@rcsb/rcsb-saguaro-app 6.3.2-dev-js-seqcoord.13 → 6.3.3

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory.d.ts

@@ -1,16 +1,16 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { SequenceAnnotations, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-export declare class PlainObservedAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
+export declare class PlainObservedAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private alignmentTrackFactory;
     private unObservedResidues;
     private readonly instanceEntityMap;
     private readonly entityInstanceNumberMap;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<RcsbFvRowConfigInterface>;
-    prepareFeatures(unObservedRegions: Array<SequenceAnnotations>): Promise<void>;
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(unObservedRegions: Array<AnnotationFeatures>): Promise<void>;
     private collectFeatureEntryProperties;
     private prepareFeaturesAlignmentMap;
     private alignedRegionToTrackElementList;

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainObservedAlignmentTrackFactory.js

@@ -108,4 +108,3 @@ export class PlainObservedAlignmentTrackFactory {
         });
     }
 }
-//# sourceMappingURL=PlainObservedAlignmentTrackFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.d.ts

@@ -1,16 +1,16 @@
 import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AlignedRegions, SequenceAnnotations, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignedRegion, AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AlignmentContextInterface, PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-export declare class PositionalScoreAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
+export declare class PositionalScoreAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private alignmentTrackFactory;
     private positionalScores;
     private readonly instanceEntityMap;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignedRegionToTrackElementList?: (region: AlignedRegions, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
-    prepareFeatures(positionalScores: Array<SequenceAnnotations>): Promise<void>;
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(positionalScores: Array<AnnotationFeatures>): Promise<void>;
     private collectFeatureEntryProperties;
     private prepareFeaturesAlignmentMap;
     private alignedRegionToTrackElementList;

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { Operator } from "../../../../RcsbUtils/Helpers/Operator";
 import { range } from "lodash";
 import { PlainAlignmentTrackFactory } from "./PlainAlignmentTrackFactory";
@@ -105,11 +105,10 @@ export class PositionalScoreAlignmentTrackFactory {
                     source: TrackUtils.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
                     provenanceName: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).name,
                     provenanceColor: TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).color,
-                    type: FeaturesType.MaQaMetricLocalTypeOther,
+                    type: Type.MaQaMetricLocalTypeOther,
                 }, alignmentContext));
             });
         }
         return outRegions;
     }
 }
-//# sourceMappingURL=PositionalScoreAlignmentTrackFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory.js

@@ -75,4 +75,3 @@ export class SequenceTrackFactory {
         return o;
     }
 }
-//# sourceMappingURL=SequenceTrackFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryInterface.js

@@ -1,2 +1 @@
 export {};
-//# sourceMappingURL=TrackFactoryInterface.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AlignmentTrackTitleFactory.d.ts

@@ -1,13 +1,13 @@
 import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-import { TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class AlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
+export declare class AlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private readonly experimentalTrackTitleFactory;
     private readonly modelTrackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
-    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
+    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
 }

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AlignmentTrackTitleFactory.js

@@ -32,4 +32,3 @@ export class AlignmentTrackTitleFactory {
         });
     }
 }
-//# sourceMappingURL=AlignmentTrackTitleFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AnnotationsTrackTitleFactory.js

@@ -32,4 +32,3 @@ export class AnnotationsTrackTitleFactory {
 function buildRowTitle(annConfig) {
     return annConfig.prefix ? FeatureTools.parseLink(annConfig.title) : annConfig.title;
 }
-//# sourceMappingURL=AnnotationsTrackTitleFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ExperimentalAlignmentTrackTitleFactory.d.ts

@@ -1,13 +1,13 @@
 import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-import { TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class ExperimentalAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
+export declare class ExperimentalAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private readonly entityInstanceTranslator;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
-    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
+    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
     private buildInstanceId;
 }

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ExperimentalAlignmentTrackTitleFactory.js

@@ -75,4 +75,3 @@ export class ExperimentalAlignmentTrackTitleFactory {
         return TagDelimiter.parseInstance(targetId).entryId + TagDelimiter.instance + (labelAsymId === authAsymId || !authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]");
     }
 }
-//# sourceMappingURL=ExperimentalAlignmentTrackTitleFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/InstanceSequenceTrackTitleFactory.js

@@ -20,4 +20,3 @@ export class InstanceSequenceTrackTitleFactory {
         });
     }
 }
-//# sourceMappingURL=InstanceSequenceTrackTitleFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ModelAlignmentTrackTitleFactory.d.ts

@@ -1,12 +1,12 @@
 import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
 import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
-import { TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class ModelAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
+export declare class ModelAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private readonly alignmentTrackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
-    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
+    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
 }

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ModelAlignmentTrackTitleFactory.js

@@ -25,4 +25,3 @@ export class ModelAlignmentTrackTitleFactory {
         });
     }
 }
-//# sourceMappingURL=ModelAlignmentTrackTitleFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/SequenceTrackTitleFactory.js

@@ -65,4 +65,3 @@ export class SequenceTrackTitleFactory {
         return (labelAsymId === authAsymId || !authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]");
     }
 }
-//# sourceMappingURL=SequenceTrackTitleFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryInterface.js

@@ -1,2 +1 @@
 export {};
-//# sourceMappingURL=TrackTitleFactoryInterface.js.map

package/lib/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.js

@@ -1,7 +1,7 @@
 import { __awaiter } from "tslib";
 import { jsx as _jsx } from "react/jsx-runtime";
 import React from "react";
-import { FieldName, OperationType, AnnotationReference, } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FieldName, OperationType, Source, } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { searchRequestProperty } from "../../RcsbSeacrh/SearchRequestProperty";
 import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
 import { RcsbTabs } from "../RcsbFvComponents/RcsbTabs";
@@ -80,34 +80,33 @@ export class GroupPfvTabs extends React.Component {
     }
     renderPositionalFeatureViewer(tabKey) {
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h;
+            var _a, _b, _c, _d, _e;
             switch (tabKey) {
                 case ALIGNMENT:
-                    this.featureViewers.set(tabKey, yield GPA.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 GPA.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 GPA.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: AnnotationReference.PdbInstance,
+                    this.featureViewers.set(tabKey, yield GPA.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: Source.PdbInstance,
                                 field: FieldName.TargetId,
                                 operation: OperationType.Equals,
-                                values: (_d = this.filterInstances) !== null && _d !== void 0 ? _d : []
+                                values: this.filterInstances
                             }] : undefined })));
                     break;
                 case STRUCTURAL_FEATURES:
-                    this.featureViewers.set(tabKey, yield GPA.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: AnnotationReference.PdbInstance,
+                    this.featureViewers.set(tabKey, yield GPA.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: Source.PdbInstance,
                                 field: FieldName.TargetId,
                                 operation: OperationType.Equals,
-                                values: (_g = this.filterInstances) !== null && _g !== void 0 ? _g : []
+                                values: this.filterInstances
                             }, {
-                                source: AnnotationReference.PdbEntity,
+                                source: Source.PdbEntity,
                                 field: FieldName.TargetId,
                                 operation: OperationType.Equals,
-                                values: (_h = this.filterEntities) !== null && _h !== void 0 ? _h : []
+                                values: this.filterEntities
                             }] : undefined })));
                     break;
             }
         });
     }
 }
-//# sourceMappingURL=GroupPfvTabs.js.map

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

@@ -3,7 +3,7 @@ import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnu
 import { RcsbFvUniprotBuilder } from "../../RcsbFvBuilder/RcsbFvUniprotBuilder";
 import { groupExternalTrackBuilder } from "../../../RcsbUtils/TrackGenerators/GroupExternalTrackBuilder";
 import { RcsbFvGroupBuilder } from "../../RcsbFvBuilder/RcsbFvGroupBuilder";
-import { FieldName, GroupReference, OperationType, SequenceReference, AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FieldName, GroupReference, OperationType, SequenceReference, Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { alignmentGlobalLigandBindingSite } from "../../../RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite";
 import { RcsbTabs } from "../../RcsbFvComponents/RcsbTabs";
 import { GroupPfvUI } from "../../../RcsbFvUI/GroupPfvUI";
@@ -32,12 +32,12 @@ export var GroupPfvApp;
                         component: 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.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
                                         first: state.first,
-                                        after: state.after
+                                        after: state.after.toString()
                                     }, excludeLogo: true }));
                             }
                         }
@@ -53,15 +53,15 @@ export 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: FieldName.Type,
-                        values: [FeaturesType.HelixP, FeaturesType.Sheet, FeaturesType.Cath, FeaturesType.Scop],
+                        values: [Type.HelixP, Type.Sheet, Type.Cath, Type.Scop],
                         operation: OperationType.Equals,
-                        source: AnnotationReference.PdbInstance
+                        source: Source.PdbInstance
                     }, {
                         field: FieldName.Type,
-                        values: [FeaturesType.Pfam],
+                        values: [Type.Pfam],
                         operation: OperationType.Equals,
-                        source: AnnotationReference.PdbEntity
-                    }], sources: [AnnotationReference.PdbInstance, AnnotationReference.PdbEntity], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: groupExternalTrackBuilder() });
+                        source: Source.PdbEntity
+                    }], sources: [Source.PdbInstance, Source.PdbEntity], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: groupExternalTrackBuilder() });
             // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
             const pfvArgs = [
                 getReferenceFromGroupProvenance(groupProvenanceId),
@@ -78,10 +78,10 @@ export 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: FieldName.Type,
-                        values: [FeaturesType.BindingSite],
+                        values: [Type.BindingSite],
                         operation: OperationType.Equals,
-                        source: AnnotationReference.PdbInstance
-                    }], sources: [AnnotationReference.PdbInstance], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: alignmentGlobalLigandBindingSite(), isAnnotationsGroupSummary: false });
+                        source: Source.PdbInstance
+                    }], sources: [Source.PdbInstance], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: alignmentGlobalLigandBindingSite() });
             // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
             const pfvArgs = [
                 getReferenceFromGroupProvenance(groupProvenanceId),
@@ -95,31 +95,25 @@ export var GroupPfvApp;
     GroupPfvApp.bindingSites = bindingSites;
 })(GroupPfvApp || (GroupPfvApp = {}));
 function annotationPositionFrequencyProcessing(nTargets) {
-    const targetValues = new Map();
-    const targetSet = new Map();
+    const targets = new Map();
     return {
         getAnnotationValue: (feature) => {
             var _a, _b, _c, _d;
-            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;
+            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;
+            }
         },
         computeAnnotationValue: (annotationTracks) => {
             annotationTracks.forEach((at, type) => {
-                var _a;
-                const isType = (type.includes(FeaturesType.Cath) || type.includes(FeaturesType.Scop) || type.includes(FeaturesType.BindingSite) || type.includes(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;
+                const N = (type.includes(Type.Cath) || type.includes(Type.Scop) || type.includes(Type.BindingSite) || type.includes(Type.Pfam)) ? targets.get(type) : nTargets;
                 at.forEach((ann, positionKey) => {
-                    if (ann.source != AnnotationReference.PdbInterface)
-                        ann.value = Math.round(100 * ann.value / (N !== null && N !== void 0 ? N : 1)) / 100;
+                    if (ann.source != Source.PdbInterface)
+                        ann.value = Math.ceil(1000 * ann.value / (N !== null && N !== void 0 ? N : 1)) / 1000;
                 });
             });
         }
@@ -135,4 +129,3 @@ export function getReferenceFromGroupProvenance(groupProvenanceId) {
             return GroupReference.MatchingUniprotAccession;
     }
 }
-//# sourceMappingURL=GroupPfvApp.js.map

package/lib/RcsbFvWeb/RcsbFvGroup/RcsbFvGroupTabsBuilder.js

@@ -10,4 +10,3 @@ export class RcsbFvGroupTabsBuilder {
         createRoot(element).render(_jsx(GroupPfvTabs, { groupProvenanceId: groupProvenanceId, groupId: groupId, searchQuery: query, additionalConfig: additionalConfig }));
     }
 }
-//# sourceMappingURL=RcsbFvGroupTabsBuilder.js.map

package/lib/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 { SequenceAlignments, SequenceAnnotations, Features, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse, AnnotationFeatures, Feature, TargetAlignment } 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<SequenceAlignments>;
-    getFeatures(): Promise<Array<Features>>;
+    getAlignmentResponse(): Promise<AlignmentResponse>;
+    getFeatures(): Promise<Array<Feature>>;
     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: SequenceAlignments, trackFactories?: {
-        alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]>;
+    protected buildAlignmentTracks(alignmentRequestContext: AlignmentRequestContextType, alignmentResponse: AlignmentResponse, trackFactories?: {
+        alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
         sequenceTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, string]>;
     }): Promise<void>;
-    protected buildAnnotationsTrack(annotationsRequestContext: AnnotationRequestContext, annotationsFeatures: SequenceAnnotations[], annotationConfigMap?: AnnotationConfigInterface): Promise<void>;
+    protected buildAnnotationsTrack(annotationsRequestContext: AnnotationRequestContext, annotationsFeatures: AnnotationFeatures[], annotationConfigMap?: AnnotationConfigInterface): Promise<void>;
     protected getBoardConfig(): Promise<RcsbFvBoardConfigInterface>;
     protected getRowsConfig(): Promise<Array<RcsbFvRowConfigInterface>>;
     private buildExternalTracks;

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.js

@@ -141,4 +141,3 @@ export class RcsbFvAbstractModule {
         });
     }
 }
-//# sourceMappingURL=RcsbFvAbstractModule.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.js

@@ -28,14 +28,14 @@ function sequenceDisplayDynamicUpdate(reference, ranges, trackWidth) {
                     from: reference,
                     to: SequenceReference.NcbiGenome
                 });
-            })).then((alignments) => {
+            })).then(alignments => {
                 const out = new RcsbFvTrackData();
                 alignments.forEach((a, n) => {
                     var _c;
                     if (a.query_sequence == null)
                         return;
                     const sequence = a.query_sequence.split("");
-                    (_c = a.target_alignments) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
+                    (_c = a.target_alignment) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
                         var _c;
                         if (!ta)
                             return;
@@ -110,12 +110,12 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
                 from: SequenceReference.PdbEntity,
                 to: to
             });
-        })).then((result) => {
+        })).then(result => {
             result.forEach(a => {
                 var _c;
                 if (!a)
                     return;
-                (_c = a.target_alignments) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
+                (_c = a.target_alignment) === 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);
                 });
@@ -141,8 +141,8 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
     collectPdbWorkerResults(ar, pdbEntityId, chrId) {
         return __awaiter(this, void 0, void 0, function* () {
             var _c, _d;
-            assertElementListDefined(ar.target_alignments);
-            const exonTracks = this.collectExons(ar.target_alignments, "target", RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, SequenceReference.PdbEntity, chrId);
+            assertElementListDefined(ar.target_alignment);
+            const exonTracks = this.collectExons(ar.target_alignment, "target", RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, SequenceReference.PdbEntity, chrId);
             this.pdbEntityTrack = this.mergeExonTracks(exonTracks, 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];
@@ -316,8 +316,8 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
             this.completeTasks++;
             const e = this.targetAlignmentList.get(reference);
             assertDefined(e);
-            assertElementListDefined(alignment.target_alignments);
-            e[index] = alignment.target_alignments;
+            assertElementListDefined(alignment.target_alignment);
+            e[index] = alignment.target_alignment;
             console.log("Completed " + Math.floor(this.completeTasks / this.nTasks * 100) + "%");
             if (forcePlot) {
                 yield this.plot();
@@ -736,4 +736,3 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
     concatAlignmentAndAnnotationTracks() {
     }
 }
-//# sourceMappingURL=RcsbFvChromosome.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvDataProvider.js

@@ -23,4 +23,3 @@ export class RcsbFvDataProvider extends RcsbFvAbstractModule {
         this.rowConfigData = this.referenceTrack ? [this.referenceTrack].concat(this.alignmentTracks) : this.alignmentTracks;
     }
 }
-//# sourceMappingURL=RcsbFvDataProvider.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvEntity.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
@@ -26,7 +26,7 @@ export class RcsbFvEntity extends RcsbFvAbstractModule {
             const annotationsRequestContext = {
                 queryId: buildConfig.entityId,
                 reference: SequenceReference.PdbEntity,
-                sources: (_d = (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.sources) !== null && _d !== void 0 ? _d : [AnnotationReference.PdbEntity, AnnotationReference.Uniprot],
+                sources: (_d = (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.sources) !== null && _d !== void 0 ? _d : [Source.PdbEntity, Source.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,
@@ -59,7 +59,7 @@ export class RcsbFvEntity extends RcsbFvAbstractModule {
         return __awaiter(this, void 0, void 0, function* () {
             if (!ann.target_id)
                 return;
-            if (this.polymerEntityInstance != null && ann.source === AnnotationReference.PdbInstance) {
+            if (this.polymerEntityInstance != null && ann.source === Source.PdbInstance) {
                 const labelAsymId = ann.target_id.split(TagDelimiter.instance)[1];
                 const authAsymId = this.polymerEntityInstance.translateAsymToAuth(labelAsymId);
                 return labelAsymId === authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]";
@@ -67,4 +67,3 @@ export class RcsbFvEntity extends RcsbFvAbstractModule {
         });
     }
 }
-//# sourceMappingURL=RcsbFvEntity.js.map