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

package/lib/RcsbCollectTools/DataCollectors/InterfaceInstanceCollector.d.ts

@@ -0,0 +1,12 @@
+import { QueryInterfacesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+export interface InterfaceInstanceInterface {
+    rcsbId: string;
+    assemblyId: string;
+    interfaceId: string;
+    asymIds: [string, string];
+    operatorIds: [Array<Array<string>>, Array<Array<string>>];
+}
+export declare class InterfaceInstanceCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryInterfacesArgs): Promise<Array<InterfaceInstanceInterface>>;
+}

package/lib/RcsbCollectTools/DataCollectors/InterfaceInstanceCollector.js

@@ -0,0 +1,41 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertElementListDefined = Assertions.assertElementListDefined;
+var assertDefined = Assertions.assertDefined;
+var assertElementMatrixDefined = Assertions.assertElementMatrixDefined;
+export class InterfaceInstanceCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const result = yield this.rcsbFvQuery.requestInterfaceInstances(requestConfig);
+                return result.map(r => parseInterfaceInstances(r));
+            }
+            catch (error) {
+                console.log(error);
+                throw error;
+            }
+        });
+    }
+}
+function parseInterfaceInstances(coreInterface) {
+    var _a, _b, _c, _d;
+    assertElementMatrixDefined(coreInterface.rcsb_interface_operator[0]);
+    assertElementMatrixDefined(coreInterface.rcsb_interface_operator[1]);
+    assertElementListDefined(coreInterface.rcsb_interface_partner);
+    assertDefined((_a = coreInterface.rcsb_interface_partner[0].interface_partner_identifier) === null || _a === void 0 ? void 0 : _a.asym_id);
+    assertDefined((_b = coreInterface.rcsb_interface_partner[1].interface_partner_identifier) === null || _b === void 0 ? void 0 : _b.asym_id);
+    return {
+        rcsbId: coreInterface.rcsb_interface_container_identifiers.rcsb_id,
+        assemblyId: coreInterface.rcsb_interface_container_identifiers.assembly_id,
+        interfaceId: coreInterface.rcsb_interface_container_identifiers.interface_id,
+        asymIds: [
+            (_c = coreInterface.rcsb_interface_partner[0].interface_partner_identifier) === null || _c === void 0 ? void 0 : _c.asym_id,
+            (_d = coreInterface.rcsb_interface_partner[1].interface_partner_identifier) === null || _d === void 0 ? void 0 : _d.asym_id
+        ],
+        operatorIds: [coreInterface.rcsb_interface_operator[0], coreInterface.rcsb_interface_operator[1]]
+    };
+}

package/lib/RcsbCollectTools/DataCollectors/MultipleEntityInstancesCollector.d.ts

@@ -0,0 +1,8 @@
+import { QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
+import { MultipleDocumentPropertyCollectorInterface } from "./DataCollectorInterface";
+export declare class MultipleEntityInstancesCollector implements MultipleDocumentPropertyCollectorInterface<"entity_ids", PolymerEntityInstanceInterface> {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<PolymerEntityInstanceInterface>>;
+    private static getEntityInstances;
+}

package/lib/RcsbCollectTools/DataCollectors/MultipleEntityInstancesCollector.js

@@ -0,0 +1,32 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { PolymerEntityInstancesCollector } from "./PolymerEntityInstancesCollector";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertElementListDefined = Assertions.assertElementListDefined;
+export class MultipleEntityInstancesCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const result = yield this.rcsbFvQuery.requestMultipleEntityInstances(requestConfig);
+                return MultipleEntityInstancesCollector.getEntityInstances(result);
+            }
+            catch (error) {
+                console.log(error);
+                throw error;
+            }
+        });
+    }
+    static getEntityInstances(polymer_entities) {
+        const out = new Array();
+        polymer_entities === null || polymer_entities === void 0 ? void 0 : polymer_entities.forEach(entity => {
+            if (Array.isArray(entity.polymer_entity_instances)) {
+                assertElementListDefined(entity.polymer_entity_instances);
+                PolymerEntityInstancesCollector.parsePolymerEntityInstances(entity.polymer_entity_instances, out);
+            }
+        });
+        return out;
+    }
+}

package/lib/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.d.ts

@@ -0,0 +1,19 @@
+import { QueryEntriesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+export interface EntryPropertyIntreface {
+    rcsbId: string;
+    entryId: string;
+    experimentalMethod: string;
+    resolution?: number;
+    name: string;
+    taxNames: Array<string>;
+    entryMolecularWeight?: number;
+    description: Array<string>;
+    entityToInstance: Map<string, Array<string>>;
+    structureDeterminationMethodology: StructureDeterminationMethodology;
+}
+export declare class MultipleEntryPropertyCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryEntriesArgs): Promise<Array<EntryPropertyIntreface>>;
+    private static getEntryProperties;
+}

package/lib/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.js

@@ -0,0 +1,28 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+export class MultipleEntryPropertyCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const result = yield this.rcsbFvQuery.requestMultipleEntriesProperties(requestConfig);
+            return result.map(r => MultipleEntryPropertyCollector.getEntryProperties(r));
+        });
+    }
+    static getEntryProperties(r) {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m;
+        return {
+            rcsbId: r.rcsb_id,
+            entryId: r.rcsb_id,
+            experimentalMethod: (_a = r.rcsb_entry_info.experimental_method) !== null && _a !== void 0 ? _a : "NA",
+            resolution: (_c = (_b = r.rcsb_entry_info.resolution_combined) === null || _b === void 0 ? void 0 : _b[0]) !== null && _c !== void 0 ? _c : undefined,
+            name: (_e = (_d = r.struct) === null || _d === void 0 ? void 0 : _d.title) !== null && _e !== void 0 ? _e : "NA",
+            description: (_g = (_f = r.pdbx_molecule_features) === null || _f === void 0 ? void 0 : _f.map(mf => mf === null || mf === void 0 ? void 0 : mf.details).filter((x) => x != null)) !== null && _g !== void 0 ? _g : [],
+            taxNames: (_j = (_h = r.polymer_entities) === null || _h === void 0 ? void 0 : _h.map((entity) => { var _a; return ((_a = entity === null || entity === void 0 ? void 0 : entity.rcsb_entity_source_organism) === null || _a === void 0 ? void 0 : _a.map((so) => (so === null || so === void 0 ? void 0 : so.ncbi_scientific_name))); }).flat().filter((x) => x != null)) !== null && _j !== void 0 ? _j : [],
+            entryMolecularWeight: (_k = r.rcsb_entry_info.molecular_weight) !== null && _k !== void 0 ? _k : undefined,
+            entityToInstance: (_m = (_l = r.polymer_entities) === null || _l === void 0 ? void 0 : _l.map(pe => { var _a; return [pe === null || pe === void 0 ? void 0 : pe.rcsb_id, (_a = pe === null || pe === void 0 ? void 0 : pe.polymer_entity_instances) === null || _a === void 0 ? void 0 : _a.map(pei => pei === null || pei === void 0 ? void 0 : pei.rcsb_id)]; }).reduce((r, x) => r.set(x[0], x[1]), new Map())) !== null && _m !== void 0 ? _m : new Map(),
+            structureDeterminationMethodology: r.rcsb_entry_info.structure_determination_methodology
+        };
+    }
+}

package/lib/RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector.d.ts

@@ -0,0 +1,11 @@
+import { MultipleDocumentPropertyCollectorInterface } from "./DataCollectorInterface";
+export interface InstanceSequenceInterface {
+    rcsbId: string;
+    sequence: string;
+}
+export declare class MultipleInstanceSequencesCollector implements MultipleDocumentPropertyCollectorInterface<"instance_ids", InstanceSequenceInterface> {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: {
+        instance_ids: string[];
+    }): Promise<InstanceSequenceInterface[]>;
+}

package/lib/RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector.js

@@ -0,0 +1,22 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertDefined = Assertions.assertDefined;
+export class MultipleInstanceSequencesCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const result = yield this.rcsbFvQuery.requestMultipleInstanceSequences(requestConfig);
+            return result.map(r => {
+                var _a, _b, _c, _d;
+                assertDefined(r.rcsb_id), assertDefined((_b = (_a = r.polymer_entity) === null || _a === void 0 ? void 0 : _a.entity_poly) === null || _b === void 0 ? void 0 : _b.pdbx_seq_one_letter_code_can);
+                return {
+                    rcsbId: r.rcsb_id,
+                    sequence: (_d = (_c = r.polymer_entity) === null || _c === void 0 ? void 0 : _c.entity_poly) === null || _d === void 0 ? void 0 : _d.pdbx_seq_one_letter_code_can
+                };
+            });
+        });
+    }
+}

package/lib/RcsbCollectTools/DataCollectors/MultiplePolymerEntityCollector.d.ts

@@ -0,0 +1,12 @@
+import { QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
+export interface PolymerEntityInterface {
+    rcsbId: string;
+    entityId: string;
+    entryId: string;
+    instances: PolymerEntityInstanceInterface[];
+}
+export declare class MultiplePolymerEntityCollector {
+    private readonly multipleEntityInstanceCollector;
+    collect(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<PolymerEntityInterface>>;
+}

package/lib/RcsbCollectTools/DataCollectors/MultiplePolymerEntityCollector.js

@@ -0,0 +1,26 @@
+import { __awaiter } from "tslib";
+import { MultipleEntityInstancesCollector } from "./MultipleEntityInstancesCollector";
+import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
+export class MultiplePolymerEntityCollector {
+    constructor() {
+        this.multipleEntityInstanceCollector = new MultipleEntityInstancesCollector();
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const results = yield this.multipleEntityInstanceCollector.collect(requestConfig);
+            const map = new Map();
+            results.forEach(r => {
+                var _a;
+                if (!map.has(`${r.entryId}${TagDelimiter.entity}${r.entityId}`))
+                    map.set(`${r.entryId}${TagDelimiter.entity}${r.entityId}`, []);
+                (_a = map.get(`${r.entryId}${TagDelimiter.entity}${r.entityId}`)) === null || _a === void 0 ? void 0 : _a.push(r);
+            });
+            return Array.from(map.entries()).map(([k, v]) => ({
+                rcsbId: v[0].rcsbId,
+                entityId: v[0].entityId,
+                entryId: v[0].entryId,
+                instances: v
+            }));
+        });
+    }
+}

package/lib/RcsbCollectTools/DataCollectors/PolymerEntityChromosomeCollector.d.ts

@@ -0,0 +1,5 @@
+export declare class PolymerEntityChromosomeCollector {
+    private readonly rcsbFvQuery;
+    collect(entityIds: Array<string>): Promise<Map<string, Array<string>>>;
+    private entityChromosomes;
+}

package/lib/RcsbCollectTools/DataCollectors/PolymerEntityChromosomeCollector.js

@@ -0,0 +1,39 @@
+import { __awaiter } from "tslib";
+import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+export class PolymerEntityChromosomeCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(entityIds) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const entityMap = new Map();
+            const result = yield Promise.all(entityIds.map(e => {
+                return this.entityChromosomes(e);
+            }));
+            result.forEach((alignment, n) => {
+                var _a;
+                (_a = alignment.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
+                    var _a, _b, _c;
+                    if (((_b = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0) {
+                        if (!entityMap.has(entityIds[n]))
+                            entityMap.set(entityIds[n], new Array());
+                        if (ta === null || ta === void 0 ? void 0 : ta.target_id)
+                            (_c = entityMap.get(entityIds[n])) === null || _c === void 0 ? void 0 : _c.push(ta.target_id);
+                    }
+                });
+            });
+            return entityMap;
+        });
+    }
+    entityChromosomes(entityId) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const request = {
+                from: SequenceReference.PdbEntity,
+                to: SequenceReference.NcbiGenome,
+                queryId: entityId
+            };
+            return yield this.rcsbFvQuery.requestAlignment(request);
+        });
+    }
+}

package/lib/RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector.d.ts

@@ -0,0 +1,24 @@
+import { CorePolymerEntityInstance, QueryEntryArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
+import { StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+export interface PolymerEntityInstanceInterface {
+    rcsbId: string;
+    entityId: string;
+    entryId: string;
+    asymId: string;
+    authId: string;
+    authResId: Array<string>;
+    name: string;
+    taxNames: Array<string>;
+    experimentalMethod: string;
+    resolution?: number;
+    sequenceLength: number;
+    entityMolecularWeight?: number;
+    entryMolecularWeight?: number;
+    structureDeterminationMethodology: StructureDeterminationMethodology;
+}
+export declare class PolymerEntityInstancesCollector {
+    private readonly rcsbFvQuery;
+    collect(requestConfig: QueryEntryArgs): Promise<Array<PolymerEntityInstanceInterface>>;
+    private static getEntryInstances;
+    static parsePolymerEntityInstances(polymerEntityInstances: Array<CorePolymerEntityInstance>, out: Array<PolymerEntityInstanceInterface>): void;
+}

package/lib/RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector.js

@@ -0,0 +1,67 @@
+import { __awaiter } from "tslib";
+import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertElementListDefined = Assertions.assertElementListDefined;
+var assertDefined = Assertions.assertDefined;
+export class PolymerEntityInstancesCollector {
+    constructor() {
+        this.rcsbFvQuery = rcsbClient;
+    }
+    collect(requestConfig) {
+        return __awaiter(this, void 0, void 0, function* () {
+            try {
+                const result = yield this.rcsbFvQuery.requestEntityInstances(requestConfig);
+                return PolymerEntityInstancesCollector.getEntryInstances(result);
+            }
+            catch (error) {
+                console.log(error);
+                throw error;
+            }
+        });
+    }
+    static getEntryInstances(entry) {
+        const out = new Array();
+        if ((entry === null || entry === void 0 ? void 0 : entry.polymer_entities) instanceof Array) {
+            entry.polymer_entities.forEach(entity => {
+                if (entity && Array.isArray(entity === null || entity === void 0 ? void 0 : entity.polymer_entity_instances)) {
+                    assertElementListDefined(entity.polymer_entity_instances);
+                    PolymerEntityInstancesCollector.parsePolymerEntityInstances(entity.polymer_entity_instances, out);
+                }
+            });
+        }
+        return out;
+    }
+    static parsePolymerEntityInstances(polymerEntityInstances, out) {
+        polymerEntityInstances.forEach(instance => {
+            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q, _r, _s, _t, _u, _v, _w, _x;
+            const taxIds = new Set();
+            if (((_a = instance === null || instance === void 0 ? void 0 : instance.polymer_entity) === null || _a === void 0 ? void 0 : _a.rcsb_entity_source_organism) instanceof Array)
+                instance.polymer_entity.rcsb_entity_source_organism.forEach(sO => {
+                    if (typeof (sO === null || sO === void 0 ? void 0 : sO.ncbi_scientific_name) === "string" && sO.ncbi_scientific_name.length > 0)
+                        taxIds.add(sO.ncbi_scientific_name);
+                });
+            const o = instance.rcsb_polymer_entity_instance_container_identifiers;
+            const p = (_b = instance.polymer_entity) === null || _b === void 0 ? void 0 : _b.entry;
+            assertDefined(o), assertDefined(o === null || o === void 0 ? void 0 : o.entity_id), assertDefined(o.auth_asym_id), assertElementListDefined(o === null || o === void 0 ? void 0 : o.auth_to_entity_poly_seq_mapping);
+            assertDefined(p);
+            assertDefined((_d = (_c = instance.polymer_entity) === null || _c === void 0 ? void 0 : _c.entity_poly) === null || _d === void 0 ? void 0 : _d.rcsb_sample_sequence_length);
+            assertDefined((_e = instance.polymer_entity.entry) === null || _e === void 0 ? void 0 : _e.rcsb_entry_info.structure_determination_methodology);
+            out.push({
+                rcsbId: instance.rcsb_id,
+                entryId: o.entry_id,
+                entityId: o.entity_id,
+                asymId: o.asym_id,
+                authId: o.auth_asym_id,
+                authResId: o.auth_to_entity_poly_seq_mapping,
+                name: (_o = ((_k = (_j = (_h = (_g = (_f = instance.polymer_entity) === null || _f === void 0 ? void 0 : _f.rcsb_polymer_entity) === null || _g === void 0 ? void 0 : _g.rcsb_polymer_name_combined) === null || _h === void 0 ? void 0 : _h.names) === null || _j === void 0 ? void 0 : _j.join(", ")) !== null && _k !== void 0 ? _k : (_m = (_l = instance === null || instance === void 0 ? void 0 : instance.polymer_entity) === null || _l === void 0 ? void 0 : _l.rcsb_polymer_entity) === null || _m === void 0 ? void 0 : _m.pdbx_description)) !== null && _o !== void 0 ? _o : "NA",
+                taxNames: Array.from(taxIds),
+                experimentalMethod: (_p = p.rcsb_entry_info.experimental_method) !== null && _p !== void 0 ? _p : "NA",
+                resolution: (_t = (_s = (_r = (_q = instance.polymer_entity) === null || _q === void 0 ? void 0 : _q.entry) === null || _r === void 0 ? void 0 : _r.rcsb_entry_info.resolution_combined) === null || _s === void 0 ? void 0 : _s[0]) !== null && _t !== void 0 ? _t : undefined,
+                sequenceLength: instance.polymer_entity.entity_poly.rcsb_sample_sequence_length,
+                entityMolecularWeight: (_v = (_u = instance.polymer_entity.rcsb_polymer_entity) === null || _u === void 0 ? void 0 : _u.formula_weight) !== null && _v !== void 0 ? _v : undefined,
+                entryMolecularWeight: (_x = (_w = instance.polymer_entity.entry) === null || _w === void 0 ? void 0 : _w.rcsb_entry_info.molecular_weight) !== null && _x !== void 0 ? _x : undefined,
+                structureDeterminationMethodology: instance.polymer_entity.entry.rcsb_entry_info.structure_determination_methodology
+            });
+        });
+    }
+}

package/lib/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.d.ts

@@ -0,0 +1,23 @@
+import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
+import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
+export interface ExternalTrackBuilderInterface {
+    processAlignmentAndFeatures?(data: {
+        annotations?: Array<AnnotationFeatures>;
+        alignments?: AlignmentResponse;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    }): Promise<void>;
+    filterAlignments?(data: {
+        alignments: AlignmentResponse;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    }): Promise<AlignmentResponse>;
+    filterFeatures?(data: {
+        annotations: Array<AnnotationFeatures>;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    }): Promise<Array<AnnotationFeatures>>;
+    addTo?(tracks: {
+        alignmentTracks?: Array<RcsbFvRowConfigInterface>;
+        annotationTracks?: Array<RcsbFvRowConfigInterface>;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    }): Promise<void>;
+}

package/lib/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.js

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

package/lib/RcsbCollectTools/FeatureTools/FeatureTools.d.ts

@@ -0,0 +1,9 @@
+import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
+import { ExternalTrackBuilderInterface } from "./ExternalTrackBuilderInterface";
+import { RcsbFvTrackDataAnnotationInterface } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface";
+export declare class FeatureTools {
+    private static readonly rcsbLigand;
+    static mergeBlocks(blocks: Array<RcsbFvTrackDataAnnotationInterface>): void;
+    static parseLink(title: string): RcsbFvLink;
+    static mergeTrackBuilders(builderA: ExternalTrackBuilderInterface, builderB?: ExternalTrackBuilderInterface): ExternalTrackBuilderInterface;
+}

package/lib/RcsbCollectTools/FeatureTools/FeatureTools.js

@@ -0,0 +1,85 @@
+import { __awaiter } from "tslib";
+import resource from "../../RcsbServerConfig/web.resources.json";
+import { RcsbAnnotationConstants } from "../../RcsbAnnotationConfig/RcsbAnnotationConstants";
+export class FeatureTools {
+    static mergeBlocks(blocks) {
+        var _a, _b;
+        let merged = false;
+        do {
+            merged = false;
+            for (let n = 0; n < (blocks.length - 1); n++) {
+                const end = blocks[n].end;
+                if (!end)
+                    return;
+                if (((_a = blocks[n].oriEnd) !== null && _a !== void 0 ? _a : Number.MIN_SAFE_INTEGER) + 1 == blocks[n + 1].oriBegin && blocks[n].color === blocks[n + 1].color) {
+                    if (blocks[n].gaps == null)
+                        blocks[n].gaps = [];
+                    (_b = blocks[n].gaps) === null || _b === void 0 ? void 0 : _b.push({ begin: end, end: blocks[n + 1].begin, isConnected: true });
+                    blocks[n].end = blocks[n + 1].end;
+                    blocks[n].oriEnd = blocks[n + 1].oriEnd;
+                    blocks.splice((n + 1), 1);
+                    merged = true;
+                    break;
+                }
+            }
+        } while (merged);
+    }
+    static parseLink(title) {
+        let match = FeatureTools.rcsbLigand.exec(title);
+        if (match) {
+            return {
+                visibleTex: match[3],
+                url: resource.rcsb_ligand.url + match[3],
+                style: {
+                    color: RcsbAnnotationConstants.provenanceColorCode.rcsbLink,
+                    fontWeight: "bold"
+                }
+            };
+        }
+        else if (title == "binding_site") {
+            return { visibleTex: "", style: { fontWeight: "bold" } };
+        }
+        return { visibleTex: title, style: { fontWeight: "bold" } };
+    }
+    static mergeTrackBuilders(builderA, builderB) {
+        return {
+            addTo(tracks) {
+                var _a, _b;
+                return __awaiter(this, void 0, void 0, function* () {
+                    yield ((_a = builderA.addTo) === null || _a === void 0 ? void 0 : _a.call(builderA, tracks));
+                    yield ((_b = builderB === null || builderB === void 0 ? void 0 : builderB.addTo) === null || _b === void 0 ? void 0 : _b.call(builderB, tracks));
+                });
+            },
+            processAlignmentAndFeatures(data) {
+                var _a, _b;
+                return __awaiter(this, void 0, void 0, function* () {
+                    yield ((_a = builderA.processAlignmentAndFeatures) === null || _a === void 0 ? void 0 : _a.call(builderA, data));
+                    yield ((_b = builderB === null || builderB === void 0 ? void 0 : builderB.processAlignmentAndFeatures) === null || _b === void 0 ? void 0 : _b.call(builderB, data));
+                });
+            },
+            filterFeatures(data) {
+                return __awaiter(this, void 0, void 0, function* () {
+                    let annotations = data.annotations;
+                    const rcsbContext = data.rcsbContext;
+                    if (builderA.filterFeatures)
+                        annotations = yield builderA.filterFeatures({ annotations, rcsbContext });
+                    if (builderB === null || builderB === void 0 ? void 0 : builderB.filterFeatures)
+                        annotations = yield builderB.filterFeatures({ annotations, rcsbContext });
+                    return annotations;
+                });
+            },
+            filterAlignments(data) {
+                return __awaiter(this, void 0, void 0, function* () {
+                    let alignments = data.alignments;
+                    const rcsbContext = data.rcsbContext;
+                    if (builderA.filterAlignments)
+                        alignments = yield builderA.filterAlignments({ alignments, rcsbContext });
+                    if (builderB === null || builderB === void 0 ? void 0 : builderB.filterAlignments)
+                        alignments = yield builderB.filterAlignments({ alignments, rcsbContext });
+                    return alignments;
+                });
+            }
+        };
+    }
+}
+FeatureTools.rcsbLigand = new RegExp(/^(ligand)(\s)(\w{1,3})$/);

package/lib/RcsbExport/FeatureType.d.ts

@@ -0,0 +1,10 @@
+import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+declare const ExtendedTypes: {
+    BurialFraction: Type;
+    BuriedResidues: Type;
+};
+type MergedType = typeof Type & typeof ExtendedTypes;
+declare const MergedType: MergedType;
+type FeatureType = typeof MergedType;
+export declare const FeatureType: FeatureType;
+export {};

package/lib/RcsbExport/FeatureType.js

@@ -0,0 +1,9 @@
+import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+const BURIAL_FRACTION = "BURIAL_FRACTION";
+const BURIED_RESIDUES = "BURIED_RESIDUES";
+const ExtendedTypes = {
+    BurialFraction: BURIAL_FRACTION,
+    BuriedResidues: BURIED_RESIDUES
+};
+const MergedType = Object.assign(Object.assign({}, Type), ExtendedTypes);
+export const FeatureType = MergedType;

package/lib/RcsbExport/RcsbFvUI.d.ts

@@ -0,0 +1,7 @@
+import { GroupedOptionsInterface, SelectOptionInterface } from "../RcsbFvWeb/RcsbFvComponents/SelectButton";
+import { SelectButtonConfigInterface } from "../RcsbFvWeb/RcsbFvComponents/ComponentsManager";
+export declare class RcsbFvUI {
+    static clearSelectButton(elementFvId: string, selectButtonId: string): void;
+    static createSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface> | Array<GroupedOptionsInterface>, config?: SelectButtonConfigInterface): void;
+    static addSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface>, config?: SelectButtonConfigInterface): void;
+}

package/lib/RcsbExport/RcsbFvUI.js

@@ -0,0 +1,12 @@
+import { RcsbFvCoreBuilder } from "../RcsbFvWeb/RcsbFvBuilder/RcsbFvCoreBuilder";
+export class RcsbFvUI {
+    static clearSelectButton(elementFvId, selectButtonId) {
+        RcsbFvCoreBuilder.clearAdditionalSelectButton(elementFvId, selectButtonId);
+    }
+    static createSelectButton(elementFvId, selectButtonId, options, config) {
+        RcsbFvCoreBuilder.buildSelectButton(elementFvId, selectButtonId, options, config);
+    }
+    static addSelectButton(elementFvId, selectButtonId, options, config) {
+        RcsbFvCoreBuilder.addSelectButton(elementFvId, selectButtonId, options, config);
+    }
+}

package/lib/RcsbFvExamples/ChromosomeFv.d.ts

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

package/lib/RcsbFvExamples/ChromosomeFv.js

@@ -0,0 +1,4 @@
+import { buildEntryChromosome } from "../RcsbFvWeb/RcsbFvBuilder";
+buildEntryChromosome("pfv", "select", "selectBis", "2uzi").then((module) => {
+    console.log(module);
+});

package/lib/RcsbFvExamples/EntitySummaryFv.d.ts

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

package/lib/RcsbFvExamples/EntitySummaryFv.js

@@ -0,0 +1,4 @@
+import { buildEntitySummaryFv } from "../RcsbFvWeb/RcsbFvBuilder";
+buildEntitySummaryFv("pfv", "select", "AF_AFQ8WZ42F1_1").then((module) => {
+    console.log(module);
+});

package/lib/RcsbFvExamples/ExternalDataProvider.d.ts

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