@rcsb/rcsb-saguaro-app 6.3.7-dev-js-seqcoord.14 → 6.3.7-react-downgrade.0

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

@@ -7,6 +7,7 @@ const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego
 const MsaAlignmentTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory");
 const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
 var assertDefined = Assertions_1.Assertions.assertDefined;
+const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
 const Operator_1 = require("../../RcsbUtils/Helpers/Operator");
 const RcsbRequestContextManager_1 = require("../../RcsbRequest/RcsbRequestContextManager");
 class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
@@ -29,15 +30,16 @@ class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
                 sequencePrefix: (_f = (_e = buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.sequencePrefix) !== null && _f !== void 0 ? _f : "",
                 externalTrackBuilder: (_g = buildConfig.additionalConfig) === null || _g === void 0 ? void 0 : _g.externalTrackBuilder
             };
+            collectNextPage(alignmentRequestContext, this.alignmentCollector, this.annotationCollector).then(() => console.log("Next page ready"));
             const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.alignmentFilter);
             const trackFactory = new MsaAlignmentTrackFactory_1.MsaAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator());
-            const targetList = yield uniqueTargetList(alignmentResponse);
+            const targetList = uniqueTargetList(alignmentResponse);
             const alignmentFeatures = yield collectFeatures({
                 groupId: buildConfig.groupId,
                 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.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 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 this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
                 alignmentTrackFactory: trackFactory
             });
@@ -54,37 +56,50 @@ class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     }
 }
 exports.RcsbFvGroupAlignment = RcsbFvGroupAlignment;
-function uniqueTargetList(alignmentResponse) {
+function collectNextPage(alignmentRequestContext, alignmentCollector, annotationCollector) {
     return tslib_1.__awaiter(this, void 0, void 0, function* () {
-        var _a, _b;
-        const entityIds = 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 ta.target_id;
-        })) !== null && _b !== void 0 ? _b : []);
-        const instanceIds = (yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntityProperties(entityIds)).map(e => e.rcsbId);
-        return Operator_1.Operator.uniqueValues(instanceIds !== null && instanceIds !== void 0 ? instanceIds : []);
+        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()
+            } }));
+        const targetList = uniqueTargetList(alignmentResponse);
+        if (alignmentRequestContext.groupId) {
+            const alignmentFeatures = yield collectFeatures({
+                groupId: alignmentRequestContext.groupId,
+                targetList
+            }, annotationCollector);
+            const featureTargetList = Operator_1.Operator.uniqueValues(alignmentFeatures.map(af => { var _a; return TagDelimiter_1.TagDelimiter.parseInstance((_a = af.target_id) !== null && _a !== void 0 ? _a : "").entryId; }));
+            Operator_1.Operator.arrayChunk(featureTargetList, 100).forEach(ids => RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntryProperties(ids));
+        }
     });
 }
+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 => {
+        assertDefined(ta === null || ta === void 0 ? void 0 : ta.target_id);
+        return TagDelimiter_1.TagDelimiter.parseEntity(ta.target_id).entryId;
+    })) !== null && _b !== void 0 ? _b : []);
+}
 function collectFeatures(annotationsContext, annotationCollector) {
     return tslib_1.__awaiter(this, void 0, void 0, function* () {
-        return yield annotationCollector.collect(Object.assign(Object.assign({}, buildGroupAnnotationQuery(annotationsContext)), { isSummary: false, externalTrackBuilder: annotationsContext.externalTrackBuilder }));
+        const annotationsRequestContext = {
+            histogram: false,
+            groupId: annotationsContext.groupId,
+            group: GqlTypes_1.GroupReference.SequenceIdentity,
+            sources: [GqlTypes_1.Source.PdbInstance],
+            filters: [{
+                    source: GqlTypes_1.Source.PdbInstance,
+                    operation: GqlTypes_1.OperationType.Equals,
+                    field: GqlTypes_1.FieldName.Type,
+                    values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
+                }, {
+                    source: GqlTypes_1.Source.PdbInstance,
+                    operation: GqlTypes_1.OperationType.Contains,
+                    field: GqlTypes_1.FieldName.TargetId,
+                    values: annotationsContext.targetList
+                }],
+            externalTrackBuilder: annotationsContext.externalTrackBuilder
+        };
+        return yield annotationCollector.collect(annotationsRequestContext);
     });
 }
-function buildGroupAnnotationQuery(annotationsContext) {
-    return {
-        group: GqlTypes_1.GroupReference.SequenceIdentity,
-        groupId: annotationsContext.groupId,
-        sources: [GqlTypes_1.AnnotationReference.PdbInstance],
-        filters: [{
-                source: GqlTypes_1.AnnotationReference.PdbInstance,
-                operation: GqlTypes_1.OperationType.Equals,
-                field: GqlTypes_1.FieldName.Type,
-                values: [GqlTypes_1.FeaturesType.UnobservedResidueXyz, GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt]
-            }, {
-                source: GqlTypes_1.AnnotationReference.PdbInstance,
-                operation: GqlTypes_1.OperationType.Equals,
-                field: GqlTypes_1.FieldName.TargetId,
-                values: annotationsContext.targetList
-            }]
-    };
-}

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

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

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

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

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

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

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

@@ -1,6 +1,6 @@
 import { RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { RcsbFv } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFv";
-import { 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/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvProteinSequence.js

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

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

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

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

@@ -30,14 +30,14 @@ class RcsbFvUniprotAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule
             const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_g = buildConfig.additionalConfig) === null || _g === void 0 ? void 0 : _g.alignmentFilter);
             const trackFactory = new MsaAlignmentTrackFactory_1.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) == 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 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 this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
                 alignmentTrackFactory: trackFactory
             });
             const annotationsRequestContext = {
                 queryId: buildConfig.upAcc,
                 reference: GqlTypes_1.SequenceReference.Uniprot,
-                sources: [GqlTypes_1.AnnotationReference.Uniprot],
+                sources: [GqlTypes_1.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
             };
@@ -63,12 +63,12 @@ function collectFeatures(upAcc) {
         return yield RcsbClient_1.rcsbClient.requestRcsbPdbAnnotations({
             queryId: upAcc,
             reference: GqlTypes_1.SequenceReference.Uniprot,
-            sources: [GqlTypes_1.AnnotationReference.PdbInstance],
+            sources: [GqlTypes_1.Source.PdbInstance],
             filters: [{
-                    source: GqlTypes_1.AnnotationReference.PdbInstance,
+                    source: GqlTypes_1.Source.PdbInstance,
                     operation: GqlTypes_1.OperationType.Equals,
                     field: GqlTypes_1.FieldName.Type,
-                    values: [GqlTypes_1.FeaturesType.UnobservedResidueXyz, GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt]
+                    values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
                 }]
         });
     });

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

@@ -24,7 +24,7 @@ class RcsbFvUniprotEntity extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
             const filters = [{
                     field: GqlTypes_1.FieldName.TargetId,
                     operation: GqlTypes_1.OperationType.Equals,
-                    source: GqlTypes_1.AnnotationReference.PdbEntity,
+                    source: GqlTypes_1.Source.PdbEntity,
                     values: [entityId]
                 }];
             const alignmentRequestContext = {
@@ -40,7 +40,7 @@ class RcsbFvUniprotEntity extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
             const annotationsRequestContext = {
                 queryId: upAcc,
                 reference: GqlTypes_1.SequenceReference.Uniprot,
-                sources: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.sources) ? additionalConfig.sources : [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.Uniprot],
+                sources: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.sources) ? additionalConfig.sources : [GqlTypes_1.Source.PdbEntity, GqlTypes_1.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,
@@ -67,7 +67,7 @@ class RcsbFvUniprotEntity extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
     titleSuffix(ann, d) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (this.polymerEntityInstance != null && ann.source === GqlTypes_1.AnnotationReference.PdbInstance) {
+            if (this.polymerEntityInstance != null && ann.source === GqlTypes_1.Source.PdbInstance) {
                 const labelAsymId = (_a = ann.target_id) === null || _a === void 0 ? void 0 : _a.split(TagDelimiter_1.TagDelimiter.instance)[1];
                 if (!labelAsymId)
                     return;

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

@@ -17,18 +17,18 @@ class RcsbFvUniprotInstance extends RcsbFvAbstractModule_1.RcsbFvAbstractModule
             const instanceId = buildConfig.instanceId;
             const additionalConfig = buildConfig.additionalConfig;
             assertDefined(entityId), assertDefined(instanceId), assertDefined(upAcc);
-            let sources = [GqlTypes_1.AnnotationReference.Uniprot, GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.PdbInstance];
+            let sources = [GqlTypes_1.Source.Uniprot, GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance];
             if (additionalConfig != null && additionalConfig.sources != null && additionalConfig.sources.length > 0)
                 sources = additionalConfig.sources;
             let filters = [{
                     field: GqlTypes_1.FieldName.TargetId,
                     operation: GqlTypes_1.OperationType.Equals,
-                    source: GqlTypes_1.AnnotationReference.PdbEntity,
+                    source: GqlTypes_1.Source.PdbEntity,
                     values: [entityId]
                 }, {
                     field: GqlTypes_1.FieldName.TargetId,
                     operation: GqlTypes_1.OperationType.Contains,
-                    source: GqlTypes_1.AnnotationReference.PdbInstance,
+                    source: GqlTypes_1.Source.PdbInstance,
                     values: [instanceId]
                 }];
             if (additionalConfig != null && additionalConfig.filters != null && additionalConfig.filters.length > 0)

package/lib/commonjs/RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip.js

@@ -60,7 +60,7 @@ 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);

package/lib/commonjs/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/commonjs/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/commonjs/RcsbGraphQL/RcsbClient.js

@@ -16,7 +16,6 @@ const RcsbQueryMultipleInstanceSequences_1 = require("./RcsbQueryMultipleInstanc
 class RcsbClientClass {
     constructor(get) {
         this.rcsbQueryAnnotations = new RcsbQueryAnnotations_1.RcsbQueryAnnotations(get.borrego);
-        this.rcsbQueryGroupAnnotationsSummary = new RcsbQueryAnnotations_1.RcsbQueryGroupAnnotationsSumary(get.borrego);
         this.rcsbQueryGroupAnnotations = new RcsbQueryAnnotations_1.RcsbQueryGroupAnnotations(get.borrego);
         this.rcsbQueryAlignment = new RcsbQueryAlignment_1.RcsbQueryAlignment(get.borrego);
         this.rcsbQueryGroupAlignment = new RcsbQueryAlignment_1.RcsbQueryGroupAlignment(get.borrego);
@@ -33,11 +32,6 @@ class RcsbClientClass {
             return yield this.rcsbQueryAnnotations.request(requestConfig);
         });
     }
-    requestRcsbPdbGroupAnnotationsSummary(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return yield this.rcsbQueryGroupAnnotationsSummary.request(requestConfig);
-        });
-    }
     requestRcsbPdbGroupAnnotations(requestConfig) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             return yield this.rcsbQueryGroupAnnotations.request(requestConfig);

package/lib/commonjs/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/commonjs/RcsbGraphQL/RcsbQueryAlignment.js

@@ -18,7 +18,7 @@ class RcsbQueryAlignment {
                     to: requestConfig.to,
                     range: requestConfig.range
                 }, QueryAlignments_graphql_1.default);
-                return result.alignments;
+                return result.alignment;
             }
             catch (error) {
                 console.error(error);
@@ -36,7 +36,7 @@ class RcsbQueryGroupAlignment {
         return tslib_1.__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 ? QueryGroupAlignmentsNoLogo_graphql_1.default : QueryGroupAlignments_graphql_1.default);
-                return result.group_alignments;
+                return result.group_alignment;
             }
             catch (error) {
                 console.error(error);

package/lib/commonjs/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>>;
 }