@rcsb/rcsb-saguaro-app 6.2.5-dev-js-seqcoord.2 → 6.2.6

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInstance.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 { buriedResidues, buriedResiduesFilter } from "../../RcsbUtils/TrackGenerators/BuriedResidues";
 import { SequenceTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory";
@@ -13,7 +13,7 @@ export class RcsbFvInstance extends RcsbFvAbstractModule {
             const buildConfig = this.buildConfig;
             const instanceId = buildConfig.instanceId;
             assertDefined(instanceId);
-            const source = [AnnotationReference.PdbEntity, AnnotationReference.PdbInstance, AnnotationReference.Uniprot];
+            const source = [Source.PdbEntity, Source.PdbInstance, Source.Uniprot];
             const alignmentRequestContext = {
                 queryId: instanceId,
                 from: SequenceReference.PdbInstance,
@@ -50,4 +50,3 @@ export class RcsbFvInstance extends RcsbFvAbstractModule {
                     this.alignmentTracks.concat(this.annotationTracks);
     }
 }
-//# sourceMappingURL=RcsbFvInstance.js.map

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

@@ -1,4 +1,4 @@
-import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures } 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<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
-export declare function filter(ann: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
+export declare function interfaceAnnotations(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+export declare function filter(ann: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.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 * as acm from "../../RcsbAnnotationConfig/RcsbAnnotationConfig.ac.json";
 import { buriedResidues, buriedResiduesFilter } from "../../RcsbUtils/TrackGenerators/BuriedResidues";
@@ -20,7 +20,7 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
             const instanceId = buildConfig.instanceId;
             assertDefined(instanceId);
             this.instanceId = instanceId;
-            const source = [AnnotationReference.PdbEntity, AnnotationReference.PdbInstance, AnnotationReference.Uniprot, AnnotationReference.PdbInterface];
+            const source = [Source.PdbEntity, Source.PdbInstance, Source.Uniprot, Source.PdbInterface];
             const alignmentRequestContext = {
                 queryId: instanceId,
                 from: SequenceReference.PdbInstance,
@@ -62,7 +62,7 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
     typeSuffix(ann, d) {
         return __awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (ann.source === AnnotationReference.PdbInterface && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_id)) {
+            if (ann.source === Source.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;
             }
         });
@@ -70,12 +70,12 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
     titleSuffix(rcsbContext) {
         return ((ann, d) => __awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (ann.source === AnnotationReference.PdbInterface) {
+            if (ann.source === Source.PdbInterface) {
                 if (!ann.target_id)
                     return "";
                 const interfaceTranslate = yield rcsbRequestCtxManager.getInterfaceToInstance(ann.target_id);
                 const chain = this.instanceId.split(TagDelimiter.instance)[1];
-                const chPair = interfaceTranslate.getInstances(ann.target_id.split(":")[0]);
+                const chPair = interfaceTranslate.getInstances(ann.target_id);
                 if (!chPair)
                     return "";
                 const asym = chPair[0] == chain ? chPair[1] : chPair[0];
@@ -98,7 +98,7 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
     }
     trackTitle(ann, d) {
         return __awaiter(this, void 0, void 0, function* () {
-            if (ann.source === AnnotationReference.PdbInterface && d.type === FeatureType.BurialFraction) {
+            if (ann.source === Source.PdbInterface && d.type === FeatureType.BurialFraction) {
                 return "BINDING CHAIN ";
             }
         });
@@ -121,4 +121,3 @@ export function filter(ann) {
         resolve(burialFractionFilter(buriedResiduesFilter(ann)));
     });
 }
-//# sourceMappingURL=RcsbFvInterface.js.map

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

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.js

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

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvPairwiseAlignment.js

@@ -19,4 +19,3 @@ export class RcsbFvPairwiseAlignment extends RcsbFvAbstractModule {
     concatAlignmentAndAnnotationTracks() {
     }
 }
-//# sourceMappingURL=RcsbFvPairwiseAlignment.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvProteinSequence.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { 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;
@@ -8,11 +8,9 @@ export class RcsbFvProteinSequence extends RcsbFvAbstractModule {
         return __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 : [AnnotationReference.Uniprot];
+            const source = (_a = buildConfig.sources) !== null && _a !== void 0 ? _a : [Source.Uniprot];
             const alignmentRequestContext = {
                 queryId: queryId,
                 from: buildConfig.from,
@@ -50,4 +48,3 @@ export class RcsbFvProteinSequence extends RcsbFvAbstractModule {
         }
     }
 }
-//# sourceMappingURL=RcsbFvProteinSequence.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprot.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FieldName, OperationType, SequenceReference, Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { MsaAlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
@@ -12,7 +12,7 @@ export class RcsbFvUniprot extends RcsbFvAbstractModule {
             const buildConfig = this.buildConfig;
             const upAcc = buildConfig.upAcc;
             assertDefined(upAcc);
-            const source = [AnnotationReference.Uniprot];
+            const source = [Source.Uniprot];
             const alignmentRequestContext = {
                 queryId: upAcc,
                 from: SequenceReference.Uniprot,
@@ -25,7 +25,7 @@ export class RcsbFvUniprot extends RcsbFvAbstractModule {
             const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.alignmentFilter);
             const trackFactory = new 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) == 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) == FeaturesType.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) == Type.UnobservedResidueXyz) })); }), alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.MaQaMetricLocalTypePlddt) })); }));
             yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
                 alignmentTrackFactory: trackFactory
             });
@@ -57,14 +57,13 @@ function collectFeatures(upAcc) {
         return yield rcsbClient.requestRcsbPdbAnnotations({
             queryId: upAcc,
             reference: SequenceReference.Uniprot,
-            sources: [AnnotationReference.PdbInstance],
+            sources: [Source.PdbInstance],
             filters: [{
-                    source: AnnotationReference.PdbInstance,
+                    source: Source.PdbInstance,
                     operation: OperationType.Equals,
                     field: FieldName.Type,
-                    values: [FeaturesType.UnobservedResidueXyz, FeaturesType.MaQaMetricLocalTypePlddt]
+                    values: [Type.UnobservedResidueXyz, Type.MaQaMetricLocalTypePlddt]
                 }]
         });
     });
 }
-//# sourceMappingURL=RcsbFvUniprot.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotAlignment.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-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 { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { MsaAlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
@@ -27,14 +27,14 @@ export class RcsbFvUniprotAlignment extends RcsbFvAbstractModule {
             const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_g = buildConfig.additionalConfig) === null || _g === void 0 ? void 0 : _g.alignmentFilter);
             const trackFactory = new MsaAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator());
             const alignmentFeatures = yield collectFeatures(buildConfig.upAcc);
-            yield trackFactory.prepareFeatures(alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == 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) == FeaturesType.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) == Type.UnobservedResidueXyz) })); }), alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.MaQaMetricLocalTypePlddt) })); }));
             yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
                 alignmentTrackFactory: trackFactory
             });
             const annotationsRequestContext = {
                 queryId: buildConfig.upAcc,
                 reference: SequenceReference.Uniprot,
-                sources: [AnnotationReference.Uniprot],
+                sources: [Source.Uniprot],
                 annotationProcessing: (_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.annotationProcessing,
                 externalTrackBuilder: (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.externalTrackBuilder
             };
@@ -59,14 +59,13 @@ function collectFeatures(upAcc) {
         return yield rcsbClient.requestRcsbPdbAnnotations({
             queryId: upAcc,
             reference: SequenceReference.Uniprot,
-            sources: [AnnotationReference.PdbInstance],
+            sources: [Source.PdbInstance],
             filters: [{
-                    source: AnnotationReference.PdbInstance,
+                    source: Source.PdbInstance,
                     operation: OperationType.Equals,
                     field: FieldName.Type,
-                    values: [FeaturesType.UnobservedResidueXyz, FeaturesType.MaQaMetricLocalTypePlddt]
+                    values: [Type.UnobservedResidueXyz, Type.MaQaMetricLocalTypePlddt]
                 }]
         });
     });
 }
-//# sourceMappingURL=RcsbFvUniprotAlignment.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotEntity.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FieldName, OperationType, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
@@ -21,7 +21,7 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
             const filters = [{
                     field: FieldName.TargetId,
                     operation: OperationType.Equals,
-                    source: AnnotationReference.PdbEntity,
+                    source: Source.PdbEntity,
                     values: [entityId]
                 }];
             const alignmentRequestContext = {
@@ -37,7 +37,7 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
             const annotationsRequestContext = {
                 queryId: upAcc,
                 reference: SequenceReference.Uniprot,
-                sources: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.sources) ? additionalConfig.sources : [AnnotationReference.PdbEntity, AnnotationReference.Uniprot],
+                sources: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.sources) ? additionalConfig.sources : [Source.PdbEntity, Source.Uniprot],
                 filters: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) instanceof Array ? additionalConfig.filters.concat(filters) : filters,
                 titleSuffix: this.titleSuffix.bind(this),
                 annotationProcessing: (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.annotationProcessing,
@@ -64,7 +64,7 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
     titleSuffix(ann, d) {
         return __awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (this.polymerEntityInstance != null && ann.source === AnnotationReference.PdbInstance) {
+            if (this.polymerEntityInstance != null && ann.source === Source.PdbInstance) {
                 const labelAsymId = (_a = ann.target_id) === null || _a === void 0 ? void 0 : _a.split(TagDelimiter.instance)[1];
                 if (!labelAsymId)
                     return;
@@ -74,4 +74,3 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
         });
     }
 }
-//# sourceMappingURL=RcsbFvUniprotEntity.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotInstance.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FieldName, OperationType, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { buriedResidues, buriedResiduesFilter } from "../../RcsbUtils/TrackGenerators/BuriedResidues";
 import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
@@ -14,18 +14,18 @@ export class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
             const instanceId = buildConfig.instanceId;
             const additionalConfig = buildConfig.additionalConfig;
             assertDefined(entityId), assertDefined(instanceId), assertDefined(upAcc);
-            let sources = [AnnotationReference.Uniprot, AnnotationReference.PdbEntity, AnnotationReference.PdbInstance];
+            let sources = [Source.Uniprot, Source.PdbEntity, Source.PdbInstance];
             if (additionalConfig != null && additionalConfig.sources != null && additionalConfig.sources.length > 0)
                 sources = additionalConfig.sources;
             let filters = [{
                     field: FieldName.TargetId,
                     operation: OperationType.Equals,
-                    source: AnnotationReference.PdbEntity,
+                    source: Source.PdbEntity,
                     values: [entityId]
                 }, {
                     field: FieldName.TargetId,
                     operation: OperationType.Contains,
-                    source: AnnotationReference.PdbInstance,
+                    source: Source.PdbInstance,
                     values: [instanceId]
                 }];
             if (additionalConfig != null && additionalConfig.filters != null && additionalConfig.filters.length > 0)
@@ -61,4 +61,3 @@ export class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
         this.rowConfigData = [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks);
     }
 }
-//# sourceMappingURL=RcsbFvUniprotInstance.js.map

package/lib/RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip.js

@@ -57,7 +57,7 @@ export class RcsbFvTooltip {
         if (d.description == null || d.description.length == 0)
             return undefined;
         const tooltipDescriptionDiv = document.createElement("div");
-        d.description.slice(0, 2).forEach(des => {
+        d.description.forEach(des => {
             const desDiv = document.createElement("div");
             desDiv.append(des);
             tooltipDescriptionDiv.append(desDiv);
@@ -80,4 +80,3 @@ export class RcsbFvTooltip {
         return b;
     }
 }
-//# sourceMappingURL=RcsbFvTooltip.js.map

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.d.ts

@@ -1,11 +1,11 @@
-import { QueryAlignmentsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { QueryAlignmentArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare class RcsbFvAlignmentCollectorQueue {
     private readonly nWorkers;
     private readonly workerList;
     private readonly taskQueue;
     private isQueueActive;
     constructor(nWorkers?: number);
-    sendTask(request: QueryAlignmentsArgs, callback: (data: any) => void): void;
+    sendTask(request: QueryAlignmentArgs, callback: (data: any) => void): void;
     private activateQueue;
     private recursiveExec;
     terminateWorkers(): void;

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.js

@@ -65,4 +65,3 @@ export class RcsbFvAlignmentCollectorQueue {
         });
     }
 }
-//# sourceMappingURL=RcsbFvAlignmentCollectorQueue.js.map

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

@@ -8,4 +8,3 @@ worker.onmessage = function (message) {
         postMessage(result);
     });
 };
-//# sourceMappingURL=RcsbFvAlignmentCollectorWorker.worker.js.map

package/lib/RcsbGraphQL/RcsbClient.d.ts

@@ -1,10 +1,9 @@
 import { RcsbQueryGroupAlignmentArguments } from "./RcsbQueryAlignment";
-import { SequenceAlignments, SequenceAnnotations, QueryAlignmentsArgs, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse, AnnotationFeatures, QueryAlignmentArgs, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { CoreAssembly, CoreEntry, CoreInterface, CorePolymerEntity, QueryAssembliesArgs, GroupPolymerEntity, QueryEntriesArgs, QueryEntryArgs, QueryInterfacesArgs, QueryPolymer_EntitiesArgs, QueryPolymer_Entity_GroupArgs, QueryPolymer_Entity_InstancesArgs, CorePolymerEntityInstance } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
 import { GraphQLRequest } from "@rcsb/rcsb-api-tools";
 declare class RcsbClientClass {
     private readonly rcsbQueryAnnotations;
-    private readonly rcsbQueryGroupAnnotationsSummary;
     private readonly rcsbQueryGroupAnnotations;
     private readonly rcsbQueryAlignment;
     private readonly rcsbQueryGroupAlignment;
@@ -19,11 +18,10 @@ declare class RcsbClientClass {
         borrego: () => GraphQLRequest;
         yosemite: () => GraphQLRequest;
     });
-    requestRcsbPdbAnnotations(requestConfig: QueryAnnotationsArgs): Promise<Array<SequenceAnnotations>>;
-    requestRcsbPdbGroupAnnotationsSummary(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<SequenceAnnotations>>;
-    requestRcsbPdbGroupAnnotations(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<SequenceAnnotations>>;
-    requestAlignment(requestConfig: QueryAlignmentsArgs): Promise<SequenceAlignments>;
-    requestGroupAlignment(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<SequenceAlignments>;
+    requestRcsbPdbAnnotations(requestConfig: QueryAnnotationsArgs): Promise<Array<AnnotationFeatures>>;
+    requestRcsbPdbGroupAnnotations(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<AnnotationFeatures>>;
+    requestAlignment(requestConfig: QueryAlignmentArgs): Promise<AlignmentResponse>;
+    requestGroupAlignment(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<AlignmentResponse>;
     requestEntityInstances(requestConfig: QueryEntryArgs): Promise<CoreEntry>;
     requestMultipleEntityInstances(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<CorePolymerEntity>>;
     requestGroupInfo(requestConfig: QueryPolymer_Entity_GroupArgs): Promise<GroupPolymerEntity>;

package/lib/RcsbGraphQL/RcsbClient.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { RcsbQueryAnnotations, RcsbQueryGroupAnnotations, RcsbQueryGroupAnnotationsSumary } from "./RcsbQueryAnnotations";
+import { RcsbQueryAnnotations, RcsbQueryGroupAnnotations } from "./RcsbQueryAnnotations";
 import { RcsbQueryAlignment, RcsbQueryGroupAlignment } from "./RcsbQueryAlignment";
 import { RcsbQueryEntryInstances } from "./RcsbQueryEntryInstances";
 import { RcsbQueryMultipleEntityInstances } from "./RcsbQueryMultipleEntityInstances";
@@ -13,7 +13,6 @@ import { RcsbQueryMultipleInstanceSequences } from "./RcsbQueryMultipleInstanceS
 class RcsbClientClass {
     constructor(get) {
         this.rcsbQueryAnnotations = new RcsbQueryAnnotations(get.borrego);
-        this.rcsbQueryGroupAnnotationsSummary = new RcsbQueryGroupAnnotationsSumary(get.borrego);
         this.rcsbQueryGroupAnnotations = new RcsbQueryGroupAnnotations(get.borrego);
         this.rcsbQueryAlignment = new RcsbQueryAlignment(get.borrego);
         this.rcsbQueryGroupAlignment = new RcsbQueryGroupAlignment(get.borrego);
@@ -30,11 +29,6 @@ class RcsbClientClass {
             return yield this.rcsbQueryAnnotations.request(requestConfig);
         });
     }
-    requestRcsbPdbGroupAnnotationsSummary(requestConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return yield this.rcsbQueryGroupAnnotationsSummary.request(requestConfig);
-        });
-    }
     requestRcsbPdbGroupAnnotations(requestConfig) {
         return __awaiter(this, void 0, void 0, function* () {
             return yield this.rcsbQueryGroupAnnotations.request(requestConfig);
@@ -87,4 +81,3 @@ class RcsbClientClass {
     }
 }
 export const rcsbClient = new RcsbClientClass({ borrego: () => rcsbRequestClient.borrego, yosemite: () => rcsbRequestClient.yosemite });
-//# sourceMappingURL=RcsbClient.js.map

package/lib/RcsbGraphQL/RcsbCoreQueryInterface.js

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

package/lib/RcsbGraphQL/RcsbQueryAlignment.d.ts

@@ -1,20 +1,20 @@
-import { SequenceAlignments, QueryAlignmentsArgs, QueryGroup_AlignmentsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse, QueryAlignmentArgs, QueryGroup_AlignmentArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
 import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
-export declare class RcsbQueryAlignment implements RcsbCoreQueryInterface<QueryAlignmentsArgs, SequenceAlignments> {
+export declare class RcsbQueryAlignment implements RcsbCoreQueryInterface<QueryAlignmentArgs, AlignmentResponse> {
     readonly getClient: () => GraphQLRequest;
     constructor(getClient: () => GraphQLRequest);
-    request(requestConfig: QueryAlignmentsArgs): Promise<SequenceAlignments>;
+    request(requestConfig: QueryAlignmentArgs): Promise<AlignmentResponse>;
 }
-export type RcsbQueryGroupAlignmentArguments = QueryGroup_AlignmentsArgs & {
+export type RcsbQueryGroupAlignmentArguments = QueryGroup_AlignmentArgs & {
     page: {
         first: number;
-        after: number;
+        after: string;
     };
     excludeLogo?: boolean;
 };
-export declare class RcsbQueryGroupAlignment implements RcsbCoreQueryInterface<RcsbQueryGroupAlignmentArguments, SequenceAlignments> {
+export declare class RcsbQueryGroupAlignment implements RcsbCoreQueryInterface<RcsbQueryGroupAlignmentArguments, AlignmentResponse> {
     readonly getClient: () => GraphQLRequest;
     constructor(getClient: () => GraphQLRequest);
-    request(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<SequenceAlignments>;
+    request(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<AlignmentResponse>;
 }

package/lib/RcsbGraphQL/RcsbQueryAlignment.js

@@ -15,7 +15,7 @@ export class RcsbQueryAlignment {
                     to: requestConfig.to,
                     range: requestConfig.range
                 }, queryAlignment);
-                return result.alignments;
+                return result.alignment;
             }
             catch (error) {
                 console.error(error);
@@ -32,7 +32,7 @@ export class RcsbQueryGroupAlignment {
         return __awaiter(this, void 0, void 0, function* () {
             try {
                 const result = yield this.getClient().request({ group: requestConfig.group, groupId: requestConfig.groupId, filter: requestConfig.filter, first: requestConfig.page.first, after: requestConfig.page.after }, requestConfig.excludeLogo ? queryGroupAlignmentNoLogo : queryGroupAlignment);
-                return result.group_alignments;
+                return result.group_alignment;
             }
             catch (error) {
                 console.error(error);
@@ -41,4 +41,3 @@ export class RcsbQueryGroupAlignment {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryAlignment.js.map

package/lib/RcsbGraphQL/RcsbQueryAnnotations.d.ts

@@ -1,18 +1,13 @@
-import { SequenceAnnotations, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbCoreQueryInterface } from "./RcsbCoreQueryInterface";
 import { GraphQLRequest } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest";
-export declare class RcsbQueryAnnotations implements RcsbCoreQueryInterface<QueryAnnotationsArgs, Array<SequenceAnnotations>> {
+export declare class RcsbQueryAnnotations implements RcsbCoreQueryInterface<QueryAnnotationsArgs, Array<AnnotationFeatures>> {
     readonly getClient: () => GraphQLRequest;
     constructor(getClient: () => GraphQLRequest);
-    request(requestConfig: QueryAnnotationsArgs): Promise<Array<SequenceAnnotations>>;
+    request(requestConfig: QueryAnnotationsArgs): Promise<Array<AnnotationFeatures>>;
 }
-export declare class RcsbQueryGroupAnnotationsSumary implements RcsbCoreQueryInterface<QueryGroup_AnnotationsArgs, Array<SequenceAnnotations>> {
+export declare class RcsbQueryGroupAnnotations implements RcsbCoreQueryInterface<QueryGroup_AnnotationsArgs, Array<AnnotationFeatures>> {
     readonly getClient: () => GraphQLRequest;
     constructor(getClient: () => GraphQLRequest);
-    request(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<SequenceAnnotations>>;
-}
-export declare class RcsbQueryGroupAnnotations implements RcsbCoreQueryInterface<QueryGroup_AnnotationsArgs, Array<SequenceAnnotations>> {
-    readonly getClient: () => GraphQLRequest;
-    constructor(getClient: () => GraphQLRequest);
-    request(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<SequenceAnnotations>>;
+    request(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<AnnotationFeatures>>;
 }

package/lib/RcsbGraphQL/RcsbQueryAnnotations.js

@@ -1,6 +1,5 @@
 import { __awaiter } from "tslib";
 import queryAnnotations from "../RcsbQueries/Borrego/QueryAnnotations.graphql";
-import queryGroupAnnotationsSummary from "../RcsbQueries/Borrego/QueryGroupAnnotationsSummary.graphql";
 import queryGroupAnnotations from "../RcsbQueries/Borrego/QueryGroupAnnotations.graphql";
 export class RcsbQueryAnnotations {
     constructor(getClient) {
@@ -9,7 +8,13 @@ export class RcsbQueryAnnotations {
     request(requestConfig) {
         return __awaiter(this, void 0, void 0, function* () {
             try {
-                const annotationsResponse = yield this.getClient().request(requestConfig, queryAnnotations);
+                const annotationsResponse = yield this.getClient().request({
+                    queryId: requestConfig.queryId,
+                    reference: requestConfig.reference,
+                    sources: requestConfig.sources,
+                    filters: requestConfig.filters,
+                    range: requestConfig.range
+                }, queryAnnotations);
                 return annotationsResponse.annotations;
             }
             catch (error) {
@@ -19,23 +24,6 @@ export class RcsbQueryAnnotations {
         });
     }
 }
-export class RcsbQueryGroupAnnotationsSumary {
-    constructor(getClient) {
-        this.getClient = getClient;
-    }
-    request(requestConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            try {
-                const annotationsResponse = yield this.getClient().request(requestConfig, queryGroupAnnotationsSummary);
-                return annotationsResponse.group_annotations_summary;
-            }
-            catch (error) {
-                console.error(error);
-                throw error;
-            }
-        });
-    }
-}
 export class RcsbQueryGroupAnnotations {
     constructor(getClient) {
         this.getClient = getClient;
@@ -53,4 +41,3 @@ export class RcsbQueryGroupAnnotations {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryAnnotations.js.map

package/lib/RcsbGraphQL/RcsbQueryAssemblyInterfaces.js

@@ -17,4 +17,3 @@ export class RcsbQueryAssemblyInterfaces {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryAssemblyInterfaces.js.map

package/lib/RcsbGraphQL/RcsbQueryEntryInstances.js

@@ -19,4 +19,3 @@ export class RcsbQueryEntryInstances {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryEntryInstances.js.map

package/lib/RcsbGraphQL/RcsbQueryGroup.js

@@ -19,4 +19,3 @@ export class RcsbQueryGroup {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryGroup.js.map

package/lib/RcsbGraphQL/RcsbQueryInterfaceInstances.js

@@ -17,4 +17,3 @@ export class RcsbQueryInterfaceInstances {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryInterfaceInstances.js.map

package/lib/RcsbGraphQL/RcsbQueryMultipleEntityInstances.js

@@ -19,4 +19,3 @@ export class RcsbQueryMultipleEntityInstances {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryMultipleEntityInstances.js.map