@rcsb/rcsb-saguaro-app 6.2.3 → 6.2.5-dev-js-seqcoord.1

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder.js

@@ -1,6 +1,27 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.buildDataProviderFv = exports.buildUniprotAlignmentFv = exports.buildSequenceIdentityAlignmentFv = exports.buildGroupFv = exports.buildChromosome = exports.buildEntityChromosome = exports.buildEntryChromosome = exports.buildFullChromosome = exports.buildPairwiseAlignment = exports.buildPfv = exports.buildUniprotEntityInstanceFv = exports.buildUniprotEntityFv = exports.buildInstanceFv = exports.buildEntityFv = exports.buildUniprotFv = exports.buildAssemblySequenceFv = exports.buildMultipleInstanceSequenceFv = exports.buildInstanceSequenceFv = exports.buildSingleEntitySummaryFv = exports.buildEntitySummaryFv = exports.buildMultipleAlignmentSequenceFv = exports.unmount = void 0;
+exports.unmount = unmount;
+exports.buildMultipleAlignmentSequenceFv = buildMultipleAlignmentSequenceFv;
+exports.buildEntitySummaryFv = buildEntitySummaryFv;
+exports.buildSingleEntitySummaryFv = buildSingleEntitySummaryFv;
+exports.buildInstanceSequenceFv = buildInstanceSequenceFv;
+exports.buildMultipleInstanceSequenceFv = buildMultipleInstanceSequenceFv;
+exports.buildAssemblySequenceFv = buildAssemblySequenceFv;
+exports.buildUniprotFv = buildUniprotFv;
+exports.buildEntityFv = buildEntityFv;
+exports.buildInstanceFv = buildInstanceFv;
+exports.buildUniprotEntityFv = buildUniprotEntityFv;
+exports.buildUniprotEntityInstanceFv = buildUniprotEntityInstanceFv;
+exports.buildPfv = buildPfv;
+exports.buildPairwiseAlignment = buildPairwiseAlignment;
+exports.buildFullChromosome = buildFullChromosome;
+exports.buildEntryChromosome = buildEntryChromosome;
+exports.buildEntityChromosome = buildEntityChromosome;
+exports.buildChromosome = buildChromosome;
+exports.buildGroupFv = buildGroupFv;
+exports.buildSequenceIdentityAlignmentFv = buildSequenceIdentityAlignmentFv;
+exports.buildUniprotAlignmentFv = buildUniprotAlignmentFv;
+exports.buildDataProviderFv = buildDataProviderFv;
 const RcsbFvCoreBuilder_1 = require("./RcsbFvBuilder/RcsbFvCoreBuilder");
 const RcsbFvChromosomeBuilder_1 = require("./RcsbFvBuilder/RcsbFvChromosomeBuilder");
 const RcsbFvPairwiseAligmentBuilder_1 = require("./RcsbFvBuilder/RcsbFvPairwiseAligmentBuilder");
@@ -16,88 +37,66 @@ const RcsbFvDataProviderBuilder_1 = require("./RcsbFvBuilder/RcsbFvDataProviderB
 function unmount(elementId) {
     RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.unmount(elementId);
 }
-exports.unmount = unmount;
 function buildMultipleAlignmentSequenceFv(elementFvId, elementSelectId, upAcc, config = {}, additionalConfig) {
     return RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotMultipleEntitySequenceFv(elementFvId, elementSelectId, upAcc, config, additionalConfig);
 }
-exports.buildMultipleAlignmentSequenceFv = buildMultipleAlignmentSequenceFv;
 function buildEntitySummaryFv(elementFvId, elementSelectId, entityId) {
     return RcsbFvEntityBuilder_1.RcsbFvEntityBuilder.buildEntitySummaryFv(elementFvId, elementSelectId, entityId);
 }
-exports.buildEntitySummaryFv = buildEntitySummaryFv;
 function buildSingleEntitySummaryFv(elementId, entityId) {
     return RcsbFvEntityBuilder_1.RcsbFvEntityBuilder.buildSingleEntitySummaryFv(elementId, entityId);
 }
-exports.buildSingleEntitySummaryFv = buildSingleEntitySummaryFv;
 function buildInstanceSequenceFv(elementFvId, elementSelectId, entryId, config = {}, additionalConfig) {
     return RcsbFvInstanceBuilder_1.RcsbFvInstanceBuilder.buildInstanceSequenceFv(elementFvId, elementSelectId, entryId, config, additionalConfig);
 }
-exports.buildInstanceSequenceFv = buildInstanceSequenceFv;
 function buildMultipleInstanceSequenceFv(elementFvId, elementEntrySelectId, elementInstanceSelectId, entryIdList, config = {}, additionalConfig) {
     return RcsbFvInstanceBuilder_1.RcsbFvInstanceBuilder.buildMultipleInstanceSequenceFv(elementFvId, elementEntrySelectId, elementInstanceSelectId, entryIdList, config, additionalConfig);
 }
-exports.buildMultipleInstanceSequenceFv = buildMultipleInstanceSequenceFv;
 function buildAssemblySequenceFv(elementFvId, elementSelectAssemblyId, elementSelectInstanceId, entryId, onAsseblyChangeCallback, onInstanceChangeCallback) {
     return RcsbFvAssemblyBuilder_1.RcsbFvAssemblyBuilder.buildAssemblySequenceFv(elementFvId, elementSelectAssemblyId, elementSelectInstanceId, entryId, onAsseblyChangeCallback, onInstanceChangeCallback);
 }
-exports.buildAssemblySequenceFv = buildAssemblySequenceFv;
 function buildUniprotFv(elementId, upAcc, additionalConfig) {
     return RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotFv(elementId, upAcc, additionalConfig);
 }
-exports.buildUniprotFv = buildUniprotFv;
 function buildEntityFv(elementId, entityId, additionalConfig) {
     return RcsbFvEntityBuilder_1.RcsbFvEntityBuilder.buildEntityFv(elementId, entityId, additionalConfig);
 }
-exports.buildEntityFv = buildEntityFv;
 function buildInstanceFv(elementId, instanceId, additionalConfig) {
     return RcsbFvInstanceBuilder_1.RcsbFvInstanceBuilder.buildInstanceFv(elementId, instanceId, additionalConfig);
 }
-exports.buildInstanceFv = buildInstanceFv;
 function buildUniprotEntityFv(elementId, upAcc, entityId, additionalConfig) {
     return RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotEntityFv(elementId, upAcc, entityId, additionalConfig);
 }
-exports.buildUniprotEntityFv = buildUniprotEntityFv;
 function buildUniprotEntityInstanceFv(elementId, upAcc, entityId, instanceId, additionalConfig) {
     return RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotEntityInstanceFv(elementId, upAcc, entityId, instanceId, additionalConfig);
 }
-exports.buildUniprotEntityInstanceFv = buildUniprotEntityInstanceFv;
 function buildPfv(elementId, config) {
     return RcsbFvProteinSequenceBuilder_1.RcsbFvProteinSequenceBuilder.buildPfv(elementId, config);
 }
-exports.buildPfv = buildPfv;
 function buildPairwiseAlignment(elementId, psa, additionalConfig) {
     return RcsbFvPairwiseAligmentBuilder_1.RcsbFvPairwiseAligmentBuilder.buildPairwiseAlignment(elementId, psa, additionalConfig);
 }
-exports.buildPairwiseAlignment = buildPairwiseAlignment;
 function buildFullChromosome(elementFvId, chrId) {
     return RcsbFvChromosomeBuilder_1.RcsbFvChromosomeBuilder.buildFullChromosome(elementFvId, chrId);
 }
-exports.buildFullChromosome = buildFullChromosome;
 function buildEntryChromosome(elementFvId, entitySelectId, chromosomeSelectId, entryId) {
     return RcsbFvChromosomeBuilder_1.RcsbFvChromosomeBuilder.buildEntryChromosome(elementFvId, entitySelectId, chromosomeSelectId, entryId);
 }
-exports.buildEntryChromosome = buildEntryChromosome;
 function buildEntityChromosome(elementFvId, elementSelectId, entityId) {
     return RcsbFvChromosomeBuilder_1.RcsbFvChromosomeBuilder.buildEntityChromosome(elementFvId, elementSelectId, entityId);
 }
-exports.buildEntityChromosome = buildEntityChromosome;
 function buildChromosome(elementFvId, entityId, chrId, elementSelectId) {
     return RcsbFvChromosomeBuilder_1.RcsbFvChromosomeBuilder.buildChromosome(elementFvId, chrId, elementSelectId);
 }
-exports.buildChromosome = buildChromosome;
 function buildGroupFv(elementId, groupProvenanceId, groupId, query, additionalConfig) {
     RcsbFvGroupTabsBuilder_1.RcsbFvGroupTabsBuilder.buildGroupTabs(elementId, groupProvenanceId, groupId, query, additionalConfig);
 }
-exports.buildGroupFv = buildGroupFv;
 function buildSequenceIdentityAlignmentFv(elementId, groupId, query, additionalConfig) {
     return RcsbFvGroupAlignmentBuilder_1.RcsbFvGroupAlignmentBuilder.buildGroupAlignmentFv(elementId, DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity, groupId, query, additionalConfig);
 }
-exports.buildSequenceIdentityAlignmentFv = buildSequenceIdentityAlignmentFv;
 function buildUniprotAlignmentFv(elementId, upAcc, query, additionalConfig) {
     return RcsbFvGroupAlignmentBuilder_1.RcsbFvGroupAlignmentBuilder.buildGroupAlignmentFv(elementId, DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession, upAcc, query, additionalConfig);
 }
-exports.buildUniprotAlignmentFv = buildUniprotAlignmentFv;
 function buildDataProviderFv(elementId, dataProvider, additionalConfig) {
     return RcsbFvDataProviderBuilder_1.RcsbFvDataProviderBuilder.buildFv(elementId, Object.assign(Object.assign({}, additionalConfig), { dataProvider: Object.assign({}, dataProvider) }));
 }
-exports.buildDataProviderFv = buildDataProviderFv;

package/lib/commonjs/RcsbFvWeb/RcsbFvComponents/ComponentsManager.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { GroupedOptionsInterface, SelectOptionInterface, SelectOptionProps } from "./SelectButton";
 export interface SelectButtonConfigInterface {
     addTitle?: boolean;

package/lib/commonjs/RcsbFvWeb/RcsbFvComponents/MountableComponent.js

@@ -5,9 +5,11 @@ const client_1 = require("react-dom/client");
 class MountableComponent {
     constructor(element) {
         var _a;
-        if (!MountableComponent.ROOT.has(element.id))
-            MountableComponent.ROOT.set(element.id, (0, client_1.createRoot)(element));
-        this.root = (_a = MountableComponent.ROOT.get(element.id)) !== null && _a !== void 0 ? _a : (0, client_1.createRoot)(element);
+        if (MountableComponent.ROOT.has(element.id)) {
+            (_a = MountableComponent.ROOT.get(element.id)) === null || _a === void 0 ? void 0 : _a.unmount();
+        }
+        this.root = (0, client_1.createRoot)(element);
+        MountableComponent.ROOT.set(element.id, this.root);
     }
     render(node) {
         this.unmount();

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

@@ -1,11 +1,11 @@
-import { AlignmentResponse, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, TargetAlignments } 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, 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[]>;
+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[]>;
 }

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

@@ -8,18 +8,18 @@ class AlignmentBlockFactory {
         this.trackConfigModifier = trackModifier;
     }
     getBlock(alignmentRequestContext, alignmentData) {
-        var _a;
         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_alignment)
+            if (!alignmentData.target_alignments)
                 return [];
-            return (yield Promise.all(alignmentData.target_alignment.map((alignment, index) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-                var _b, _c;
-                if (alignmentRequestContext.filterByTargetContains != null && !((_b = alignment === null || alignment === void 0 ? void 0 : alignment.target_id) === null || _b === void 0 ? void 0 : _b.includes(alignmentRequestContext.filterByTargetContains)))
+            return (yield Promise.all(alignmentData.target_alignments.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;
                 if ((alignment === null || alignment === void 0 ? void 0 : alignment.target_sequence) == null)
                     return;
-                return Object.assign(Object.assign({}, yield this.trackFactory.getTrack(alignmentRequestContext, alignment)), yield ((_c = this.trackConfigModifier) === null || _c === void 0 ? void 0 : _c.call(this, alignmentRequestContext, alignment, alignmentData, index)));
+                return Object.assign(Object.assign({}, yield this.trackFactory.getTrack(alignmentRequestContext, alignment)), yield ((_b = this.trackConfigModifier) === null || _b === void 0 ? void 0 : _b.call(this, alignmentRequestContext, alignment, alignmentData, index)));
             })))).filter((x) => x != undefined);
         });
     }

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

@@ -1,15 +1,15 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations } 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, AnnotationFeatures[]], [TrackManagerInterface]> {
+export declare class AnnotationsBlockFactory implements BlockFactoryInterface<[AnnotationRequestContext, SequenceAnnotations[]], [TrackManagerInterface]> {
     private readonly annotationBlockManager;
     private readonly annotationsBlockData;
     readonly trackFactory: TrackFactoryInterface<[TrackManagerInterface]>;
     readonly trackConfigModifier?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>;
-    constructor(annotationBlockManager: BlockManagerInterface<[AnnotationRequestContext, AnnotationFeatures[]]>, annotationTrackFactory: TrackFactoryInterface<[TrackManagerInterface]>, trackModifier?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>);
-    getBlock(annotationsRequestContext: AnnotationRequestContext, annotations: AnnotationFeatures[]): Promise<RcsbFvRowConfigInterface[]>;
+    constructor(annotationBlockManager: BlockManagerInterface<[AnnotationRequestContext, SequenceAnnotations[]]>, annotationTrackFactory: TrackFactoryInterface<[TrackManagerInterface]>, trackModifier?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>);
+    getBlock(annotationsRequestContext: AnnotationRequestContext, annotations: SequenceAnnotations[]): Promise<RcsbFvRowConfigInterface[]>;
 }

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

@@ -1,17 +1,17 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations } 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, AnnotationFeatures[]]> {
+export declare class AnnotationBlockManager implements BlockManagerInterface<[AnnotationRequestContext, SequenceAnnotations[]]> {
     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<AnnotationFeatures>): Promise<void>;
+    setData(requestConfig: AnnotationRequestContext, data: Array<SequenceAnnotations>): Promise<void>;
     getTracks(): Array<TrackManagerInterface>;
     private has;
     private orderedTypes;

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

@@ -36,8 +36,8 @@ class AnnotationBlockManager {
         ].flat();
     }
     processAnnotations(requestConfig, data) {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             yield Promise.all(data.map(ann => {
                 var _a, _b;
                 return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.map((feature) => tslib_1.__awaiter(this, void 0, void 0, function* () {
@@ -49,8 +49,8 @@ class AnnotationBlockManager {
         });
     }
     addFeature(requestConfig, ann, feature) {
-        var _a, _b, _c, _d, _e;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c, _d, _e;
             if (feature.type && ((_a = this.rcsbAnnotationConfig.getConfig(feature.type)) === null || _a === void 0 ? void 0 : _a.ignore))
                 return;
             const type = yield this.rcsbAnnotationConfig.getAnnotationType(requestConfig, ann, feature);

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

@@ -1,9 +1,9 @@
 import { RcsbFvTrackDataElementGapInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { FeaturePosition } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FeaturesFeaturePositions } 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 FeaturePosition {
+export interface FeaturePositionGaps extends FeaturesFeaturePositions {
     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.Source.PdbInstance && this.entityInstanceTranslator != null ?
+        const sourceId = source == GqlTypes_1.AnnotationReference.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 { Feature, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Features, SequenceReference, AnnotationReference } 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: Source;
+        source: AnnotationReference;
         targetId: string;
-        feature: Feature;
+        feature: Features;
     }, 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 { AlignedRegion, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignedRegions, TargetAlignments } 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, TargetAlignment]> {
+export declare class AlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
     private readonly sequenceTrackFactory;
     private readonly trackTitleFactory;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate, trackTitleFactory?: TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate, trackTitleFactory?: TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignments]>);
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignedRegionToTrackElementList?: (region: AlignedRegions, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
     private getAlignmentTrackConfiguration;
-    alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
+    alignedRegionToTrackElementList(region: AlignedRegions, 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, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare namespace TrackUtils {
-    function getProvenanceConfigFormTarget(targetId: string, targetSource: SequenceReference | Source): {
+    function getProvenanceConfigFormTarget(targetId: string, targetSource: SequenceReference | AnnotationReference): {
         name: string;
         color: string;
     };
-    function transformSourceFromTarget(targetId: string, source: SequenceReference | Source): string;
+    function transformSourceFromTarget(targetId: string, source: SequenceReference | AnnotationReference): string;
     function getProvenanceColorFromProvenance(provenance?: string): string;
 }

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

@@ -1,12 +1,12 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class MsaAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+export declare class MsaAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
     private observedAlignmentTrackFactory;
     private positionalScoreAlignmentTrackFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<RcsbFvRowConfigInterface>;
-    prepareFeatures(unObservedRegions: Array<AnnotationFeatures>, positionalScores: Array<AnnotationFeatures>): Promise<void>;
+    getTrack(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(unObservedRegions: Array<SequenceAnnotations>, positionalScores: Array<SequenceAnnotations>): Promise<void>;
 }

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

@@ -1,6 +1,6 @@
 import { RcsbFvColorGradient, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AlignedRegion, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignedRegions, TargetAlignments } 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";
@@ -8,16 +8,16 @@ import { RcsbFvTrackDataAnnotationInterface } from "../RcsbFvTrackDataAnnotation
 export type AlignmentRequestContextType = AlignmentCollectConfig & {
     querySequence?: string;
 };
-export declare class PlainAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+export declare class PlainAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
     private readonly sequenceTrackFactory;
     private readonly trackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>, alignmentColor?: RcsbFvColorGradient): Promise<RcsbFvRowConfigInterface>;
-    getAlignmentTrackConfiguration(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): {
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignedRegionToTrackElementList?: (region: AlignedRegions, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>, alignmentColor?: RcsbFvColorGradient): Promise<RcsbFvRowConfigInterface>;
+    getAlignmentTrackConfiguration(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignedRegionToTrackElementList: (region: AlignedRegions, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): {
         alignedBlocks: Array<RcsbFvTrackDataElementInterface>;
         mismatchData: Array<RcsbFvTrackDataElementInterface>;
         sequenceData: Array<RcsbFvTrackDataElementInterface>;
     };
-    alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
+    alignedRegionToTrackElementList(region: AlignedRegions, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
     addAuthorResIds(e: RcsbFvTrackDataAnnotationInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
 }

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

@@ -1,16 +1,16 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-export declare class PlainObservedAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+export declare class PlainObservedAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
     private alignmentTrackFactory;
     private unObservedResidues;
     private readonly instanceEntityMap;
     private readonly entityInstanceNumberMap;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<RcsbFvRowConfigInterface>;
-    prepareFeatures(unObservedRegions: Array<AnnotationFeatures>): Promise<void>;
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(unObservedRegions: Array<SequenceAnnotations>): Promise<void>;
     private collectFeatureEntryProperties;
     private prepareFeaturesAlignmentMap;
     private alignedRegionToTrackElementList;

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

@@ -1,16 +1,16 @@
 import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AlignedRegion, AnnotationFeatures, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignedRegions, SequenceAnnotations, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AlignmentContextInterface, PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { TrackFactoryInterface } from "../TrackFactoryInterface";
 import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-export declare class PositionalScoreAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+export declare class PositionalScoreAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
     private alignmentTrackFactory;
     private positionalScores;
     private readonly instanceEntityMap;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
-    prepareFeatures(positionalScores: Array<AnnotationFeatures>): Promise<void>;
+    getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignedRegionToTrackElementList?: (region: AlignedRegions, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
+    prepareFeatures(positionalScores: Array<SequenceAnnotations>): Promise<void>;
     private collectFeatureEntryProperties;
     private prepareFeaturesAlignmentMap;
     private alignedRegionToTrackElementList;

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PositionalScoreAlignmentTrackFactory.js

@@ -108,7 +108,7 @@ class PositionalScoreAlignmentTrackFactory {
                     source: TrackUtils_1.TrackUtils.transformSourceFromTarget(alignmentContext.targetId, alignmentContext.to),
                     provenanceName: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).name,
                     provenanceColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(alignmentContext.targetId, alignmentContext.to).color,
-                    type: GqlTypes_1.Type.MaQaMetricLocalTypeOther,
+                    type: GqlTypes_1.FeaturesType.MaQaMetricLocalTypeOther,
                 }, alignmentContext));
             });
         }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory.js

@@ -15,8 +15,8 @@ class SequenceTrackFactory {
         this.trackTitleFactory = trackTitleFactory !== null && trackTitleFactory !== void 0 ? trackTitleFactory : new SequenceTrackTitleFactory_1.SequenceTrackTitleFactory(entityInstanceTranslator);
     }
     getTrack(alignmentQueryContext, querySequence) {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const queryId = (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : alignmentQueryContext.groupId;
             assertDefined(queryId);
             return {

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AlignmentTrackTitleFactory.d.ts

@@ -1,13 +1,13 @@
 import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class AlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+export declare class AlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
     private readonly experimentalTrackTitleFactory;
     private readonly modelTrackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
-    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string | RcsbFvLink>;
+    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
 }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AnnotationsTrackTitleFactory.js

@@ -12,8 +12,8 @@ class AnnotationsTrackTitleFactory {
         });
     }
     getTrackTitleFlagColor(trackManager) {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const provenance = Array.from((_b = (_a = trackManager.getConfig()) === null || _a === void 0 ? void 0 : _a.provenanceList) !== null && _b !== void 0 ? _b : []);
             if (provenance.length == 1
                 &&
@@ -26,8 +26,8 @@ class AnnotationsTrackTitleFactory {
         });
     }
     getTrackTitlePrefix(trackManager) {
-        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             return (_b = (_a = trackManager.getConfig()) === null || _a === void 0 ? void 0 : _a.prefix) !== null && _b !== void 0 ? _b : "";
         });
     }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ExperimentalAlignmentTrackTitleFactory.d.ts

@@ -1,13 +1,13 @@
 import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class ExperimentalAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+export declare class ExperimentalAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
     private readonly entityInstanceTranslator;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
-    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string | RcsbFvLink>;
+    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
     private buildInstanceId;
 }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ModelAlignmentTrackTitleFactory.d.ts

@@ -1,12 +1,12 @@
 import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
 import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
-import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class ModelAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+export declare class ModelAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
     private readonly alignmentTrackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
-    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string | RcsbFvLink>;
+    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignments): Promise<string>;
 }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/SequenceTrackTitleFactory.js

@@ -15,8 +15,8 @@ class SequenceTrackTitleFactory {
         this.entityInstanceTranslator = entityInstanceTranslator;
     }
     getTrackTitle(alignmentQueryContext) {
-        var _a, _b, _c;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a, _b, _c;
             let rowTitle;
             if (!alignmentQueryContext.excludeFirstRowLink && alignmentQueryContext.from === GqlTypes_1.SequenceReference.Uniprot) {
                 rowTitle = {
@@ -48,14 +48,14 @@ class SequenceTrackTitleFactory {
         });
     }
     getTrackTitlePrefix(alignmentQueryContext) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a;
             return (alignmentQueryContext.from && !alignmentQueryContext.from.includes("PDB")) ? alignmentQueryContext.from.replace("_", " ") + " " + TagDelimiter_1.TagDelimiter.sequenceTitle : ((_a = alignmentQueryContext.sequencePrefix) !== null && _a !== void 0 ? _a : "");
         });
     }
     getTrackTitleFlagColor(alignmentQueryContext) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a;
             const queryId = (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : alignmentQueryContext.groupId;
             assertDefined(queryId), assertDefined(alignmentQueryContext.from);
             return TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(queryId, alignmentQueryContext.from).color;