@rcsb/rcsb-saguaro-app/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.js

RCSB 1D Saguaro Web App

import { __awaiter } from "tslib";
import { AnnotationCollector } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollector";
import { ComponentsManager } from "../RcsbFvComponents/ComponentsManager";
import { SingletonMap } from "../../RcsbUtils/Helpers/SingletonMap";
import { AlignmentCollector } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollector";
import { AlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
import { SequenceTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory";
import { AlignmentBlockFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory";
import { AnnotationsBlockFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory";
import { AnnotationsTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory";
import * as acm from "../../RcsbAnnotationConfig/RcsbAnnotationConfig.ac.json";
import { AnnotationBlockManager } from "../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager";
import { RcsbAnnotationConfig } from "../../RcsbAnnotationConfig/RcsbAnnotationConfig";
import { AnnotationTrackManagerFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
export class RcsbFvAbstractModule {
    constructor(elementId, rcsbFv) {
        this.boardConfigData = {
            length: 0
        };
        this.rowConfigData = new Array();
        this.alignmentCollector = new AlignmentCollector();
        this.annotationCollector = new AnnotationCollector();
        this.alignmentTracks = [];
        this.annotationTracks = [];
        this.activeDisplayFlag = false;
        this.rcsbFv = rcsbFv;
        this.elementId = elementId;
        ComponentsManager.buildLoaderSpinner(elementId);
    }
    setPolymerEntityInstanceTranslator(polymerEntityInstance) {
        this.polymerEntityInstance = polymerEntityInstance;
    }
    getPolymerEntityInstanceTranslator() {
        return this.polymerEntityInstance;
    }
    display() {
        return __awaiter(this, void 0, void 0, function* () {
            console.info(`Starting display ${this.elementId}`);
            yield this.rcsbFv.updateBoardConfig({
                boardConfigData: yield this.getBoardConfig(),
                rowConfigData: []
            });
            ComponentsManager.unmountLoaderSpinner(this.elementId);
            console.info(`Rendering tracks ${this.elementId}`);
            this.rcsbFvRowUpdatePromise = this.rcsbFv.updateBoardConfig({
                rowConfigData: yield this.getRowsConfig()
            });
            this.activeDisplayFlag = true;
            return void 0;
        });
    }
    activeDisplay() {
        return this.activeDisplayFlag;
    }
    getFv() {
        return this.rcsbFv;
    }
    getTargets() {
        return __awaiter(this, void 0, void 0, function* () {
            return yield this.alignmentCollector.getTargets();
        });
    }
    getAlignmentResponse() {
        return __awaiter(this, void 0, void 0, function* () {
            return yield this.alignmentCollector.getAlignment();
        });
    }
    getFeatures() {
        return __awaiter(this, void 0, void 0, function* () {
            //return (await this.annotationCollector.getAnnotationFeatures()).map(af=>af.features).flat();
            return yield this.annotationCollector.getFeatures();
        });
    }
    getAnnotationConfigData() {
        return __awaiter(this, void 0, void 0, function* () {
            return this.annotationTracks;
        });
    }
    build(buildConfig) {
        return __awaiter(this, void 0, void 0, function* () {
            SingletonMap.update(this.elementId, this);
            this.buildConfig = buildConfig;
            yield this.protectedBuild();
            yield this.buildExternalTracks();
            this.concatAlignmentAndAnnotationTracks();
            yield this.display();
            return void 0;
        });
    }
    wait() {
        return this.rcsbFvRowUpdatePromise;
    }
    buildAlignmentTracks(alignmentRequestContext, alignmentResponse, trackFactories) {
        return __awaiter(this, void 0, void 0, function* () {
            var _a, _b, _c, _d;
            const sequenceTrackFactory = (_a = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.sequenceTrackFactory) !== null && _a !== void 0 ? _a : new SequenceTrackFactory(this.getPolymerEntityInstanceTranslator());
            if (alignmentResponse.query_sequence)
                this.referenceTrack = yield sequenceTrackFactory.getTrack(alignmentRequestContext, alignmentResponse.query_sequence);
            const alignmentBlockFactory = new AlignmentBlockFactory((_b = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.alignmentTrackFactory) !== null && _b !== void 0 ? _b : new AlignmentTrackFactory(this.getPolymerEntityInstanceTranslator()), (_d = (_c = this.buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.trackConfigModifier) === null || _d === void 0 ? void 0 : _d.alignment);
            this.alignmentTracks = yield alignmentBlockFactory.getBlock(alignmentRequestContext, alignmentResponse);
        });
    }
    buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap) {
        return __awaiter(this, void 0, void 0, function* () {
            var _a, _b;
            const defaultAnnotationConfigMap = annotationConfigMap !== null && annotationConfigMap !== void 0 ? annotationConfigMap : acm;
            const annotationsBlockFactory = new AnnotationsBlockFactory(new AnnotationBlockManager(new AnnotationTrackManagerFactory(), new RcsbAnnotationConfig(defaultAnnotationConfigMap), this.getPolymerEntityInstanceTranslator()), new AnnotationsTrackFactory(), (_b = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.trackConfigModifier) === null || _b === void 0 ? void 0 : _b.annotations);
            this.annotationTracks = yield annotationsBlockFactory.getBlock(annotationsRequestContext, annotationsFeatures);
        });
    }
    getBoardConfig() {
        return __awaiter(this, void 0, void 0, function* () {
            return this.boardConfigData;
        });
    }
    getRowsConfig() {
        return __awaiter(this, void 0, void 0, function* () {
            return this.rowConfigData;
        });
    }
    buildExternalTracks() {
        return __awaiter(this, void 0, void 0, function* () {
            var _a, _b;
            const externalTrackBuilder = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder;
            const rcsbContext = (_b = this.buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.rcsbContext;
            if (!externalTrackBuilder)
                return;
            if (typeof externalTrackBuilder.processAlignmentAndFeatures === "function")
                yield externalTrackBuilder.processAlignmentAndFeatures({
                    annotations: yield this.annotationCollector.getAnnotationFeatures(),
                    alignments: yield this.alignmentCollector.getAlignment(),
                    rcsbContext: rcsbContext
                });
            if (typeof externalTrackBuilder.addTo === "function")
                yield externalTrackBuilder.addTo({
                    alignmentTracks: this.alignmentTracks,
                    annotationTracks: this.annotationTracks,
                    rcsbContext: rcsbContext
                });
            return void 0;
        });
    }
}
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