@rcsb/rcsb-saguaro-app 6.3.0 → 6.3.2-dev-js-seqcoord.13

package/lib/commonjs/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.js

@@ -11,6 +11,7 @@ const RcsbTabs_1 = require("../RcsbFvComponents/RcsbTabs");
 const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
 const SearchQueryTools_1 = require("../../RcsbSeacrh/SearchQueryTools");
 const GroupPfvApp_1 = require("./GroupTabs/GroupPfvApp");
+const rxjs_1 = require("rxjs");
 const ALIGNMENT = "alignment";
 const STRUCTURAL_FEATURES = "structural-features";
 const BINDING_SITES = "binding-sites";
@@ -72,38 +73,40 @@ class GroupPfvTabs extends react_1.default.Component {
     }
     onSelect(tabKey) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            if (!this.featureViewers.has(tabKey))
-                yield this.renderPositionalFeatureViewer(tabKey);
-            this.syncPositionAndHighlight(tabKey);
-            this.currentTab = tabKey;
+            rxjs_1.asyncScheduler.schedule(() => tslib_1.__awaiter(this, void 0, void 0, function* () {
+                if (!this.featureViewers.has(tabKey))
+                    yield this.renderPositionalFeatureViewer(tabKey);
+                this.syncPositionAndHighlight(tabKey);
+                this.currentTab = tabKey;
+            }), 10);
         });
     }
     renderPositionalFeatureViewer(tabKey) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
+            var _a, _b, _c, _d, _e, _f, _g, _h;
             switch (tabKey) {
                 case ALIGNMENT:
-                    this.featureViewers.set(tabKey, yield GroupPfvApp_1.GroupPfvApp.alignment(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_a = this.entityCount) !== null && _a !== void 0 ? _a : 0, Object.assign(Object.assign({ page: { first: 50, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.filterEntities })));
+                    this.featureViewers.set(tabKey, yield GroupPfvApp_1.GroupPfvApp.alignment(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_a = this.entityCount) !== null && _a !== void 0 ? _a : 0, Object.assign(Object.assign({ page: { first: 50, after: 0 } }, this.props.additionalConfig), { alignmentFilter: this.filterEntities })));
                     break;
                 case BINDING_SITES:
-                    this.featureViewers.set(tabKey, yield GroupPfvApp_1.GroupPfvApp.bindingSites(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_c = (_b = this.filterInstances) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0, Object.assign(Object.assign({ page: { first: 0, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.props.searchQuery ? this.filterEntities : undefined, filters: this.props.searchQuery ? [{
-                                source: GqlTypes_1.Source.PdbInstance,
+                    this.featureViewers.set(tabKey, yield GroupPfvApp_1.GroupPfvApp.bindingSites(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_c = (_b = this.filterInstances) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0, Object.assign(Object.assign({ page: { first: 1, after: 0 } }, this.props.additionalConfig), { alignmentFilter: this.props.searchQuery ? this.filterEntities : undefined, filters: this.props.searchQuery ? [{
+                                source: GqlTypes_1.AnnotationReference.PdbInstance,
                                 field: GqlTypes_1.FieldName.TargetId,
                                 operation: GqlTypes_1.OperationType.Equals,
-                                values: this.filterInstances
+                                values: (_d = this.filterInstances) !== null && _d !== void 0 ? _d : []
                             }] : undefined })));
                     break;
                 case STRUCTURAL_FEATURES:
-                    this.featureViewers.set(tabKey, yield GroupPfvApp_1.GroupPfvApp.structure(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_e = (_d = this.filterInstances) === null || _d === void 0 ? void 0 : _d.length) !== null && _e !== void 0 ? _e : 0, Object.assign(Object.assign({ page: { first: 0, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.props.searchQuery ? this.filterEntities : undefined, filters: this.props.searchQuery ? [{
-                                source: GqlTypes_1.Source.PdbInstance,
+                    this.featureViewers.set(tabKey, yield GroupPfvApp_1.GroupPfvApp.structure(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_f = (_e = this.filterInstances) === null || _e === void 0 ? void 0 : _e.length) !== null && _f !== void 0 ? _f : 0, Object.assign(Object.assign({ page: { first: 1, after: 0 } }, this.props.additionalConfig), { alignmentFilter: this.props.searchQuery ? this.filterEntities : undefined, filters: this.props.searchQuery ? [{
+                                source: GqlTypes_1.AnnotationReference.PdbInstance,
                                 field: GqlTypes_1.FieldName.TargetId,
                                 operation: GqlTypes_1.OperationType.Equals,
-                                values: this.filterInstances
+                                values: (_g = this.filterInstances) !== null && _g !== void 0 ? _g : []
                             }, {
-                                source: GqlTypes_1.Source.PdbEntity,
+                                source: GqlTypes_1.AnnotationReference.PdbEntity,
                                 field: GqlTypes_1.FieldName.TargetId,
                                 operation: GqlTypes_1.OperationType.Equals,
-                                values: this.filterEntities
+                                values: (_h = this.filterEntities) !== null && _h !== void 0 ? _h : []
                             }] : undefined })));
                     break;
             }

package/lib/commonjs/RcsbFvWeb/RcsbFvGroup/GroupTabs/GroupPfvApp.js

@@ -36,12 +36,12 @@ var GroupPfvApp;
                         component: PaginationItemComponent_1.PaginationItemComponent,
                         props: {
                             count: entityCount,
-                            after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : "0",
+                            after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : 0,
                             first: (_d = (_c = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _c === void 0 ? void 0 : _c.first) !== null && _d !== void 0 ? _d : 50,
                             stateChange: (state, prevState) => {
                                 paginationCallback(elementId, pfv, RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
                                         first: state.first,
-                                        after: state.after.toString()
+                                        after: state.after
                                     }, excludeLogo: true }));
                             }
                         }
@@ -57,15 +57,15 @@ var GroupPfvApp;
             var _a;
             additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
                         field: GqlTypes_1.FieldName.Type,
-                        values: [GqlTypes_1.Type.HelixP, GqlTypes_1.Type.Sheet, GqlTypes_1.Type.Cath, GqlTypes_1.Type.Scop],
+                        values: [GqlTypes_1.FeaturesType.HelixP, GqlTypes_1.FeaturesType.Sheet, GqlTypes_1.FeaturesType.Cath, GqlTypes_1.FeaturesType.Scop],
                         operation: GqlTypes_1.OperationType.Equals,
-                        source: GqlTypes_1.Source.PdbInstance
+                        source: GqlTypes_1.AnnotationReference.PdbInstance
                     }, {
                         field: GqlTypes_1.FieldName.Type,
-                        values: [GqlTypes_1.Type.Pfam],
+                        values: [GqlTypes_1.FeaturesType.Pfam],
                         operation: GqlTypes_1.OperationType.Equals,
-                        source: GqlTypes_1.Source.PdbEntity
-                    }], sources: [GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.PdbEntity], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: (0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)() });
+                        source: GqlTypes_1.AnnotationReference.PdbEntity
+                    }], sources: [GqlTypes_1.AnnotationReference.PdbInstance, GqlTypes_1.AnnotationReference.PdbEntity], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: (0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)() });
             // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
             const pfvArgs = [
                 getReferenceFromGroupProvenance(groupProvenanceId),
@@ -82,10 +82,10 @@ var GroupPfvApp;
             var _a;
             additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
                         field: GqlTypes_1.FieldName.Type,
-                        values: [GqlTypes_1.Type.BindingSite],
+                        values: [GqlTypes_1.FeaturesType.BindingSite],
                         operation: GqlTypes_1.OperationType.Equals,
-                        source: GqlTypes_1.Source.PdbInstance
-                    }], sources: [GqlTypes_1.Source.PdbInstance], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: (0, AlignmentGlobalBindingSite_1.alignmentGlobalLigandBindingSite)() });
+                        source: GqlTypes_1.AnnotationReference.PdbInstance
+                    }], sources: [GqlTypes_1.AnnotationReference.PdbInstance], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: (0, AlignmentGlobalBindingSite_1.alignmentGlobalLigandBindingSite)(), isAnnotationsGroupSummary: false });
             // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
             const pfvArgs = [
                 getReferenceFromGroupProvenance(groupProvenanceId),
@@ -99,25 +99,31 @@ var GroupPfvApp;
     GroupPfvApp.bindingSites = bindingSites;
 })(GroupPfvApp || (exports.GroupPfvApp = GroupPfvApp = {}));
 function annotationPositionFrequencyProcessing(nTargets) {
-    const targets = new Map();
+    const targetValues = new Map();
+    const targetSet = new Map();
     return {
         getAnnotationValue: (feature) => {
             var _a, _b, _c, _d;
-            if (!targets.has(feature.type)) {
-                if (feature.d.value)
-                    targets.set(feature.type, feature.d.value);
-                return (_b = (_a = feature.p.values) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : 0;
-            }
-            else {
-                return (_d = (_c = feature.p.values) === null || _c === void 0 ? void 0 : _c[0]) !== null && _d !== void 0 ? _d : 0;
-            }
+            if (!targetValues.has(feature.type))
+                targetValues.set(feature.type, 0);
+            if (!targetSet.has(feature.type))
+                targetSet.set(feature.type, new Set());
+            if (feature.type === "SCOP:Prokaryotic (50S subunit)")
+                console.log(feature);
+            if (typeof feature.d.value === "number")
+                targetValues.set(feature.type, (_a = feature.d.value) !== null && _a !== void 0 ? _a : 0);
+            else
+                (_b = targetSet.get(feature.type)) === null || _b === void 0 ? void 0 : _b.add(feature.targetId);
+            return (_d = (_c = feature.p.values) === null || _c === void 0 ? void 0 : _c[0]) !== null && _d !== void 0 ? _d : 1;
         },
         computeAnnotationValue: (annotationTracks) => {
             annotationTracks.forEach((at, type) => {
-                const N = (type.includes(GqlTypes_1.Type.Cath) || type.includes(GqlTypes_1.Type.Scop) || type.includes(GqlTypes_1.Type.BindingSite) || type.includes(GqlTypes_1.Type.Pfam)) ? targets.get(type) : nTargets;
+                var _a;
+                const isType = (type.includes(GqlTypes_1.FeaturesType.Cath) || type.includes(GqlTypes_1.FeaturesType.Scop) || type.includes(GqlTypes_1.FeaturesType.BindingSite) || type.includes(GqlTypes_1.FeaturesType.Pfam));
+                const N = isType ? (targetValues.get(type) != 0 ? targetValues.get(type) : (_a = targetSet.get(type)) === null || _a === void 0 ? void 0 : _a.size) : nTargets;
                 at.forEach((ann, positionKey) => {
-                    if (ann.source != GqlTypes_1.Source.PdbInterface)
-                        ann.value = Math.ceil(1000 * ann.value / (N !== null && N !== void 0 ? N : 1)) / 1000;
+                    if (ann.source != GqlTypes_1.AnnotationReference.PdbInterface)
+                        ann.value = Math.round(100 * ann.value / (N !== null && N !== void 0 ? N : 1)) / 100;
                 });
             });
         }

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.d.ts

@@ -4,7 +4,7 @@ import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/Poly
 import { AlignmentCollectorInterface } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
 import { AnnotationRequestContext, AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface } from "./RcsbFvModuleInterface";
-import { AlignmentResponse, AnnotationFeatures, Feature, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, SequenceAnnotations, Features, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { TrackFactoryInterface } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryInterface";
 import { AlignmentRequestContextType } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
 import { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
@@ -29,18 +29,18 @@ export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterf
     activeDisplay(): boolean;
     getFv(): RcsbFv;
     getTargets(): Promise<Array<string>>;
-    getAlignmentResponse(): Promise<AlignmentResponse>;
-    getFeatures(): Promise<Array<Feature>>;
+    getAlignmentResponse(): Promise<SequenceAlignments>;
+    getFeatures(): Promise<Array<Features>>;
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
     build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     wait(): Promise<void>;
     protected abstract protectedBuild(): Promise<void>;
     protected abstract concatAlignmentAndAnnotationTracks(): void;
-    protected buildAlignmentTracks(alignmentRequestContext: AlignmentRequestContextType, alignmentResponse: AlignmentResponse, trackFactories?: {
-        alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
+    protected buildAlignmentTracks(alignmentRequestContext: AlignmentRequestContextType, alignmentResponse: SequenceAlignments, trackFactories?: {
+        alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]>;
         sequenceTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, string]>;
     }): Promise<void>;
-    protected buildAnnotationsTrack(annotationsRequestContext: AnnotationRequestContext, annotationsFeatures: AnnotationFeatures[], annotationConfigMap?: AnnotationConfigInterface): Promise<void>;
+    protected buildAnnotationsTrack(annotationsRequestContext: AnnotationRequestContext, annotationsFeatures: SequenceAnnotations[], annotationConfigMap?: AnnotationConfigInterface): Promise<void>;
     protected getBoardConfig(): Promise<RcsbFvBoardConfigInterface>;
     protected getRowsConfig(): Promise<Array<RcsbFvRowConfigInterface>>;
     private buildExternalTracks;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.js

@@ -31,14 +31,14 @@ function sequenceDisplayDynamicUpdate(reference, ranges, trackWidth) {
                     from: reference,
                     to: GqlTypes_1.SequenceReference.NcbiGenome
                 });
-            })).then(alignments => {
+            })).then((alignments) => {
                 const out = new RcsbDataManager_1.RcsbFvTrackData();
                 alignments.forEach((a, n) => {
                     var _c;
                     if (a.query_sequence == null)
                         return;
                     const sequence = a.query_sequence.split("");
-                    (_c = a.target_alignment) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
+                    (_c = a.target_alignments) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
                         var _c;
                         if (!ta)
                             return;
@@ -113,12 +113,12 @@ class RcsbFvChromosome extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
                 from: GqlTypes_1.SequenceReference.PdbEntity,
                 to: to
             });
-        })).then(result => {
+        })).then((result) => {
             result.forEach(a => {
                 var _c;
                 if (!a)
                     return;
-                (_c = a.target_alignment) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
+                (_c = a.target_alignments) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
                     if ((ta === null || ta === void 0 ? void 0 : ta.target_id) && (ta === null || ta === void 0 ? void 0 : ta.coverage))
                         this.targetCoverages.set(ta.target_id, ta.coverage);
                 });
@@ -144,8 +144,8 @@ class RcsbFvChromosome extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     collectPdbWorkerResults(ar, pdbEntityId, chrId) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             var _c, _d;
-            assertElementListDefined(ar.target_alignment);
-            const exonTracks = this.collectExons(ar.target_alignment, "target", RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, GqlTypes_1.SequenceReference.PdbEntity, chrId);
+            assertElementListDefined(ar.target_alignments);
+            const exonTracks = this.collectExons(ar.target_alignments, "target", RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, GqlTypes_1.SequenceReference.PdbEntity, chrId);
             this.pdbEntityTrack = this.mergeExonTracks(exonTracks, GqlTypes_1.SequenceReference.PdbEntity)[0];
             (_d = (_c = this.pdbEntityTrack.displayConfig) === null || _c === void 0 ? void 0 : _c[0].displayData) === null || _d === void 0 ? void 0 : _d.forEach(d => {
                 d.description = [pdbEntityId];
@@ -319,8 +319,8 @@ class RcsbFvChromosome extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
             this.completeTasks++;
             const e = this.targetAlignmentList.get(reference);
             assertDefined(e);
-            assertElementListDefined(alignment.target_alignment);
-            e[index] = alignment.target_alignment;
+            assertElementListDefined(alignment.target_alignments);
+            e[index] = alignment.target_alignments;
             console.log("Completed " + Math.floor(this.completeTasks / this.nTasks * 100) + "%");
             if (forcePlot) {
                 yield this.plot();

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvEntity.js

@@ -29,7 +29,7 @@ class RcsbFvEntity extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
             const annotationsRequestContext = {
                 queryId: buildConfig.entityId,
                 reference: GqlTypes_1.SequenceReference.PdbEntity,
-                sources: (_d = (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.sources) !== null && _d !== void 0 ? _d : [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.Uniprot],
+                sources: (_d = (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.sources) !== null && _d !== void 0 ? _d : [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.Uniprot],
                 titleSuffix: this.titleSuffix.bind(this),
                 filters: (_e = buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.filters,
                 annotationProcessing: (_f = buildConfig.additionalConfig) === null || _f === void 0 ? void 0 : _f.annotationProcessing,
@@ -62,7 +62,7 @@ class RcsbFvEntity extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             if (!ann.target_id)
                 return;
-            if (this.polymerEntityInstance != null && ann.source === GqlTypes_1.Source.PdbInstance) {
+            if (this.polymerEntityInstance != null && ann.source === GqlTypes_1.AnnotationReference.PdbInstance) {
                 const labelAsymId = ann.target_id.split(TagDelimiter_1.TagDelimiter.instance)[1];
                 const authAsymId = this.polymerEntityInstance.translateAsymToAuth(labelAsymId);
                 return labelAsymId === authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]";

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAlignment.js

@@ -10,6 +10,7 @@ var assertDefined = Assertions_1.Assertions.assertDefined;
 const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
 const Operator_1 = require("../../RcsbUtils/Helpers/Operator");
 const RcsbRequestContextManager_1 = require("../../RcsbRequest/RcsbRequestContextManager");
+const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
 class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     protectedBuild() {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
@@ -30,7 +31,6 @@ class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
                 sequencePrefix: (_f = (_e = buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.sequencePrefix) !== null && _f !== void 0 ? _f : "",
                 externalTrackBuilder: (_g = buildConfig.additionalConfig) === null || _g === void 0 ? void 0 : _g.externalTrackBuilder
             };
-            collectNextPage(alignmentRequestContext, this.alignmentCollector, this.annotationCollector).then(() => console.log("Next page ready"));
             const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.alignmentFilter);
             const trackFactory = new MsaAlignmentTrackFactory_1.MsaAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator());
             const targetList = uniqueTargetList(alignmentResponse);
@@ -39,10 +39,11 @@ class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
                 externalTrackBuilder: (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.externalTrackBuilder,
                 targetList
             }, this.annotationCollector);
-            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) == GqlTypes_1.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) == GqlTypes_1.Type.MaQaMetricLocalTypePlddt) })); }));
+            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) == GqlTypes_1.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) == GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt) })); }));
             yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
                 alignmentTrackFactory: trackFactory
             });
+            collectNextPage(alignmentRequestContext, this.alignmentCollector, this.annotationCollector).then(() => console.log("Next page ready"));
             return void 0;
         });
     }
@@ -58,16 +59,21 @@ class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
 exports.RcsbFvGroupAlignment = RcsbFvGroupAlignment;
 function collectNextPage(alignmentRequestContext, alignmentCollector, annotationCollector) {
     return tslib_1.__awaiter(this, void 0, void 0, function* () {
-        const alignmentResponse = yield alignmentCollector.collect(Object.assign(Object.assign({}, alignmentRequestContext), { excludeLogo: true, page: {
+        const alignmentResponse = yield RcsbClient_1.rcsbClient.requestGroupAlignment({
+            group: alignmentRequestContext.group,
+            groupId: alignmentRequestContext.groupId,
+            page: {
                 first: alignmentRequestContext.page.first,
-                after: (parseInt(alignmentRequestContext.page.after) + alignmentRequestContext.page.first).toString()
-            } }));
+                after: alignmentRequestContext.page.after + alignmentRequestContext.page.first
+            },
+            excludeLogo: true
+        });
         const targetList = uniqueTargetList(alignmentResponse);
         if (alignmentRequestContext.groupId) {
-            const alignmentFeatures = yield collectFeatures({
+            const alignmentFeatures = yield RcsbClient_1.rcsbClient.requestRcsbPdbGroupAnnotations(buildGroupAnnotationQuery({
                 groupId: alignmentRequestContext.groupId,
                 targetList
-            }, annotationCollector);
+            }));
             const featureTargetList = Operator_1.Operator.uniqueValues(alignmentFeatures.map(af => { var _a; return TagDelimiter_1.TagDelimiter.parseInstance((_a = af.target_id) !== null && _a !== void 0 ? _a : "").entryId; }));
             Operator_1.Operator.arrayChunk(featureTargetList, 100).forEach(ids => RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntryProperties(ids));
         }
@@ -75,31 +81,31 @@ function collectNextPage(alignmentRequestContext, alignmentCollector, annotation
 }
 function uniqueTargetList(alignmentResponse) {
     var _a, _b;
-    return Operator_1.Operator.uniqueValues((_b = (_a = alignmentResponse.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => {
+    return Operator_1.Operator.uniqueValues((_b = (_a = alignmentResponse.target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => {
         assertDefined(ta === null || ta === void 0 ? void 0 : ta.target_id);
         return TagDelimiter_1.TagDelimiter.parseEntity(ta.target_id).entryId;
     })) !== null && _b !== void 0 ? _b : []);
 }
 function collectFeatures(annotationsContext, annotationCollector) {
     return tslib_1.__awaiter(this, void 0, void 0, function* () {
-        const annotationsRequestContext = {
-            histogram: false,
-            groupId: annotationsContext.groupId,
-            group: GqlTypes_1.GroupReference.SequenceIdentity,
-            sources: [GqlTypes_1.Source.PdbInstance],
-            filters: [{
-                    source: GqlTypes_1.Source.PdbInstance,
-                    operation: GqlTypes_1.OperationType.Equals,
-                    field: GqlTypes_1.FieldName.Type,
-                    values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
-                }, {
-                    source: GqlTypes_1.Source.PdbInstance,
-                    operation: GqlTypes_1.OperationType.Contains,
-                    field: GqlTypes_1.FieldName.TargetId,
-                    values: annotationsContext.targetList
-                }],
-            externalTrackBuilder: annotationsContext.externalTrackBuilder
-        };
-        return yield annotationCollector.collect(annotationsRequestContext);
+        return yield annotationCollector.collect(Object.assign(Object.assign({}, buildGroupAnnotationQuery(annotationsContext)), { isSummary: false, externalTrackBuilder: annotationsContext.externalTrackBuilder }));
     });
 }
+function buildGroupAnnotationQuery(annotationsContext) {
+    return {
+        group: GqlTypes_1.GroupReference.SequenceIdentity,
+        groupId: annotationsContext.groupId,
+        sources: [GqlTypes_1.AnnotationReference.PdbInstance],
+        filters: [{
+                source: GqlTypes_1.AnnotationReference.PdbInstance,
+                operation: GqlTypes_1.OperationType.Equals,
+                field: GqlTypes_1.FieldName.Type,
+                values: [GqlTypes_1.FeaturesType.UnobservedResidueXyz, GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt]
+            }, {
+                source: GqlTypes_1.AnnotationReference.PdbInstance,
+                operation: GqlTypes_1.OperationType.Contains,
+                field: GqlTypes_1.FieldName.TargetId,
+                values: annotationsContext.targetList
+            }]
+    };
+}

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAnnotation.js

@@ -11,7 +11,7 @@ const annotationConfigMap = acm;
 class RcsbFvGroupAnnotation extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     protectedBuild() {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
+            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o;
             const buildConfig = this.buildConfig;
             assertDefined(buildConfig.group), assertDefined(buildConfig.groupId), assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page);
             const alignmentRequestContext = {
@@ -34,10 +34,11 @@ class RcsbFvGroupAnnotation extends RcsbFvAbstractModule_1.RcsbFvAbstractModule
             const annotationsRequestContext = {
                 group: buildConfig.group,
                 groupId: buildConfig.groupId,
-                sources: (_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.sources,
-                filters: (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.filters,
-                annotationProcessing: (_k = buildConfig.additionalConfig) === null || _k === void 0 ? void 0 : _k.annotationProcessing,
-                externalTrackBuilder: (_l = buildConfig.additionalConfig) === null || _l === void 0 ? void 0 : _l.externalTrackBuilder
+                isSummary: typeof ((_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.isAnnotationsGroupSummary) === "boolean" ? buildConfig.additionalConfig.isAnnotationsGroupSummary : true,
+                sources: (_k = (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.sources) !== null && _k !== void 0 ? _k : [],
+                filters: (_l = buildConfig.additionalConfig) === null || _l === void 0 ? void 0 : _l.filters,
+                annotationProcessing: (_m = buildConfig.additionalConfig) === null || _m === void 0 ? void 0 : _m.annotationProcessing,
+                externalTrackBuilder: (_o = buildConfig.additionalConfig) === null || _o === void 0 ? void 0 : _o.externalTrackBuilder
             };
             const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
             yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap);

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvInstance.js

@@ -16,7 +16,7 @@ class RcsbFvInstance extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
             const buildConfig = this.buildConfig;
             const instanceId = buildConfig.instanceId;
             assertDefined(instanceId);
-            const source = [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.Uniprot];
+            const source = [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.PdbInstance, GqlTypes_1.AnnotationReference.Uniprot];
             const alignmentRequestContext = {
                 queryId: instanceId,
                 from: GqlTypes_1.SequenceReference.PdbInstance,

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.d.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 export declare class RcsbFvInterface extends RcsbFvAbstractModule {
     private instanceId;
@@ -8,5 +8,5 @@ export declare class RcsbFvInterface extends RcsbFvAbstractModule {
     private titleSuffix;
     private trackTitle;
 }
-export declare function interfaceAnnotations(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
-export declare function filter(ann: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+export declare function interfaceAnnotations(annotations: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
+export declare function filter(ann: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.js

@@ -25,7 +25,7 @@ class RcsbFvInterface extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
             const instanceId = buildConfig.instanceId;
             assertDefined(instanceId);
             this.instanceId = instanceId;
-            const source = [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.Uniprot, GqlTypes_1.Source.PdbInterface];
+            const source = [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.PdbInstance, GqlTypes_1.AnnotationReference.Uniprot, GqlTypes_1.AnnotationReference.PdbInterface];
             const alignmentRequestContext = {
                 queryId: instanceId,
                 from: GqlTypes_1.SequenceReference.PdbInstance,
@@ -67,7 +67,7 @@ class RcsbFvInterface extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     typeSuffix(ann, d) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (ann.source === GqlTypes_1.Source.PdbInterface && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_id)) {
+            if (ann.source === GqlTypes_1.AnnotationReference.PdbInterface && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_id)) {
                 return ann.target_identifiers.interface_id + "|" + ann.target_identifiers.interface_partner_index;
             }
         });
@@ -75,26 +75,28 @@ class RcsbFvInterface extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     titleSuffix(rcsbContext) {
         return ((ann, d) => tslib_1.__awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (ann.source === GqlTypes_1.Source.PdbInterface) {
-                if (!ann.target_id)
+            if (ann.source === GqlTypes_1.AnnotationReference.PdbInterface) {
+                if (!ann.target_id || !ann.target_identifiers)
                     return "";
                 const interfaceTranslate = yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getInterfaceToInstance(ann.target_id);
                 const chain = this.instanceId.split(TagDelimiter_1.TagDelimiter.instance)[1];
-                const chPair = interfaceTranslate.getInstances(ann.target_id);
+                const interfaceId = TagDelimiter_1.TagDelimiter.getInterfaceId(ann.target_identifiers);
+                const chPair = interfaceTranslate.getInstances(interfaceId);
                 if (!chPair)
                     return "";
                 const asym = chPair[0] == chain ? chPair[1] : chPair[0];
                 const auth = (yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntityToInstance(this.instanceId.split(TagDelimiter_1.TagDelimiter.instance)[0])).translateAsymToAuth(asym);
-                const operators = interfaceTranslate.getOperatorIds(ann.target_id);
+                const operators = interfaceTranslate.getOperatorIds(interfaceId);
                 let partnerOperator = "";
-                if (operators && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_partner_index) && rcsbContext && Array.isArray(rcsbContext.operatorIds)) {
-                    const opIndex = operators[ann.target_identifiers.interface_partner_index].map(o => o.join("-")).indexOf(rcsbContext.operatorIds.join("-"));
+                const partner_idx = (_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_partner_index;
+                if (operators && typeof partner_idx == "number" && rcsbContext && Array.isArray(rcsbContext.operatorIds)) {
+                    const opIndex = operators[partner_idx].map(o => o.join("-")).indexOf(rcsbContext.operatorIds.join("-"));
                     if (opIndex < 0) {
                         console.error(`Operator Id ${rcsbContext.operatorIds.join("-")} not found in [[${operators[0]}],[${operators[1]}]]`);
                         console.error(ann.target_identifiers);
                     }
                     else {
-                        partnerOperator = TagDelimiter_1.TagDelimiter.operatorComposition + operators[1 - ann.target_identifiers.interface_partner_index][opIndex].join(TagDelimiter_1.TagDelimiter.operatorComposition);
+                        partnerOperator = TagDelimiter_1.TagDelimiter.operatorComposition + operators[1 - partner_idx][opIndex].join(TagDelimiter_1.TagDelimiter.operatorComposition);
                     }
                 }
                 return (asym == auth ? asym : `${asym}[auth ${auth}]`) + partnerOperator;
@@ -103,7 +105,7 @@ class RcsbFvInterface extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     }
     trackTitle(ann, d) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            if (ann.source === GqlTypes_1.Source.PdbInterface && d.type === FeatureType_1.FeatureType.BurialFraction) {
+            if (ann.source === GqlTypes_1.AnnotationReference.PdbInterface && d.type === FeatureType_1.FeatureType.BurialFraction) {
                 return "BINDING CHAIN ";
             }
         });

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.d.ts

@@ -1,6 +1,6 @@
 import { RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { RcsbFv } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFv";
-import { AlignmentResponse, Feature, FilterInput, GroupReference, SequenceReference, Source, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, Features, AnnotationFilterInput, GroupReference, SequenceReference, AnnotationReference, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AnnotationCollectorInterface, AnnotationProcessingInterface, AnnotationsCollectConfig } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
@@ -22,8 +22,8 @@ export type RcsbContextType = Partial<{
     operatorIds: Array<string>;
 }>;
 export interface RcsbFvAdditionalConfig {
-    sources?: Array<Source>;
-    filters?: Array<FilterInput>;
+    sources?: Array<AnnotationReference>;
+    filters?: Array<AnnotationFilterInput>;
     alignmentFilter?: Array<string>;
     hideAlignments?: boolean;
     bottomAlignments?: boolean;
@@ -33,12 +33,12 @@ export interface RcsbFvAdditionalConfig {
     externalTrackBuilder?: ExternalTrackBuilderInterface;
     page?: {
         first: number;
-        after: string;
+        after: number;
     };
     excludeLogo?: boolean;
     rcsbContext?: RcsbContextType;
     trackConfigModifier?: {
-        alignment?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignmentResponse: AlignmentResponse, alignmentIndex: number) => Promise<Partial<RcsbFvRowConfigInterface>>;
+        alignment?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignmentResponse: SequenceAlignments, alignmentIndex: number) => Promise<Partial<RcsbFvRowConfigInterface>>;
         annotations?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>;
     };
     externalUiComponents?: {
@@ -46,13 +46,14 @@ export interface RcsbFvAdditionalConfig {
         replace?: UiComponentType<any>[];
     };
     dataProvider?: RcsbModuleDataProviderInterface;
+    isAnnotationsGroupSummary?: boolean;
 }
 export interface RcsbModuleDataProviderInterface {
     alignments?: {
         collector: AlignmentCollectorInterface;
         context: AlignmentCollectConfig;
         trackFactories?: {
-            alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
+            alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]>;
             sequenceTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, string]>;
         };
     };
@@ -67,7 +68,7 @@ export interface RcsbFvModuleBuildInterface {
     queryId?: string;
     from?: SequenceReference;
     to?: SequenceReference;
-    sources?: Array<Source>;
+    sources?: Array<AnnotationReference>;
     entityId?: string;
     instanceId?: string;
     upAcc?: string;
@@ -95,8 +96,8 @@ export interface RcsbFvModulePublicInterface<P extends {
     [k: string]: any;
 } = {}> {
     getTargets(): Promise<Array<string>>;
-    getAlignmentResponse(): Promise<AlignmentResponse>;
-    getFeatures(): Promise<Array<Feature>>;
+    getAlignmentResponse(): Promise<SequenceAlignments>;
+    getFeatures(): Promise<Array<Features>>;
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface<P, S, R, M>>>;
     getFv(): RcsbFv<P, S, R, M>;
     wait(): Promise<void>;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvProteinSequence.js

@@ -11,9 +11,11 @@ class RcsbFvProteinSequence extends RcsbFvAbstractModule_1.RcsbFvAbstractModule
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             var _a, _b, _c, _d, _e;
             const buildConfig = this.buildConfig;
+            if (!buildConfig.from || !buildConfig.to)
+                return;
             const queryId = buildConfig.queryId;
             assertDefined(queryId);
-            const source = (_a = buildConfig.sources) !== null && _a !== void 0 ? _a : [GqlTypes_1.Source.Uniprot];
+            const source = (_a = buildConfig.sources) !== null && _a !== void 0 ? _a : [GqlTypes_1.AnnotationReference.Uniprot];
             const alignmentRequestContext = {
                 queryId: queryId,
                 from: buildConfig.from,

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvUniprot.js

@@ -15,7 +15,7 @@ class RcsbFvUniprot extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
             const buildConfig = this.buildConfig;
             const upAcc = buildConfig.upAcc;
             assertDefined(upAcc);
-            const source = [GqlTypes_1.Source.Uniprot];
+            const source = [GqlTypes_1.AnnotationReference.Uniprot];
             const alignmentRequestContext = {
                 queryId: upAcc,
                 from: GqlTypes_1.SequenceReference.Uniprot,
@@ -28,7 +28,7 @@ class RcsbFvUniprot extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
             const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.alignmentFilter);
             const trackFactory = new MsaAlignmentTrackFactory_1.MsaAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator());
             const alignmentFeatures = yield collectFeatures(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) == GqlTypes_1.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) == GqlTypes_1.Type.MaQaMetricLocalTypePlddt) })); }));
+            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) == GqlTypes_1.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) == GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt) })); }));
             yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
                 alignmentTrackFactory: trackFactory
             });
@@ -61,12 +61,12 @@ function collectFeatures(upAcc) {
         return yield RcsbClient_1.rcsbClient.requestRcsbPdbAnnotations({
             queryId: upAcc,
             reference: GqlTypes_1.SequenceReference.Uniprot,
-            sources: [GqlTypes_1.Source.PdbInstance],
+            sources: [GqlTypes_1.AnnotationReference.PdbInstance],
             filters: [{
-                    source: GqlTypes_1.Source.PdbInstance,
+                    source: GqlTypes_1.AnnotationReference.PdbInstance,
                     operation: GqlTypes_1.OperationType.Equals,
                     field: GqlTypes_1.FieldName.Type,
-                    values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
+                    values: [GqlTypes_1.FeaturesType.UnobservedResidueXyz, GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt]
                 }]
         });
     });