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@@ -22,8 +22,8 @@ import {
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} from "molstar/lib/mol-model/structure";
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import {OrderedSet} from "molstar/lib/mol-data/int";
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import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin-state/objects';
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-import {State} from "molstar/lib/mol-state";
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-import {StructureRef} from "molstar/lib/mol-plugin-state/manager/structure/hierarchy-state";
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+import {State, StateObject} from "molstar/lib/mol-state";
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+import {StructureComponentRef, StructureRef} from "molstar/lib/mol-plugin-state/manager/structure/hierarchy-state";
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import {RcsbFvSelection, ResidueSelectionInterface} from "../../RcsbFvSelection/RcsbFvSelection";
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import {AbstractPlugin} from "./AbstractPlugin";
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import {Subscription} from "rxjs";
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@@ -33,6 +33,7 @@ import {MolScriptBuilder} from "molstar/lib/mol-script/language/builder";
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import {SetUtils} from "molstar/lib/mol-util/set";
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import {StructureRepresentationRegistry} from "molstar/lib/mol-repr/structure/registry";
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import {ColorTheme} from "molstar/lib/mol-theme/color";
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+import {StateObjectCell} from "molstar/lib/mol-state/object";
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export enum LoadMethod {
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loadPdbId = "loadPdbId",
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@@ -60,7 +61,7 @@ interface LoadParams {
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}
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export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterface {
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- private plugin: Viewer;
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+ private viewer: Viewer;
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private innerSelectionFlag: boolean = false;
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private loadingFlag: boolean = false;
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private selectCallbackSubs: Subscription;
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@@ -75,12 +76,11 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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public init(target: string | HTMLElement, props?: Partial<ViewerProps>) {
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- this.plugin = new Viewer(target, {layoutShowControls:false, layoutShowSequence: true, ...props});
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- this.plugin.getPlugin().representation.structure.registry
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+ this.viewer = new Viewer(target, {layoutShowControls:false, layoutShowSequence: true, ...props});
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}
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public clear(): void{
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- this.plugin.clear();
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+ this.viewer.clear();
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}
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async load(loadConfig: LoadMolstarInterface): Promise<void>{
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@@ -88,24 +88,24 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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if(MolstarPlugin.checkLoadData(loadConfig)) {
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if (loadConfig.method == LoadMethod.loadPdbId) {
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const config: LoadParams = loadConfig.params as LoadParams;
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- await this.plugin.loadPdbId(config.pdbId!, config.props, config.matrix);
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+ await this.viewer.loadPdbId(config.pdbId!, config.props, config.matrix);
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} else if (loadConfig.method == LoadMethod.loadPdbIds) {
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const config: Array<LoadParams> = loadConfig.params as Array<LoadParams>;
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- await this.plugin.loadPdbIds(config.map((d) => {
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+ await this.viewer.loadPdbIds(config.map((d) => {
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return {pdbId: d.pdbId!, props: d.props, matrix: d.matrix}
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}));
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} else if (loadConfig.method == LoadMethod.loadStructureFromUrl) {
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const config: LoadParams = loadConfig.params as LoadParams;
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- await this.plugin.loadStructureFromUrl(config.url!, config.format!, config.isBinary!);
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+ await this.viewer.loadStructureFromUrl(config.url!, config.format!, config.isBinary!);
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} else if (loadConfig.method == LoadMethod.loadSnapshotFromUrl) {
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const config: LoadParams = loadConfig.params as LoadParams;
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- await this.plugin.loadSnapshotFromUrl(config.url!, config.type!);
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+ await this.viewer.loadSnapshotFromUrl(config.url!, config.type!);
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} else if (loadConfig.method == LoadMethod.loadStructureFromData) {
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const config: LoadParams = loadConfig.params as LoadParams;
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- await this.plugin.loadStructureFromData(config.data!, config.format!, config.isBinary!);
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+ await this.viewer.loadStructureFromData(config.data!, config.format!, config.isBinary!);
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}
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}
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- this.plugin.getPlugin().selectionMode = true;
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+ this.viewer.plugin.selectionMode = true;
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this.loadingFlag = false;
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this.mapModels(loadConfig.params);
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this.modelChangeCallback(this.getChains());
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@@ -156,40 +156,41 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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if(mode == null || mode === 'select') {
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this.innerSelectionFlag = true;
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}
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- this.plugin.select(this.getModelId(modelId), asymId, begin, end, mode, operation);
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+ this.viewer.select({modelId:this.getModelId(modelId), label_asym_id: asymId, label_seq_range:{beg: begin, end:end}}, mode,operation);
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this.innerSelectionFlag = false;
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}
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private selectSet(selection: Array<{modelId:string; asymId: string; position: number;}>, mode: 'select'|'hover', operation:'add'|'set'): void {
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if(mode == null || mode === 'select') {
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this.innerSelectionFlag = true;
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}
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- this.plugin.select(selection.map(r=>{return{modelId: this.getModelId(r.modelId), position:r.position, asymId: r.asymId}}), mode, operation);
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+ this.viewer.select(selection.map(r=>({modelId: this.getModelId(r.modelId), label_seq_id:r.position, label_asym_id: r.asymId})), mode, operation);
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this.innerSelectionFlag = false;
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}
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private selectMultipleRanges(selection: Array<{modelId:string; asymId: string; begin: number; end:number;}>, mode: 'select'|'hover', operation:'add'|'set'): void {
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if(mode == null || mode === 'select') {
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this.innerSelectionFlag = true;
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}
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- this.plugin.select(selection.map(r=>{return{modelId: this.getModelId(r.modelId), begin:r.begin, end: r.end, asymId: r.asymId}}), mode, operation);
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+ this.viewer.select(selection.map(r=>({modelId: this.getModelId(r.modelId), label_asym_id: r.asymId, label_seq_range:{beg:r.begin, end: r.end}})), mode, operation);
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this.innerSelectionFlag = false;
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}
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+
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public clearSelection(mode:'select'|'hover', option?:{modelId:string; labelAsymId:string;}): void {
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if(mode === 'select') {
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- this.plugin.clearFocus();
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+ this.viewer.clearFocus();
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this.innerSelectionFlag = true;
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}
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if(option != null)
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- this.plugin.clearSelection(mode, {modelId: this.getModelId(option.modelId), labelAsymId: option.labelAsymId});
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+ this.viewer.clearSelection(mode, {modelId: this.getModelId(option.modelId), label_asym_id: option.labelAsymId});
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else
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- this.plugin.clearSelection(mode);
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+ this.viewer.clearSelection(mode);
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this.innerSelectionFlag = false;
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}
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public setFocus(modelId: string, asymId: string, begin: number, end: number): void{
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- this.plugin.setFocus(this.getModelId(modelId), asymId, begin, end);
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+ this.viewer.setFocus({modelId: this.getModelId(modelId), label_asym_id: asymId, label_seq_range:{beg:begin, end: end}});
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}
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public clearFocus(): void {
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- this.plugin.clearFocus();
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+ this.viewer.clearFocus();
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}
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public cameraFocus(modelId: string, asymId: string, positions:Array<number>): void;
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@@ -202,7 +203,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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}
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private focusPositions(modelId: string, asymId: string, positions:Array<number>): void{
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- const data: Structure | undefined = getStructureWithModelId(this.plugin.getPlugin().managers.structure.hierarchy.current.structures, this.getModelId(modelId));
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+ const data: Structure | undefined = getStructureWithModelId(this.viewer.plugin.managers.structure.hierarchy.current.structures, this.getModelId(modelId));
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if (data == null) return;
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const sel: StructureSelection = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
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'chain-test': Q.core.rel.eq([asymId, MolScriptBuilder.ammp('label_asym_id')]),
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@@ -210,9 +211,9 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}), data);
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const loci: Loci = StructureSelection.toLociWithSourceUnits(sel);
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if(!StructureElement.Loci.isEmpty(loci))
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- this.plugin.getPlugin().managers.camera.focusLoci(loci);
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+ this.viewer.plugin.managers.camera.focusLoci(loci);
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else
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- this.plugin.getPlugin().managers.camera.reset();
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+ this.viewer.plugin.managers.camera.reset();
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}
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private focusRange(modelId: string, asymId: string, begin: number, end: number): void{
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const seqIds: Array<number> = new Array<number>();
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@@ -230,14 +231,24 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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this.removeComponent(args[0]);
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this.componentVisibility.set(args[0], true);
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this.componentSet.add(args[0]);
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- if(args.length === 4)
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- await this.plugin.createComponent(args[0], this.getModelId(args[1]), args[2], args[3]);
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- else if(args.length === 6)
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- await this.plugin.createComponent(args[0], this.getModelId(args[1]), args[2], args[3], args[4], args[5]);
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+ if(args.length === 4){
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+ if( args[2] instanceof Array && args[2].length > 0 ) {
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+ if(typeof args[2][0].position === "number"){
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+ await this.viewer.createComponent(args[0], args[2].map(r=>({modelId: this.getModelId(args[1]), label_asym_id: r.asymId, label_seq_id: r.position})), args[3]);
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+ }else{
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+ await this.viewer.createComponent(args[0], args[2].map(r=>({modelId: this.getModelId(args[1]), label_asym_id: r.asymId, label_seq_range:{beg:r.begin, end: r.end}})), args[3]);
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+ }
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+ }else{
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+ await this.viewer.createComponent(args[0], {modelId: this.getModelId(args[1]), label_asym_id:args[2]}, args[3]);
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+ }
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+ }
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+ else if(args.length === 6){
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+ await this.viewer.createComponent(args[0], {modelId: this.getModelId(args[1]), label_asym_id: args[2], label_seq_range:{beg:args[3], end:args[4]}}, args[5]);
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+ }
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}
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public isComponent(componentLabel: string): boolean{
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- for(const c of this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups){
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+ for(const c of this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups){
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for(const comp of c){
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if(comp.cell.obj?.label === componentLabel) {
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return true;
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@@ -248,10 +259,10 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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public async colorComponent(componentLabel: string, color: ColorTheme.BuiltIn): Promise<void>{
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- for(const c of this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups){
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+ for(const c of this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups){
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for(const comp of c){
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if(comp.cell.obj?.label === componentLabel) {
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- await this.plugin.getPlugin().managers.structure.component.updateRepresentationsTheme([comp], { color: color });
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+ await this.viewer.plugin.managers.structure.component.updateRepresentationsTheme([comp], { color: color });
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return;
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}
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}
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@@ -260,7 +271,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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public getComponentSet(): Set<string>{
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const out: Set<string> = new Set<string>();
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- this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups.forEach(c=>{
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+ this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups.forEach((c)=>{
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for(const comp of c){
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if(comp.cell.obj?.label != null && out.has(comp.cell.obj?.label)) {
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break;
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@@ -275,12 +286,12 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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public removeComponent(componentLabel?: string): void{
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if(componentLabel == null){
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this.componentSet.forEach(id=>{
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- this.plugin.removeComponent(id);
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+ this.viewer.removeComponent(id);
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})
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this.componentSet.clear();
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this.componentVisibility.clear();
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}else{
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- this.plugin.removeComponent(componentLabel);
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+ this.viewer.removeComponent(componentLabel);
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this.componentSet.delete(componentLabel);
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this.componentVisibility.delete(componentLabel);
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}
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@@ -298,11 +309,11 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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if(this.isComponent(componentLabel) && !this.componentVisibility.has(componentLabel))
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this.componentVisibility.set(componentLabel, true);
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if(this.componentVisibility.get(componentLabel) != visibilityFlag) {
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- for (const c of this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups) {
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+ for (const c of this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups) {
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for (const comp of c) {
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if (comp.cell.obj?.label === componentLabel) {
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if(this.getComponentDisplay(componentLabel) != visibilityFlag)
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- this.plugin.getPlugin().managers.structure.component.toggleVisibility([comp]);
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+ this.viewer.plugin.managers.structure.component.toggleVisibility([comp]);
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return void 0;
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}
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}
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@@ -310,7 +321,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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}
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private getComponentDisplay(componentLabel: string): boolean{
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- for (const c of this.plugin.getPlugin().managers.structure.hierarchy.currentComponentGroups) {
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+ for (const c of this.viewer.plugin.managers.structure.hierarchy.currentComponentGroups) {
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for (const comp of c) {
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if (comp.cell.obj?.label === componentLabel) {
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return this.componentVisibility.get(componentLabel) ?? false;
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@@ -321,7 +332,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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public setRepresentationChangeCallback(g:()=>void){
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- this.plugin.getPlugin().state.events.cell.stateUpdated.subscribe(o=>{
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+ this.viewer.plugin.state.events.cell.stateUpdated.subscribe((o)=>{
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if(o.cell.obj?.type.name === "Structure" && this.componentSet.has(o.cell.obj?.label)){
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if(o.cell.state.isHidden != null) {
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this.componentVisibility.set(o.cell.obj?.label, !o.cell.state.isHidden);
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@@ -331,9 +342,9 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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public setHoverCallback(g:()=>void){
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- this.plugin.getPlugin().behaviors.interaction.hover.subscribe((r: InteractivityManager.HoverEvent)=>{
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+ this.viewer.plugin.behaviors.interaction.hover.subscribe((r)=>{
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const sequenceData: Array<ResidueSelectionInterface> = new Array<ResidueSelectionInterface>();
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- const loci: Loci = r.current.loci;
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+ const loci:Loci = r.current.loci;
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if(StructureElement.Loci.is(loci)){
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const loc = StructureElement.Location.create(loci.structure);
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for (const e of loci.elements) {
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@@ -357,12 +368,12 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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public setSelectCallback(g:(flag?:boolean)=>void){
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- this.selectCallbackSubs = this.plugin.getPlugin().managers.structure.selection.events.changed.subscribe(()=>{
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+ this.selectCallbackSubs = this.viewer.plugin.managers.structure.selection.events.changed.subscribe(()=>{
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if(this.innerSelectionFlag) {
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return;
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}
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- if(this.plugin.getPlugin().managers.structure.selection.additionsHistory.length > 0) {
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- const currentLoci: Loci = this.plugin.getPlugin().managers.structure.selection.additionsHistory[0].loci;
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+ if(this.viewer.plugin.managers.structure.selection.additionsHistory.length > 0) {
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+ const currentLoci: Loci = this.viewer.plugin.managers.structure.selection.additionsHistory[0].loci;
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const loc: StructureElement.Location = StructureElement.Location.create(currentLoci.structure);
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StructureElement.Location.set(
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loc,
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@@ -387,7 +398,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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this.innerSelectionFlag = true;
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const sel: StructureSelection = StructureQuery.run(query, currentLoci.structure);
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const surroundingsLoci: Loci = StructureSelection.toLociWithSourceUnits(sel);
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- this.plugin.getPlugin().managers.structure.selection.fromLoci('add', surroundingsLoci);
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+ this.viewer.plugin.managers.structure.selection.fromLoci('add', surroundingsLoci);
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const surroundingsLoc = StructureElement.Location.create(surroundingsLoci.structure);
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for (const e of surroundingsLoci.elements) {
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StructureElement.Location.set(surroundingsLoc, surroundingsLoci.structure, e.unit, e.unit.elements[0]);
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@@ -415,10 +426,10 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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this.selection.setLastSelection('select', null);
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}
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const sequenceData: Array<ResidueSelectionInterface> = new Array<ResidueSelectionInterface>();
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- for(const structure of this.plugin.getPlugin().managers.structure.hierarchy.current.structures){
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+ for(const structure of this.viewer.plugin.managers.structure.hierarchy.current.structures){
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const data: Structure | undefined = structure.cell.obj?.data;
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if(data == null) return;
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- const loci: Loci = this.plugin.getPlugin().managers.structure.selection.getLoci(data);
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+ const loci: Loci = this.viewer.plugin.managers.structure.selection.getLoci(data);
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if(StructureElement.Loci.is(loci)){
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const loc = StructureElement.Location.create(loci.structure);
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for (const e of loci.elements) {
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@@ -443,12 +454,12 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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public pluginCall(f: (plugin: PluginContext) => void){
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- this.plugin.pluginCall(f);
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+ this.viewer.pluginCall(f);
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}
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public setModelChangeCallback(f:(modelMap:SaguaroPluginModelMapType)=>void){
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this.modelChangeCallback = f;
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- this.modelChangeCallbackSubs = this.plugin.getPlugin().state.events.object.updated.subscribe((o)=>{
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+ this.modelChangeCallbackSubs = this.viewer.plugin.state.events.object.updated.subscribe((o:{obj: StateObject, action: "in-place" | "recreate"})=>{
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if(this.loadingFlag)
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return;
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if(o.obj.type.name === "Behavior" && o.action === "in-place") {
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@@ -460,10 +471,10 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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private getChains(): SaguaroPluginModelMapType{
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- const structureRefList = getStructureOptions(this.plugin.getPlugin());
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+ const structureRefList = getStructureOptions(this.viewer.plugin);
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const out: SaguaroPluginModelMapType = new Map<string, {entryId: string; chains: Array<{label:string;auth:string;entityId:string;title:string;type:ChainType;}>}>();
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structureRefList.forEach((structureRef,i)=>{
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- const structure = getStructure(structureRef[0], this.plugin.getPlugin().state.data);
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+ const structure = getStructure(structureRef[0], this.viewer.plugin.state.data);
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let modelEntityId = getModelEntityOptions(structure)[0][0];
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const chains: [{modelId:string;entryId:string},{auth:string;label:string;entityId:string;title:string;type:ChainType;}[]] = getChainValues(structure, modelEntityId);
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out.set(this.getModelId(chains[0].modelId),{entryId:chains[0].entryId, chains: chains[1]});
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@@ -473,9 +484,9 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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private mapModels(loadParams: LoadParams | Array<LoadParams>): void{
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const loadParamList: Array<LoadParams> = loadParams instanceof Array ? loadParams : [loadParams];
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- const structureRefList = getStructureOptions(this.plugin.getPlugin());
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+ const structureRefList = getStructureOptions(this.viewer.plugin);
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structureRefList.forEach((structureRef,i)=>{
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- const structure = getStructure(structureRef[0], this.plugin.getPlugin().state.data);
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+ const structure = getStructure(structureRef[0], this.viewer.plugin.state.data);
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let modelEntityId = getModelEntityOptions(structure)[0][0];
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const chains: [{modelId:string, entryId:string},{auth:string,label:string;entityId:string;title:string;type:ChainType;}[]] = getChainValues(structure, modelEntityId);
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this.modelMap.set(chains[0].modelId,loadParamList[i].id);
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@@ -494,7 +505,7 @@ export class MolstarPlugin extends AbstractPlugin implements SaguaroPluginInterf
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}
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public resetCamera(): void {
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- this.plugin.getPlugin().managers.camera.reset();
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+ this.viewer.plugin.managers.camera.reset();
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}
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}
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bioinsilico