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

package/lib/RcsbFvExamples/UniprotGroupFv.js

@@ -1,7 +1,6 @@
 import { buildGroupFv } from "../RcsbFvWeb/RcsbFvBuilder";
 import { GroupProvenanceId } from "@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": [
@@ -65,8 +64,7 @@ import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnu
             "experimental"
         ]
     }
-}*/
-// buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "Q8WZ42");
-// buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "P69905", query);
-buildGroupFv("pfv", GroupProvenanceId.ProvenanceSequenceIdentity, "10_30");
-//# sourceMappingURL=UniprotGroupFv.js.map
+};
+//buildGroupFv("pfv",GroupProvenanceId.ProvenanceMatchingUniprotAccession, "Q8WZ42");
+buildGroupFv("pfv", GroupProvenanceId.ProvenanceMatchingUniprotAccession, "P69905", query);
+//buildGroupFv("pfv",GroupProvenanceId.ProvenanceSequenceIdentity, "1_30");

package/lib/RcsbFvExamples/utils/events.js

@@ -13,4 +13,3 @@ export function onLoad(f) {
         f();
     });
 }
-//# sourceMappingURL=events.js.map

package/lib/RcsbFvUI/AbstractMenuItemComponent.js

@@ -4,4 +4,3 @@ export class AbstractMenuItemComponent extends React.Component {
         this.props.stateChange(this.state, prevState);
     }
 }
-//# sourceMappingURL=AbstractMenuItemComponent.js.map

package/lib/RcsbFvUI/Components/FilterItemComponent.js

@@ -14,4 +14,3 @@ export class FilterItemComponent extends AbstractMenuItemComponent {
         return (_jsxs(_Fragment, { children: [_jsx(ItemComponent, { onClick: () => this.setState({ collapseIn: !this.state.collapseIn }), children: "FILTER" }), _jsx(Collapse, { in: this.state.collapseIn, children: _jsx("div", { className: "position-absolute" }) })] }));
     }
 }
-//# sourceMappingURL=FilterItemComponent.js.map

package/lib/RcsbFvUI/Components/ItemComponent.js

@@ -5,4 +5,3 @@ export class ItemComponent extends React.Component {
         return (_jsx("div", Object.assign({ role: "button" }, this.props, { className: `user-select-none d-inline-block text-white text-center bg-primary bg-gradient rounded bg-opacity-75${this.props.className ? " " + this.props.className : ''}`, style: Object.assign(Object.assign({}, this.props.style), { width: 130, marginRight: 3, MozUserSelect: "none", WebkitUserSelect: "none", msUserSelect: "none" }) })));
     }
 }
-//# sourceMappingURL=ItemComponent.js.map

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

@@ -4,7 +4,7 @@ export class PaginationItemComponent extends AbstractMenuItemComponent {
     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
         };
     }
@@ -79,4 +79,3 @@ export class PaginationItemComponent extends AbstractMenuItemComponent {
         return x.out();
     }
 }
-//# sourceMappingURL=PaginationItemComponent.js.map

package/lib/RcsbFvUI/GroupPfvUI.js

@@ -23,4 +23,3 @@ export class GroupPfvUI {
         return uiDiv;
     }
 }
-//# sourceMappingURL=GroupPfvUI.js.map

package/lib/RcsbFvUI/Helper/ActionMethods.js

@@ -27,4 +27,3 @@ export var ActionMethods;
     }
     ActionMethods.paginationCallback = paginationCallback;
 })(ActionMethods || (ActionMethods = {}));
-//# sourceMappingURL=ActionMethods.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvAssemblyBuilder.js

@@ -38,4 +38,3 @@ export class RcsbFvAssemblyBuilder {
         });
     }
 }
-//# sourceMappingURL=RcsbFvAssemblyBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvChromosomeBuilder.js

@@ -91,4 +91,3 @@ export class RcsbFvChromosomeBuilder {
         });
     }
 }
-//# sourceMappingURL=RcsbFvChromosomeBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvContextManager.js

@@ -46,4 +46,3 @@ function buildRcsbFvSingleViewer(elementId, boardConfig) {
     });
 }
 export const rcsbFvCtxManager = new RcsbFvContextManager();
-//# sourceMappingURL=RcsbFvContextManager.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvCoreBuilder.js

@@ -89,4 +89,3 @@ export class RcsbFvCoreBuilder {
         (_a = document.getElementById(elementId)) === null || _a === void 0 ? void 0 : _a.append(domElement);
     }
 }
-//# sourceMappingURL=RcsbFvCoreBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvDataProviderBuilder.js

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

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvEntityBuilder.js

@@ -1,6 +1,6 @@
 import { __awaiter } from "tslib";
 import { RcsbFvEntity } from "../RcsbFvModule/RcsbFvEntity";
-import { FieldName, OperationType, AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FieldName, OperationType, Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvCoreBuilder } from "./RcsbFvCoreBuilder";
 import { RcsbFvUniprotBuilder } from "./RcsbFvUniprotBuilder";
 import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
@@ -33,7 +33,7 @@ export class RcsbFvEntityBuilder {
                                     yield RcsbFvUniprotBuilder.buildUniprotEntityFv(elementFvId, t, entityId, Object.assign({ alignmentFilter: [entityId] }, customAdditionalConfig({
                                         field: FieldName.TargetId,
                                         operation: OperationType.Contains,
-                                        source: AnnotationReference.PdbInstance,
+                                        source: Source.PdbInstance,
                                         values: [pdbId + TagDelimiter.instance]
                                     })));
                                 }
@@ -76,14 +76,13 @@ function customAdditionalConfig(f) {
     const filters = [{
             field: FieldName.Type,
             operation: OperationType.Equals,
-            source: AnnotationReference.PdbInstance,
-            values: [FeaturesType.UnobservedResidueXyz, FeaturesType.UnobservedAtomXyz, FeaturesType.MaQaMetricLocalTypeOther, FeaturesType.MaQaMetricLocalTypePlddt]
+            source: Source.PdbInstance,
+            values: [Type.UnobservedResidueXyz, Type.UnobservedAtomXyz, Type.MaQaMetricLocalTypeOther, Type.MaQaMetricLocalTypePlddt]
         }];
     if (f)
         filters.push(f);
     return {
-        sources: [AnnotationReference.PdbEntity, AnnotationReference.PdbInstance],
+        sources: [Source.PdbEntity, Source.PdbInstance],
         filters: filters
     };
 }
-//# sourceMappingURL=RcsbFvEntityBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupAlignmentBuilder.js

@@ -34,7 +34,7 @@ export class RcsbFvGroupAlignmentBuilder {
             else {
                 entityCount = yield searchRequestProperty.requestCount({ query: SQT.searchGroupQuery(groupProvenance, groupId), return_type: 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.mergeTrackBuilders(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.mergeTrackBuilders(groupExternalTrackBuilder(), additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalTrackBuilder) });
             // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
             const pfvArgs = [
                 getReferenceFromGroupProvenance(groupProvenance),
@@ -57,20 +57,20 @@ export class RcsbFvGroupAlignmentBuilder {
                 component: 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 GroupProvenanceId.ProvenanceSequenceIdentity:
                                 sequenceIdentityCallback(elementId, pfv, RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
                                         first: state.first,
-                                        after: state.after
+                                        after: state.after.toString()
                                     }, excludeLogo: true }));
                                 break;
                             case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
                                 uniprotCallback(elementId, pfv, RcsbFvUniprotBuilder.buildUniprotAlignmentFv, [groupId], Object.assign(Object.assign({}, additionalConfig), { page: {
                                         first: state.first,
-                                        after: state.after
+                                        after: state.after.toString()
                                     } }));
                                 break;
                         }
@@ -82,4 +82,3 @@ export class RcsbFvGroupAlignmentBuilder {
         });
     }
 }
-//# sourceMappingURL=RcsbFvGroupAlignmentBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupBuilder.js

@@ -51,4 +51,3 @@ export class RcsbFvGroupBuilder {
         });
     }
 }
-//# sourceMappingURL=RcsbFvGroupBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.js

@@ -108,4 +108,3 @@ export class RcsbFvInstanceBuilder {
         });
     }
 }
-//# sourceMappingURL=RcsbFvInstanceBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvPairwiseAligmentBuilder.js

@@ -26,4 +26,3 @@ export class RcsbFvPairwiseAligmentBuilder {
         });
     }
 }
-//# sourceMappingURL=RcsbFvPairwiseAligmentBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-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 { RcsbFvProteinSequence } from "../RcsbFvModule/RcsbFvProteinSequence";
 import { RcsbFvCoreBuilder } from "./RcsbFvCoreBuilder";
 export class RcsbFvProteinSequenceBuilder {
@@ -7,11 +7,11 @@ export class RcsbFvProteinSequenceBuilder {
         return __awaiter(this, void 0, void 0, function* () {
             var _a;
             const alignmentSource = (_a = config.alignmentSource) !== null && _a !== void 0 ? _a : config.reference;
-            const sources = [AnnotationReference.Uniprot];
+            const sources = [Source.Uniprot];
             if (config.reference == SequenceReference.PdbEntity)
-                sources.unshift(AnnotationReference.PdbEntity);
+                sources.unshift(Source.PdbEntity);
             if (config.reference == SequenceReference.PdbInstance)
-                sources.unshift(AnnotationReference.PdbInstance);
+                sources.unshift(Source.PdbInstance);
             return new Promise((resolve, reject) => {
                 try {
                     RcsbFvCoreBuilder.createFv({
@@ -40,4 +40,3 @@ export class RcsbFvProteinSequenceBuilder {
         });
     }
 }
-//# sourceMappingURL=RcsbFvProteinSequenceBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvUniprotBuilder.js

@@ -157,4 +157,3 @@ export class RcsbFvUniprotBuilder {
         });
     }
 }
-//# sourceMappingURL=RcsbFvUniprotBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvBuilder.js

@@ -76,4 +76,3 @@ export function buildUniprotAlignmentFv(elementId, upAcc, query, additionalConfi
 export function buildDataProviderFv(elementId, dataProvider, additionalConfig) {
     return RcsbFvDataProviderBuilder.buildFv(elementId, Object.assign(Object.assign({}, additionalConfig), { dataProvider: Object.assign({}, dataProvider) }));
 }
-//# sourceMappingURL=RcsbFvBuilder.js.map

package/lib/RcsbFvWeb/RcsbFvComponents/ComponentsManager.js

@@ -61,4 +61,3 @@ export class ComponentsManager {
 ComponentsManager.loaderSpinner = "_loaderSpinner";
 ComponentsManager.selectButtonMap = new Map();
 ComponentsManager.nodeMap = new Map();
-//# sourceMappingURL=ComponentsManager.js.map

package/lib/RcsbFvWeb/RcsbFvComponents/LoaderSpinner.js

@@ -6,4 +6,3 @@ export class LoaderSpinner extends React.Component {
         return (_jsx("div", { style: { position: "absolute", left: 0, right: 0, marginLeft: "auto", zIndex: Number.MAX_SAFE_INTEGER, marginRight: "auto" }, children: _jsx("div", { className: classes.loadSpinnerComponentScope, children: _jsx("div", { className: "loader" }) }) }));
     }
 }
-//# sourceMappingURL=LoaderSpinner.js.map

package/lib/RcsbFvWeb/RcsbFvComponents/MountableComponent.js

@@ -17,4 +17,3 @@ export class MountableComponent {
     }
 }
 MountableComponent.ROOT = new Map();
-//# sourceMappingURL=MountableComponent.js.map

package/lib/RcsbFvWeb/RcsbFvComponents/RcsbTabs.js

@@ -18,4 +18,3 @@ export class RcsbTabs extends React.Component {
 }
 RcsbTabs.UI_SUFFIX = "_" + uniqid() + "_UI_DIV";
 RcsbTabs.SELECT_SUFFIX = "_" + uniqid() + "_SELECT_DIV";
-//# sourceMappingURL=RcsbTabs.js.map

package/lib/RcsbFvWeb/RcsbFvComponents/SelectButton.js

@@ -114,4 +114,3 @@ export class SelectButton extends React.Component {
     }
 }
 SelectButton.BUTTON_CONTAINER_DIV_SUFFIX = "_buttonContainerDiv";
-//# sourceMappingURL=SelectButton.js.map

package/lib/RcsbFvWeb/RcsbFvComponents/SelectButtonManager.js

@@ -52,4 +52,3 @@ export class SelectButtonManager {
 SelectButtonManager.MAIN_BUTTON_SUFFIX = "_buttonDiv";
 SelectButtonManager.ADDITIONAL_BUTTON_SUFFIX = "_additionalButtonDiv";
 SelectButtonManager.SELECT_TITLE_DIV = "_selectButtonTitleDiv";
-//# sourceMappingURL=SelectButtonManager.js.map

package/lib/RcsbFvWeb/RcsbFvComponents/SelectButtonTitle.js

@@ -5,4 +5,3 @@ export class SelectButtonTitle extends React.Component {
         return (_jsx("div", { style: { marginLeft: 20 }, children: this.props.title }));
     }
 }
-//# sourceMappingURL=SelectButtonTitle.js.map

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

@@ -8,9 +8,9 @@ export class AlignmentBlockFactory {
         return __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) => __awaiter(this, void 0, void 0, function* () {
+            return (yield Promise.all(alignmentData.target_alignment.map((alignment, index) => __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;
@@ -21,4 +21,3 @@ export class AlignmentBlockFactory {
         });
     }
 }
-//# sourceMappingURL=AlignmentBlockFactory.js.map

package/lib/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/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory.js

@@ -17,4 +17,3 @@ export class AnnotationsBlockFactory {
         });
     }
 }
-//# sourceMappingURL=AnnotationsBlockFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockFactoryInterface.js

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

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

@@ -96,4 +96,3 @@ export class AnnotationBlockManager {
         });
     }
 }
-//# sourceMappingURL=AnnotationBlockManager.js.map

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

@@ -1,4 +1,4 @@
-import { AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { TrackUtils } from "../../RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils";
 import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
 var assertElementListDefined = Assertions.assertElementListDefined;
@@ -81,7 +81,7 @@ class AnnotationTrackManager {
             if (value < this.valueRange.min)
                 this.valueRange.min = value;
         }
-        const sourceId = source == AnnotationReference.PdbInstance && this.entityInstanceTranslator != null ?
+        const sourceId = source == Source.PdbInstance && this.entityInstanceTranslator != null ?
             TagDelimiter.parseInstance(targetId).entryId + TagDelimiter.instance + this.entityInstanceTranslator.translateAsymToAuth(TagDelimiter.parseInstance(targetId).instanceId) : targetId;
         assertDefined(p.beg_seq_id);
         return {
@@ -239,4 +239,3 @@ function computeFeatureGaps(featurePositions) {
     });
     return out;
 }
-//# sourceMappingURL=AnnotationTrackManager.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/BlockManagerInterface.js

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

package/lib/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/RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface.js

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

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface.js

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

package/lib/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/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory.js

@@ -126,4 +126,3 @@ function findMismatch(seqA, seqB) {
     }
     return out;
 }
-//# sourceMappingURL=AlignmentTrackFactory.js.map

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory.js

@@ -143,4 +143,3 @@ function buildRcsbFvRowConfigTrack(annotationTrack, type, rcsbAnnotationConfig)
     }
     return Object.assign(Object.assign({}, rcsbAnnotationConfig), { trackId: "annotationTrack_" + type, displayType: displayType, trackColor: "#F9F9F9", displayColor: displayColor, trackData: data });
 }
-//# sourceMappingURL=AnnotationsTrackFactory.js.map

package/lib/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;
 }

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils.js

@@ -34,4 +34,3 @@ export var TrackUtils;
     }
     TrackUtils.getProvenanceColorFromProvenance = getProvenanceColorFromProvenance;
 })(TrackUtils || (TrackUtils = {}));
-//# sourceMappingURL=TrackUtils.js.map

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

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory.js

@@ -22,4 +22,3 @@ export class MsaAlignmentTrackFactory {
         });
     }
 }
-//# sourceMappingURL=MsaAlignmentTrackFactory.js.map

package/lib/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 { 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";
@@ -8,16 +8,16 @@ import { RcsbFvTrackDataAnnotationInterface } from "../RcsbFvTrackDataAnnotation
 export type AlignmentRequestContextType = AlignmentCollectConfig & {
     querySequence?: string;
 };
-export declare class PlainAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]> {
+export declare class PlainAlignmentTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private readonly sequenceTrackFactory;
     private readonly trackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    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>): {
+    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>): {
         alignedBlocks: Array<RcsbFvTrackDataElementInterface>;
         mismatchData: Array<RcsbFvTrackDataElementInterface>;
         sequenceData: Array<RcsbFvTrackDataElementInterface>;
     };
-    alignedRegionToTrackElementList(region: AlignedRegions, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
+    alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
     addAuthorResIds(e: RcsbFvTrackDataAnnotationInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
 }

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory.js

@@ -126,4 +126,3 @@ function findMismatch(seqA, seqB) {
     }
     return out;
 }
-//# sourceMappingURL=PlainAlignmentTrackFactory.js.map