@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.2

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

@@ -0,0 +1,21 @@
+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

@@ -0,0 +1,76 @@
+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) {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function* () {
+            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
+            };
+            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

@@ -0,0 +1,4 @@
+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

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

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

@@ -0,0 +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 { 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

@@ -0,0 +1,34 @@
+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

@@ -0,0 +1,8 @@
+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

@@ -0,0 +1,34 @@
+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) {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function* () {
+            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) {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function* () {
+            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

@@ -0,0 +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 { 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

@@ -0,0 +1,77 @@
+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

@@ -0,0 +1,11 @@
+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

@@ -0,0 +1,22 @@
+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

@@ -0,0 +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 { 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

@@ -0,0 +1,27 @@
+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

@@ -0,0 +1,12 @@
+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

@@ -0,0 +1,67 @@
+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) {
+        var _a, _b, _c;
+        return __awaiter(this, void 0, void 0, function* () {
+            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) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            return (alignmentQueryContext.from && !alignmentQueryContext.from.includes("PDB")) ? alignmentQueryContext.from.replace("_", " ") + " " + TagDelimiter.sequenceTitle : ((_a = alignmentQueryContext.sequencePrefix) !== null && _a !== void 0 ? _a : "");
+        });
+    }
+    getTrackTitleFlagColor(alignmentQueryContext) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function* () {
+            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

@@ -0,0 +1,6 @@
+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

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

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

@@ -0,0 +1,28 @@
+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

@@ -0,0 +1,109 @@
+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";
+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* () {
+            if (!this.featureViewers.has(tabKey))
+                yield this.renderPositionalFeatureViewer(tabKey);
+            this.syncPositionAndHighlight(tabKey);
+            this.currentTab = tabKey;
+        });
+    }
+    renderPositionalFeatureViewer(tabKey) {
+        var _a, _b, _c, _d, _e;
+        return __awaiter(this, void 0, void 0, function* () {
+            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

@@ -0,0 +1,10 @@
+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;