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

package/lib/RcsbRequest/RcsbRequestTools.js

@@ -17,23 +17,20 @@ export var RcsbRequestTools;
             if (!Array.isArray(ids))
                 ids = [ids];
             const missing = ids.filter(id => !map.has(id));
-            if (missing.length > 0) {
-                const collectorPromise = collector.collect({ [collectorKey]: missing });
-                missing.forEach(id => {
-                    map.set(id, new Promise((resolve, reject) => {
-                        collectorPromise.then(t => {
-                            const d = t.find(t => propertyKey(t) == id);
-                            if (d)
-                                resolve(d);
-                            else
-                                reject(`${id} not available`);
-                        });
-                    }));
-                });
-            }
+            const collectorPromise = collector.collect({ [collectorKey]: missing });
+            missing.forEach(id => {
+                map.set(id, new Promise((resolve, reject) => {
+                    collectorPromise.then(t => {
+                        const d = t.find(t => propertyKey(t) == id);
+                        if (d)
+                            resolve(d);
+                        else
+                            reject(`${id} not available`);
+                    });
+                }));
+            });
             return Promise.all(ids.map(i => map.get(i)).filter((x) => typeof x !== undefined));
         });
     }
     RcsbRequestTools.getMultipleObjectProperties = getMultipleObjectProperties;
 })(RcsbRequestTools || (RcsbRequestTools = {}));
-//# sourceMappingURL=RcsbRequestTools.js.map

package/lib/RcsbSeacrh/FacetStore/DepositionGroupFacetStore.js

@@ -67,4 +67,3 @@ class DepositionGroupFacetStore {
     }
 }
 export const depositionGroupFacetStore = new DepositionGroupFacetStore();
-//# sourceMappingURL=DepositionGroupFacetStore.js.map

package/lib/RcsbSeacrh/FacetStore/EntityGranularitySearchFacetStore.js

@@ -32,4 +32,3 @@ class EntityGranularitySearchFacetStore {
     }
 }
 export const entityGranularityGroupFacetStore = new EntityGranularitySearchFacetStore();
-//# sourceMappingURL=EntityGranularitySearchFacetStore.js.map

package/lib/RcsbSeacrh/FacetStore/FacetMemberInterface.js

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

package/lib/RcsbSeacrh/FacetStore/FacetStoreInterface.js

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

package/lib/RcsbSeacrh/FacetStore/SequenceGroupFacetStore.js

@@ -68,4 +68,3 @@ class SequenceGroupFacetStore {
     }
 }
 export const sequenceGroupFacetStore = new SequenceGroupFacetStore();
-//# sourceMappingURL=SequenceGroupFacetStore.js.map

package/lib/RcsbSeacrh/FacetStore/SingleFacets.js

@@ -785,4 +785,3 @@ export const SearchFacets = {
 function goFacetTransform(bucket, facetConfig) {
     return bucket.map(d => (Object.assign(Object.assign({}, d), { label: d.labelPath[0] })));
 }
-//# sourceMappingURL=SingleFacets.js.map

package/lib/RcsbSeacrh/FacetStore/UniprotGroupFacetStore.js

@@ -68,4 +68,3 @@ class UniprotGroupFacetStore {
     }
 }
 export const uniprotGroupFacetStore = new UniprotGroupFacetStore();
-//# sourceMappingURL=UniprotGroupFacetStore.js.map

package/lib/RcsbSeacrh/FacetTools.js

@@ -95,4 +95,3 @@ function mergeDomainMaxValue(data, domMaxValue) {
         labelPath: [domMaxValue.toString()]
     }) : data;
 }
-//# sourceMappingURL=FacetTools.js.map

package/lib/RcsbSeacrh/SearchQueryTools.js

@@ -112,4 +112,3 @@ export var SearchQueryTools;
         }
     }
 })(SearchQueryTools || (SearchQueryTools = {}));
-//# sourceMappingURL=SearchQueryTools.js.map

package/lib/RcsbSeacrh/SearchRequestProperty.js

@@ -68,4 +68,3 @@ class SearchRequestProperty {
     }
 }
 export const searchRequestProperty = new SearchRequestProperty(() => rcsbRequestClient.arches);
-//# sourceMappingURL=SearchRequestProperty.js.map

package/lib/RcsbServerConfig/ServerConfig.js

@@ -1,3 +1,2 @@
 import * as path from "path";
 export const rcsbFvWebAppPath = path.resolve(__dirname);
-//# sourceMappingURL=ServerConfig.js.map

package/lib/RcsbServerConfig/codegen.borrego.json

@@ -1,4 +1,4 @@
 {
-    "schema": "https://sequence-coordinates.rcsb.org/graphql",
+    "schema": "https://1d-coordinates.rcsb.org/graphql",
     "documents": "src/RcsbQueries/Borrego/Query*.graphql"
 }

package/lib/RcsbUtils/Groups/GroupGapLessTransformer.d.ts

@@ -1,8 +1,8 @@
-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";
 export declare class GroupGapLessTransformer {
     private readonly gapLessReference;
     private refLength;
     private processAlignments;
-    gapLessAlignments(alignments: SequenceAlignments): void;
-    gapLessFeatures(annotations: Array<SequenceAnnotations>): void;
+    gapLessAlignments(alignments: AlignmentResponse): void;
+    gapLessFeatures(annotations: Array<AnnotationFeatures>): void;
 }

package/lib/RcsbUtils/Groups/GroupGapLessTransformer.js

@@ -29,20 +29,31 @@ export class GroupGapLessTransformer {
         this.refLength = newIndex - 1;
     }
     gapLessAlignments(alignments) {
-        var _a, _b;
+        var _a, _b, _c, _d;
         this.processAlignments(alignments);
         if (this.gapLessReference.length == 0)
             return;
-        (_a = alignments.target_alignments) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
-            var _a;
-            (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.forEach(region => {
-                if (region === null || region === void 0 ? void 0 : region.query_begin)
-                    region.query_begin = this.gapLessReference[region.query_begin];
-                if (region === null || region === void 0 ? void 0 : region.query_end)
-                    region.query_end = this.gapLessReference[region.query_end];
+        if (alignments.target_alignment)
+            (_a = alignments.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
+                var _a;
+                (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.forEach(region => {
+                    if (region === null || region === void 0 ? void 0 : region.query_begin)
+                        region.query_begin = this.gapLessReference[region.query_begin];
+                    if (region === null || region === void 0 ? void 0 : region.query_end)
+                        region.query_end = this.gapLessReference[region.query_end];
+                });
             });
-        });
-        alignments.alignment_logo = (_b = alignments.alignment_logo) === null || _b === void 0 ? void 0 : _b.filter((al, n) => this.gapLessReference[n + 1] != -1);
+        else
+            (_c = (_b = alignments.target_alignment_subset) === null || _b === void 0 ? void 0 : _b.edges) === null || _c === void 0 ? void 0 : _c.forEach(edge => {
+                var _a, _b;
+                (_b = (_a = edge === null || edge === void 0 ? void 0 : edge.node) === null || _a === void 0 ? void 0 : _a.aligned_regions) === null || _b === void 0 ? void 0 : _b.forEach(region => {
+                    if (region === null || region === void 0 ? void 0 : region.query_begin)
+                        region.query_begin = this.gapLessReference[region.query_begin];
+                    if (region === null || region === void 0 ? void 0 : region.query_end)
+                        region.query_end = this.gapLessReference[region.query_end];
+                });
+            });
+        alignments.alignment_logo = (_d = alignments.alignment_logo) === null || _d === void 0 ? void 0 : _d.filter((al, n) => this.gapLessReference[n + 1] != -1);
         if (alignments.alignment_length)
             alignments.alignment_length = this.refLength;
     }
@@ -63,4 +74,3 @@ export class GroupGapLessTransformer {
         });
     }
 }
-//# sourceMappingURL=GroupGapLessTransformer.js.map

package/lib/RcsbUtils/Groups/GroupPropertiesProvider.js

@@ -25,4 +25,3 @@ export class GroupPropertiesProvider {
         }
     }
 }
-//# sourceMappingURL=GroupPropertiesProvider.js.map

package/lib/RcsbUtils/Groups/GroupProvenanceToAggregationType.js

@@ -5,4 +5,3 @@ export const groupProvenanceToReturnType = {
     [GroupProvenanceId.ProvenanceMatchingUniprotAccession]: ReturnType.PolymerEntity,
     [GroupProvenanceId.ProvenanceSequenceIdentity]: ReturnType.PolymerEntity,
 };
-//# sourceMappingURL=GroupProvenanceToAggregationType.js.map

package/lib/RcsbUtils/Helpers/Assertions.js

@@ -24,4 +24,3 @@ export var Assertions;
     }
     Assertions.assertElementMatrixDefined = assertElementMatrixDefined;
 })(Assertions || (Assertions = {}));
-//# sourceMappingURL=Assertions.js.map

package/lib/RcsbUtils/Helpers/DataContainer.js

@@ -10,4 +10,3 @@ export class DataContainer {
         this.data = data;
     }
 }
-//# sourceMappingURL=DataContainer.js.map

package/lib/RcsbUtils/Helpers/ObservableHelper.js

@@ -10,4 +10,3 @@ export class ObservableHelper {
         });
     }
 }
-//# sourceMappingURL=ObservableHelper.js.map

package/lib/RcsbUtils/Helpers/Operator.js

@@ -13,4 +13,3 @@ export class Operator {
         return parseFloat(x).toLocaleString('en-US');
     }
 }
-//# sourceMappingURL=Operator.js.map

package/lib/RcsbUtils/Helpers/SingletonMap.js

@@ -9,4 +9,3 @@ export class SingletonMap {
     }
 }
 SingletonMap.map = new Map();
-//# sourceMappingURL=SingletonMap.js.map

package/lib/RcsbUtils/Helpers/UrlTools.js

@@ -29,4 +29,3 @@ export var UrlTools;
         return encodeURIComponent(JSON.stringify(p));
     }
 })(UrlTools || (UrlTools = {}));
-//# sourceMappingURL=UrlTools.js.map

package/lib/RcsbUtils/PairwiseAlignmentTools/AlignmentReference.d.ts

@@ -1,4 +1,4 @@
-import { SequenceAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 type AlignmentRefType = (number | undefined)[];
 export declare class AlignmentReference {
     private readonly alignmentRefMap;
@@ -7,7 +7,7 @@ export declare class AlignmentReference {
     private readonly memberRefList;
     constructor(refId: string, targetId: string, alignment: AlignmentRefType, target: AlignmentRefType);
     addAlignment(id: string, alignment: AlignmentRefType, target: AlignmentRefType): void;
-    buildAlignments(): SequenceAlignments;
+    buildAlignments(): AlignmentResponse;
     private addRef;
     private addEnd;
     private addBeg;

package/lib/RcsbUtils/PairwiseAlignmentTools/AlignmentReference.js

@@ -92,14 +92,14 @@ export class AlignmentReference {
 }
 function buildAlignments(refId, alignmentRefMap, alignmentMembers) {
     const out = {};
-    out.target_alignments = [];
-    out.target_alignments.push({
+    out.target_alignment = [];
+    out.target_alignment.push({
         aligned_regions: buildRegions(alignmentRefMap),
         target_id: refId
     });
     alignmentMembers.forEach(am => {
         var _a;
-        (_a = out.target_alignments) === null || _a === void 0 ? void 0 : _a.push({
+        (_a = out.target_alignment) === null || _a === void 0 ? void 0 : _a.push({
             target_id: am.id,
             aligned_regions: buildRegions(am.map.map((v, n) => typeof v === "number" ? am.target[v] : undefined))
         });
@@ -163,4 +163,3 @@ function findGaps(alignment) {
         out[gapBeg] = gapLength;
     return out;
 }
-//# sourceMappingURL=AlignmentReference.js.map

package/lib/RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder.js

@@ -289,4 +289,3 @@ export class PairwiseAlignmentBuilder {
         FeatureTools.mergeBlocks(alignedBlocks);
     }
 }
-//# sourceMappingURL=PairwiseAlignmentBuilder.js.map

package/lib/RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite.js

@@ -63,36 +63,37 @@ export function alignmentGlobalLigandBindingSite() {
                 var _a;
                 if (d)
                     (_a = d.feature_positions) === null || _a === void 0 ? void 0 : _a.forEach(p => {
-                        var _a, _b;
-                        if (p === null || p === void 0 ? void 0 : p.beg_seq_id) {
-                            const key = (p.beg_seq_id).toString();
-                            if (!ligandMap.has(key))
-                                ligandMap.set(key, new Set());
-                            else if (d.name && !((_a = ligandMap.get(key)) === null || _a === void 0 ? void 0 : _a.has(d.name)))
-                                (_b = ligandMap.get(key)) === null || _b === void 0 ? void 0 : _b.add(d.name);
-                            else
-                                return;
-                            const bs = bindingSiteMap.get(key);
-                            if (!bs) {
-                                bindingSiteMap.set(key, {
-                                    begin: p.beg_seq_id,
-                                    type: trackName,
-                                    value: 1
-                                });
-                                if (max == 0)
-                                    max = 1;
-                            }
-                            else {
-                                if (bs) {
-                                    bs.value += 1;
-                                    if (bs.value > max)
-                                        max = bs.value;
+                        var _a;
+                        if (p === null || p === void 0 ? void 0 : p.beg_seq_id)
+                            (_a = p.values) === null || _a === void 0 ? void 0 : _a.forEach((v, n) => {
+                                var _a, _b;
+                                const key = (p.beg_seq_id + n).toString();
+                                if (!ligandMap.has(key))
+                                    ligandMap.set(key, new Set());
+                                else if (d.name && !((_a = ligandMap.get(key)) === null || _a === void 0 ? void 0 : _a.has(d.name)))
+                                    (_b = ligandMap.get(key)) === null || _b === void 0 ? void 0 : _b.add(d.name);
+                                else
+                                    return;
+                                const bs = bindingSiteMap.get(key);
+                                if (!bs) {
+                                    bindingSiteMap.set(key, {
+                                        begin: p.beg_seq_id + n,
+                                        type: trackName,
+                                        value: 1
+                                    });
+                                    if (max == 0)
+                                        max = 1;
                                 }
-                            }
-                        }
+                                else {
+                                    if (bs) {
+                                        bs.value += 1;
+                                        if (bs.value > max)
+                                            max = bs.value;
+                                    }
+                                }
+                            });
                     });
             });
         });
     }
 }
-//# sourceMappingURL=AlignmentGlobalBindingSite.js.map

package/lib/RcsbUtils/TrackGenerators/BurialFraction.d.ts

@@ -1,3 +1,3 @@
-import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare function burialFraction(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
-export declare function burialFractionFilter(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
+import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare function burialFraction(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+export declare function burialFractionFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;

package/lib/RcsbUtils/TrackGenerators/BurialFraction.js

@@ -1,16 +1,16 @@
-import { AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { cloneDeep } from "lodash";
 import { FeatureType } from "../../RcsbExport/FeatureType";
 export function burialFraction(annotations) {
     const burialFractionOut = new Array();
     const asaUnboundAnn = cloneDeep(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === FeatureType.AsaUnbound));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === Type.AsaUnbound));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
     const asaBoundAnn = cloneDeep(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === FeatureType.AsaBound));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === Type.AsaBound));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
     asaUnboundAnn.forEach((asaUnbound) => {
@@ -56,8 +56,7 @@ export function burialFraction(annotations) {
 export function burialFractionFilter(annotations) {
     return cloneDeep(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== AnnotationReference.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType.BurialFraction));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== Source.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType.BurialFraction));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
 }
-//# sourceMappingURL=BurialFraction.js.map

package/lib/RcsbUtils/TrackGenerators/BuriedResidues.d.ts

@@ -1,3 +1,3 @@
-import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare function buriedResidues(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
-export declare function buriedResiduesFilter(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
+import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare function buriedResidues(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+export declare function buriedResiduesFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;

package/lib/RcsbUtils/TrackGenerators/BuriedResidues.js

@@ -1,4 +1,4 @@
-import { AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { cloneDeep } from "lodash";
 import { FeatureType } from "../../RcsbExport/FeatureType";
 export function buriedResidues(annotations) {
@@ -7,11 +7,11 @@ export function buriedResidues(annotations) {
     let buriedResidues = {};
     let nBuried = 0;
     mainloop: for (const ann of annotations) {
-        if (ann.source === AnnotationReference.PdbInstance) {
+        if (ann.source === Source.PdbInstance) {
             for (const f of (_a = ann.features) !== null && _a !== void 0 ? _a : []) {
-                if ((f === null || f === void 0 ? void 0 : f.type) === FeatureType.Asa) {
+                if ((f === null || f === void 0 ? void 0 : f.type) === Type.Asa) {
                     buriedResidues = cloneDeep(ann);
-                    buriedResidues.source = AnnotationReference.PdbInstance;
+                    buriedResidues.source = Source.PdbInstance;
                     const feature = cloneDeep(f);
                     feature.type = FeatureType.BuriedResidues;
                     feature.name = "Unbound chain core residues";
@@ -41,8 +41,7 @@ export function buriedResidues(annotations) {
 export function buriedResiduesFilter(annotations) {
     return cloneDeep(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== FeatureType.Asa));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== Type.Asa));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
 }
-//# sourceMappingURL=BuriedResidues.js.map

package/lib/RcsbUtils/TrackGenerators/GroupExternalTrackBuilder.js

@@ -94,4 +94,3 @@ export function groupExternalTrackBuilder() {
             }];
     }
 }
-//# sourceMappingURL=GroupExternalTrackBuilder.js.map

package/lib/RcsbUtils/TrackGenerators/Logo.js

@@ -43,4 +43,3 @@ export class Logo {
         return -this.aaTypes().map(aa => (this.get(aa) != 0 ? (this.get(aa) / this.n) * (Math.log(this.get(aa) / this.n) / Math.log(this.aaTypes().length)) : 0)).reduce((p, v) => (p + v));
     }
 }
-//# sourceMappingURL=Logo.js.map

package/lib/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.d.ts

@@ -1,4 +1,4 @@
-import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 import { RcsbFvTooltipInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvTooltip/RcsbFvTooltipInterface";
 import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
@@ -6,9 +6,9 @@ export declare function addUnmodeledTrackBuilder(unmodeledTrackBuilder: Unmodele
 export declare class UnmodeledTrackBuilder {
     private readonly unmodeledDescription;
     filterFeatures(data: {
-        annotations: Array<SequenceAnnotations>;
+        annotations: Array<AnnotationFeatures>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<Array<SequenceAnnotations>>;
+    }): Promise<Array<AnnotationFeatures>>;
     getTooltip(): RcsbFvTooltipInterface;
     private buildUnobserved;
 }

package/lib/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { range } from "lodash";
 import { rcsbRequestCtxManager } from "../../RcsbRequest/RcsbRequestContextManager";
 import { RcsbFvTooltip } from "../../RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip";
@@ -43,10 +43,10 @@ export class UnmodeledTrackBuilder {
             const nInstances = (yield rcsbRequestCtxManager.getEntityProperties((_a = rcsbContext.entityId) !== null && _a !== void 0 ? _a : "none"))[0].instances.length;
             const featurePositions = Array.from(annotations.filter(ann => {
                 var _a, _b, _c;
-                return (_c = (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == FeaturesType.UnobservedResidueXyz)) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0 > 0;
+                return (_c = (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.UnobservedResidueXyz)) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0 > 0;
             }).map(ann => {
                 var _a, _b;
-                return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter((f) => (f === null || f === void 0 ? void 0 : f.type) == FeaturesType.UnobservedResidueXyz)) !== null && _b !== void 0 ? _b : [];
+                return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter((f) => (f === null || f === void 0 ? void 0 : f.type) == Type.UnobservedResidueXyz)) !== null && _b !== void 0 ? _b : [];
             }).flat().map(feature => {
                 var _a, _b;
                 return (_b = (_a = feature.feature_positions) === null || _a === void 0 ? void 0 : _a.filter((p) => typeof p != "undefined")) !== null && _b !== void 0 ? _b : [];
@@ -58,7 +58,7 @@ export class UnmodeledTrackBuilder {
                 };
             });
             return [{
-                    source: AnnotationReference.PdbEntity,
+                    source: Source.PdbEntity,
                     target_id: rcsbContext.entityId,
                     features: [{
                             type: UNMODELED,
@@ -94,8 +94,7 @@ class UnobservedToolTip {
 function filterUnobserved(annotations) {
     return annotations.map(ann => {
         var _a;
-        return Object.assign(Object.assign({}, ann), { features: (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) != FeaturesType.UnobservedResidueXyz && (f === null || f === void 0 ? void 0 : f.type) != FeaturesType.UnobservedAtomXyz) });
+        return Object.assign(Object.assign({}, ann), { features: (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) != Type.UnobservedResidueXyz && (f === null || f === void 0 ? void 0 : f.type) != Type.UnobservedAtomXyz) });
     });
 }
 const UNMODELED = "UNMODELED";
-//# sourceMappingURL=UnmodeledTrackBuilder.js.map

package/lib/RcsbUtils/Translators/AssemblyInterfacesTranslate.js

@@ -13,4 +13,3 @@ export class AssemblyInterfacesTranslate {
         return this.rawData;
     }
 }
-//# sourceMappingURL=AssemblyInterfacesTranslate.js.map

package/lib/RcsbUtils/Translators/EntryAssemblyTranslate.js

@@ -6,4 +6,3 @@ export class EntryAssemblyTranslate {
         return this.rawData;
     }
 }
-//# sourceMappingURL=EntryAssemblyTranslate.js.map

package/lib/RcsbUtils/Translators/InterfaceInstanceTranslate.js

@@ -18,4 +18,3 @@ export class InterfaceInstanceTranslate {
         return this.rawData;
     }
 }
-//# sourceMappingURL=InterfaceInstanceTranslate.js.map

package/lib/RcsbUtils/Translators/MultipleEntityInstanceTranslate.js

@@ -31,4 +31,3 @@ export class MultipleEntityInstanceTranslate {
         return Operator.uniqueValues(Array.from(this.entityInstanceTranslateMap.values()).map(peit => peit.getData()).flat().map(e => e.asymId));
     }
 }
-//# sourceMappingURL=MultipleEntityInstanceTranslate.js.map

package/lib/RcsbUtils/Translators/PolymerEntityChromosomeTranslate.js

@@ -6,4 +6,3 @@ export class PolymerEntityChromosomeTranslate {
         return this.rawData;
     }
 }
-//# sourceMappingURL=PolymerEntityChromosomeTranslate.js.map

package/lib/RcsbUtils/Translators/PolymerEntityInstanceTranslate.d.ts

@@ -1,11 +1,11 @@
 import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-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 interface AlignmentContextInterface {
     queryId: string;
     targetId: string;
     from: SequenceReference | undefined;
-    to: SequenceReference | AnnotationReference | undefined;
+    to: SequenceReference | Source | undefined;
     targetSequenceLength?: number;
     querySequenceLength?: number;
 }

package/lib/RcsbUtils/Translators/PolymerEntityInstanceTranslate.js

@@ -1,4 +1,4 @@
-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 { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
 export class PolymerEntityInstanceTranslate {
     constructor(data) {
@@ -67,7 +67,7 @@ export class PolymerEntityInstanceTranslate {
         const authResIds = this.instanceAuthResIds.get(asymId);
         if (!authResIds)
             return out;
-        if (reference === SequenceReference.PdbInstance || (reference === SequenceReference.PdbEntity && source === AnnotationReference.PdbInstance)) {
+        if (reference === SequenceReference.PdbInstance || (reference === SequenceReference.PdbEntity && source === Source.PdbInstance)) {
             const x = authResIds[e.begin - 1];
             if (typeof e.end === "number" && authResIds[e.end - 1] != x) {
                 out.beginName = x;
@@ -77,7 +77,7 @@ export class PolymerEntityInstanceTranslate {
                 out.beginName = x;
             }
         }
-        else if (source === AnnotationReference.PdbInstance && e.oriBegin) {
+        else if (source === Source.PdbInstance && e.oriBegin) {
             const x = authResIds[e.oriBegin - 1];
             if (typeof e.oriEnd === "number" && authResIds[e.oriEnd - 1] != x) {
                 out.oriBeginName = x;
@@ -90,4 +90,3 @@ export class PolymerEntityInstanceTranslate {
         return out;
     }
 }
-//# sourceMappingURL=PolymerEntityInstanceTranslate.js.map

package/lib/app.js

@@ -9,4 +9,3 @@ export { PlainAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTr
 export { MsaAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
 export { AnnotationsTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory";
 export { AlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
-//# sourceMappingURL=app.js.map

package/lib/commonjs/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/commonjs/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;
 }