@rcsb/rcsb-saguaro-app 6.2.3 → 6.2.5-dev-js-seqcoord.1

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

@@ -79,31 +79,31 @@ class GroupPfvTabs extends react_1.default.Component {
         });
     }
     renderPositionalFeatureViewer(tabKey) {
-        var _a, _b, _c, _d, _e;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getReferenceFromGroupProvenance = exports.GroupPfvApp = void 0;
+exports.GroupPfvApp = void 0;
+exports.getReferenceFromGroupProvenance = getReferenceFromGroupProvenance;
 const tslib_1 = require("tslib");
 const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
 const RcsbFvUniprotBuilder_1 = require("../../RcsbFvBuilder/RcsbFvUniprotBuilder");
@@ -15,8 +16,8 @@ const PaginationItemComponent_1 = require("../../../RcsbFvUI/Components/Paginati
 var GroupPfvApp;
 (function (GroupPfvApp) {
     function alignment(elementId, groupProvenanceId, groupId, entityCount, additionalConfig) {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
             switch (groupProvenanceId) {
                 case DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession:
                     return RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotMultipleEntitySequenceFv(elementId, elementId + RcsbTabs_1.RcsbTabs.SELECT_SUFFIX, groupId, {}, additionalConfig);
@@ -35,12 +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 }));
                             }
                         }
@@ -52,19 +53,19 @@ var GroupPfvApp;
     }
     GroupPfvApp.alignment = alignment;
     function structure(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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),
@@ -77,14 +78,14 @@ var GroupPfvApp;
     }
     GroupPfvApp.structure = structure;
     function bindingSites(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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),
@@ -98,25 +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;
                 });
             });
         }
@@ -132,4 +139,3 @@ function getReferenceFromGroupProvenance(groupProvenanceId) {
             return GqlTypes_1.GroupReference.MatchingUniprotAccession;
     }
 }
-exports.getReferenceFromGroupProvenance = getReferenceFromGroupProvenance;

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/RcsbFvAbstractModule.js

@@ -94,8 +94,8 @@ class RcsbFvAbstractModule {
         return this.rcsbFvRowUpdatePromise;
     }
     buildAlignmentTracks(alignmentRequestContext, alignmentResponse, trackFactories) {
-        var _a, _b, _c, _d;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c, _d;
             const sequenceTrackFactory = (_a = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.sequenceTrackFactory) !== null && _a !== void 0 ? _a : new SequenceTrackFactory_1.SequenceTrackFactory(this.getPolymerEntityInstanceTranslator());
             if (alignmentResponse.query_sequence)
                 this.referenceTrack = yield sequenceTrackFactory.getTrack(alignmentRequestContext, alignmentResponse.query_sequence);
@@ -104,8 +104,8 @@ class RcsbFvAbstractModule {
         });
     }
     buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap) {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const defaultAnnotationConfigMap = annotationConfigMap !== null && annotationConfigMap !== void 0 ? annotationConfigMap : acm;
             const annotationsBlockFactory = new AnnotationsBlockFactory_1.AnnotationsBlockFactory(new AnnotationBlockManager_1.AnnotationBlockManager(new AnnotationTrackManager_1.AnnotationTrackManagerFactory(), new RcsbAnnotationConfig_1.RcsbAnnotationConfig(defaultAnnotationConfigMap), this.getPolymerEntityInstanceTranslator()), new AnnotationsTrackFactory_1.AnnotationsTrackFactory(), (_b = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.trackConfigModifier) === null || _b === void 0 ? void 0 : _b.annotations);
             this.annotationTracks = yield annotationsBlockFactory.getBlock(annotationsRequestContext, annotationsFeatures);
@@ -122,8 +122,8 @@ class RcsbFvAbstractModule {
         });
     }
     buildExternalTracks() {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const externalTrackBuilder = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder;
             const rcsbContext = (_b = this.buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.rcsbContext;
             if (!externalTrackBuilder)

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);
                 });
@@ -142,10 +142,10 @@ class RcsbFvChromosome extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
         this.collectChromosomeAlignments(chrId, GqlTypes_1.SequenceReference.NcbiProtein);
     }
     collectPdbWorkerResults(ar, pdbEntityId, chrId) {
-        var _c, _d;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            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);
+            var _c, _d;
+            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();
@@ -624,8 +624,8 @@ class RcsbFvChromosome extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
         });
     }
     setDisplayView() {
-        var _c, _d, _e, _f, _g, _h, _j;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _c, _d, _e, _f, _g, _h, _j;
             if (this.entityBegin == 0 && this.entityEnd == 0 && ((_e = (_d = (_c = this.pdbEntityTrack) === null || _c === void 0 ? void 0 : _c.displayConfig) === null || _d === void 0 ? void 0 : _d.length) !== null && _e !== void 0 ? _e : 0) > 0) {
                 const d = (_f = this.pdbEntityTrack.displayConfig) === null || _f === void 0 ? void 0 : _f[0].displayData;
                 if (!d)
@@ -662,8 +662,8 @@ class RcsbFvChromosome extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
         });
     }
     plot() {
-        var _c, _d, _e, _f;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _c, _d, _e, _f;
             console.log("PROCESSING");
             let tracks = new Array();
             let ncbiTracks = new Array();

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

@@ -6,8 +6,8 @@ const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
 const PlainAlignmentTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory");
 class RcsbFvDataProvider extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     protectedBuild() {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o;
             if ((_b = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.dataProvider) === null || _b === void 0 ? void 0 : _b.alignments) {
                 this.alignmentCollector = this.buildConfig.additionalConfig.dataProvider.alignments.collector;
                 const alignmentResponse = yield this.alignmentCollector.collect(Object.assign({}, (_d = (_c = this.buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.dataProvider) === null || _d === void 0 ? void 0 : _d.alignments.context), (_e = this.buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.alignmentFilter);

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

@@ -14,8 +14,8 @@ class RcsbFvEntity extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
         this.unmodeledTrackBuilder = new UnmodeledTrackBuilder_1.UnmodeledTrackBuilder();
     }
     protectedBuild() {
-        var _a, _b, _c, _d, _e, _f, _g;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c, _d, _e, _f, _g;
             const buildConfig = this.buildConfig;
             assertDefined(buildConfig.entityId);
             const alignmentRequestContext = {
@@ -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

@@ -12,8 +12,8 @@ const Operator_1 = require("../../RcsbUtils/Helpers/Operator");
 const RcsbRequestContextManager_1 = require("../../RcsbRequest/RcsbRequestContextManager");
 class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     protectedBuild() {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
             const buildConfig = this.buildConfig;
             assertDefined(buildConfig.groupId), assertDefined(buildConfig.group), assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page);
             const alignmentRequestContext = {
@@ -39,7 +39,7 @@ 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
             });
@@ -60,7 +60,7 @@ function collectNextPage(alignmentRequestContext, alignmentCollector, annotation
     return tslib_1.__awaiter(this, void 0, void 0, function* () {
         const alignmentResponse = yield alignmentCollector.collect(Object.assign(Object.assign({}, alignmentRequestContext), { excludeLogo: true, page: {
                 first: alignmentRequestContext.page.first,
-                after: (parseInt(alignmentRequestContext.page.after) + alignmentRequestContext.page.first).toString()
+                after: alignmentRequestContext.page.after + alignmentRequestContext.page.first
             } }));
         const targetList = uniqueTargetList(alignmentResponse);
         if (alignmentRequestContext.groupId) {
@@ -75,7 +75,7 @@ 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 : []);
@@ -83,17 +83,17 @@ function uniqueTargetList(alignmentResponse) {
 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],
+            sources: [GqlTypes_1.AnnotationReference.PdbInstance],
+            isSummary: false,
             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]
                 }, {
-                    source: GqlTypes_1.Source.PdbInstance,
+                    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

@@ -10,8 +10,8 @@ var assertDefined = Assertions_1.Assertions.assertDefined;
 const annotationConfigMap = acm;
 class RcsbFvGroupAnnotation extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     protectedBuild() {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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

@@ -11,12 +11,12 @@ const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
 var assertDefined = Assertions_1.Assertions.assertDefined;
 class RcsbFvInstance extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     protectedBuild() {
-        var _a, _b, _c, _d;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c, _d;
             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

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.filter = exports.interfaceAnnotations = exports.RcsbFvInterface = void 0;
+exports.RcsbFvInterface = void 0;
+exports.interfaceAnnotations = interfaceAnnotations;
+exports.filter = filter;
 const tslib_1 = require("tslib");
 const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
 const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
@@ -17,13 +19,13 @@ const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimite
 const annotationConfigMap = acm;
 class RcsbFvInterface extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     protectedBuild() {
-        var _a, _b, _c, _d, _e;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c, _d, _e;
             const buildConfig = this.buildConfig;
             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,
@@ -63,9 +65,9 @@ class RcsbFvInterface extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
                     this.alignmentTracks.concat(this.annotationTracks);
     }
     typeSuffix(ann, d) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            if (ann.source === GqlTypes_1.Source.PdbInterface && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_id)) {
+            var _a;
+            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;
             }
         });
@@ -73,7 +75,7 @@ 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.source === GqlTypes_1.AnnotationReference.PdbInterface) {
                 if (!ann.target_id)
                     return "";
                 const interfaceTranslate = yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getInterfaceToInstance(ann.target_id);
@@ -101,7 +103,7 @@ 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 ";
             }
         });
@@ -120,10 +122,8 @@ function interfaceAnnotations(annotations) {
         resolve(out);
     });
 }
-exports.interfaceAnnotations = interfaceAnnotations;
 function filter(ann) {
     return new Promise(resolve => {
         resolve((0, BurialFraction_1.burialFractionFilter)((0, BuriedResidues_1.buriedResiduesFilter)(ann)));
     });
 }
-exports.filter = filter;

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/RcsbFvPairwiseAlignment.js

@@ -8,8 +8,8 @@ const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
 var assertDefined = Assertions_1.Assertions.assertDefined;
 class RcsbFvPairwiseAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     protectedBuild() {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a;
             const buildConfig = this.buildConfig;
             assertDefined(buildConfig.psa);
             const pab = new PairwiseAlignmentBuilder_1.PairwiseAlignmentBuilder(buildConfig.psa);