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

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.Type.UnobservedResidueXyz) })); }), alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == GqlTypes_1.Type.MaQaMetricLocalTypePlddt) })); }));
+            yield trackFactory.prepareFeatures(alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == GqlTypes_1.FeaturesType.UnobservedResidueXyz) })); }), alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt) })); }));
             yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
                 alignmentTrackFactory: trackFactory
             });
             const annotationsRequestContext = {
                 queryId: buildConfig.upAcc,
                 reference: GqlTypes_1.SequenceReference.Uniprot,
-                sources: [GqlTypes_1.Source.Uniprot],
+                sources: [GqlTypes_1.AnnotationReference.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.Source.PdbInstance],
+            sources: [GqlTypes_1.AnnotationReference.PdbInstance],
             filters: [{
-                    source: GqlTypes_1.Source.PdbInstance,
+                    source: GqlTypes_1.AnnotationReference.PdbInstance,
                     operation: GqlTypes_1.OperationType.Equals,
                     field: GqlTypes_1.FieldName.Type,
-                    values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
+                    values: [GqlTypes_1.FeaturesType.UnobservedResidueXyz, GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt]
                 }]
         });
     });

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.Source.PdbEntity,
+                    source: GqlTypes_1.AnnotationReference.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.Source.PdbEntity, GqlTypes_1.Source.Uniprot],
+                sources: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.sources) ? additionalConfig.sources : [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.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.Source.PdbInstance) {
+            if (this.polymerEntityInstance != null && ann.source === GqlTypes_1.AnnotationReference.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.Source.Uniprot, GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance];
+            let sources = [GqlTypes_1.AnnotationReference.Uniprot, GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.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.Source.PdbEntity,
+                    source: GqlTypes_1.AnnotationReference.PdbEntity,
                     values: [entityId]
                 }, {
                     field: GqlTypes_1.FieldName.TargetId,
                     operation: GqlTypes_1.OperationType.Contains,
-                    source: GqlTypes_1.Source.PdbInstance,
+                    source: GqlTypes_1.AnnotationReference.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.forEach(des => {
+        d.description.slice(0, 2).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 { QueryAlignmentArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { QueryAlignmentsArgs } 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: QueryAlignmentArgs, callback: (data: any) => void): void;
+    sendTask(request: QueryAlignmentsArgs, callback: (data: any) => void): void;
     private activateQueue;
     private recursiveExec;
     terminateWorkers(): void;

package/lib/commonjs/RcsbGraphQL/RcsbClient.d.ts

@@ -1,9 +1,10 @@
 import { RcsbQueryGroupAlignmentArguments } from "./RcsbQueryAlignment";
-import { AlignmentResponse, AnnotationFeatures, QueryAlignmentArgs, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, SequenceAnnotations, QueryAlignmentsArgs, 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;
@@ -18,10 +19,11 @@ declare class RcsbClientClass {
         borrego: () => GraphQLRequest;
         yosemite: () => GraphQLRequest;
     });
-    requestRcsbPdbAnnotations(requestConfig: QueryAnnotationsArgs): Promise<Array<AnnotationFeatures>>;
-    requestRcsbPdbGroupAnnotations(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<AnnotationFeatures>>;
-    requestAlignment(requestConfig: QueryAlignmentArgs): Promise<AlignmentResponse>;
-    requestGroupAlignment(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<AlignmentResponse>;
+    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>;
     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

@@ -16,6 +16,7 @@ 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);
@@ -32,6 +33,11 @@ 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 { AlignmentResponse, QueryAlignmentArgs, QueryGroup_AlignmentArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, QueryAlignmentsArgs, QueryGroup_AlignmentsArgs } 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<QueryAlignmentArgs, AlignmentResponse> {
+export declare class RcsbQueryAlignment implements RcsbCoreQueryInterface<QueryAlignmentsArgs, SequenceAlignments> {
     readonly getClient: () => GraphQLRequest;
     constructor(getClient: () => GraphQLRequest);
-    request(requestConfig: QueryAlignmentArgs): Promise<AlignmentResponse>;
+    request(requestConfig: QueryAlignmentsArgs): Promise<SequenceAlignments>;
 }
-export type RcsbQueryGroupAlignmentArguments = QueryGroup_AlignmentArgs & {
+export type RcsbQueryGroupAlignmentArguments = QueryGroup_AlignmentsArgs & {
     page: {
         first: number;
-        after: string;
+        after: number;
     };
     excludeLogo?: boolean;
 };
-export declare class RcsbQueryGroupAlignment implements RcsbCoreQueryInterface<RcsbQueryGroupAlignmentArguments, AlignmentResponse> {
+export declare class RcsbQueryGroupAlignment implements RcsbCoreQueryInterface<RcsbQueryGroupAlignmentArguments, SequenceAlignments> {
     readonly getClient: () => GraphQLRequest;
     constructor(getClient: () => GraphQLRequest);
-    request(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<AlignmentResponse>;
+    request(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<SequenceAlignments>;
 }

package/lib/commonjs/RcsbGraphQL/RcsbQueryAlignment.js

@@ -18,7 +18,7 @@ class RcsbQueryAlignment {
                     to: requestConfig.to,
                     range: requestConfig.range
                 }, QueryAlignments_graphql_1.default);
-                return result.alignment;
+                return result.alignments;
             }
             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_alignment;
+                return result.group_alignments;
             }
             catch (error) {
                 console.error(error);

package/lib/commonjs/RcsbGraphQL/RcsbQueryAnnotations.d.ts

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

package/lib/commonjs/RcsbGraphQL/RcsbQueryAnnotations.js

@@ -1,8 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbQueryGroupAnnotations = exports.RcsbQueryAnnotations = void 0;
+exports.RcsbQueryGroupAnnotations = exports.RcsbQueryGroupAnnotationsSumary = exports.RcsbQueryAnnotations = void 0;
 const tslib_1 = require("tslib");
 const QueryAnnotations_graphql_1 = tslib_1.__importDefault(require("../RcsbQueries/Borrego/QueryAnnotations.graphql"));
+const QueryGroupAnnotationsSummary_graphql_1 = tslib_1.__importDefault(require("../RcsbQueries/Borrego/QueryGroupAnnotationsSummary.graphql"));
 const QueryGroupAnnotations_graphql_1 = tslib_1.__importDefault(require("../RcsbQueries/Borrego/QueryGroupAnnotations.graphql"));
 class RcsbQueryAnnotations {
     constructor(getClient) {
@@ -11,13 +12,7 @@ class RcsbQueryAnnotations {
     request(requestConfig) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             try {
-                const annotationsResponse = yield this.getClient().request({
-                    queryId: requestConfig.queryId,
-                    reference: requestConfig.reference,
-                    sources: requestConfig.sources,
-                    filters: requestConfig.filters,
-                    range: requestConfig.range
-                }, QueryAnnotations_graphql_1.default);
+                const annotationsResponse = yield this.getClient().request(requestConfig, QueryAnnotations_graphql_1.default);
                 return annotationsResponse.annotations;
             }
             catch (error) {
@@ -28,6 +23,24 @@ class RcsbQueryAnnotations {
     }
 }
 exports.RcsbQueryAnnotations = RcsbQueryAnnotations;
+class RcsbQueryGroupAnnotationsSumary {
+    constructor(getClient) {
+        this.getClient = getClient;
+    }
+    request(requestConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            try {
+                const annotationsResponse = yield this.getClient().request(requestConfig, QueryGroupAnnotationsSummary_graphql_1.default);
+                return annotationsResponse.group_annotations_summary;
+            }
+            catch (error) {
+                console.error(error);
+                throw error;
+            }
+        });
+    }
+}
+exports.RcsbQueryGroupAnnotationsSumary = RcsbQueryGroupAnnotationsSumary;
 class RcsbQueryGroupAnnotations {
     constructor(getClient) {
         this.getClient = getClient;

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/ResidueChartTools.js

@@ -56,7 +56,7 @@ var ResidueChartTools;
             const annotationsRequestContext = {
                 queryId: instanceId,
                 reference: GqlTypes_1.SequenceReference.PdbInstance,
-                sources: [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.Uniprot, GqlTypes_1.Source.PdbInterface],
+                sources: [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.PdbInstance, GqlTypes_1.AnnotationReference.Uniprot, GqlTypes_1.AnnotationReference.PdbInterface],
                 annotationGenerator: RcsbFvInterface_1.interfaceAnnotations,
                 annotationFilter: RcsbFvInterface_1.filter
             };

package/lib/commonjs/RcsbQueries/Borrego/QueryAlignments.graphql

@@ -1,12 +1,12 @@
-query QueryAlignment($queryId: String!, $from: SequenceReference, $to:SequenceReference, $range:[Int]){
-    alignment(
+query QueryAlignment($queryId: String!, $from: SequenceReference!, $to:SequenceReference!, $range:[Int!]){
+    alignments(
         queryId:$queryId
         from:$from
         to:$to
         range:$range
     ){
         query_sequence
-        target_alignment {
+        target_alignments {
             target_id
             orientation
             target_sequence

package/lib/commonjs/RcsbQueries/Borrego/QueryAnnotations.graphql

@@ -1,4 +1,10 @@
-query QueryAnnotations($queryId: String!, $reference: SequenceReference, $sources:[Source], $range:[Int], $filters: [FilterInput]){
+query QueryAnnotations(
+    $queryId: String!,
+    $reference: SequenceReference!,
+    $sources:[AnnotationReference!]!,
+    $range:[Int!],
+    $filters: [AnnotationFilterInput!]
+){
     annotations(
         queryId:$queryId
         reference:$reference

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAlignments.graphql

@@ -1,42 +1,37 @@
-query QueryGroupAlignment($group: GroupReference!, $groupId: String!, $filter: [String], $first: Int!, $after: String){
-    group_alignment(
+query QueryGroupAlignment(
+    $group: GroupReference!,
+    $groupId: String!,
+    $filter: [String!],
+    $first: Int,
+    $after: Int
+){
+    group_alignments(
         group: $group
         groupId: $groupId
         filter: $filter
     ){
         alignment_length
-        alignment_logo{
+        alignment_logo {
             symbol
             value
         }
         query_sequence
-        target_alignment_subset(first: $first, after: $after) {
-            pageInfo{
-                startCursor
-                endCursor
-                hasNextPage
-                hasPreviousPage
+        target_alignments(first: $first, offset: $after) {
+            target_id
+            orientation
+            target_sequence
+            coverage {
+                query_coverage
+                query_length
+                target_coverage
+                target_length
             }
-            edges{
-                node{
-                    target_id
-                    orientation
-                    target_sequence
-                    coverage {
-                        query_coverage
-                        query_length
-                        target_coverage
-                        target_length
-                    }
-                    aligned_regions {
-                        query_begin
-                        query_end
-                        target_begin
-                        target_end
-                        exon_shift
-                    }
-                }
-                cursor
+            aligned_regions {
+                query_begin
+                query_end
+                target_begin
+                target_end
+                exon_shift
             }
         }
     }

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAlignmentsNoLogo.graphql

@@ -1,38 +1,32 @@
-query QueryGroupAlignmentNoLogo($group: GroupReference!, $groupId: String!, $filter: [String], $first: Int!, $after: String){
-    group_alignment(
+query QueryGroupAlignmentNoLogo(
+    $group: GroupReference!,
+    $groupId: String!,
+    $filter: [String!],
+    $first: Int!,
+    $after: Int!){
+    group_alignments(
         group: $group
         groupId: $groupId
         filter: $filter
     ){
         alignment_length
         query_sequence
-        target_alignment_subset(first: $first, after: $after) {
-            pageInfo{
-                startCursor
-                endCursor
-                hasNextPage
-                hasPreviousPage
+        target_alignments(first: $first, offset: $after) {
+            target_id
+            orientation
+            target_sequence
+            coverage {
+                query_coverage
+                query_length
+                target_coverage
+                target_length
             }
-            edges{
-                node{
-                    target_id
-                    orientation
-                    target_sequence
-                    coverage {
-                        query_coverage
-                        query_length
-                        target_coverage
-                        target_length
-                    }
-                    aligned_regions {
-                        query_begin
-                        query_end
-                        target_begin
-                        target_end
-                        exon_shift
-                    }
-                }
-                cursor
+            aligned_regions {
+                query_begin
+                query_end
+                target_begin
+                target_end
+                exon_shift
             }
         }
     }

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAnnotations.graphql

@@ -1,10 +1,14 @@
-query QueryGroupAnnotations($group: GroupReference!, $groupId: String!, $sources:[Source], $filters: [FilterInput], $histogram:Boolean){
+query QueryGroupAnnotations(
+    $group: GroupReference!,
+    $groupId: String!,
+    $sources: [AnnotationReference!]!,
+    $filters: [AnnotationFilterInput!]
+){
     group_annotations(
         group:$group
         groupId:$groupId
         sources:$sources
         filters:$filters
-        histogram:$histogram
     ){
         source
         target_id

package/lib/commonjs/RcsbQueries/Borrego/QueryGroupAnnotationsSummary.graphql

@@ -0,0 +1,35 @@
+query QueryGroupAnnotationsSummary(
+    $group: GroupReference!,
+    $groupId: String!,
+    $sources: [AnnotationReference!]!,
+    $filters: [AnnotationFilterInput!]
+){
+    group_annotations_summary(
+        group:$group
+        groupId:$groupId
+        sources:$sources
+        filters:$filters
+    ){
+        source
+        target_id
+        features {
+            type
+            provenance_source
+            description
+            feature_id
+            name
+            value
+            feature_positions {
+                beg_seq_id
+                end_seq_id
+                beg_ori_id
+                end_ori_id
+                range_id
+                open_begin
+                open_end
+                value
+                values
+            }
+        }
+    }
+}

package/lib/commonjs/RcsbQueries/Borrego/graphql.config.yml

@@ -0,0 +1,8 @@
+schema: schema.graphql
+extensions:
+  endpoints:
+    Default GraphQL Endpoint:
+      url: https://sequence-coordinates.rcsb.org/graphql
+      headers:
+        user-agent: JS GraphQL
+      introspect: false