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

package/lib/commonjs/RcsbCollectTools/AlignmentCollector/AlignmentCollector.js

@@ -17,15 +17,15 @@ class AlignmentCollector {
     }
     collect(requestConfig, filter) {
         return tslib_1.__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;
         });
@@ -35,7 +35,7 @@ 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);
                 }
@@ -71,7 +71,7 @@ class AlignmentCollector {
     requestAlignment(requestConfig) {
         return tslib_1.__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,
@@ -79,7 +79,7 @@ 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,
@@ -97,7 +97,7 @@ 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);

package/lib/commonjs/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/commonjs/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/commonjs/RcsbCollectTools/AnnotationCollector/AnnotationCollector.js

@@ -58,22 +58,7 @@ class AnnotationCollector {
     }
     requestAnnotations(requestConfig) {
         return tslib_1.__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,
@@ -81,6 +66,14 @@ 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`);
         });
     }

package/lib/commonjs/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/commonjs/RcsbCollectTools/DataCollectors/PolymerEntityChromosomeCollector.js

@@ -16,7 +16,7 @@ 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]))

package/lib/commonjs/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/commonjs/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/commonjs/RcsbExport/FeatureType.js

@@ -8,5 +8,5 @@ const ExtendedTypes = {
     BurialFraction: BURIAL_FRACTION,
     BuriedResidues: BURIED_RESIDUES
 };
-const MergedType = Object.assign(Object.assign({}, GqlTypes_1.FeaturesType), ExtendedTypes);
+const MergedType = Object.assign(Object.assign({}, GqlTypes_1.Type), ExtendedTypes);
 exports.FeatureType = MergedType;

package/lib/commonjs/RcsbFvExamples/ExternalDataProvider.js

@@ -861,7 +861,7 @@ class RcsbStructuralAlignmentProvider {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             return new Promise((resolve) => tslib_1.__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 : []);
             }));
         });
     }
@@ -869,7 +869,7 @@ class RcsbStructuralAlignmentProvider {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             return new Promise((resolve) => tslib_1.__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));
             }));
@@ -888,10 +888,10 @@ 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 RcsbRequestContextManager_1.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)

package/lib/commonjs/RcsbFvExamples/InstanceSequenceFv.js

@@ -36,7 +36,7 @@ function externalTrackBuilder() {
                     var _a;
                     (_a = a.features) === null || _a === void 0 ? void 0 : _a.forEach(f => {
                         var _a, _b;
-                        if (f != null && f.type === GqlTypes_1.FeaturesType.RegionOfInterest) {
+                        if (f != null && f.type === GqlTypes_1.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;

package/lib/commonjs/RcsbFvExamples/SequenceIdentityGroupAlignmentFv.js

@@ -14,7 +14,7 @@ class UiComponent extends react_1.default.Component {
             }, children: this.props.text }));
     }
 }
-(0, RcsbFvBuilder_1.buildSequenceIdentityAlignmentFv)("pfv", "1_30", undefined, {
+(0, RcsbFvBuilder_1.buildSequenceIdentityAlignmentFv)("pfv", "5_30", undefined, {
     boardConfig: {
         selectionChangeCallback: (selection) => {
             console.log(selection);
@@ -22,7 +22,7 @@ class UiComponent extends react_1.default.Component {
     },
     page: {
         first: 200,
-        after: 0
+        after: "0"
     },
     externalTrackBuilder: {
         filterAlignments: (data) => {

package/lib/commonjs/RcsbFvExamples/UniprotGroupFv.js

@@ -2,8 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const RcsbFvBuilder_1 = require("../RcsbFvWeb/RcsbFvBuilder");
 const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
-// import {SearchQuery} from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-/* const query: SearchQuery = {
+const query = {
     "query": {
         "type": "group",
         "nodes": [
@@ -67,7 +66,7 @@ const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
             "experimental"
         ]
     }
-}*/
-// buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "Q8WZ42");
-// buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "P69905", query);
-(0, RcsbFvBuilder_1.buildGroupFv)("pfv", DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity, "10_30");
+};
+//buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "Q8WZ42");
+(0, RcsbFvBuilder_1.buildGroupFv)("pfv", DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession, "P69905", query);
+//buildGroupFv("pfv",GroupProvenanceId.ProvenanceSequenceIdentity, "1_30");

package/lib/commonjs/RcsbFvUI/Components/PaginationItemComponent.d.ts

@@ -5,7 +5,7 @@ export interface PaginationItemState {
 }
 export interface PaginationItemProps {
     count: number;
-    after: number;
+    after: string;
     first: number;
     stateChange(state: PaginationItemState, prevState: PaginationItemState): void;
 }

package/lib/commonjs/RcsbFvUI/Components/PaginationItemComponent.js

@@ -7,7 +7,7 @@ class PaginationItemComponent extends AbstractMenuItemComponent_1.AbstractMenuIt
     constructor() {
         super(...arguments);
         this.state = {
-            after: this.props.after,
+            after: parseInt(this.props.after),
             first: this.props.first > this.props.count ? this.props.count : this.props.first
         };
     }

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvEntityBuilder.js

@@ -36,7 +36,7 @@ class RcsbFvEntityBuilder {
                                     yield RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotEntityFv(elementFvId, t, entityId, Object.assign({ alignmentFilter: [entityId] }, customAdditionalConfig({
                                         field: GqlTypes_1.FieldName.TargetId,
                                         operation: GqlTypes_1.OperationType.Contains,
-                                        source: GqlTypes_1.AnnotationReference.PdbInstance,
+                                        source: GqlTypes_1.Source.PdbInstance,
                                         values: [pdbId + TagDelimiter_1.TagDelimiter.instance]
                                     })));
                                 }
@@ -80,13 +80,13 @@ function customAdditionalConfig(f) {
     const filters = [{
             field: GqlTypes_1.FieldName.Type,
             operation: GqlTypes_1.OperationType.Equals,
-            source: GqlTypes_1.AnnotationReference.PdbInstance,
-            values: [GqlTypes_1.FeaturesType.UnobservedResidueXyz, GqlTypes_1.FeaturesType.UnobservedAtomXyz, GqlTypes_1.FeaturesType.MaQaMetricLocalTypeOther, GqlTypes_1.FeaturesType.MaQaMetricLocalTypePlddt]
+            source: GqlTypes_1.Source.PdbInstance,
+            values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.UnobservedAtomXyz, GqlTypes_1.Type.MaQaMetricLocalTypeOther, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
         }];
     if (f)
         filters.push(f);
     return {
-        sources: [GqlTypes_1.AnnotationReference.PdbEntity, GqlTypes_1.AnnotationReference.PdbInstance],
+        sources: [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance],
         filters: filters
     };
 }

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupAlignmentBuilder.js

@@ -37,7 +37,7 @@ class RcsbFvGroupAlignmentBuilder {
             else {
                 entityCount = yield SearchRequestProperty_1.searchRequestProperty.requestCount({ query: SearchQueryTools_1.SearchQueryTools.searchGroupQuery(groupProvenance, groupId), return_type: SearchEnums_1.ReturnType.PolymerEntity });
             }
-            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { page: Object.assign({ first: 50, after: 0 }, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page), alignmentFilter: filterEntities, externalTrackBuilder: FeatureTools_1.FeatureTools.mergeTrackBuilders((0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)(), additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalTrackBuilder) });
+            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { page: Object.assign({ first: 50, after: "0" }, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page), alignmentFilter: filterEntities, externalTrackBuilder: FeatureTools_1.FeatureTools.mergeTrackBuilders((0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)(), additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalTrackBuilder) });
             // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
             const pfvArgs = [
                 (0, GroupPfvApp_1.getReferenceFromGroupProvenance)(groupProvenance),
@@ -60,20 +60,20 @@ class RcsbFvGroupAlignmentBuilder {
                 component: PaginationItemComponent_1.PaginationItemComponent,
                 props: {
                     count: entityCount,
-                    after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : 0,
+                    after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : "0",
                     first: (_d = (_c = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _c === void 0 ? void 0 : _c.first) !== null && _d !== void 0 ? _d : 50,
                     stateChange: (state, prevState) => {
                         switch (groupProvenance) {
                             case DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity:
                                 sequenceIdentityCallback(elementId, pfv, RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
                                         first: state.first,
-                                        after: state.after
+                                        after: state.after.toString()
                                     }, excludeLogo: true }));
                                 break;
                             case DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession:
                                 uniprotCallback(elementId, pfv, RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotAlignmentFv, [groupId], Object.assign(Object.assign({}, additionalConfig), { page: {
                                         first: state.first,
-                                        after: state.after
+                                        after: state.after.toString()
                                     } }));
                                 break;
                         }

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.js

@@ -10,11 +10,11 @@ class RcsbFvProteinSequenceBuilder {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             var _a;
             const alignmentSource = (_a = config.alignmentSource) !== null && _a !== void 0 ? _a : config.reference;
-            const sources = [GqlTypes_1.AnnotationReference.Uniprot];
+            const sources = [GqlTypes_1.Source.Uniprot];
             if (config.reference == GqlTypes_1.SequenceReference.PdbEntity)
-                sources.unshift(GqlTypes_1.AnnotationReference.PdbEntity);
+                sources.unshift(GqlTypes_1.Source.PdbEntity);
             if (config.reference == GqlTypes_1.SequenceReference.PdbInstance)
-                sources.unshift(GqlTypes_1.AnnotationReference.PdbInstance);
+                sources.unshift(GqlTypes_1.Source.PdbInstance);
             return new Promise((resolve, reject) => {
                 try {
                     RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.createFv({

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory.d.ts

@@ -1,11 +1,11 @@
-import { SequenceAlignments, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { AlignmentRequestContextType } from "../RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
 import { BlockFactoryInterface } from "./BlockFactoryInterface";
 import { TrackFactoryInterface } from "../RcsbFvTrackFactory/TrackFactoryInterface";
-export declare class AlignmentBlockFactory implements BlockFactoryInterface<[AlignmentRequestContextType, SequenceAlignments], [AlignmentRequestContextType, TargetAlignments, SequenceAlignments, number]> {
-    readonly trackFactory: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]>;
-    readonly trackConfigModifier?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignmentResponse: SequenceAlignments, indexResponse: number) => Promise<Partial<RcsbFvRowConfigInterface>>;
-    constructor(alignmentTrackFactory: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]>, trackModifier?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignmentResponse: SequenceAlignments, indexResponse: number) => Promise<Partial<RcsbFvRowConfigInterface>>);
-    getBlock(alignmentRequestContext: AlignmentRequestContextType, alignmentData: SequenceAlignments): Promise<RcsbFvRowConfigInterface[]>;
+export declare class AlignmentBlockFactory implements BlockFactoryInterface<[AlignmentRequestContextType, AlignmentResponse], [AlignmentRequestContextType, TargetAlignment, AlignmentResponse, number]> {
+    readonly trackFactory: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
+    readonly trackConfigModifier?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignmentResponse: AlignmentResponse, indexResponse: number) => Promise<Partial<RcsbFvRowConfigInterface>>;
+    constructor(alignmentTrackFactory: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>, trackModifier?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignmentResponse: AlignmentResponse, indexResponse: number) => Promise<Partial<RcsbFvRowConfigInterface>>);
+    getBlock(alignmentRequestContext: AlignmentRequestContextType, alignmentData: AlignmentResponse): Promise<RcsbFvRowConfigInterface[]>;
 }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory.js

@@ -11,9 +11,9 @@ class AlignmentBlockFactory {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             var _a;
             alignmentRequestContext = Object.assign(Object.assign({}, alignmentRequestContext), { querySequence: (_a = alignmentData.query_sequence) !== null && _a !== void 0 ? _a : undefined });
-            if (!alignmentData.target_alignments)
+            if (!alignmentData.target_alignment)
                 return [];
-            return (yield Promise.all(alignmentData.target_alignments.map((alignment, index) => tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return (yield Promise.all(alignmentData.target_alignment.map((alignment, index) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a, _b;
                 if (alignmentRequestContext.filterByTargetContains != null && !((_a = alignment === null || alignment === void 0 ? void 0 : alignment.target_id) === null || _a === void 0 ? void 0 : _a.includes(alignmentRequestContext.filterByTargetContains)))
                     return;

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory.d.ts

@@ -1,15 +1,15 @@
-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 { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { AnnotationRequestContext } from "../../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { BlockFactoryInterface } from "./BlockFactoryInterface";
 import { TrackFactoryInterface } from "../RcsbFvTrackFactory/TrackFactoryInterface";
 import { BlockManagerInterface } from "./BlockManager/BlockManagerInterface";
 import { TrackManagerInterface } from "./BlockManager/TrackManagerInterface";
-export declare class AnnotationsBlockFactory implements BlockFactoryInterface<[AnnotationRequestContext, SequenceAnnotations[]], [TrackManagerInterface]> {
+export declare class AnnotationsBlockFactory implements BlockFactoryInterface<[AnnotationRequestContext, AnnotationFeatures[]], [TrackManagerInterface]> {
     private readonly annotationBlockManager;
     private readonly annotationsBlockData;
     readonly trackFactory: TrackFactoryInterface<[TrackManagerInterface]>;
     readonly trackConfigModifier?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>;
-    constructor(annotationBlockManager: BlockManagerInterface<[AnnotationRequestContext, SequenceAnnotations[]]>, annotationTrackFactory: TrackFactoryInterface<[TrackManagerInterface]>, trackModifier?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>);
-    getBlock(annotationsRequestContext: AnnotationRequestContext, annotations: SequenceAnnotations[]): Promise<RcsbFvRowConfigInterface[]>;
+    constructor(annotationBlockManager: BlockManagerInterface<[AnnotationRequestContext, AnnotationFeatures[]]>, annotationTrackFactory: TrackFactoryInterface<[TrackManagerInterface]>, trackModifier?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>);
+    getBlock(annotationsRequestContext: AnnotationRequestContext, annotations: AnnotationFeatures[]): Promise<RcsbFvRowConfigInterface[]>;
 }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager.d.ts

@@ -1,17 +1,17 @@
-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 { RcsbAnnotationConfig } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConfig";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AnnotationRequestContext } from "../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { BlockManagerInterface } from "./BlockManagerInterface";
 import { TrackManagerFactoryInterface, TrackManagerInterface } from "./TrackManagerInterface";
 import { RcsbAnnotationConfigInterface } from "../../../../RcsbAnnotationConfig/AnnotationConfigInterface";
-export declare class AnnotationBlockManager implements BlockManagerInterface<[AnnotationRequestContext, SequenceAnnotations[]]> {
+export declare class AnnotationBlockManager implements BlockManagerInterface<[AnnotationRequestContext, AnnotationFeatures[]]> {
     private readonly rcsbAnnotationConfig;
     private readonly annotationTracks;
     private readonly polymerEntityInstanceTranslator?;
     private readonly trackManagerFactory;
     constructor(trackManagerFactory: TrackManagerFactoryInterface<[string, RcsbAnnotationConfigInterface, PolymerEntityInstanceTranslate]>, rcsbAnnotationConfig: RcsbAnnotationConfig, polymerEntityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    setData(requestConfig: AnnotationRequestContext, data: Array<SequenceAnnotations>): Promise<void>;
+    setData(requestConfig: AnnotationRequestContext, data: Array<AnnotationFeatures>): Promise<void>;
     getTracks(): Array<TrackManagerInterface>;
     private has;
     private orderedTypes;

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager.d.ts

@@ -1,9 +1,9 @@
 import { RcsbFvTrackDataElementGapInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { FeaturesFeaturePositions } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FeaturePosition } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbAnnotationConfigInterface } from "../../../../RcsbAnnotationConfig/AnnotationConfigInterface";
 import { TrackManagerFactoryInterface, TrackManagerInterface } from "./TrackManagerInterface";
-export interface FeaturePositionGaps extends FeaturesFeaturePositions {
+export interface FeaturePositionGaps extends FeaturePosition {
     gaps?: Array<RcsbFvTrackDataElementGapInterface>;
 }
 export declare class AnnotationTrackManagerFactory implements TrackManagerFactoryInterface<[string, RcsbAnnotationConfigInterface, PolymerEntityInstanceTranslate]> {

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager.js

@@ -85,7 +85,7 @@ class AnnotationTrackManager {
             if (value < this.valueRange.min)
                 this.valueRange.min = value;
         }
-        const sourceId = source == GqlTypes_1.AnnotationReference.PdbInstance && this.entityInstanceTranslator != null ?
+        const sourceId = source == GqlTypes_1.Source.PdbInstance && this.entityInstanceTranslator != null ?
             TagDelimiter_1.TagDelimiter.parseInstance(targetId).entryId + TagDelimiter_1.TagDelimiter.instance + this.entityInstanceTranslator.translateAsymToAuth(TagDelimiter_1.TagDelimiter.parseInstance(targetId).instanceId) : targetId;
         assertDefined(p.beg_seq_id);
         return {

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface.d.ts

@@ -1,6 +1,6 @@
 import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
 import { RcsbAnnotationConfigInterface } from "../../../../RcsbAnnotationConfig/AnnotationConfigInterface";
-import { Features, SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Feature, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AnnotationProcessingInterface } from "../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { RcsbFvTrackDataAnnotationInterface } from "../../RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface";
 export interface TrackManagerFactoryInterface<T extends any[]> {
@@ -16,9 +16,9 @@ export interface TrackManagerInterface {
     addFeature(ann: {
         reference: SequenceReference | undefined;
         queryId: string;
-        source: AnnotationReference;
+        source: Source;
         targetId: string;
-        feature: Features;
+        feature: Feature;
     }, annotationProcessing?: AnnotationProcessingInterface): void;
     size(): number;
     forEach(f: (ann: RcsbFvTrackDataAnnotationInterface, loc: string) => void): void;

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory.d.ts

@@ -1,6 +1,6 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { AlignedRegions, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignedRegion, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { AlignmentCollectConfig } from "../../../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
@@ -8,12 +8,12 @@ import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
 export type AlignmentRequestContextType = AlignmentCollectConfig & {
     querySequence?: string;
 };
-export declare class AlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
+export declare class AlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private readonly sequenceTrackFactory;
     private readonly trackTitleFactory;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate, trackTitleFactory?: TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignments]>);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignedRegionToTrackElementList?: (region: AlignedRegions, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate, trackTitleFactory?: TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>);
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
     private getAlignmentTrackConfiguration;
-    alignedRegionToTrackElementList(region: AlignedRegions, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
+    alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
     addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
 }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils.d.ts

@@ -1,9 +1,9 @@
-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";
 export declare namespace TrackUtils {
-    function getProvenanceConfigFormTarget(targetId: string, targetSource: SequenceReference | AnnotationReference): {
+    function getProvenanceConfigFormTarget(targetId: string, targetSource: SequenceReference | Source): {
         name: string;
         color: string;
     };
-    function transformSourceFromTarget(targetId: string, source: SequenceReference | AnnotationReference): string;
+    function transformSourceFromTarget(targetId: string, source: SequenceReference | Source): string;
     function getProvenanceColorFromProvenance(provenance?: string): string;
 }