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

package/lib/ExternalResources/NcbiData/NcbiGenomeSequenceData.js

@@ -63,4 +63,3 @@ export class NcbiGenomeSequenceData {
 }
 NcbiGenomeSequenceData.urlPrefix = resource.ncbi_genome_sequence.url;
 NcbiGenomeSequenceData.urlSuffix = resource.ncbi_genome_sequence.url_suffix;
-//# sourceMappingURL=NcbiGenomeSequenceData.js.map

package/lib/ExternalResources/NcbiData/NcbiSummary.js

@@ -79,4 +79,3 @@ export class NcbiSummary {
 NcbiSummary.timeout = 3000;
 NcbiSummary.httpTimeout = 10000;
 NcbiSummary.jobTask = null;
-//# sourceMappingURL=NcbiSummary.js.map

package/lib/RcsbAnnotationConfig/AnnotationConfigInterface.js

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

package/lib/RcsbAnnotationConfig/RcsbAnnotationConfig.d.ts

@@ -1,4 +1,4 @@
-import { SequenceAnnotations, Features } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvDisplayTypes } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvDefaultConfigValues";
 import { AnnotationConfigInterface, RcsbAnnotationConfigInterface } from "./AnnotationConfigInterface";
 import { AnnotationRequestContext } from "../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
@@ -19,7 +19,7 @@ export declare class RcsbAnnotationConfig {
     uniprotOrder(): Array<string>;
     instanceOrder(): Array<string>;
     entityOrder(): Array<string>;
-    getAnnotationType(requestConfig: AnnotationRequestContext, ann: SequenceAnnotations, feature: Features): Promise<string>;
+    getAnnotationType(requestConfig: AnnotationRequestContext, ann: AnnotationFeatures, feature: Feature): Promise<string>;
     isMergedType(type: string): boolean;
     getMergeConfig(type: string): RcsbMergedTypesInterface | undefined;
     private addNewType;

package/lib/RcsbAnnotationConfig/RcsbAnnotationConfig.js

@@ -181,4 +181,3 @@ class ArraySuffix extends Array {
         return this.length;
     }
 }
-//# sourceMappingURL=RcsbAnnotationConfig.js.map

package/lib/RcsbAnnotationConfig/RcsbAnnotationConstants.js

@@ -15,4 +15,3 @@ export const RcsbAnnotationConstants = {
         userInput: "USER INPUT"
     }
 };
-//# sourceMappingURL=RcsbAnnotationConstants.js.map

package/lib/RcsbAnnotationConfig/RcsbDistributionConfig.js

@@ -29,4 +29,3 @@ export class RcsbDistributionConfig {
         });
     }
 }
-//# sourceMappingURL=RcsbDistributionConfig.js.map

package/lib/RcsbChartWeb/AbsractChartComponent.js

@@ -46,4 +46,3 @@ export class AbstractChartComponent extends React.Component {
         }, x);
     }
 }
-//# sourceMappingURL=AbsractChartComponent.js.map

package/lib/RcsbChartWeb/BarChartComponent.js

@@ -8,4 +8,3 @@ export class BarChartComponent extends AbstractChartComponent {
         return (_jsx(ChartComponent, { data: this.state.data, chartComponentImplementation: ChartJsBarComponent, dataProvider: new BarChartDataProvider(), chartConfig: this.props.chartConfig }));
     }
 }
-//# sourceMappingURL=BarChartComponent.js.map

package/lib/RcsbChartWeb/HistogramChartComponent.js

@@ -8,4 +8,3 @@ export class HistogramChartComponent extends AbstractChartComponent {
         return (_jsx(ChartComponent, { data: this.state.data.map(d => d.map(d => { var _a, _b; return (Object.assign(Object.assign({}, d), { label: (parseFloat(d.label.toString()) + ((_b = (_a = this.props.chartConfig) === null || _a === void 0 ? void 0 : _a.histogramBinIncrement) !== null && _b !== void 0 ? _b : 0) * 0.5) })); })), chartComponentImplementation: ChartJsHistogramComponent, dataProvider: new HistogramChartDataProvider(), chartConfig: this.props.chartConfig }));
     }
 }
-//# sourceMappingURL=HistogramChartComponent.js.map

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollector.d.ts

@@ -1,6 +1,6 @@
 import { AlignmentCollectConfig, AlignmentCollectorInterface } from "./AlignmentCollectorInterface";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { SequenceAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare class AlignmentCollector implements AlignmentCollectorInterface {
     private requestStatus;
     readonly rcsbFvQuery: RcsbClient;
@@ -8,10 +8,10 @@ export declare class AlignmentCollector implements AlignmentCollectorInterface {
     private alignmentResponse;
     private readonly alignmentResponseSubject;
     private readonly alignmentLengthSubject;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<SequenceAlignments>;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
     getTargets(): Promise<Array<string>>;
-    getAlignment(): Promise<SequenceAlignments>;
+    getAlignment(): Promise<AlignmentResponse>;
     getAlignmentLength(): Promise<number>;
-    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<SequenceAlignments>;
+    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<AlignmentResponse>;
     private complete;
 }

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollector.js

@@ -14,15 +14,15 @@ export class AlignmentCollector {
     }
     collect(requestConfig, filter) {
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
+            var _a, _b, _c, _d, _e, _f;
             this.requestStatus = "pending";
             this.alignmentResponse = yield this.requestAlignment(requestConfig);
-            const targetAlignment = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignments;
+            const targetAlignment = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) !== null && _b !== void 0 ? _b : (_e = (_d = (_c = this.alignmentResponse) === null || _c === void 0 ? void 0 : _c.target_alignment_subset) === null || _d === void 0 ? void 0 : _d.edges) === null || _e === void 0 ? void 0 : _e.map(e => e === null || e === void 0 ? void 0 : e.node);
             if (targetAlignment) {
                 assertElementListDefined(targetAlignment);
-                this.alignmentResponse.target_alignments = !filter ? targetAlignment : targetAlignment === null || targetAlignment === void 0 ? void 0 : targetAlignment.filter(ta => { var _a; return filter.includes((_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "not-included"); });
+                this.alignmentResponse.target_alignment = !filter ? targetAlignment : targetAlignment === null || targetAlignment === void 0 ? void 0 : targetAlignment.filter(ta => { var _a; return filter.includes((_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "not-included"); });
             }
-            this.alignmentResponse = typeof ((_b = requestConfig.externalTrackBuilder) === null || _b === void 0 ? void 0 : _b.filterAlignments) === "function" ? yield requestConfig.externalTrackBuilder.filterAlignments({ alignments: this.alignmentResponse }) : this.alignmentResponse;
+            this.alignmentResponse = typeof ((_f = requestConfig.externalTrackBuilder) === null || _f === void 0 ? void 0 : _f.filterAlignments) === "function" ? yield requestConfig.externalTrackBuilder.filterAlignments({ alignments: this.alignmentResponse }) : this.alignmentResponse;
             this.complete();
             return this.alignmentResponse;
         });
@@ -32,7 +32,7 @@ export class AlignmentCollector {
             return new Promise((resolve, reject) => {
                 var _a, _b;
                 if (this.requestStatus === "complete") {
-                    const targetIds = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignments) === null || _b === void 0 ? void 0 : _b.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
+                    const targetIds = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) === null || _b === void 0 ? void 0 : _b.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
                     assertElementListDefined(targetIds);
                     resolve(targetIds);
                 }
@@ -68,7 +68,7 @@ export class AlignmentCollector {
     requestAlignment(requestConfig) {
         return __awaiter(this, void 0, void 0, function* () {
             this.requestStatus = "pending";
-            if (requestConfig.queryId && requestConfig.from && requestConfig.to) {
+            if (requestConfig.queryId) {
                 return yield this.rcsbFvQuery.requestAlignment({
                     queryId: requestConfig.queryId,
                     from: requestConfig.from,
@@ -76,7 +76,7 @@ export class AlignmentCollector {
                 });
             }
             else {
-                if (requestConfig.group && requestConfig.groupId && requestConfig.page) {
+                if (requestConfig.group && requestConfig.page) {
                     return yield this.rcsbFvQuery.requestGroupAlignment({
                         group: requestConfig.group,
                         groupId: requestConfig.groupId,
@@ -94,7 +94,7 @@ export class AlignmentCollector {
     complete() {
         var _a, _b, _c, _d, _e;
         this.requestStatus = "complete";
-        const targetIds = (_b = (_a = this.alignmentResponse.target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id)) !== null && _b !== void 0 ? _b : [];
+        const targetIds = (_b = (_a = this.alignmentResponse.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id)) !== null && _b !== void 0 ? _b : [];
         assertElementListDefined(targetIds);
         this.targetsSubject.next(targetIds);
         this.alignmentResponseSubject.next(this.alignmentResponse);
@@ -102,4 +102,3 @@ export class AlignmentCollector {
         console.info("Alignment Processing Complete");
     }
 }
-//# sourceMappingURL=AlignmentCollector.js.map

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.d.ts

@@ -1,4 +1,4 @@
-import { SequenceAlignments, QueryAlignmentsArgs, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse, QueryAlignmentArgs, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbQueryGroupAlignmentArguments } from "../../RcsbGraphQL/RcsbQueryAlignment";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 interface CommonAlignmentInterface {
@@ -10,7 +10,7 @@ interface CommonAlignmentInterface {
     excludeFirstRowLink?: boolean;
 }
 type QueryAlignmentArgsTypes = {
-    [K in keyof QueryAlignmentsArgs]: NonNullable<QueryAlignmentsArgs[K]>;
+    [K in keyof QueryAlignmentArgs]: NonNullable<QueryAlignmentArgs[K]>;
 };
 export interface CollectAlignmentInterface extends QueryAlignmentArgsTypes, CommonAlignmentInterface {
 }
@@ -22,8 +22,8 @@ export interface CollectGroupAlignmentInterface extends RcsbQueryGroupAlignmentA
 export type AlignmentCollectConfig = Partial<CollectAlignmentInterface & CollectGroupAlignmentInterface>;
 export interface AlignmentCollectorInterface {
     getTargets(): Promise<Array<string>>;
-    getAlignment(): Promise<SequenceAlignments>;
+    getAlignment(): Promise<AlignmentResponse>;
     getAlignmentLength(): Promise<number>;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<SequenceAlignments>;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
 }
 export {};

package/lib/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.js

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

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollector.d.ts

@@ -1,4 +1,4 @@
-import { SequenceAnnotations, Features } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AnnotationRequestContext, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
 export declare class AnnotationCollector implements AnnotationCollectorInterface {
@@ -8,9 +8,9 @@ export declare class AnnotationCollector implements AnnotationCollectorInterface
     private annotationFeatures;
     private readonly rawFeaturesSubject;
     private readonly annotationFeaturesSubject;
-    collect(requestConfig: AnnotationRequestContext): Promise<Array<SequenceAnnotations>>;
-    getFeatures(): Promise<Array<Features>>;
-    getAnnotationFeatures(): Promise<Array<SequenceAnnotations>>;
+    collect(requestConfig: AnnotationRequestContext): Promise<Array<AnnotationFeatures>>;
+    getFeatures(): Promise<Array<Feature>>;
+    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
     private requestAnnotations;
     private complete;
 }

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollector.js

@@ -55,22 +55,7 @@ export class AnnotationCollector {
     }
     requestAnnotations(requestConfig) {
         return __awaiter(this, void 0, void 0, function* () {
-            if (requestConfig.group && requestConfig.groupId && requestConfig.sources)
-                if (requestConfig.isSummary)
-                    return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotationsSummary({
-                        group: requestConfig.group,
-                        groupId: requestConfig.groupId,
-                        sources: requestConfig.sources,
-                        filters: requestConfig.filters
-                    });
-                else
-                    return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotations({
-                        group: requestConfig.group,
-                        groupId: requestConfig.groupId,
-                        sources: requestConfig.sources,
-                        filters: requestConfig.filters
-                    });
-            else if (requestConfig.queryId && requestConfig.reference && requestConfig.sources)
+            if (requestConfig.queryId)
                 return yield this.rcsbFvQuery.requestRcsbPdbAnnotations({
                     queryId: requestConfig.queryId,
                     reference: requestConfig.reference,
@@ -78,6 +63,14 @@ export class AnnotationCollector {
                     filters: requestConfig.filters,
                     range: requestConfig.range
                 });
+            else if (requestConfig.group && requestConfig.groupId)
+                return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotations({
+                    group: requestConfig.group,
+                    groupId: requestConfig.groupId,
+                    sources: requestConfig.sources,
+                    filters: requestConfig.filters,
+                    histogram: requestConfig.histogram
+                });
             throw new Error(`Annotation query error`);
         });
     }
@@ -88,4 +81,3 @@ export class AnnotationCollector {
         console.info("Features Processing Complete");
     }
 }
-//# sourceMappingURL=AnnotationCollector.js.map

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.d.ts

@@ -1,4 +1,4 @@
-import { SequenceAnnotations, Features, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures, Feature, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { FeaturePositionGaps } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
@@ -7,7 +7,7 @@ export type IncreaseAnnotationValueType = (feature: {
     type: string;
     targetId: string;
     positionKey: string;
-    d: Features;
+    d: Feature;
     p: FeaturePositionGaps;
 }) => number;
 export interface AnnotationProcessingInterface {
@@ -19,20 +19,19 @@ export interface CommonAnnotationInterface {
     rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     annotationProcessing?: AnnotationProcessingInterface;
     externalTrackBuilder?: ExternalTrackBuilderInterface;
-    annotationGenerator?(annotations: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
-    annotationFilter?(annotations: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
-    titleSuffix?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
-    trackTitle?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
-    typeSuffix?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
+    annotationGenerator?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+    annotationFilter?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+    titleSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+    trackTitle?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+    typeSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
 }
 export interface AnnotationsCollectConfig extends QueryAnnotationsArgs, CommonAnnotationInterface {
 }
 export interface CollectGroupAnnotationsInterface extends QueryGroup_AnnotationsArgs, CommonAnnotationInterface {
-    isSummary: boolean;
 }
 export type AnnotationRequestContext = Partial<AnnotationsCollectConfig & CollectGroupAnnotationsInterface>;
 export interface AnnotationCollectorInterface {
-    collect(requestConfig: AnnotationsCollectConfig | CollectGroupAnnotationsInterface): Promise<Array<SequenceAnnotations>>;
-    getAnnotationFeatures(): Promise<Array<SequenceAnnotations>>;
-    getFeatures(): Promise<Array<Features>>;
+    collect(requestConfig: AnnotationsCollectConfig | CollectGroupAnnotationsInterface): Promise<Array<AnnotationFeatures>>;
+    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
+    getFeatures(): Promise<Array<Feature>>;
 }

package/lib/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.js

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

package/lib/RcsbCollectTools/DataCollectors/AssemblyInterfacesCollector.js

@@ -29,4 +29,3 @@ function parseAssemblyInterfaces(assemblyInterfaces) {
         })) !== null && _b !== void 0 ? _b : []
     };
 }
-//# sourceMappingURL=AssemblyInterfacesCollector.js.map

package/lib/RcsbCollectTools/DataCollectors/DataCollectorInterface.js

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

package/lib/RcsbCollectTools/DataCollectors/EntryAssembliesCollector.js

@@ -90,4 +90,3 @@ export class EntryAssembliesCollector {
     }
 }
 EntryAssembliesCollector.modelKey = "Model";
-//# sourceMappingURL=EntryAssembliesCollector.js.map

package/lib/RcsbCollectTools/DataCollectors/GroupMemberCollector.js

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

package/lib/RcsbCollectTools/DataCollectors/GroupPropertyCollector.js

@@ -24,4 +24,3 @@ export class GroupPropertyCollector {
         };
     }
 }
-//# sourceMappingURL=GroupPropertyCollector.js.map

package/lib/RcsbCollectTools/DataCollectors/InterfaceInstanceCollector.js

@@ -39,4 +39,3 @@ function parseInterfaceInstances(coreInterface) {
         operatorIds: [coreInterface.rcsb_interface_operator[0], coreInterface.rcsb_interface_operator[1]]
     };
 }
-//# sourceMappingURL=InterfaceInstanceCollector.js.map

package/lib/RcsbCollectTools/DataCollectors/MultipleEntityInstancesCollector.js

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

package/lib/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.js

@@ -51,4 +51,3 @@ export class MultipleEntryPropertyCollector {
         return out;
     }
 }
-//# sourceMappingURL=MultipleEntryPropertyCollector.js.map

package/lib/RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector.js

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

package/lib/RcsbCollectTools/DataCollectors/MultiplePolymerEntityCollector.js

@@ -24,4 +24,3 @@ export class MultiplePolymerEntityCollector {
         });
     }
 }
-//# sourceMappingURL=MultiplePolymerEntityCollector.js.map

package/lib/RcsbCollectTools/DataCollectors/PolymerEntityChromosomeCollector.js

@@ -13,7 +13,7 @@ export class PolymerEntityChromosomeCollector {
             }));
             result.forEach((alignment, n) => {
                 var _a;
-                (_a = alignment.target_alignments) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
+                (_a = alignment.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
                     var _a, _b, _c;
                     if (((_b = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0) {
                         if (!entityMap.has(entityIds[n]))
@@ -37,4 +37,3 @@ export class PolymerEntityChromosomeCollector {
         });
     }
 }
-//# sourceMappingURL=PolymerEntityChromosomeCollector.js.map

package/lib/RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector.js

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

package/lib/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.d.ts

@@ -1,20 +1,20 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { SequenceAlignments, SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
 export interface ExternalTrackBuilderInterface {
     processAlignmentAndFeatures?(data: {
-        annotations?: Array<SequenceAnnotations>;
-        alignments?: SequenceAlignments;
+        annotations?: Array<AnnotationFeatures>;
+        alignments?: AlignmentResponse;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     }): Promise<void>;
     filterAlignments?(data: {
-        alignments: SequenceAlignments;
+        alignments: AlignmentResponse;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<SequenceAlignments>;
+    }): Promise<AlignmentResponse>;
     filterFeatures?(data: {
-        annotations: Array<SequenceAnnotations>;
+        annotations: Array<AnnotationFeatures>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<Array<SequenceAnnotations>>;
+    }): Promise<Array<AnnotationFeatures>>;
     addTo?(tracks: {
         alignmentTracks?: Array<RcsbFvRowConfigInterface>;
         annotationTracks?: Array<RcsbFvRowConfigInterface>;

package/lib/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.js

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

package/lib/RcsbCollectTools/FeatureTools/FeatureTools.js

@@ -83,4 +83,3 @@ export class FeatureTools {
     }
 }
 FeatureTools.rcsbLigand = new RegExp(/^(ligand)(\s)(\w{1,3})$/);
-//# sourceMappingURL=FeatureTools.js.map

package/lib/RcsbExport/FeatureType.d.ts

@@ -1,9 +1,9 @@
-import { FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 declare const ExtendedTypes: {
-    BurialFraction: FeaturesType;
-    BuriedResidues: FeaturesType;
+    BurialFraction: Type;
+    BuriedResidues: Type;
 };
-type MergedType = typeof FeaturesType & typeof ExtendedTypes;
+type MergedType = typeof Type & typeof ExtendedTypes;
 declare const MergedType: MergedType;
 type FeatureType = typeof MergedType;
 export declare const FeatureType: FeatureType;

package/lib/RcsbExport/FeatureType.js

@@ -1,10 +1,9 @@
-import { FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 const BURIAL_FRACTION = "BURIAL_FRACTION";
 const BURIED_RESIDUES = "BURIED_RESIDUES";
 const ExtendedTypes = {
     BurialFraction: BURIAL_FRACTION,
     BuriedResidues: BURIED_RESIDUES
 };
-const MergedType = Object.assign(Object.assign({}, FeaturesType), ExtendedTypes);
+const MergedType = Object.assign(Object.assign({}, Type), ExtendedTypes);
 export const FeatureType = MergedType;
-//# sourceMappingURL=FeatureType.js.map

package/lib/RcsbExport/RcsbFvUI.js

@@ -10,4 +10,3 @@ export class RcsbFvUI {
         RcsbFvCoreBuilder.addSelectButton(elementFvId, selectButtonId, options, config);
     }
 }
-//# sourceMappingURL=RcsbFvUI.js.map

package/lib/RcsbFvExamples/ChromosomeFv.js

@@ -2,4 +2,3 @@ import { buildEntryChromosome } from "../RcsbFvWeb/RcsbFvBuilder";
 buildEntryChromosome("pfv", "select", "selectBis", "2uzi").then((module) => {
     console.log(module);
 });
-//# sourceMappingURL=ChromosomeFv.js.map

package/lib/RcsbFvExamples/EntitySummaryFv.js

@@ -6,4 +6,3 @@ onLoad(() => {
         console.log(module);
     });
 });
-//# sourceMappingURL=EntitySummaryFv.js.map

package/lib/RcsbFvExamples/ExternalDataProvider.js

@@ -859,7 +859,7 @@ class RcsbStructuralAlignmentProvider {
         return __awaiter(this, void 0, void 0, function* () {
             return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
                 var _a, _b;
-                resolve((_b = (_a = (yield this.data()).target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a; return (_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "NA"; })) !== null && _b !== void 0 ? _b : []);
+                resolve((_b = (_a = (yield this.data()).target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a; return (_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "NA"; })) !== null && _b !== void 0 ? _b : []);
             }));
         });
     }
@@ -867,7 +867,7 @@ class RcsbStructuralAlignmentProvider {
         return __awaiter(this, void 0, void 0, function* () {
             return new Promise((resolve) => __awaiter(this, void 0, void 0, function* () {
                 var _a;
-                const ends = (_a = (yield this.data()).target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a, _b, _c; return (_c = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a[((_b = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _b === void 0 ? void 0 : _b.length) - 1]) === null || _c === void 0 ? void 0 : _c.query_end; });
+                const ends = (_a = (yield this.data()).target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => { var _a, _b, _c; return (_c = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a[((_b = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _b === void 0 ? void 0 : _b.length) - 1]) === null || _c === void 0 ? void 0 : _c.query_end; });
                 assertElementListDefined(ends);
                 resolve(Math.max(...ends));
             }));
@@ -886,10 +886,10 @@ function alignmentTransform(alignment) {
         var _a, _b;
         const alignmentRef = mergeAlignments(alignment.results);
         const out = alignmentRef.buildAlignments();
-        const instance_ids = (_a = out.target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
+        const instance_ids = (_a = out.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
         assertElementListDefined(instance_ids);
         const seqs = yield rcsbRequestCtxManager.getInstanceSequences(instance_ids);
-        (_b = out.target_alignments) === null || _b === void 0 ? void 0 : _b.forEach(ta => {
+        (_b = out.target_alignment) === null || _b === void 0 ? void 0 : _b.forEach(ta => {
             var _a;
             const seq = (_a = seqs.find(s => s.rcsbId === (ta === null || ta === void 0 ? void 0 : ta.target_id))) === null || _a === void 0 ? void 0 : _a.sequence;
             if (seq && ta)
@@ -949,4 +949,3 @@ function transformToGapedDomain(regions) {
     });
     return out;
 }
-//# sourceMappingURL=ExternalDataProvider.js.map

package/lib/RcsbFvExamples/GroupHistogram.js

@@ -26,4 +26,3 @@ buildGroup("pfv_2", GroupProvenanceId.ProvenanceSequenceIdentity, groupId, undef
     PHENOTYPE_FACET.attributeName
 ]).then((m) => {
 });
-//# sourceMappingURL=GroupHistogram.js.map

package/lib/RcsbFvExamples/InstanceFv.js

@@ -18,4 +18,3 @@ buildInstanceFv("pfv", "2UZI.C").then((module) => {
         });
     });
 });
-//# sourceMappingURL=InstanceFv.js.map

package/lib/RcsbFvExamples/InstanceSequenceFv.js

@@ -1,4 +1,4 @@
-import { FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { buildInstanceSequenceFv } from "../RcsbFvWeb/RcsbFvBuilder";
 buildInstanceSequenceFv("pfv", "select", "8PDU", {
     module: "interface",
@@ -34,7 +34,7 @@ function externalTrackBuilder() {
                     var _a;
                     (_a = a.features) === null || _a === void 0 ? void 0 : _a.forEach(f => {
                         var _a, _b;
-                        if (f != null && f.type === FeaturesType.RegionOfInterest) {
+                        if (f != null && f.type === Type.RegionOfInterest) {
                             if (f.feature_positions)
                                 (_a = myComputedTrack.trackData) === null || _a === void 0 ? void 0 : _a.push(...(_b = f.feature_positions) === null || _b === void 0 ? void 0 : _b.map(p => {
                                     var _a, _b;
@@ -65,4 +65,3 @@ function externalTrackBuilder() {
         }
     };
 }
-//# sourceMappingURL=InstanceSequenceFv.js.map

package/lib/RcsbFvExamples/ResidueDistribution.js

@@ -3,4 +3,3 @@ buildResidueDistribution("pfv", "entry", "MA_MABAKCEPC0005", ["MA_QA_METRIC_LOCA
     paddingLeft: 100,
     constWidth: 250
 });
-//# sourceMappingURL=ResidueDistribution.js.map

package/lib/RcsbFvExamples/SequenceIdentityGroupAlignmentFv.js

@@ -11,7 +11,7 @@ class UiComponent extends React.Component {
             }, children: this.props.text }));
     }
 }
-buildSequenceIdentityAlignmentFv("pfv", "1_30", undefined, {
+buildSequenceIdentityAlignmentFv("pfv", "5_30", undefined, {
     boardConfig: {
         selectionChangeCallback: (selection) => {
             console.log(selection);
@@ -19,7 +19,7 @@ buildSequenceIdentityAlignmentFv("pfv", "1_30", undefined, {
     },
     page: {
         first: 200,
-        after: 0
+        after: "0"
     },
     externalTrackBuilder: {
         filterAlignments: (data) => {
@@ -58,4 +58,3 @@ buildSequenceIdentityAlignmentFv("pfv", "1_30", undefined, {
     fvContainer.set(pfv);
     console.log(pfv, "rendered");
 });
-//# sourceMappingURL=SequenceIdentityGroupAlignmentFv.js.map

package/lib/RcsbFvExamples/SequenceIdentityGroupFv.js

@@ -39,4 +39,3 @@ const query = {
 };
 buildGroupFv("pfv", GroupProvenanceId.ProvenanceSequenceIdentity, "1_30", query);
 //buildGroupFv("pfv",GroupProvenanceId.ProvenanceSequenceIdentity, "P12694");
-//# sourceMappingURL=SequenceIdentityGroupFv.js.map

package/lib/RcsbFvExamples/SingleEntitySummaryFv.js

@@ -1,3 +1,2 @@
 import { buildSingleEntitySummaryFv } from "../RcsbFvWeb/RcsbFvBuilder";
 buildSingleEntitySummaryFv("pfv", "2UZI_3").then(m => console.log(m));
-//# sourceMappingURL=SingleEntitySummaryFv.js.map

package/lib/RcsbFvExamples/TestCollectors.js

@@ -110,4 +110,3 @@ function test() {
     });
 }
 test();
-//# sourceMappingURL=TestCollectors.js.map

package/lib/RcsbFvExamples/UniprotAlignmentFv.js

@@ -1,3 +1,2 @@
 import { buildUniprotAlignmentFv } from "../RcsbFvWeb/RcsbFvBuilder";
 buildUniprotAlignmentFv("pfv", "P12694");
-//# sourceMappingURL=UniprotAlignmentFv.js.map

package/lib/RcsbFvExamples/UniprotEntityInstanceFv.js

@@ -40,4 +40,3 @@ buildUniprotEntityInstanceFv("pfv", "P01112", "2UZI_3", "2UZI.C", { boardConfig:
         });
     });
 });
-//# sourceMappingURL=UniprotEntityInstanceFv.js.map

package/lib/RcsbFvExamples/UniprotFv.js

@@ -8,4 +8,3 @@ buildMultipleAlignmentSequenceFv("pfv", "select", "P01112", {}, {
 }).then(() => {
     console.log("render done");
 });
-//# sourceMappingURL=UniprotFv.js.map