@rcsb/rcsb-saguaro-app
Version:
RCSB 1D Saguaro Web App
72 lines • 4.94 kB
JavaScript
import { __awaiter } from "tslib";
import { FieldName, GroupReference, OperationType, SequenceReference, AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
import { MsaAlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
var assertDefined = Assertions.assertDefined;
export class RcsbFvUniprotAlignment extends RcsbFvAbstractModule {
protectedBuild() {
return __awaiter(this, void 0, void 0, function* () {
var _a, _b, _c, _d, _e, _f, _g, _h, _j;
const buildConfig = this.buildConfig;
assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page), assertDefined(buildConfig.upAcc);
const alignmentRequestContext = {
group: GroupReference.MatchingUniprotAccession,
groupId: buildConfig.upAcc,
filter: (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.alignmentFilter,
page: (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.page,
from: SequenceReference.Uniprot,
to: SequenceReference.PdbEntity,
dynamicDisplay: false,
fitTitleWidth: true,
excludeFirstRowLink: true,
sequencePrefix: (_e = (_d = buildConfig.additionalConfig) === null || _d === void 0 ? void 0 : _d.sequencePrefix) !== null && _e !== void 0 ? _e : "",
externalTrackBuilder: (_f = buildConfig.additionalConfig) === null || _f === void 0 ? void 0 : _f.externalTrackBuilder
};
const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_g = buildConfig.additionalConfig) === null || _g === void 0 ? void 0 : _g.alignmentFilter);
const trackFactory = new MsaAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator());
const alignmentFeatures = yield collectFeatures(buildConfig.upAcc);
yield trackFactory.prepareFeatures(alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == FeaturesType.UnobservedResidueXyz) })); }), alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == FeaturesType.MaQaMetricLocalTypePlddt) })); }));
yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
alignmentTrackFactory: trackFactory
});
const annotationsRequestContext = {
queryId: buildConfig.upAcc,
reference: SequenceReference.Uniprot,
sources: [AnnotationReference.Uniprot],
annotationProcessing: (_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.annotationProcessing,
externalTrackBuilder: (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.externalTrackBuilder
};
const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures);
this.boardConfigData.length = yield this.alignmentCollector.getAlignmentLength();
this.boardConfigData.includeAxis = true;
return void 0;
});
}
concatAlignmentAndAnnotationTracks() {
var _a;
const buildConfig = this.buildConfig;
this.rowConfigData = !((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.hideAlignments) ?
[this.referenceTrack].concat(this.annotationTracks).concat(this.alignmentTracks)
:
[this.referenceTrack].concat(this.annotationTracks);
}
}
function collectFeatures(upAcc) {
return __awaiter(this, void 0, void 0, function* () {
return yield rcsbClient.requestRcsbPdbAnnotations({
queryId: upAcc,
reference: SequenceReference.Uniprot,
sources: [AnnotationReference.PdbInstance],
filters: [{
source: AnnotationReference.PdbInstance,
operation: OperationType.Equals,
field: FieldName.Type,
values: [FeaturesType.UnobservedResidueXyz, FeaturesType.MaQaMetricLocalTypePlddt]
}]
});
});
}
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