@rcsb/rcsb-saguaro-app/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory.js

RCSB 1D Saguaro Web App

import { __awaiter } from "tslib";
import { SequenceReference } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
import { SequenceTrackTitleFactory } from "../TrackTitleFactoryImpl/SequenceTrackTitleFactory";
import { TrackUtils } from "./Helper/TrackUtils";
import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
var assertDefined = Assertions.assertDefined;
import { TagDelimiter } from "@rcsb/rcsb-api-tools/lib/RcsbUtils/TagDelimiter";
export class SequenceTrackFactory {
    constructor(entityInstanceTranslator, trackTitleFactory) {
        this.entityInstanceTranslator = undefined;
        this.entityInstanceTranslator = entityInstanceTranslator;
        this.trackTitleFactory = trackTitleFactory !== null && trackTitleFactory !== void 0 ? trackTitleFactory : new SequenceTrackTitleFactory(entityInstanceTranslator);
    }
    getTrack(alignmentQueryContext, querySequence) {
        return __awaiter(this, void 0, void 0, function* () {
            var _a, _b;
            const queryId = (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : alignmentQueryContext.groupId;
            assertDefined(queryId);
            return {
                trackId: "mainSequenceTrack_" + ((_b = alignmentQueryContext.queryId) !== null && _b !== void 0 ? _b : alignmentQueryContext.groupId),
                displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
                trackColor: "#F9F9F9",
                displayColor: "#000000",
                rowTitle: yield this.trackTitleFactory.getTrackTitle(alignmentQueryContext),
                rowPrefix: yield this.trackTitleFactory.getTrackTitlePrefix(alignmentQueryContext),
                titleFlagColor: yield this.trackTitleFactory.getTrackTitleFlagColor(alignmentQueryContext),
                nonEmptyDisplay: true,
                overlap: true,
                trackData: this.buildSequenceData({
                    sequence: querySequence,
                    begin: 1,
                    oriBegin: undefined,
                    queryId,
                    targetId: "",
                    from: alignmentQueryContext.from,
                    to: undefined
                }, "from")
            };
        });
    }
    buildSequenceData(config, source) {
        const sequenceData = new Array();
        const id = source === "from" ? config.queryId : config.targetId;
        config.sequence.split("").forEach((s, i) => {
            const c = config[source];
            if (!c)
                return;
            const o = {
                begin: (config.begin + i),
                oriBegin: typeof config.oriBegin === "number" ? config.oriBegin + i : undefined,
                sourceId: id,
                source: TrackUtils.transformSourceFromTarget(id, c),
                provenanceName: TrackUtils.getProvenanceConfigFormTarget(id, c).name,
                provenanceColor: TrackUtils.getProvenanceConfigFormTarget(id, c).color,
                label: s,
                name: `RES ${s}`
            };
            sequenceData.push(this.addAuthorResIds(o, {
                from: config.from,
                to: config.to,
                queryId: config.queryId,
                targetId: config.targetId
            }));
        });
        return sequenceData;
    }
    //TODO this method can be defined in a helper
    addAuthorResIds(e, alignmentContext) {
        let o = e;
        if (this.entityInstanceTranslator != null) {
            this.entityInstanceTranslator.addAuthorResIds(o, alignmentContext);
        }
        if (alignmentContext.to == SequenceReference.PdbInstance && o.sourceId != null && this.entityInstanceTranslator != null)
            o.sourceId = o.sourceId.split(TagDelimiter.instance)[0] + TagDelimiter.instance + this.entityInstanceTranslator.translateAsymToAuth(o.sourceId.split(TagDelimiter.instance)[1]);
        return o;
    }
}
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