@rcsb/rcsb-saguaro-app
Version:
RCSB 1D Saguaro Web App
64 lines • 3.83 kB
JavaScript
import { __awaiter } from "tslib";
import { FieldName, OperationType, SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes";
import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
import { buriedResidues, buriedResiduesFilter } from "../../RcsbUtils/TrackGenerators/BuriedResidues";
import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
var assertDefined = Assertions.assertDefined;
export class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
protectedBuild() {
return __awaiter(this, void 0, void 0, function* () {
var _a, _b, _c;
const buildConfig = this.buildConfig;
const upAcc = buildConfig.upAcc;
const entityId = buildConfig.entityId;
const instanceId = buildConfig.instanceId;
const additionalConfig = buildConfig.additionalConfig;
assertDefined(entityId), assertDefined(instanceId), assertDefined(upAcc);
let sources = [AnnotationReference.Uniprot, AnnotationReference.PdbEntity, AnnotationReference.PdbInstance];
if (additionalConfig != null && additionalConfig.sources != null && additionalConfig.sources.length > 0)
sources = additionalConfig.sources;
let filters = [{
field: FieldName.TargetId,
operation: OperationType.Equals,
source: AnnotationReference.PdbEntity,
values: [entityId]
}, {
field: FieldName.TargetId,
operation: OperationType.Contains,
source: AnnotationReference.PdbInstance,
values: [instanceId]
}];
if (additionalConfig != null && additionalConfig.filters != null && additionalConfig.filters.length > 0)
filters = additionalConfig.filters;
const alignmentRequestContext = {
queryId: upAcc,
from: SequenceReference.Uniprot,
to: SequenceReference.PdbInstance,
filterByTargetContains: instanceId,
excludeFirstRowLink: true,
externalTrackBuilder: (_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder
};
const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, [instanceId]);
yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse);
const annotationsRequestContext = {
queryId: upAcc,
reference: SequenceReference.Uniprot,
sources: sources,
filters: filters,
annotationGenerator: (ann) => (new Promise((r) => (r(buriedResidues(ann))))),
annotationFilter: (ann) => (new Promise((r) => (r(buriedResiduesFilter(ann))))),
annotationProcessing: (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.annotationProcessing,
externalTrackBuilder: (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.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() {
this.rowConfigData = [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks);
}
}
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