@rcsb/rcsb-saguaro-app 5.1.5 → 6.0.0-development.2

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotAlignment.js

@@ -0,0 +1,71 @@
+import { __awaiter } from "tslib";
+import { FieldName, GroupReference, OperationType, SequenceReference, Source, Type } from "@rcsb/rcsb-api-tools/build/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() {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
+        return __awaiter(this, void 0, void 0, function* () {
+            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) == Type.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) == Type.MaQaMetricLocalTypePlddt) })); }));
+            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
+                alignmentTrackFactory: trackFactory
+            });
+            const annotationsRequestContext = {
+                queryId: buildConfig.upAcc,
+                reference: SequenceReference.Uniprot,
+                sources: [Source.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: [Source.PdbInstance],
+            filters: [{
+                    source: Source.PdbInstance,
+                    operation: OperationType.Equals,
+                    field: FieldName.Type,
+                    values: [Type.UnobservedResidueXyz, Type.MaQaMetricLocalTypePlddt]
+                }]
+        });
+    });
+}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotEntity.js

@@ -0,0 +1,63 @@
+import { __awaiter } from "tslib";
+import { FieldName, OperationType, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertDefined = Assertions.assertDefined;
+import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
+export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
+    protectedBuild() {
+        var _a, _b, _c;
+        return __awaiter(this, void 0, void 0, function* () {
+            const buildConfig = this.buildConfig;
+            const upAcc = buildConfig.upAcc;
+            const entityId = buildConfig.entityId;
+            const additionalConfig = buildConfig.additionalConfig;
+            assertDefined(upAcc), assertDefined(entityId);
+            const filters = [{
+                    field: FieldName.TargetId,
+                    operation: OperationType.Equals,
+                    source: Source.PdbEntity,
+                    values: [entityId]
+                }];
+            const alignmentRequestContext = {
+                queryId: upAcc,
+                from: SequenceReference.Uniprot,
+                to: SequenceReference.PdbEntity,
+                filterByTargetContains: entityId,
+                excludeAlignmentLinks: true,
+                externalTrackBuilder: (_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder
+            };
+            const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, [entityId]);
+            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse);
+            const annotationsRequestContext = {
+                queryId: upAcc,
+                reference: SequenceReference.Uniprot,
+                sources: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.sources) ? additionalConfig.sources : [Source.PdbEntity, Source.Uniprot],
+                filters: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) instanceof Array ? additionalConfig.filters.concat(filters) : filters,
+                titleSuffix: this.titleSuffix.bind(this),
+                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);
+    }
+    titleSuffix(ann, d) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            if (this.polymerEntityInstance != null && ann.source === Source.PdbInstance) {
+                const labelAsymId = (_a = ann.target_id) === null || _a === void 0 ? void 0 : _a.split(TagDelimiter.instance)[1];
+                if (!labelAsymId)
+                    return;
+                const authAsymId = this.polymerEntityInstance.translateAsymToAuth(labelAsymId);
+                return labelAsymId === authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]";
+            }
+        });
+    }
+}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotInstance.js

@@ -0,0 +1,63 @@
+import { __awaiter } from "tslib";
+import { FieldName, OperationType, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/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() {
+        var _a, _b, _c;
+        return __awaiter(this, void 0, void 0, function* () {
+            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 = [Source.Uniprot, Source.PdbEntity, Source.PdbInstance];
+            if (additionalConfig != null && additionalConfig.sources != null && additionalConfig.sources.length > 0)
+                sources = additionalConfig.sources;
+            let filters = [{
+                    field: FieldName.TargetId,
+                    operation: OperationType.Equals,
+                    source: Source.PdbEntity,
+                    values: [entityId]
+                }, {
+                    field: FieldName.TargetId,
+                    operation: OperationType.Contains,
+                    source: Source.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);
+    }
+}

package/lib/RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip.d.ts

@@ -0,0 +1,8 @@
+import { RcsbFvTooltipInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvTooltip/RcsbFvTooltipInterface";
+import { RcsbFvTrackDataAnnotationInterface } from "../RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface";
+export declare class RcsbFvTooltip implements RcsbFvTooltipInterface {
+    showTooltip(d: RcsbFvTrackDataAnnotationInterface): HTMLElement;
+    showTooltipDescription(d: RcsbFvTrackDataAnnotationInterface): HTMLElement | undefined;
+    private static buildIndexNames;
+    private static bNode;
+}

package/lib/RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip.js

@@ -0,0 +1,82 @@
+export class RcsbFvTooltip {
+    showTooltip(d) {
+        const tooltipDiv = document.createElement("div");
+        let region = "Position: " + d.begin.toString();
+        if (typeof d.end === "number" && d.end != d.begin)
+            region += " - " + d.end.toString();
+        const spanRegion = document.createElement("span");
+        spanRegion.append(region);
+        if (typeof d.beginName === "string" && d.indexName != undefined) {
+            spanRegion.append(RcsbFvTooltip.buildIndexNames(d.beginName, d.endName, d.indexName));
+        }
+        if (typeof d.oriBegin === "number") {
+            let ori_region = d.oriBegin.toString();
+            if (typeof d.oriEnd === "number")
+                ori_region += " - " + d.oriEnd.toString();
+            const spanOriRegion = document.createElement("span");
+            if (d.source != undefined)
+                spanOriRegion.append(" | [" + d.source.replace("_", " ") + "] " + d.sourceId + ": " + ori_region);
+            spanOriRegion.style.color = "#888888";
+            if (typeof d.oriBeginName === "string" && d.indexName != undefined)
+                spanOriRegion.append(RcsbFvTooltip.buildIndexNames(d.oriBeginName, d.oriEndName, d.indexName));
+            spanRegion.append(spanOriRegion);
+        }
+        let title = d.title;
+        if (typeof d.name === "string")
+            title = d.name;
+        else if (typeof d.featureId === "string")
+            title = d.featureId;
+        if (title != undefined)
+            tooltipDiv.append(title);
+        if (typeof d.provenanceName === "string") {
+            const spanProvenance = document.createElement("span");
+            const spanProvenanceString = document.createElement("span");
+            spanProvenanceString.append(d.provenanceName);
+            if (typeof d.provenanceColor === "string")
+                spanProvenanceString.style.color = d.provenanceColor;
+            else
+                spanProvenanceString.style.color = "#888888";
+            spanProvenance.append(" [", spanProvenanceString, "]");
+            spanProvenance.style.color = "#888888";
+            tooltipDiv.append(spanProvenance);
+            tooltipDiv.append(RcsbFvTooltip.bNode());
+        }
+        else if (title != undefined) {
+            tooltipDiv.append(RcsbFvTooltip.bNode());
+        }
+        if (typeof d.value === "number") {
+            const valueRegion = document.createElement("span");
+            valueRegion.append(" value: " + d.value);
+            tooltipDiv.append(valueRegion);
+            tooltipDiv.append(RcsbFvTooltip.bNode());
+        }
+        tooltipDiv.append(spanRegion);
+        return tooltipDiv;
+    }
+    showTooltipDescription(d) {
+        if (d.description == null || d.description.length == 0)
+            return undefined;
+        const tooltipDescriptionDiv = document.createElement("div");
+        d.description.forEach(des => {
+            const desDiv = document.createElement("div");
+            desDiv.append(des);
+            tooltipDescriptionDiv.append(desDiv);
+        });
+        return tooltipDescriptionDiv;
+    }
+    static buildIndexNames(beginName, endName, name) {
+        const spanAuthRegion = document.createElement("span");
+        let authRegion = beginName;
+        if (typeof endName === "string")
+            authRegion += " - " + endName;
+        spanAuthRegion.append(" [" + name + ": " + authRegion + "]");
+        spanAuthRegion.style.color = "#888888";
+        return spanAuthRegion;
+    }
+    static bNode() {
+        const b = document.createElement("span");
+        b.append(" | ");
+        b.style.fontWeight = "bold";
+        return b;
+    }
+}

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.js

@@ -0,0 +1,67 @@
+import { asyncScheduler } from "rxjs";
+export class RcsbFvAlignmentCollectorQueue {
+    constructor(nWorkers) {
+        this.workerList = new Array();
+        this.taskQueue = new Array();
+        this.isQueueActive = false;
+        if (nWorkers != null)
+            this.nWorkers = nWorkers;
+        else
+            this.nWorkers = self.navigator.hardwareConcurrency;
+        for (let i = 0; i < this.nWorkers; i++) {
+            this.workerList.push({
+                available: true,
+                worker: new Worker("/saguaro/worker.js")
+            });
+        }
+    }
+    sendTask(request, callback) {
+        const available = this.workerList.filter(d => d.available);
+        if (available.length > 0) {
+            available[0].available = false;
+            available[0].worker.postMessage(request);
+            available[0].worker.onmessage = (e) => {
+                callback(e.data);
+                available[0].available = true;
+            };
+        }
+        else {
+            this.taskQueue.push({ request: request, callback: callback });
+            if (!this.isQueueActive)
+                this.activateQueue();
+        }
+    }
+    activateQueue() {
+        this.isQueueActive = true;
+        this.recursiveExec();
+    }
+    recursiveExec() {
+        if (this.taskQueue.length == 0) {
+            this.isQueueActive = false;
+        }
+        else {
+            this.isQueueActive = true;
+            this.workerList.filter(d => d.available).forEach(aW => {
+                if (this.taskQueue.length > 0) {
+                    aW.available = false;
+                    const task = this.taskQueue.shift();
+                    if (!task)
+                        return;
+                    aW.worker.postMessage(task.request);
+                    aW.worker.onmessage = (e) => {
+                        task.callback(e.data);
+                        aW.available = true;
+                    };
+                }
+            });
+            asyncScheduler.schedule(() => {
+                this.recursiveExec();
+            }, 1000);
+        }
+    }
+    terminateWorkers() {
+        this.workerList.forEach(w => {
+            w.worker.terminate();
+        });
+    }
+}

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorWorker.worker.d.ts

@@ -0,0 +1 @@
+export {};

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorWorker.worker.js

@@ -0,0 +1,10 @@
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+const worker = self;
+worker.onmessage = function (message) {
+    const request = message.data;
+    const rcsbFvQuery = rcsbClient;
+    rcsbFvQuery.requestAlignment(request).then((result) => {
+        // @ts-ignore
+        postMessage(result);
+    });
+};

package/lib/RcsbGraphQL/RcsbClient.js

@@ -0,0 +1,83 @@
+import { __awaiter } from "tslib";
+import { RcsbQueryAnnotations, RcsbQueryGroupAnnotations } from "./RcsbQueryAnnotations";
+import { RcsbQueryAlignment, RcsbQueryGroupAlignment } from "./RcsbQueryAlignment";
+import { RcsbQueryEntryInstances } from "./RcsbQueryEntryInstances";
+import { RcsbQueryMultipleEntityInstances } from "./RcsbQueryMultipleEntityInstances";
+import { RcsbQueryGroup } from "./RcsbQueryGroup";
+import { RcsbQueryMultipleEntriesProperties } from "./RcsbQueryMultipleEntriesProperties";
+import { RcsbQueryInterfaceInstances } from "./RcsbQueryInterfaceInstances";
+import { RcsbQueryAssemblyInterfaces } from "./RcsbQueryAssemblyInterfaces";
+import { rcsbRequestClient } from "../RcsbRequest/RcsbRequestClient";
+import { RcsbQueryMultipleInstanceSequences } from "./RcsbQueryMultipleInstanceSequences";
+//TODO Implement a cache to store requests and avoid duplication
+class RcsbClientClass {
+    constructor(get) {
+        this.rcsbQueryAnnotations = new RcsbQueryAnnotations(get.borrego);
+        this.rcsbQueryGroupAnnotations = new RcsbQueryGroupAnnotations(get.borrego);
+        this.rcsbQueryAlignment = new RcsbQueryAlignment(get.borrego);
+        this.rcsbQueryGroupAlignment = new RcsbQueryGroupAlignment(get.borrego);
+        this.rcsbQueryEntityInstances = new RcsbQueryEntryInstances(get.yosemite);
+        this.rcsbQueryMutipleEntityInstances = new RcsbQueryMultipleEntityInstances(get.yosemite);
+        this.rcsbQueryEntryProperties = new RcsbQueryMultipleEntriesProperties(get.yosemite);
+        this.rcsbQueryInterfaceInstances = new RcsbQueryInterfaceInstances(get.yosemite);
+        this.rcsbQueryAssemblyInterfaces = new RcsbQueryAssemblyInterfaces(get.yosemite);
+        this.rcsbQueryGroup = new RcsbQueryGroup(get.yosemite);
+        this.rcsbQueryMultipleInstanceSequences = new RcsbQueryMultipleInstanceSequences(get.yosemite);
+    }
+    requestRcsbPdbAnnotations(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryAnnotations.request(requestConfig);
+        });
+    }
+    requestRcsbPdbGroupAnnotations(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryGroupAnnotations.request(requestConfig);
+        });
+    }
+    requestAlignment(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryAlignment.request(requestConfig);
+        });
+    }
+    requestGroupAlignment(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryGroupAlignment.request(requestConfig);
+        });
+    }
+    requestEntityInstances(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryEntityInstances.request(requestConfig);
+        });
+    }
+    requestMultipleEntityInstances(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryMutipleEntityInstances.request(requestConfig);
+        });
+    }
+    requestGroupInfo(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryGroup.request(requestConfig);
+        });
+    }
+    requestMultipleEntriesProperties(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryEntryProperties.request(requestConfig);
+        });
+    }
+    requestInterfaceInstances(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryInterfaceInstances.request(requestConfig);
+        });
+    }
+    requestAssemblyInterfaces(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryAssemblyInterfaces.request(requestConfig);
+        });
+    }
+    requestMultipleInstanceSequences(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return yield this.rcsbQueryMultipleInstanceSequences.request(requestConfig);
+        });
+    }
+}
+export const rcsbClient = new RcsbClientClass({ borrego: () => rcsbRequestClient.borrego, yosemite: () => rcsbRequestClient.yosemite });

package/lib/RcsbGraphQL/RcsbCoreQueryInterface.js

@@ -0,0 +1 @@
+export {};

package/lib/RcsbGraphQL/RcsbQueryAlignment.js

@@ -0,0 +1,43 @@
+import { __awaiter } from "tslib";
+import queryAlignment from "../RcsbQueries/Borrego/QueryAlignments.graphql";
+import queryGroupAlignment from "../RcsbQueries/Borrego/QueryGroupAlignments.graphql";
+import queryGroupAlignmentNoLogo from "../RcsbQueries/Borrego/QueryGroupAlignmentsNoLogo.graphql";
+export class RcsbQueryAlignment {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const result = yield this.getClient().request({
+                    queryId: requestConfig.queryId,
+                    from: requestConfig.from,
+                    to: requestConfig.to,
+                    range: requestConfig.range
+                }, queryAlignment);
+                return result.alignment;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}
+export class RcsbQueryGroupAlignment {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const result = yield this.getClient().request({ group: requestConfig.group, groupId: requestConfig.groupId, filter: requestConfig.filter, first: requestConfig.page.first, after: requestConfig.page.after }, requestConfig.excludeLogo ? queryGroupAlignmentNoLogo : queryGroupAlignment);
+                return result.group_alignment;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}

package/lib/RcsbGraphQL/RcsbQueryAnnotations.js

@@ -0,0 +1,43 @@
+import { __awaiter } from "tslib";
+import queryAnnotations from "../RcsbQueries/Borrego/QueryAnnotations.graphql";
+import queryGroupAnnotations from "../RcsbQueries/Borrego/QueryGroupAnnotations.graphql";
+export class RcsbQueryAnnotations {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const annotationsResponse = yield this.getClient().request({
+                    queryId: requestConfig.queryId,
+                    reference: requestConfig.reference,
+                    sources: requestConfig.sources,
+                    filters: requestConfig.filters,
+                    range: requestConfig.range
+                }, queryAnnotations);
+                return annotationsResponse.annotations;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}
+export class RcsbQueryGroupAnnotations {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const annotationsResponse = yield this.getClient().request(requestConfig, queryGroupAnnotations);
+                return annotationsResponse.group_annotations;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}

package/lib/RcsbGraphQL/RcsbQueryAssemblyInterfaces.js

@@ -0,0 +1,19 @@
+import { __awaiter } from "tslib";
+import query from "../RcsbQueries/Yosemite/QueryAssemblyInterfaces.graphql";
+export class RcsbQueryAssemblyInterfaces {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const response = yield this.getClient().request(requestConfig, query);
+                return response.assemblies;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}

package/lib/RcsbGraphQL/RcsbQueryEntryInstances.js

@@ -0,0 +1,21 @@
+import { __awaiter } from "tslib";
+import query from "../RcsbQueries/Yosemite/QueryEntryInstances.graphql";
+export class RcsbQueryEntryInstances {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const response = yield this.getClient().request({
+                    entry_id: requestConfig.entry_id,
+                }, query);
+                return response.entry;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}

package/lib/RcsbGraphQL/RcsbQueryGroup.js

@@ -0,0 +1,21 @@
+import { __awaiter } from "tslib";
+import query from "../RcsbQueries/Yosemite/QueryGroup.graphql";
+export class RcsbQueryGroup {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const response = yield this.getClient().request({
+                    group_id: requestConfig.group_id
+                }, query);
+                return response.group;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}

package/lib/RcsbGraphQL/RcsbQueryInterfaceInstances.js

@@ -0,0 +1,19 @@
+import { __awaiter } from "tslib";
+import query from "../RcsbQueries/Yosemite/QueryInterfaceInstances.graphql";
+export class RcsbQueryInterfaceInstances {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const response = yield this.getClient().request(requestConfig, query);
+                return response.interfaces;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}

package/lib/RcsbGraphQL/RcsbQueryMultipleEntityInstances.js

@@ -0,0 +1,21 @@
+import { __awaiter } from "tslib";
+import query from "../RcsbQueries/Yosemite/QueryMultipleEntityInstances.graphql";
+export class RcsbQueryMultipleEntityInstances {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const result = yield this.getClient().request({
+                    entity_ids: requestConfig.entity_ids,
+                }, query);
+                return result.polymer_entities;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}