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

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

package/lib/RcsbGraphQL/RcsbQueryMultipleEntriesProperties.js

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

package/lib/RcsbGraphQL/RcsbQueryMultipleInstanceSequences.js

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

package/lib/RcsbGroupWeb/RcsbGroupBuilder.js

@@ -26,4 +26,3 @@ export const searchQueryContextManager = {
         return SearchQueryContextManager.subscribe(f);
     }
 };
-//# sourceMappingURL=RcsbGroupBuilder.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartAdditionalProperties.js

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

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartEvents.js

@@ -126,4 +126,3 @@ export var GroupChartEvents;
         }
     }
 })(GroupChartEvents || (GroupChartEvents = {}));
-//# sourceMappingURL=GroupChartEvents.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartLayout.js

@@ -32,4 +32,3 @@ function histogramChart(attributeName, chart) {
 function barChart(attributeName, chart) {
     return (_jsx("div", { id: `chart:${chart[0].attributeName}`, children: _jsx(BarChartComponent, { data: chart.map(c => c.data), chartConfig: chart[0].chartConfig, attributeName: attributeName }) }));
 }
-//# sourceMappingURL=GroupChartLayout.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartTools.js

@@ -89,4 +89,3 @@ export var GroupChartMap;
         });
     }
 })(GroupChartMap || (GroupChartMap = {}));
-//# sourceMappingURL=GroupChartTools.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbGroupChartComponent.js

@@ -47,4 +47,3 @@ function applyLayoutConfig(layout, chartMap, layoutConfig) {
         }
     });
 }
-//# sourceMappingURL=RcsbGroupChartComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbStatsChartComponent.js

@@ -34,4 +34,3 @@ export class RcsbStatsChartComponent extends React.Component {
         });
     }
 }
-//# sourceMappingURL=RcsbStatsChartComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupContent/RcsbGroupContentComponent.js

@@ -74,4 +74,3 @@ export class RcsbGroupContentComponent extends React.Component {
         };
     }
 }
-//# sourceMappingURL=RcsbGroupContentComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupDisplay.js

@@ -39,4 +39,3 @@ export class RcsbGroupDisplay {
         createRoot(e).render(_jsx(RcsbResidueChartComponent, { granularity: granularity, rcsbId: rcsbId, facetLayoutGrid: facetLayoutGrid, chartDisplayConfig: chartDisplayConfig }));
     }
 }
-//# sourceMappingURL=RcsbGroupDisplay.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/Components/Slider.js

@@ -17,4 +17,3 @@ export class Slider extends React.Component {
 export function actionIcon(action) {
     return (_jsx("span", { style: { cursor: "pointer" }, className: "h1 user-select-none", children: action == "prev" ? "❮" : "❯" }));
 }
-//# sourceMappingURL=Slider.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.js

@@ -67,4 +67,3 @@ function imageIcon(ei) {
                     transform: "translate(-50%, -50%)"
                 }, className: `fa ${isExperimental ? "fa-flask" : "fa-desktop"}` }) }) }));
 }
-//# sourceMappingURL=GroupMemberItem.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMembersGrid.js

@@ -96,4 +96,3 @@ function parseItems(groupProvenanceId, propsList) {
         :
             propsList.map((o) => (o.instances)).flat().map((o) => (Object.assign(Object.assign({}, o), { molecularWeight: o.entityMolecularWeight })));
 }
-//# sourceMappingURL=GroupMembersGrid.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/RcsbGroupMembersComponent.js

@@ -90,4 +90,3 @@ function mod(n, p) {
     const r = n % p;
     return r < 0 ? p + r : r;
 }
-//# sourceMappingURL=RcsbGroupMembersComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/RcsbGroupSeacrhQueryComponent.js

@@ -84,4 +84,3 @@ class RcsbGroupSearchQueryComponent extends React.Component {
         ]);
     }
 }
-//# sourceMappingURL=RcsbGroupSeacrhQueryComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/SearchQueryContextManager.js

@@ -89,4 +89,3 @@ SearchQueryContextManager.attributeList = [];
 SearchQueryContextManager.currentSearchQuery = new DataContainer();
 SearchQueryContextManager.groupProvenanceId = new DataContainer();
 SearchQueryContextManager.groupId = new DataContainer();
-//# sourceMappingURL=SearchQueryContextManager.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/RcsbResidueChartComponent.js

@@ -30,4 +30,3 @@ export class RcsbResidueChartComponent extends React.Component {
         });
     }
 }
-//# sourceMappingURL=RcsbResidueChartComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/DistributionChartFactoryImpl/DistributionChartFactory.js

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

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/MultipleTrackDistributionFactory.js

@@ -30,4 +30,3 @@ export class MultipleTrackDistributionFactory {
         };
     }
 }
-//# sourceMappingURL=MultipleTrackDistributionFactory.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/NumericalTrackDistributionFactory.js

@@ -35,4 +35,3 @@ export class NumericalTrackDistributionFactory {
         };
     }
 }
-//# sourceMappingURL=NumericalTrackDistributionFactory.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/TrackDistributionFactory.js

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

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryInterface.js

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

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/TrackBlockFactoryImpl/TrackBlockFactory.js

@@ -17,4 +17,3 @@ export class TrackBlockFactory {
         return Array.from(trackMap.entries()).map(e => ({ blockType: e[0], tracks: e[1] }));
     }
 }
-//# sourceMappingURL=TrackBlockFactory.js.map

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

@@ -20,4 +20,3 @@ export var Helper;
         });
     }
 })(Helper || (Helper = {}));
-//# sourceMappingURL=Helper.js.map

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

@@ -1,6 +1,6 @@
 import { __awaiter } from "tslib";
 import { AnnotationCollector } from "../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollector";
-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 { filter, interfaceAnnotations } from "../../../../RcsbFvWeb/RcsbFvModule/RcsbFvInterface";
 import * as rcm from "../../../../RcsbAnnotationConfig/RcsbResidueConfig.ac.json";
 import { AnnotationBlockManager } from "../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager";
@@ -53,7 +53,7 @@ export var ResidueChartTools;
             const annotationsRequestContext = {
                 queryId: instanceId,
                 reference: SequenceReference.PdbInstance,
-                sources: [AnnotationReference.PdbEntity, AnnotationReference.PdbInstance, AnnotationReference.Uniprot, AnnotationReference.PdbInterface],
+                sources: [Source.PdbEntity, Source.PdbInstance, Source.Uniprot, Source.PdbInterface],
                 annotationGenerator: interfaceAnnotations,
                 annotationFilter: filter
             };
@@ -85,4 +85,3 @@ export var ResidueChartTools;
     const annotationCollector = new AnnotationCollector();
     const alignmentCollector = new AlignmentCollector();
 })(ResidueChartTools || (ResidueChartTools = {}));
-//# sourceMappingURL=ResidueChartTools.js.map

package/lib/RcsbQueries/Borrego/.graphqlconfig

@@ -0,0 +1,15 @@
+{
+  "name": "Untitled GraphQL Schema",
+  "schemaPath": "schema.graphql",
+  "extensions": {
+    "endpoints": {
+      "Default GraphQL Endpoint": {
+        "url": "https://1d-coordinates.rcsb.org/graphql",
+        "headers": {
+          "user-agent": "JS GraphQL"
+        },
+        "introspect": false
+      }
+    }
+  }
+}

package/lib/RcsbQueries/Borrego/QueryAlignments.graphql

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

package/lib/RcsbQueries/Borrego/QueryAnnotations.graphql

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

package/lib/RcsbQueries/Borrego/QueryGroupAlignments.graphql

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

package/lib/RcsbQueries/Borrego/QueryGroupAlignmentsNoLogo.graphql

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

package/lib/RcsbQueries/Borrego/QueryGroupAnnotations.graphql

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