+export const structureLocationProvider = new RcsbStructureLocationProvider(structuralAlignment);

src/examples/alignment-provider/providers/alignment-response.d.ts

@@ -0,0 +1,194 @@
+/* tslint:disable */
+/**
+ * This file was automatically generated by json-schema-to-typescript.
+ * DO NOT MODIFY IT BY HAND. Instead, modify the source JSONSchema file,
+ * and run json-schema-to-typescript to regenerate this file.
+ */
+
+export type StructureFileFormat = 'pdb' | 'mmcif';
+
+/**
+ * Container for structure alignment results
+ */
+export interface StructureAlignmentResponse {
+    info: ResponseInfo;
+    meta?: StructureAlignmentMetadata;
+    /**
+     * Stores of a set of alignment alternatives or solutions
+     */
+    results?: Alignment[];
+}
+/**
+ * Provides additional metadata about a job
+ */
+export interface ResponseInfo {
+    /**
+     * Unique job ID
+     */
+    uuid: string;
+    /**
+     * Indicates whether a job is successfully completed, in progress or resulted in error
+     */
+    status: 'RUNNING' | 'COMPLETE' | 'ERROR';
+    /**
+     * Provides additional information about the request
+     */
+    message?: string;
+}
+export interface StructureAlignmentMetadata {
+    alignment_mode: 'pairwise' | 'multiple';
+    alignment_method?: string;
+}
+/**
+ * Store the core information of a structure alignment
+ */
+export interface Alignment {
+    /**
+     * Identifies aligned structures
+     */
+    structures: (StructureEntry | StructureURL)[];
+    /**
+     * List of size K that holds structural alignment data, where K - number of blocks. Blocks divide the alignment into structurally equivalent parts. The division can be due to non-topological rearrangements (e.g. circular permutations) or due to flexible parts (e.g. domain or region swaps).
+     */
+    structure_alignment: StructureAlignmentBlock[];
+    /**
+     * List of size M that codifies sequence alignment, where M - the number of aligned structures
+     */
+    sequence_alignment?: SequenceAlignment[];
+    summary?: AlignmentSummary;
+}
+/**
+ * Structure available in the PDB archive
+ */
+export interface StructureEntry {
+    entry_id: string;
+    selection?: StructureInstanceSelection | StructureMotifSelection;
+}
+export interface StructureInstanceSelection {
+    /**
+     * Case sensitive chain ID (label_asym_id)
+     */
+    asym_id: string;
+    /**
+     * First residue number as it appears in the deposited sequences. In mmCIF terminology it corresponds to label_seq_id
+     */
+    beg_seq_id?: number;
+    /**
+     * Last residue number as it appears in the deposited sequences. In mmCIF terminology it corresponds to label_seq_id
+     */
+    end_seq_id?: number;
+}
+export interface StructureMotifSelection {
+    /**
+     * Collection of residue identifiers
+     */
+    residue_ids: ResidueIdentifier[];
+}
+export interface ResidueIdentifier {
+    /**
+     * Chain identifier of this residue. In mmCIF terminology it corresponds to label_asym_id
+     */
+    asym_id: string;
+    /**
+     * Identifier of the assembly generating operation that was used to determine the coordinates of this residue. Chaining of operations is expressed by '1stx2nd'.
+     */
+    struct_oper_id?: string;
+    /**
+     * Sequence identifier of this residue. In mmCIF terminology it corresponds to label_seq_id
+     */
+    seq_id: number;
+}
+/**
+ * Structure provided via web-link or via uploading the file content together with the query
+ */
+export interface StructureURL {
+    /**
+     * File will be fetched from the specified location
+     */
+    url: string;
+    format: StructureFileFormat;
+    is_binary: boolean;
+    name?: string;
+    selection?: StructureInstanceSelection | StructureMotifSelection;
+}
+/**
+ * Stores a sequential (reverse or forward) part of a structural alignment: aligned positions and 3D transformations
+ */
+export interface StructureAlignmentBlock {
+    /**
+     * List of size M that describes structurally equivalent residues, where M - the number of aligned structures
+     */
+    regions?: AlignmentRegion[][];
+    /**
+     * List of size M that holds block transformations, where M - the number of aligned structures. Each transformation is a 4x4 matrix in a column major (j * 4 + i indexing) format.
+     */
+    transformations: number[][];
+    summary?: AlignmentSummary;
+}
+export interface AlignmentRegion {
+    /**
+     * Chain ID assigned by the PDB (or selected by the author at the time of deposition)
+     */
+    asym_id: string;
+    /**
+     * PDB residue number of the alignment position (sequential number from 1-N to match residues as they appear in the deposited sequences)
+     */
+    beg_seq_id: number;
+    /**
+     * 0-based index of the alignment position in sequence alignment
+     */
+    beg_index: number;
+    length: number;
+}
+export interface AlignmentSummary {
+    scores?: {
+        /**
+         * Similarity score value
+         */
+        value?: number;
+        /**
+         * Similarity score type: RMSD: a simple root mean square deviation between the superposed residues; TM-score: template modeling score - topological similarity of structures; similarity-score: similarity score specific to the method; sequence-identity: the percent of residues in the alignment that are sequence-identical; sequence-similarity: the percent of residues in the alignment that are sequence-similar
+         */
+        type?: 'RMSD' | 'TM-score' | 'similarity-score' | 'sequence-similarity' | 'sequence-identity';
+    }[];
+    /**
+     * Number of residue (alpha carbon) pairs matched by the superposition
+     */
+    n_aln_residue_pairs?: number;
+    /**
+     * Number of residues with coordinates used for structure alignment
+     */
+    n_modeled_residues?: number[];
+    /**
+     * Sequence alignment length (including gaps)
+     */
+    seq_aln_len?: number;
+    /**
+     * Fraction of residues matched by the superposition (related by spacial proximity) relative to the total number of modeled residues being aligned
+     */
+    aln_coverage?: number[];
+}
+/**
+ * Codifies the alignment data a sequence of one-letter residue codes and the information on the chain and residue numbers for the aligned regions
+ */
+export interface SequenceAlignment {
+    /**
+     * A sequence of one-letter residue codes in the order they appear in the alignment (gap characters are permitted). Gaps that have been introduced into the sequences to make them align are indicated by the '-' character
+     */
+    sequence?: string;
+    regions: AlignmentRegion[];
+    /**
+     * List of empty regions (gaps) in the alignment sequence
+     */
+    gaps?: AlignmentGap[];
+}
+/**
+ * Defines the placement of introduced gaps in sequence alignment
+ */
+export interface AlignmentGap {
+    /**
+     * 0-based index of the alignment position in sequence alignment
+     */
+    beg_index: number;
+    length: number;
+}

src/examples/multiple-chain/index.tsx

@@ -20,7 +20,7 @@ import {
 } from "../../RcsbFvStructure/StructureViewerInterface";
 import {
     LoadMethod,
-    LoadMolstarInterface
+    LoadMolstarInterface, LoadMolstarReturnType
 } from "../../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {RcsbFvStateManager} from "../../RcsbFvState/RcsbFvStateManager";
@@ -84,7 +84,7 @@ const rowConfigChainB: Array<RcsbFvRowConfigInterface> = [
     }
 ];
 
-const fvConfigChainA: FeatureViewInterface<LoadMolstarInterface> = {
+const fvConfigChainA: FeatureViewInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     boardId:"1acb.A_board",
     boardConfig: {
         range: {
@@ -95,7 +95,7 @@ const fvConfigChainA: FeatureViewInterface<LoadMolstarInterface> = {
         includeAxis: true
     },
     rowConfig: rowConfigChainA,
-    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => {
+    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => {
         stateManager.selectionState.clearSelection("select", {modelId:"1acb_board", labelAsymId:"A"});
         plugin.clearSelection("select", {modelId: "1acb_board", labelAsymId: "A"})
         if(sequenceRegion.length > 0) {
@@ -114,11 +114,11 @@ const fvConfigChainA: FeatureViewInterface<LoadMolstarInterface> = {
             plugin.resetCamera();
         }
     },
-    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
+    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
         if(d!=null)
             plugin.cameraFocus("1acb_board", "A", d.begin, d.end ?? d.begin);
     },
-    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
+    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
         if(elements == null || elements.length == 0)
             plugin.clearSelection("hover");
         else
@@ -129,7 +129,7 @@ const fvConfigChainA: FeatureViewInterface<LoadMolstarInterface> = {
                 end: e.end ?? e.begin
             })), "hover", "set");
     },
-    structureSelectionCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
+    structureSelectionCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("1acb_board", "A", "select");
         if(sel == null) {
             pfv.clearSelection("select");
@@ -138,7 +138,7 @@ const fvConfigChainA: FeatureViewInterface<LoadMolstarInterface> = {
             pfv.setSelection({elements: sel.regions, mode: "select"});
         }
     },
-    structureHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
+    structureHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("1acb_board", "A", "hover");
         if(sel == null)
             pfv.clearSelection("hover");
@@ -147,7 +147,7 @@ const fvConfigChainA: FeatureViewInterface<LoadMolstarInterface> = {
     }
 }
 
-const fvConfigChainB: FeatureViewInterface<LoadMolstarInterface> = {
+const fvConfigChainB: FeatureViewInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     boardId:"1acb.B_board",
     boardConfig: {
         range: {
@@ -158,7 +158,7 @@ const fvConfigChainB: FeatureViewInterface<LoadMolstarInterface> = {
         includeAxis: true
     },
     rowConfig: rowConfigChainB,
-    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => {
+    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => {
         stateManager.selectionState.clearSelection("select", {modelId:"1acb_board", labelAsymId:"B"});
         plugin.clearSelection("select", {modelId: "1acb_board", labelAsymId: "B"})
         if(sequenceRegion.length > 0) {
@@ -177,11 +177,11 @@ const fvConfigChainB: FeatureViewInterface<LoadMolstarInterface> = {
             plugin.resetCamera();
         }
     },
-    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
+    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
         if(d!=null)
             plugin.cameraFocus("1acb_board", "B", d.begin, d.end ?? d.begin);
     },
-    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
+    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
         if(elements == null || elements.length == 0)
             plugin.clearSelection("hover");
         else
@@ -192,7 +192,7 @@ const fvConfigChainB: FeatureViewInterface<LoadMolstarInterface> = {
                 end: e.end ?? e.begin
             })), "hover", "set");
     },
-    structureSelectionCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
+    structureSelectionCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("1acb_board", "B", "select");
         if(sel == null) {
             pfv.clearSelection("select");
@@ -201,7 +201,7 @@ const fvConfigChainB: FeatureViewInterface<LoadMolstarInterface> = {
             pfv.setSelection({elements: sel.regions, mode: "select"});
         }
     },
-    structureHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
+    structureHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("1acb_board", "B", "hover");
         if(sel == null)
             pfv.clearSelection("hover");
@@ -210,12 +210,12 @@ const fvConfigChainB: FeatureViewInterface<LoadMolstarInterface> = {
     }
 }
 
-const blockChainA: FeatureBlockInterface<LoadMolstarInterface> = {
+const blockChainA: FeatureBlockInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     blockId:"chainA",
     featureViewConfig: [fvConfigChainA]
 };
 
-const blockChainB: FeatureBlockInterface<LoadMolstarInterface> = {
+const blockChainB: FeatureBlockInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     blockId:"chainB",
     featureViewConfig: [fvConfigChainB]
 };
@@ -233,7 +233,7 @@ const blockSelectorElement: (blockSelectorManager: BlockSelectorManager) => JSX.
     );
 }
 
-const customConfig: CustomViewInterface<LoadMolstarInterface> = {
+const customConfig: CustomViewInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     blockConfig:[blockChainA, blockChainB],
     blockSelectorElement: blockSelectorElement
 }
@@ -244,7 +244,7 @@ const sequenceConfig = {
     config: customConfig
 };
 
-const molstarConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface,{viewerProps:Partial<ViewerProps>}> = {
+const molstarConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface<undefined,undefined>,{viewerProps:Partial<ViewerProps>}> = {
     loadConfig: {
         loadMethod: LoadMethod.loadPdbId,
         loadParams: {

src/examples/single-chain/index.ts

@@ -20,7 +20,7 @@ import {
 } from "../../RcsbFvStructure/StructureViewerInterface";
 import {
     LoadMethod,
-    LoadMolstarInterface
+    LoadMolstarInterface, LoadMolstarReturnType
 } from "../../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {RcsbFvStateManager} from "../../RcsbFvState/RcsbFvStateManager";
@@ -53,7 +53,7 @@ const rowConfig: Array<RcsbFvRowConfigInterface> = [
     }
 ];
 
-const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
+const fvConfig: FeatureViewInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     boardId:"1ash_board",
     boardConfig: {
         range: {
@@ -64,7 +64,7 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
         includeAxis: true
     },
     rowConfig: rowConfig,
-    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => {
+    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => {
         stateManager.selectionState.clearSelection("select", {modelId:"1ash_model", labelAsymId:"A"});
         if(sequenceRegion.length > 0) {
             const regions = sequenceRegion.map(r => ({
@@ -83,11 +83,11 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
             plugin.resetCamera();
         }
     },
-    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
+    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
         if(d!=null)
             plugin.cameraFocus("1ash_model", "A", d.begin, d.end ?? d.begin);
     },
-    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
+    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
         if(elements == null || elements.length == 0)
             plugin.clearSelection("hover");
         else
@@ -98,7 +98,7 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
                 end: e.end ?? e.begin
             })), "hover", "set");
     },
-    structureSelectionCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
+    structureSelectionCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("1ash_model", "A", "select");
         if(sel == null) {
             pfv.clearSelection("select");
@@ -107,7 +107,7 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
             pfv.setSelection({elements: sel.regions, mode: "select"});
         }
     },
-    structureHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
+    structureHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("1ash_model", "A", "hover");
         if(sel == null)
             pfv.clearSelection("hover");
@@ -116,12 +116,12 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
     }
 }
 
-const block: FeatureBlockInterface<LoadMolstarInterface> = {
+const block: FeatureBlockInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     blockId:"MyBlock_1",
     featureViewConfig: [fvConfig]
 };
 
-const customConfig: CustomViewInterface<LoadMolstarInterface> = {
+const customConfig: CustomViewInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     blockConfig:[block]
 }
 
@@ -131,7 +131,7 @@ const sequenceConfig = {
     config: customConfig
 };
 
-const molstarConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface,{viewerProps:Partial<ViewerProps>}> = {
+const molstarConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface<undefined,undefined>,{viewerProps:Partial<ViewerProps>}> = {
     loadConfig: {
         loadMethod: LoadMethod.loadPdbId,
         loadParams: {

src/examples/structural-alignment/index.ts

@@ -17,7 +17,7 @@ import {AlignmentManager} from "./AlignmentManager";
 import {Mat4} from "molstar/lib/mol-math/linear-algebra";
 import {
     LoadMethod,
-    LoadMolstarInterface
+    LoadMolstarInterface, LoadMolstarReturnType
 } from "../../RcsbFvStructure/StructureViewers/MolstarViewer/MolstarActionManager";
 import {ViewerProps} from "@rcsb/rcsb-molstar/build/src/viewer";
 import {RcsbFvStateManager} from "../../RcsbFvState/RcsbFvStateManager";
@@ -97,7 +97,7 @@ const rowConfig: Array<RcsbFvRowConfigInterface> = [
     }
 ];
 
-const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
+const fvConfig: FeatureViewInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     boardId:"1ash_board",
     boardConfig: {
         range: {
@@ -110,7 +110,7 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
         includeAxis: true
     },
     rowConfig: rowConfig,
-    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => {
+    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => {
         stateManager.selectionState.clearSelection("select", {modelId:"1ash_model", labelAsymId:"A"});
         stateManager.selectionState.clearSelection("select", {modelId:"101m_model", labelAsymId:"A"});
         if(sequenceRegion.length > 0) {
@@ -137,7 +137,7 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
             plugin.resetCamera();
         }
     },
-    sequenceElementClickCallback: async (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
+    sequenceElementClickCallback: async (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, d: RcsbFvTrackDataElementInterface) => {
         plugin.removeComponent("1ash_component");
         plugin.removeComponent("101m_component");
         if(d.begin === d.end || !d.end){
@@ -145,7 +145,7 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
             await plugin.createComponent("101m_component", "101m_model", "A", alignmentManager.getTargetPosition(d.begin)!, alignmentManager.getTargetPosition(d.begin)!, "ball-and-stick");
         }
     },
-    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
+    sequenceHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, stateManager: RcsbFvStateManager, elements: Array<RcsbFvTrackDataElementInterface>) => {
         if (elements == null || elements.length == 0){
             plugin.clearSelection("hover");
         }else {
@@ -165,7 +165,7 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
                 ), "hover", "set");
         }
     },
-    structureSelectionCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
+    structureSelectionCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel_1ash: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("1ash_model", "A", "select");
         const sel_101m: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("101m_model", "A", "select");
         pfv.clearSelection("select");
@@ -182,7 +182,7 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
                     })), mode: "select"});
         }
     },
-    structureHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
+    structureHoverCallback: (plugin: StructureViewerPublicInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType>, pfv: RcsbFv, stateManager: RcsbFvStateManager) => {
         const sel_1ash: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("1ash_model", "A", "hover");
         const sel_101m: SaguaroRegionList | undefined = stateManager.selectionState.getSelectionWithCondition("101m_model", "A", "hover");
         if(sel_1ash == null && sel_101m == null)
@@ -198,12 +198,12 @@ const fvConfig: FeatureViewInterface<LoadMolstarInterface> = {
     }
 }
 
-const block: FeatureBlockInterface<LoadMolstarInterface> = {
+const block: FeatureBlockInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     blockId:"MyBlock_1",
     featureViewConfig: [fvConfig]
 };
 
-const customConfig: CustomViewInterface<LoadMolstarInterface> = {
+const customConfig: CustomViewInterface<LoadMolstarInterface<undefined,undefined>,LoadMolstarReturnType> = {
     blockConfig:[block]
 }
 
@@ -213,7 +213,7 @@ const sequenceConfig = {
     config: customConfig
 };
 
-const molstarConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface,{viewerProps:Partial<ViewerProps>}> = {
+const molstarConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface<undefined,undefined>,{viewerProps:Partial<ViewerProps>}> = {
     loadConfig: [{
         loadMethod: LoadMethod.loadPdbId,
         loadParams: {

tsconfig.json

@@ -9,9 +9,11 @@
     "allowJs": true,
     "declaration": true,
     "sourceMap": true,
+    //"noUnusedLocals": true,
     "strictNullChecks": true,
     "declarationDir": "./build/dist",
-    "esModuleInterop": true
+    "esModuleInterop": true,
+    "skipLibCheck": true
   },
   "include": [ "src/*", "src/**/*", "src/**/**/*", "src/**/**/**/*" ],
   "exclude": [

webpack.server.dev.config.js

@@ -39,7 +39,7 @@ const commonConfig = {
     devtool: 'source-map'
 };
 
-const examples = ['assembly','uniprot','structural-alignment','sequence-identity','single-chain','multiple-chain'];
+const examples = ['assembly','uniprot','structural-alignment','sequence-identity','single-chain','multiple-chain','alignment-provider'];
 const entries = examples.reduce((prev,current)=>{
         prev[current]= fs.existsSync(`./src/examples/${current}/index.ts`) ? `./src/examples/${current}/index.ts` : `./src/examples/${current}/index.tsx`;
         return prev;