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

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvEntityBuilder.js

@@ -0,0 +1,92 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvEntityBuilder = void 0;
+const tslib_1 = require("tslib");
+const RcsbFvEntity_1 = require("../RcsbFvModule/RcsbFvEntity");
+const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
+const RcsbFvCoreBuilder_1 = require("./RcsbFvCoreBuilder");
+const RcsbFvUniprotBuilder_1 = require("./RcsbFvUniprotBuilder");
+const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
+class RcsbFvEntityBuilder {
+    static buildEntitySummaryFv(elementFvId, elementSelectId, entityId) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                const pdbId = TagDelimiter_1.TagDelimiter.parseEntity(entityId).entryId;
+                const createSelectAndFvBuilder = (p) => tslib_1.__awaiter(this, void 0, void 0, function* () {
+                    const rcsbFvEntity = yield RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.createFv({
+                        elementId: elementFvId,
+                        fvModuleI: RcsbFvEntity_1.RcsbFvEntity,
+                        p: p,
+                        config: {
+                            entityId: entityId,
+                            elementSelectId: elementSelectId,
+                            additionalConfig: Object.assign({ rcsbContext: TagDelimiter_1.TagDelimiter.parseEntity(entityId) }, additionalConfig()),
+                            resolve: resolve
+                        }
+                    });
+                    const targets = yield rcsbFvEntity.getTargets();
+                    RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.buildSelectButton(elementFvId, elementSelectId, [entityId].concat(targets).map(t => {
+                        return {
+                            label: t,
+                            onChange: () => tslib_1.__awaiter(this, void 0, void 0, function* () {
+                                if (t === entityId) {
+                                    yield RcsbFvEntityBuilder.buildSingleEntitySummaryFv(elementFvId, entityId);
+                                }
+                                else {
+                                    yield RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotEntityFv(elementFvId, t, entityId, Object.assign({ alignmentFilter: [entityId] }, additionalConfig({
+                                        field: GqlTypes_1.FieldName.TargetId,
+                                        operation: GqlTypes_1.OperationType.Contains,
+                                        source: GqlTypes_1.Source.PdbInstance,
+                                        values: [pdbId + TagDelimiter_1.TagDelimiter.instance]
+                                    })));
+                                }
+                            })
+                        };
+                    }));
+                    return rcsbFvEntity;
+                });
+                const entryId = TagDelimiter_1.TagDelimiter.parseEntity(entityId).entryId;
+                RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.getPolymerEntityInstanceMapAndCustomBuildFv(entryId, createSelectAndFvBuilder);
+            });
+        });
+    }
+    static buildSingleEntitySummaryFv(elementId, entityId) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                const entryId = TagDelimiter_1.TagDelimiter.parseEntity(entityId).entryId;
+                RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.getPolymerEntityInstanceMapAndBuildFv(elementId, entryId, RcsbFvEntity_1.RcsbFvEntity, {
+                    entityId: entityId,
+                    additionalConfig: Object.assign({ rcsbContext: TagDelimiter_1.TagDelimiter.parseEntity(entityId) }, additionalConfig()),
+                    resolve: resolve
+                });
+            });
+        });
+    }
+    static buildEntityFv(elementId, entityId, additionalConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                const entryId = TagDelimiter_1.TagDelimiter.parseEntity(entityId).entryId;
+                RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.getPolymerEntityInstanceMapAndBuildFv(elementId, entryId, RcsbFvEntity_1.RcsbFvEntity, {
+                    entityId: entityId,
+                    additionalConfig: Object.assign({ rcsbContext: TagDelimiter_1.TagDelimiter.parseEntity(entityId) }, additionalConfig),
+                    resolve: resolve
+                });
+            });
+        });
+    }
+}
+exports.RcsbFvEntityBuilder = RcsbFvEntityBuilder;
+function additionalConfig(f) {
+    const filters = [{
+            field: GqlTypes_1.FieldName.Type,
+            operation: GqlTypes_1.OperationType.Equals,
+            source: GqlTypes_1.Source.PdbInstance,
+            values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.UnobservedAtomXyz, GqlTypes_1.Type.MaQaMetricLocalTypeOther, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
+        }];
+    if (f)
+        filters.push(f);
+    return {
+        sources: [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance],
+        filters: filters
+    };
+}

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupAlignmentBuilder.d.ts

@@ -0,0 +1,8 @@
+import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
+import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
+import { RcsbFvAdditionalConfig, RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
+import { ActionMethods } from "../../RcsbFvUI/Helper/ActionMethods";
+export declare class RcsbFvGroupAlignmentBuilder {
+    static buildUniprotAlignmentFv(elementId: string, upAcc: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig & ActionMethods.FvChangeConfigInterface): Promise<RcsbFvModulePublicInterface>;
+    static buildGroupAlignmentFv(elementId: string, groupProvenance: GroupProvenanceId, groupId: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig & ActionMethods.FvChangeConfigInterface): Promise<RcsbFvModulePublicInterface>;
+}

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupAlignmentBuilder.js

@@ -0,0 +1,88 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvGroupAlignmentBuilder = void 0;
+const tslib_1 = require("tslib");
+const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
+const SearchRequestProperty_1 = require("../../RcsbSeacrh/SearchRequestProperty");
+const SearchQueryTools_1 = require("../../RcsbSeacrh/SearchQueryTools");
+const SearchEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums");
+const GroupPfvApp_1 = require("../RcsbFvGroup/GroupTabs/GroupPfvApp");
+const ActionMethods_1 = require("../../RcsbFvUI/Helper/ActionMethods");
+const RcsbFvUniprotBuilder_1 = require("./RcsbFvUniprotBuilder");
+const GroupExternalTrackBuilder_1 = require("../../RcsbUtils/TrackGenerators/GroupExternalTrackBuilder");
+const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
+const RcsbFvGroupBuilder_1 = require("./RcsbFvGroupBuilder");
+const GroupPfvUI_1 = require("../../RcsbFvUI/GroupPfvUI");
+const PaginationItemComponent_1 = require("../../RcsbFvUI/Components/PaginationItemComponent");
+const FeatureTools_1 = require("../../RcsbCollectTools/FeatureTools/FeatureTools");
+class RcsbFvGroupAlignmentBuilder {
+    static buildUniprotAlignmentFv(elementId, upAcc, query, additionalConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            let filterEntities = undefined;
+            if (query && query.query) {
+                filterEntities = yield SearchRequestProperty_1.searchRequestProperty.requestMembers(Object.assign(Object.assign({}, query), { query: SearchQueryTools_1.SearchQueryTools.addGroupNodeToSearchQuery(DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession, upAcc, query.query), return_type: SearchEnums_1.ReturnType.PolymerEntity }));
+            }
+            return RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotFv(elementId, upAcc, Object.assign(Object.assign({}, additionalConfig), { alignmentFilter: filterEntities }));
+        });
+    }
+    static buildGroupAlignmentFv(elementId, groupProvenance, groupId, query, additionalConfig) {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            let entityCount = -1;
+            let filterEntities = undefined;
+            if (query && query.query) {
+                filterEntities = yield SearchRequestProperty_1.searchRequestProperty.requestMembers(Object.assign(Object.assign({}, query), { query: SearchQueryTools_1.SearchQueryTools.addGroupNodeToSearchQuery(groupProvenance, groupId, query.query), return_type: SearchEnums_1.ReturnType.PolymerEntity }));
+                entityCount = filterEntities.length;
+            }
+            else {
+                entityCount = yield SearchRequestProperty_1.searchRequestProperty.requestCount({ query: SearchQueryTools_1.SearchQueryTools.searchGroupQuery(groupProvenance, groupId), return_type: SearchEnums_1.ReturnType.PolymerEntity });
+            }
+            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { page: Object.assign({ first: 50, after: "0" }, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page), alignmentFilter: filterEntities, externalTrackBuilder: FeatureTools_1.FeatureTools.mergeTrackBuilders((0, GroupExternalTrackBuilder_1.groupExternalTrackBuilder)(), additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalTrackBuilder) });
+            // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
+            const pfvArgs = [
+                (0, GroupPfvApp_1.getReferenceFromGroupProvenance)(groupProvenance),
+                groupId,
+                GqlTypes_1.SequenceReference.PdbEntity,
+                GqlTypes_1.SequenceReference.Uniprot
+            ];
+            let pfv = Object();
+            switch (groupProvenance) {
+                case DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity:
+                    pfv = yield RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAlignmentFv(elementId, ...pfvArgs, additionalConfig);
+                    break;
+                case DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession:
+                    pfv = yield RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotAlignmentFv(elementId, groupId, additionalConfig);
+                    break;
+            }
+            const sequenceIdentityCallback = ActionMethods_1.ActionMethods.paginationCallback();
+            const uniprotCallback = ActionMethods_1.ActionMethods.paginationCallback();
+            const uiComp = {
+                component: PaginationItemComponent_1.PaginationItemComponent,
+                props: {
+                    count: entityCount,
+                    after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : "0",
+                    first: (_d = (_c = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _c === void 0 ? void 0 : _c.first) !== null && _d !== void 0 ? _d : 50,
+                    stateChange: (state, prevState) => {
+                        switch (groupProvenance) {
+                            case DwEnums_1.GroupProvenanceId.ProvenanceSequenceIdentity:
+                                sequenceIdentityCallback(elementId, pfv, RcsbFvGroupBuilder_1.RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
+                                        first: state.first,
+                                        after: state.after.toString()
+                                    }, excludeLogo: true }));
+                                break;
+                            case DwEnums_1.GroupProvenanceId.ProvenanceMatchingUniprotAccession:
+                                uniprotCallback(elementId, pfv, RcsbFvUniprotBuilder_1.RcsbFvUniprotBuilder.buildUniprotAlignmentFv, [groupId], Object.assign(Object.assign({}, additionalConfig), { page: {
+                                        first: state.first,
+                                        after: state.after.toString()
+                                    } }));
+                                break;
+                        }
+                    }
+                }
+            };
+            GroupPfvUI_1.GroupPfvUI.fvUI(GroupPfvUI_1.GroupPfvUI.addBootstrapElement(elementId), (_f = (_e = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalUiComponents) === null || _e === void 0 ? void 0 : _e.replace) !== null && _f !== void 0 ? _f : (entityCount > ((_h = (_g = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _g === void 0 ? void 0 : _g.first) !== null && _h !== void 0 ? _h : 50) ? [uiComp] : []).concat(((_j = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalUiComponents) === null || _j === void 0 ? void 0 : _j.add) ? additionalConfig.externalUiComponents.add : []));
+            return pfv;
+        });
+    }
+}
+exports.RcsbFvGroupAlignmentBuilder = RcsbFvGroupAlignmentBuilder;

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupBuilder.d.ts

@@ -0,0 +1,6 @@
+import { RcsbFvAdditionalConfig, RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
+import { GroupReference, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare class RcsbFvGroupBuilder {
+    static buildGroupAnnotationFv(elementId: string, group: GroupReference, groupId: string, to: SequenceReference, from?: SequenceReference, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+    static buildGroupAlignmentFv(elementId: string, group: GroupReference, groupId: string, to: SequenceReference, from?: SequenceReference, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+}

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupBuilder.js

@@ -0,0 +1,57 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvGroupBuilder = void 0;
+const tslib_1 = require("tslib");
+const RcsbFvCoreBuilder_1 = require("./RcsbFvCoreBuilder");
+const RcsbFvGroupAnnotation_1 = require("../RcsbFvModule/RcsbFvGroupAnnotation");
+const RcsbFvGroupAlignment_1 = require("../RcsbFvModule/RcsbFvGroupAlignment");
+class RcsbFvGroupBuilder {
+    //TODO How to make this method more general. Variables from, to and group should be parameters. What happens when from cannot be defined ?
+    static buildGroupAnnotationFv(elementId, group, groupId, to, from, additionalConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                try {
+                    RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.createFv({
+                        elementId: elementId,
+                        fvModuleI: RcsbFvGroupAnnotation_1.RcsbFvGroupAnnotation,
+                        config: {
+                            group: group,
+                            groupId: groupId,
+                            from: from,
+                            to: to,
+                            additionalConfig: additionalConfig,
+                            resolve: resolve
+                        }
+                    });
+                }
+                catch (e) {
+                    reject(e);
+                }
+            });
+        });
+    }
+    static buildGroupAlignmentFv(elementId, group, groupId, to, from, additionalConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                try {
+                    RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.createFv({
+                        elementId: elementId,
+                        fvModuleI: RcsbFvGroupAlignment_1.RcsbFvGroupAlignment,
+                        config: {
+                            group: group,
+                            groupId: groupId,
+                            from: from,
+                            to: to,
+                            additionalConfig: Object.assign({}, additionalConfig),
+                            resolve: resolve
+                        }
+                    });
+                }
+                catch (e) {
+                    reject(e);
+                }
+            });
+        });
+    }
+}
+exports.RcsbFvGroupBuilder = RcsbFvGroupBuilder;

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.d.ts

@@ -0,0 +1,25 @@
+/// <reference types="react" />
+import { RcsbContextType, RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
+import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
+import { SelectOptionProps } from "../RcsbFvComponents/SelectButton";
+import { RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
+export interface InstanceSequenceOnchangeInterface extends PolymerEntityInstanceInterface {
+}
+type InstanceModuleType = "interface" | "instance";
+export interface InstanceSequenceConfig {
+    dropdownTitle?: string;
+    defaultValue?: string | undefined | null;
+    beforeChangeCallback?: (x: InstanceSequenceOnchangeInterface, module: RcsbFvModulePublicInterface | undefined) => undefined | RcsbContextType;
+    onChangeCallback?: (x: InstanceSequenceOnchangeInterface, module: RcsbFvModulePublicInterface) => void;
+    filterInstances?: Set<string>;
+    displayAuthId?: boolean;
+    selectButtonOptionProps?: (props: SelectOptionProps) => JSX.Element;
+    module?: InstanceModuleType;
+}
+export declare class RcsbFvInstanceBuilder {
+    static buildMultipleInstanceSequenceFv(elementFvId: string, elementEntrySelectId: string, elementInstanceSelectId: string, entryIdList: Array<string>, config?: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+    static buildInstanceSequenceFv(elementFvId: string, elementSelectId: string, entryId: string, config: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+    static buildSelectorInstanceFv(instanceList: Array<PolymerEntityInstanceInterface>, elementFvId: string, elementSelectId: string, entryId: string, config: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+    static buildInstanceFv(elementId: string, instanceId: string, additionalConfig?: RcsbFvAdditionalConfig, module?: InstanceModuleType): Promise<RcsbFvModulePublicInterface>;
+}
+export {};

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.js

@@ -0,0 +1,114 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvInstanceBuilder = void 0;
+const tslib_1 = require("tslib");
+const RcsbFvInstance_1 = require("../RcsbFvModule/RcsbFvInstance");
+const RcsbFvCoreBuilder_1 = require("./RcsbFvCoreBuilder");
+const RcsbFvInterface_1 = require("../RcsbFvModule/RcsbFvInterface");
+const RcsbRequestContextManager_1 = require("../../RcsbRequest/RcsbRequestContextManager");
+const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
+//TODO Find a better structure for change callbacks
+class RcsbFvInstanceBuilder {
+    static buildMultipleInstanceSequenceFv(elementFvId, elementEntrySelectId, elementInstanceSelectId, entryIdList, config = {}, additionalConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.buildSelectButton(elementFvId, elementEntrySelectId, entryIdList.map(entryId => {
+                return {
+                    label: entryId,
+                    shortLabel: entryId,
+                    onChange: () => {
+                        RcsbFvInstanceBuilder.buildInstanceSequenceFv(elementFvId, elementInstanceSelectId, entryId, Object.assign(Object.assign({}, config), { displayAuthId: true }), additionalConfig);
+                    }
+                };
+            }), { addTitle: true, dropdownTitle: "PDB" });
+            const entryId = entryIdList[0];
+            return yield RcsbFvInstanceBuilder.buildInstanceSequenceFv(elementFvId, elementInstanceSelectId, entryId, Object.assign(Object.assign({}, config), { displayAuthId: true }), additionalConfig);
+        });
+    }
+    static buildInstanceSequenceFv(elementFvId, elementSelectId, entryId, config, additionalConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            const entityInstanceTranslator = yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntityToInstance(entryId);
+            const result = entityInstanceTranslator.getData();
+            if (result.length == 0) {
+                RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.showMessage(elementFvId, "No sequence features are available");
+                throw new Error("No sequence features are available");
+            }
+            else {
+                return RcsbFvInstanceBuilder.buildSelectorInstanceFv(result, elementFvId, elementSelectId, entryId, config, additionalConfig);
+            }
+        });
+    }
+    static buildSelectorInstanceFv(instanceList, elementFvId, elementSelectId, entryId, config, additionalConfig) {
+        var _a;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            const filteredInstanceList = instanceList.filter(i => (config.filterInstances == null || config.filterInstances.has(i.asymId)));
+            const groupedInstances = new Map();
+            filteredInstanceList.forEach((instance) => {
+                var _a;
+                if (!groupedInstances.has(instance.entityId))
+                    groupedInstances.set(instance.entityId, new Array());
+                const label = instance.asymId === instance.authId ? instance.asymId : `${instance.asymId} [auth ${instance.authId}]`;
+                (_a = groupedInstances.get(instance.entityId)) === null || _a === void 0 ? void 0 : _a.push({
+                    name: instance.name + " - " + instance.taxNames.join(", "),
+                    label: label,
+                    groupLabel: `ENTITY ${instance.entityId} - ${instance.name}`,
+                    shortLabel: config.displayAuthId === true ? instance.authId : label,
+                    optId: instance.asymId,
+                    onChange: () => tslib_1.__awaiter(this, void 0, void 0, function* () {
+                        out.getFv().reset();
+                        let externalContext;
+                        if (typeof config.beforeChangeCallback === "function")
+                            externalContext = config.beforeChangeCallback(instance, out);
+                        const rcsbContext = Object.assign(Object.assign(Object.assign({}, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.rcsbContext), externalContext), instance);
+                        yield RcsbFvInstanceBuilder.buildInstanceFv(elementFvId, instance.rcsbId, Object.assign(Object.assign({}, additionalConfig), { rcsbContext: rcsbContext }), config.module);
+                        if (typeof config.onChangeCallback === "function")
+                            config.onChangeCallback(instance, out);
+                    })
+                });
+            });
+            let index = 0;
+            if (config.defaultValue != null) {
+                const n = filteredInstanceList.findIndex(a => {
+                    return a.asymId === config.defaultValue;
+                });
+                if (n >= 0)
+                    index = n;
+                else
+                    config.defaultValue = undefined;
+            }
+            RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.buildSelectButton(elementFvId, elementSelectId, Array.from(groupedInstances.values()).map((group, n) => {
+                var _a;
+                return ({
+                    label: (_a = group[0].groupLabel) !== null && _a !== void 0 ? _a : `Group ${n}`,
+                    options: group
+                });
+            }), { addTitle: true, defaultValue: config.defaultValue, dropdownTitle: ((_a = config.dropdownTitle) !== null && _a !== void 0 ? _a : "INSTANCE"), width: config.displayAuthId === true ? 70 : undefined, optionProps: config.selectButtonOptionProps });
+            let externalContext;
+            if (typeof config.beforeChangeCallback === "function")
+                externalContext = config.beforeChangeCallback(filteredInstanceList[index], undefined);
+            const rcsbContext = Object.assign(Object.assign(Object.assign({}, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.rcsbContext), externalContext), filteredInstanceList[index]);
+            const out = yield RcsbFvInstanceBuilder.buildInstanceFv(elementFvId, filteredInstanceList[index].rcsbId, Object.assign(Object.assign({}, additionalConfig), { rcsbContext: rcsbContext }), config.module);
+            if (typeof config.onChangeCallback === "function")
+                config.onChangeCallback(filteredInstanceList[index], out);
+            return out;
+        });
+    }
+    static buildInstanceFv(elementId, instanceId, additionalConfig, module) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                try {
+                    const entryId = instanceId.split(TagDelimiter_1.TagDelimiter.instance)[0];
+                    const asymId = instanceId.split(TagDelimiter_1.TagDelimiter.instance)[1];
+                    RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.getPolymerEntityInstanceMapAndBuildFv(elementId, entryId, module === "interface" ? RcsbFvInterface_1.RcsbFvInterface : RcsbFvInstance_1.RcsbFvInstance, {
+                        instanceId: instanceId,
+                        additionalConfig: Object.assign(Object.assign({}, additionalConfig), { rcsbContext: Object.assign(Object.assign({}, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.rcsbContext), { entryId: entryId, asymId: asymId }) }),
+                        resolve: resolve
+                    });
+                }
+                catch (e) {
+                    reject(e);
+                }
+            });
+        });
+    }
+}
+exports.RcsbFvInstanceBuilder = RcsbFvInstanceBuilder;

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvPairwiseAligmentBuilder.d.ts

@@ -0,0 +1,5 @@
+import { RcsbFvAdditionalConfig, RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
+import { PairwiseAlignmentInterface } from "../../RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder";
+export declare class RcsbFvPairwiseAligmentBuilder {
+    static buildPairwiseAlignment(elementId: string, psa: PairwiseAlignmentInterface, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+}

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvPairwiseAligmentBuilder.js

@@ -0,0 +1,32 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvPairwiseAligmentBuilder = void 0;
+const tslib_1 = require("tslib");
+const RcsbFvCoreBuilder_1 = require("./RcsbFvCoreBuilder");
+const RcsbFvPairwiseAlignment_1 = require("../RcsbFvModule/RcsbFvPairwiseAlignment");
+class RcsbFvPairwiseAligmentBuilder {
+    static buildPairwiseAlignment(elementId, psa, additionalConfig) {
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            return new Promise((resolve, reject) => {
+                try {
+                    RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.createFv({
+                        elementId: elementId,
+                        fvModuleI: RcsbFvPairwiseAlignment_1.RcsbFvPairwiseAlignment,
+                        config: {
+                            psa: psa,
+                            additionalConfig: Object.assign({ rcsbContext: {
+                                    queryId: psa.queryId,
+                                    targetId: psa.targetId
+                                } }, additionalConfig),
+                            resolve: resolve
+                        }
+                    });
+                }
+                catch (e) {
+                    reject(e);
+                }
+            });
+        });
+    }
+}
+exports.RcsbFvPairwiseAligmentBuilder = RcsbFvPairwiseAligmentBuilder;

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.d.ts

@@ -0,0 +1,12 @@
+import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
+export interface PfvBuilderInterface {
+    queryId: string;
+    reference: SequenceReference;
+    alignmentSource?: SequenceReference;
+    hideAlignments?: boolean;
+    bottomAlignments?: boolean;
+}
+export declare class RcsbFvProteinSequenceBuilder {
+    static buildPfv(elementId: string, config: PfvBuilderInterface): Promise<RcsbFvModulePublicInterface>;
+}

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.js

@@ -0,0 +1,46 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvProteinSequenceBuilder = void 0;
+const tslib_1 = require("tslib");
+const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
+const RcsbFvProteinSequence_1 = require("../RcsbFvModule/RcsbFvProteinSequence");
+const RcsbFvCoreBuilder_1 = require("./RcsbFvCoreBuilder");
+class RcsbFvProteinSequenceBuilder {
+    static buildPfv(elementId, config) {
+        var _a;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            const alignmentSource = (_a = config.alignmentSource) !== null && _a !== void 0 ? _a : config.reference;
+            const sources = [GqlTypes_1.Source.Uniprot];
+            if (config.reference == GqlTypes_1.SequenceReference.PdbEntity)
+                sources.unshift(GqlTypes_1.Source.PdbEntity);
+            if (config.reference == GqlTypes_1.SequenceReference.PdbInstance)
+                sources.unshift(GqlTypes_1.Source.PdbInstance);
+            return new Promise((resolve, reject) => {
+                try {
+                    RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.createFv({
+                        elementId: elementId,
+                        fvModuleI: RcsbFvProteinSequence_1.RcsbFvProteinSequence,
+                        config: {
+                            queryId: config.queryId,
+                            from: config.reference,
+                            to: alignmentSource,
+                            sources: sources,
+                            additionalConfig: {
+                                rcsbContext: {
+                                    queryId: config.queryId
+                                },
+                                hideAlignments: config.hideAlignments,
+                                bottomAlignments: config.bottomAlignments
+                            },
+                            resolve: resolve
+                        }
+                    });
+                }
+                catch (e) {
+                    reject(e);
+                }
+            });
+        });
+    }
+}
+exports.RcsbFvProteinSequenceBuilder = RcsbFvProteinSequenceBuilder;

package/lib/commonjs/RcsbFvWeb/RcsbFvBuilder/RcsbFvUniprotBuilder.d.ts

@@ -0,0 +1,17 @@
+import { RcsbContextType, RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
+import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
+import { RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
+export interface UniprotSequenceOnchangeInterface extends Partial<PolymerEntityInstanceInterface> {
+    upAcc: string;
+}
+export interface UniprotSequenceConfig {
+    beforeChangeCallback?: (x: UniprotSequenceOnchangeInterface, module: RcsbFvModulePublicInterface | undefined) => undefined | RcsbContextType;
+    onChangeCallback?: (x: UniprotSequenceOnchangeInterface, module: RcsbFvModulePublicInterface) => void;
+}
+export declare class RcsbFvUniprotBuilder {
+    static buildUniprotMultipleEntitySequenceFv(elementFvId: string, elementSelectId: string, upAcc: string, config?: UniprotSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+    static buildUniprotFv(elementId: string, upAcc: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+    static buildUniprotEntityFv(elementId: string, upAcc: string, entityId: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+    static buildUniprotEntityInstanceFv(elementId: string, upAcc: string, entityId: string, instanceId: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+    static buildUniprotAlignmentFv(elementId: string, upAcc: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
+}