@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory.d.ts

@@ -1,21 +0,0 @@
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { AlignmentContextInterface, PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { TrackFactoryInterface } from "../TrackFactoryInterface";
-import { AlignmentRequestContextType } from "./AlignmentTrackFactory";
-import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-import { RcsbFvTrackDataAnnotationInterface } from "../RcsbFvTrackDataAnnotationInterface";
-interface BuildSequenceDataInterface extends AlignmentContextInterface {
-    sequence: string;
-    begin: number;
-    oriBegin?: number;
-}
-export declare class SequenceTrackFactory implements TrackFactoryInterface<[AlignmentRequestContextType, string]> {
-    private readonly entityInstanceTranslator;
-    private readonly trackTitleFactory;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate, trackTitleFactory?: TrackTitleFactoryInterface<[AlignmentRequestContextType]>);
-    getTrack(alignmentQueryContext: AlignmentRequestContextType, querySequence: string): Promise<RcsbFvRowConfigInterface>;
-    buildSequenceData(config: BuildSequenceDataInterface, source: "from" | "to"): Array<RcsbFvTrackDataElementInterface>;
-    addAuthorResIds(e: RcsbFvTrackDataAnnotationInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;
-}
-export {};

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

@@ -1,77 +0,0 @@
-import { __awaiter } from "tslib";
-import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { SequenceTrackTitleFactory } from "../TrackTitleFactoryImpl/SequenceTrackTitleFactory";
-import { TrackUtils } from "./Helper/TrackUtils";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class SequenceTrackFactory {
-    constructor(entityInstanceTranslator, trackTitleFactory) {
-        this.entityInstanceTranslator = undefined;
-        this.entityInstanceTranslator = entityInstanceTranslator;
-        this.trackTitleFactory = trackTitleFactory !== null && trackTitleFactory !== void 0 ? trackTitleFactory : new SequenceTrackTitleFactory(entityInstanceTranslator);
-    }
-    getTrack(alignmentQueryContext, querySequence) {
-        return __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 {
-                trackId: (_b = "mainSequenceTrack_" + alignmentQueryContext.queryId) !== null && _b !== void 0 ? _b : alignmentQueryContext.groupId,
-                displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
-                trackColor: "#F9F9F9",
-                displayColor: "#000000",
-                rowTitle: yield this.trackTitleFactory.getTrackTitle(alignmentQueryContext),
-                rowPrefix: yield this.trackTitleFactory.getTrackTitlePrefix(alignmentQueryContext),
-                titleFlagColor: yield this.trackTitleFactory.getTrackTitleFlagColor(alignmentQueryContext),
-                nonEmptyDisplay: true,
-                overlap: true,
-                trackData: this.buildSequenceData({
-                    sequence: querySequence,
-                    begin: 1,
-                    oriBegin: undefined,
-                    queryId,
-                    targetId: "",
-                    from: alignmentQueryContext.from,
-                    to: undefined
-                }, "from")
-            };
-        });
-    }
-    buildSequenceData(config, source) {
-        const sequenceData = new Array();
-        const id = source === "from" ? config.queryId : config.targetId;
-        config.sequence.split("").forEach((s, i) => {
-            const c = config[source];
-            if (!c)
-                return;
-            const o = {
-                begin: (config.begin + i),
-                oriBegin: typeof config.oriBegin === "number" ? config.oriBegin + i : undefined,
-                sourceId: id,
-                source: TrackUtils.transformSourceFromTarget(id, c),
-                provenanceName: TrackUtils.getProvenanceConfigFormTarget(id, c).name,
-                provenanceColor: TrackUtils.getProvenanceConfigFormTarget(id, c).color,
-                label: s,
-                name: `RES ${s}`
-            };
-            sequenceData.push(this.addAuthorResIds(o, {
-                from: config.from,
-                to: config.to,
-                queryId: config.queryId,
-                targetId: config.targetId
-            }));
-        });
-        return sequenceData;
-    }
-    //TODO this method can be defined in a helper
-    addAuthorResIds(e, alignmentContext) {
-        let o = e;
-        if (this.entityInstanceTranslator != null) {
-            this.entityInstanceTranslator.addAuthorResIds(o, alignmentContext);
-        }
-        if (alignmentContext.to == SequenceReference.PdbInstance && o.sourceId != null && this.entityInstanceTranslator != null)
-            o.sourceId = o.sourceId.split(TagDelimiter.instance)[0] + TagDelimiter.instance + this.entityInstanceTranslator.translateAsymToAuth(o.sourceId.split(TagDelimiter.instance)[1]);
-        return o;
-    }
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryInterface.d.ts

@@ -1,4 +0,0 @@
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-export interface TrackFactoryInterface<T extends any[]> {
-    getTrack(...args: T): Promise<RcsbFvRowConfigInterface>;
-}

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

@@ -1 +0,0 @@
-export {};

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

@@ -1,13 +0,0 @@
-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 { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
-import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class AlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
-    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>;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AlignmentTrackTitleFactory.js

@@ -1,34 +0,0 @@
-import { __awaiter } from "tslib";
-import { ExperimentalAlignmentTrackTitleFactory } from "./ExperimentalAlignmentTrackTitleFactory";
-import { ModelAlignmentTrackTitleFactory } from "./ModelAlignmentTrackTitleFactory";
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class AlignmentTrackTitleFactory {
-    constructor(entityInstanceTranslator) {
-        this.experimentalTrackTitleFactory = new ExperimentalAlignmentTrackTitleFactory(entityInstanceTranslator);
-        this.modelTrackTitleFactory = new ModelAlignmentTrackTitleFactory(entityInstanceTranslator);
-    }
-    getTrackTitle(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (targetAlignment.target_id && TagDelimiter.isModel(targetAlignment.target_id))
-                return this.modelTrackTitleFactory.getTrackTitle(alignmentQueryContext, targetAlignment);
-            else
-                return this.experimentalTrackTitleFactory.getTrackTitle(alignmentQueryContext, targetAlignment);
-        });
-    }
-    getTrackTitlePrefix(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (targetAlignment.target_id && TagDelimiter.isModel(targetAlignment.target_id))
-                return this.modelTrackTitleFactory.getTrackTitlePrefix(alignmentQueryContext, targetAlignment);
-            else
-                return this.experimentalTrackTitleFactory.getTrackTitlePrefix(alignmentQueryContext, targetAlignment);
-        });
-    }
-    getTrackTitleFlagColor(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (targetAlignment.target_id && TagDelimiter.isModel(targetAlignment.target_id))
-                return this.modelTrackTitleFactory.getTrackTitleFlagColor(alignmentQueryContext, targetAlignment);
-            else
-                return this.experimentalTrackTitleFactory.getTrackTitleFlagColor(alignmentQueryContext, targetAlignment);
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AnnotationsTrackTitleFactory.d.ts

@@ -1,8 +0,0 @@
-import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-import { TrackManagerInterface } from "../../RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-export declare class AnnotationsTrackTitleFactory implements TrackTitleFactoryInterface<[TrackManagerInterface]> {
-    getTrackTitle(trackManager: TrackManagerInterface): Promise<string | RcsbFvLink>;
-    getTrackTitleFlagColor(trackManager: TrackManagerInterface): Promise<string>;
-    getTrackTitlePrefix(trackManager: TrackManagerInterface): Promise<string>;
-}

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

@@ -1,34 +0,0 @@
-import { __awaiter } from "tslib";
-import { RcsbAnnotationConstants } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConstants";
-import { FeatureTools } from "../../../../RcsbCollectTools/FeatureTools/FeatureTools";
-export class AnnotationsTrackTitleFactory {
-    getTrackTitle(trackManager) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const c = trackManager.getConfig();
-            return c ? buildRowTitle(c) : trackManager.getId();
-        });
-    }
-    getTrackTitleFlagColor(trackManager) {
-        return __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
-                &&
-                    (provenance[0] === RcsbAnnotationConstants.provenanceName.pdb || provenance[0] === RcsbAnnotationConstants.provenanceName.promotif)) {
-                return RcsbAnnotationConstants.provenanceColorCode.rcsbPdb;
-            }
-            else {
-                return RcsbAnnotationConstants.provenanceColorCode.external;
-            }
-        });
-    }
-    getTrackTitlePrefix(trackManager) {
-        return __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 : "";
-        });
-    }
-}
-function buildRowTitle(annConfig) {
-    return annConfig.prefix ? FeatureTools.parseLink(annConfig.title) : annConfig.title;
-}

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

@@ -1,13 +0,0 @@
-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 { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
-import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class ExperimentalAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
-    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>;
-    private buildInstanceId;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ExperimentalAlignmentTrackTitleFactory.js

@@ -1,77 +0,0 @@
-import { __awaiter } from "tslib";
-import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import resource from "../../../../RcsbServerConfig/web.resources.json";
-import { RcsbAnnotationConstants } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConstants";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class ExperimentalAlignmentTrackTitleFactory {
-    constructor(entityInstanceTranslator) {
-        this.entityInstanceTranslator = undefined;
-        this.entityInstanceTranslator = entityInstanceTranslator;
-    }
-    getTrackTitle(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            let rowTitle;
-            assertDefined(targetAlignment.target_id);
-            if (alignmentQueryContext.excludeAlignmentLinks) {
-                rowTitle = targetAlignment.target_id;
-            }
-            else if (alignmentQueryContext.to === SequenceReference.PdbInstance && this.entityInstanceTranslator != null) {
-                const entityId = this.entityInstanceTranslator.translateAsymToEntity(TagDelimiter.parseInstance(targetAlignment.target_id).instanceId);
-                assertDefined(entityId);
-                rowTitle = {
-                    visibleTex: this.buildInstanceId(targetAlignment.target_id),
-                    url: resource.rcsb_entry.url + TagDelimiter.parseInstance(targetAlignment.target_id).entryId + "#entity-" + entityId,
-                    style: {
-                        fontWeight: "bold",
-                        color: RcsbAnnotationConstants.provenanceColorCode.rcsbLink
-                    }
-                };
-            }
-            else if (alignmentQueryContext.to === SequenceReference.PdbEntity) {
-                const entityId = TagDelimiter.parseEntity(targetAlignment.target_id).entityId;
-                rowTitle = {
-                    visibleTex: targetAlignment.target_id,
-                    url: resource.rcsb_entry.url + TagDelimiter.parseEntity(targetAlignment.target_id).entryId + "#entity-" + entityId,
-                    style: {
-                        fontWeight: "bold",
-                        color: RcsbAnnotationConstants.provenanceColorCode.rcsbLink
-                    }
-                };
-            }
-            else if (alignmentQueryContext.to === SequenceReference.Uniprot) {
-                rowTitle = {
-                    visibleTex: targetAlignment.target_id,
-                    url: resource.rcsb_uniprot.url + targetAlignment.target_id,
-                    style: {
-                        fontWeight: "bold",
-                        color: RcsbAnnotationConstants.provenanceColorCode.rcsbLink
-                    }
-                };
-            }
-            else {
-                rowTitle = targetAlignment.target_id;
-            }
-            return rowTitle;
-        });
-    }
-    getTrackTitlePrefix(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return alignmentQueryContext.to && !alignmentQueryContext.to.includes("PDB") ? alignmentQueryContext.to.replace("_", " ") + " " + TagDelimiter.alignmentTitle : "";
-        });
-    }
-    getTrackTitleFlagColor(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (alignmentQueryContext.to === SequenceReference.Uniprot)
-                return RcsbAnnotationConstants.provenanceColorCode.external;
-            return RcsbAnnotationConstants.provenanceColorCode.rcsbPdb;
-        });
-    }
-    buildInstanceId(targetId) {
-        var _a;
-        const labelAsymId = TagDelimiter.parseInstance(targetId).instanceId;
-        const authAsymId = (_a = this.entityInstanceTranslator) === null || _a === void 0 ? void 0 : _a.translateAsymToAuth(labelAsymId);
-        return TagDelimiter.parseInstance(targetId).entryId + TagDelimiter.instance + (labelAsymId === authAsymId || !authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]");
-    }
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/InstanceSequenceTrackTitleFactory.d.ts

@@ -1,11 +0,0 @@
-import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
-import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class InstanceSequenceTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType]> {
-    private readonly trackTitleFactory;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType): Promise<string>;
-    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType): Promise<string>;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/InstanceSequenceTrackTitleFactory.js

@@ -1,22 +0,0 @@
-import { __awaiter } from "tslib";
-import { SequenceTrackTitleFactory } from "./SequenceTrackTitleFactory";
-export class InstanceSequenceTrackTitleFactory {
-    constructor(entityInstanceTranslator) {
-        this.trackTitleFactory = new SequenceTrackTitleFactory(entityInstanceTranslator);
-    }
-    getTrackTitle(alignmentQueryContext) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.trackTitleFactory.getTrackTitle(alignmentQueryContext);
-        });
-    }
-    getTrackTitlePrefix(alignmentQueryContext) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return "CHAIN";
-        });
-    }
-    getTrackTitleFlagColor(alignmentQueryContext) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.trackTitleFactory.getTrackTitleFlagColor(alignmentQueryContext);
-        });
-    }
-}

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

@@ -1,12 +0,0 @@
-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 { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class ModelAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
-    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>;
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ModelAlignmentTrackTitleFactory.js

@@ -1,27 +0,0 @@
-import { __awaiter } from "tslib";
-import { RcsbAnnotationConstants } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConstants";
-import { ExperimentalAlignmentTrackTitleFactory } from "./ExperimentalAlignmentTrackTitleFactory";
-export class ModelAlignmentTrackTitleFactory {
-    constructor(entityInstanceTranslator) {
-        this.alignmentTrackTitleFactory = new ExperimentalAlignmentTrackTitleFactory(entityInstanceTranslator);
-    }
-    getTrackTitle(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const rowTitle = yield this.alignmentTrackTitleFactory.getTrackTitle(alignmentQueryContext, targetAlignment);
-            return typeof rowTitle === "string" ? rowTitle : Object.assign(Object.assign({}, rowTitle), { style: {
-                    fontWeight: "bold",
-                    color: RcsbAnnotationConstants.provenanceColorCode.rcsbLink
-                } });
-        });
-    }
-    getTrackTitlePrefix(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.alignmentTrackTitleFactory.getTrackTitlePrefix(alignmentQueryContext, targetAlignment);
-        });
-    }
-    getTrackTitleFlagColor(alignmentQueryContext, targetAlignment) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return RcsbAnnotationConstants.provenanceColorCode.csm;
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/SequenceTrackTitleFactory.d.ts

@@ -1,12 +0,0 @@
-import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
-import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
-import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-export declare class SequenceTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType]> {
-    private readonly entityInstanceTranslator;
-    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
-    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType): Promise<string>;
-    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType): Promise<string>;
-    private buildInstanceId;
-}

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

@@ -1,67 +0,0 @@
-import { __awaiter } from "tslib";
-import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import resource from "../../../../RcsbServerConfig/web.resources.json";
-import { RcsbAnnotationConstants } from "../../../../RcsbAnnotationConfig/RcsbAnnotationConstants";
-import { TrackUtils } from "../TrackFactoryImpl/Helper/TrackUtils";
-import { Assertions } from "../../../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-export class SequenceTrackTitleFactory {
-    constructor(entityInstanceTranslator) {
-        this.entityInstanceTranslator = undefined;
-        this.entityInstanceTranslator = entityInstanceTranslator;
-    }
-    getTrackTitle(alignmentQueryContext) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
-            let rowTitle;
-            if (!alignmentQueryContext.excludeFirstRowLink && alignmentQueryContext.from === SequenceReference.Uniprot) {
-                rowTitle = {
-                    visibleTex: (_a = alignmentQueryContext.queryId) !== null && _a !== void 0 ? _a : "",
-                    url: resource.rcsb_uniprot.url + alignmentQueryContext.queryId,
-                    style: {
-                        fontWeight: "bold",
-                        color: RcsbAnnotationConstants.provenanceColorCode.rcsbLink
-                    }
-                };
-            }
-            else if (!alignmentQueryContext.excludeFirstRowLink && alignmentQueryContext.from === SequenceReference.PdbInstance && this.entityInstanceTranslator != null) {
-                rowTitle = {
-                    visibleTex: alignmentQueryContext.queryId ? this.buildInstanceId(alignmentQueryContext.queryId) : "",
-                    style: {
-                        fontWeight: "bold",
-                    }
-                };
-            }
-            else {
-                rowTitle = {
-                    visibleTex: (_b = alignmentQueryContext.queryId) !== null && _b !== void 0 ? _b : ((_c = alignmentQueryContext.groupId) !== null && _c !== void 0 ? _c : ""),
-                    style: {
-                        fontWeight: "bold",
-                    }
-                };
-            }
-            return rowTitle;
-        });
-    }
-    getTrackTitlePrefix(alignmentQueryContext) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            return (alignmentQueryContext.from && !alignmentQueryContext.from.includes("PDB")) ? alignmentQueryContext.from.replace("_", " ") + " " + TagDelimiter.sequenceTitle : ((_a = alignmentQueryContext.sequencePrefix) !== null && _a !== void 0 ? _a : "");
-        });
-    }
-    getTrackTitleFlagColor(alignmentQueryContext) {
-        return __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.getProvenanceConfigFormTarget(queryId, alignmentQueryContext.from).color;
-        });
-    }
-    buildInstanceId(targetId) {
-        var _a;
-        const labelAsymId = targetId.split(TagDelimiter.instance)[1];
-        const authAsymId = (_a = this.entityInstanceTranslator) === null || _a === void 0 ? void 0 : _a.translateAsymToAuth(labelAsymId);
-        return (labelAsymId === authAsymId || !authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]");
-    }
-}

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryInterface.d.ts

@@ -1,6 +0,0 @@
-import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-export interface TrackTitleFactoryInterface<T extends any[]> {
-    getTrackTitle(...args: T): Promise<string | RcsbFvLink>;
-    getTrackTitlePrefix(...args: T): Promise<string>;
-    getTrackTitleFlagColor(...args: T): Promise<string>;
-}

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

@@ -1 +0,0 @@
-export {};

package/lib/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.d.ts

@@ -1,28 +0,0 @@
-import React from "react";
-import { RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
-import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-interface SequenceTabInterface {
-    groupProvenanceId: GroupProvenanceId;
-    groupId: string;
-    searchQuery?: SearchQuery;
-    additionalConfig?: RcsbFvAdditionalConfig;
-}
-export declare class GroupPfvTabs extends React.Component<SequenceTabInterface> {
-    private readonly featureViewers;
-    private filterInstances;
-    private filterEntities;
-    private entityCount;
-    private currentTab;
-    constructor(props: {
-        groupProvenanceId: GroupProvenanceId;
-        groupId: string;
-        searchQuery: SearchQuery;
-    });
-    render(): JSX.Element;
-    private onMount;
-    private syncPositionAndHighlight;
-    private onSelect;
-    private renderPositionalFeatureViewer;
-}
-export {};

package/lib/RcsbFvWeb/RcsbFvGroup/GroupPfvTabs.js

@@ -1,112 +0,0 @@
-import { __awaiter } from "tslib";
-import { jsx as _jsx } from "react/jsx-runtime";
-import React from "react";
-import { FieldName, OperationType, Source, } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { searchRequestProperty } from "../../RcsbSeacrh/SearchRequestProperty";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { RcsbTabs } from "../RcsbFvComponents/RcsbTabs";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { SearchQueryTools as SQT } from "../../RcsbSeacrh/SearchQueryTools";
-import { GroupPfvApp as GPA } from "./GroupTabs/GroupPfvApp";
-import { asyncScheduler } from "rxjs";
-const ALIGNMENT = "alignment";
-const STRUCTURAL_FEATURES = "structural-features";
-const BINDING_SITES = "binding-sites";
-export class GroupPfvTabs extends React.Component {
-    constructor(props) {
-        super(props);
-        this.featureViewers = new Map();
-        this.filterInstances = undefined;
-        this.filterEntities = undefined;
-        this.entityCount = undefined;
-        this.currentTab = ALIGNMENT;
-    }
-    render() {
-        const additionalComponent = {
-            additionalComponent: this.props.groupProvenanceId === GroupProvenanceId.ProvenanceMatchingUniprotAccession ? _jsx("div", { id: ALIGNMENT + RcsbTabs.SELECT_SUFFIX, style: { height: 38 } }) : undefined
-        };
-        return (_jsx(RcsbTabs, { id: "group-id", tabList: [
-                Object.assign({ key: ALIGNMENT, title: "Sequence Alignments" }, additionalComponent),
-                Object.assign({ key: STRUCTURAL_FEATURES, title: "Structural Features" }, additionalComponent),
-                Object.assign({ key: BINDING_SITES, title: "Binding Sites" }, additionalComponent)
-            ], default: "alignment", onMount: this.onMount.bind(this), onSelect: this.onSelect.bind(this) }));
-    }
-    onMount() {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (this.props.searchQuery && this.props.searchQuery.query) {
-                this.filterEntities = yield searchRequestProperty.requestMembers(Object.assign(Object.assign({}, this.props.searchQuery), { query: SQT.addGroupNodeToSearchQuery(this.props.groupProvenanceId, this.props.groupId, this.props.searchQuery.query), return_type: ReturnType.PolymerEntity }));
-                this.entityCount = this.filterEntities.length;
-                this.filterInstances = yield searchRequestProperty.requestMembers(Object.assign(Object.assign({}, this.props.searchQuery), { query: SQT.addGroupNodeToSearchQuery(this.props.groupProvenanceId, this.props.groupId, this.props.searchQuery.query), return_type: ReturnType.PolymerInstance }));
-                yield this.onSelect(this.currentTab);
-            }
-            else {
-                this.filterInstances = yield searchRequestProperty.requestMembers({ query: SQT.searchGroupQuery(this.props.groupProvenanceId, this.props.groupId), return_type: ReturnType.PolymerInstance });
-                this.entityCount = yield searchRequestProperty.requestCount({ query: SQT.searchGroupQuery(this.props.groupProvenanceId, this.props.groupId), return_type: ReturnType.PolymerEntity });
-                yield this.onSelect(this.currentTab);
-            }
-        });
-    }
-    syncPositionAndHighlight(tabKey) {
-        var _a, _b, _c, _d, _e, _f, _g;
-        if (tabKey !== this.currentTab) {
-            const dom = (_a = this.featureViewers.get(this.currentTab)) === null || _a === void 0 ? void 0 : _a.getFv().getDomain();
-            if (dom)
-                (_b = this.featureViewers.get(tabKey)) === null || _b === void 0 ? void 0 : _b.getFv().setDomain(dom);
-            const sel = (_c = this.featureViewers.get(this.currentTab)) === null || _c === void 0 ? void 0 : _c.getFv().getSelection("select");
-            if (sel && (sel === null || sel === void 0 ? void 0 : sel.length) > 0) {
-                (_d = this.featureViewers.get(tabKey)) === null || _d === void 0 ? void 0 : _d.getFv().clearSelection("select");
-                (_e = this.featureViewers.get(tabKey)) === null || _e === void 0 ? void 0 : _e.getFv().setSelection({
-                    elements: (_f = sel === null || sel === void 0 ? void 0 : sel.map((s) => ({
-                        begin: s.rcsbFvTrackDataElement.begin,
-                        end: s.rcsbFvTrackDataElement.end
-                    }))) !== null && _f !== void 0 ? _f : [],
-                    mode: "select"
-                });
-            }
-            else {
-                (_g = this.featureViewers.get(tabKey)) === null || _g === void 0 ? void 0 : _g.getFv().clearSelection("select");
-            }
-        }
-    }
-    onSelect(tabKey) {
-        return __awaiter(this, void 0, void 0, function* () {
-            asyncScheduler.schedule(() => __awaiter(this, void 0, void 0, function* () {
-                if (!this.featureViewers.has(tabKey))
-                    yield this.renderPositionalFeatureViewer(tabKey);
-                this.syncPositionAndHighlight(tabKey);
-                this.currentTab = tabKey;
-            }), 10);
-        });
-    }
-    renderPositionalFeatureViewer(tabKey) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
-            switch (tabKey) {
-                case ALIGNMENT:
-                    this.featureViewers.set(tabKey, yield GPA.alignment(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_a = this.entityCount) !== null && _a !== void 0 ? _a : 0, Object.assign(Object.assign({ page: { first: 50, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.filterEntities })));
-                    break;
-                case BINDING_SITES:
-                    this.featureViewers.set(tabKey, yield GPA.bindingSites(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_c = (_b = this.filterInstances) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0, Object.assign(Object.assign({ page: { first: 0, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.props.searchQuery ? this.filterEntities : undefined, filters: this.props.searchQuery ? [{
-                                source: Source.PdbInstance,
-                                field: FieldName.TargetId,
-                                operation: OperationType.Equals,
-                                values: this.filterInstances
-                            }] : undefined })));
-                    break;
-                case STRUCTURAL_FEATURES:
-                    this.featureViewers.set(tabKey, yield GPA.structure(tabKey.toString(), this.props.groupProvenanceId, this.props.groupId, (_e = (_d = this.filterInstances) === null || _d === void 0 ? void 0 : _d.length) !== null && _e !== void 0 ? _e : 0, Object.assign(Object.assign({ page: { first: 0, after: "0" } }, this.props.additionalConfig), { alignmentFilter: this.props.searchQuery ? this.filterEntities : undefined, filters: this.props.searchQuery ? [{
-                                source: Source.PdbInstance,
-                                field: FieldName.TargetId,
-                                operation: OperationType.Equals,
-                                values: this.filterInstances
-                            }, {
-                                source: Source.PdbEntity,
-                                field: FieldName.TargetId,
-                                operation: OperationType.Equals,
-                                values: this.filterEntities
-                            }] : undefined })));
-                    break;
-            }
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvGroup/GroupTabs/GroupPfvApp.d.ts

@@ -1,10 +0,0 @@
-import { RcsbFvAdditionalConfig, RcsbFvModulePublicInterface } from "../../RcsbFvModule/RcsbFvModuleInterface";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { GroupReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { ActionMethods } from "../../../RcsbFvUI/Helper/ActionMethods";
-export declare namespace GroupPfvApp {
-    function alignment(elementId: string, groupProvenanceId: GroupProvenanceId, groupId: string, entityCount: number, additionalConfig?: RcsbFvAdditionalConfig & ActionMethods.FvChangeConfigInterface): Promise<RcsbFvModulePublicInterface>;
-    function structure(elementId: string, groupProvenanceId: GroupProvenanceId, groupId: string, nTargets: number, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-    function bindingSites(elementId: string, groupProvenanceId: GroupProvenanceId, groupId: string, nTargets: number, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-}
-export declare function getReferenceFromGroupProvenance(groupProvenanceId: GroupProvenanceId): GroupReference;