@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupAlignmentBuilder.js

@@ -1,84 +0,0 @@
-import { __awaiter } from "tslib";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { searchRequestProperty } from "../../RcsbSeacrh/SearchRequestProperty";
-import { SearchQueryTools as SQT } from "../../RcsbSeacrh/SearchQueryTools";
-import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
-import { getReferenceFromGroupProvenance } from "../RcsbFvGroup/GroupTabs/GroupPfvApp";
-import { ActionMethods } from "../../RcsbFvUI/Helper/ActionMethods";
-import { RcsbFvUniprotBuilder } from "./RcsbFvUniprotBuilder";
-import { groupExternalTrackBuilder } from "../../RcsbUtils/TrackGenerators/GroupExternalTrackBuilder";
-import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvGroupBuilder } from "./RcsbFvGroupBuilder";
-import { GroupPfvUI } from "../../RcsbFvUI/GroupPfvUI";
-import { PaginationItemComponent } from "../../RcsbFvUI/Components/PaginationItemComponent";
-import { FeatureTools } from "../../RcsbCollectTools/FeatureTools/FeatureTools";
-export class RcsbFvGroupAlignmentBuilder {
-    static buildUniprotAlignmentFv(elementId, upAcc, query, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            let filterEntities = undefined;
-            if (query && query.query) {
-                filterEntities = yield searchRequestProperty.requestMembers(Object.assign(Object.assign({}, query), { query: SQT.addGroupNodeToSearchQuery(GroupProvenanceId.ProvenanceMatchingUniprotAccession, upAcc, query.query), return_type: ReturnType.PolymerEntity }));
-            }
-            return RcsbFvUniprotBuilder.buildUniprotFv(elementId, upAcc, Object.assign(Object.assign({}, additionalConfig), { alignmentFilter: filterEntities }));
-        });
-    }
-    static buildGroupAlignmentFv(elementId, groupProvenance, groupId, query, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
-            let entityCount = -1;
-            let filterEntities = undefined;
-            if (query && query.query) {
-                filterEntities = yield searchRequestProperty.requestMembers(Object.assign(Object.assign({}, query), { query: SQT.addGroupNodeToSearchQuery(groupProvenance, groupId, query.query), return_type: ReturnType.PolymerEntity }));
-                entityCount = filterEntities.length;
-            }
-            else {
-                entityCount = yield searchRequestProperty.requestCount({ query: SQT.searchGroupQuery(groupProvenance, groupId), return_type: ReturnType.PolymerEntity });
-            }
-            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { page: Object.assign({ first: 50, after: "0" }, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page), alignmentFilter: filterEntities, externalTrackBuilder: FeatureTools.mergeTrackBuilders(groupExternalTrackBuilder(), additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalTrackBuilder) });
-            // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
-            const pfvArgs = [
-                getReferenceFromGroupProvenance(groupProvenance),
-                groupId,
-                SequenceReference.PdbEntity,
-                SequenceReference.Uniprot
-            ];
-            let pfv = Object();
-            switch (groupProvenance) {
-                case GroupProvenanceId.ProvenanceSequenceIdentity:
-                    pfv = yield RcsbFvGroupBuilder.buildGroupAlignmentFv(elementId, ...pfvArgs, additionalConfig);
-                    break;
-                case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
-                    pfv = yield RcsbFvUniprotBuilder.buildUniprotAlignmentFv(elementId, groupId, additionalConfig);
-                    break;
-            }
-            const sequenceIdentityCallback = ActionMethods.paginationCallback();
-            const uniprotCallback = ActionMethods.paginationCallback();
-            const uiComp = {
-                component: PaginationItemComponent,
-                props: {
-                    count: entityCount,
-                    after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : "0",
-                    first: (_d = (_c = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _c === void 0 ? void 0 : _c.first) !== null && _d !== void 0 ? _d : 50,
-                    stateChange: (state, prevState) => {
-                        switch (groupProvenance) {
-                            case GroupProvenanceId.ProvenanceSequenceIdentity:
-                                sequenceIdentityCallback(elementId, pfv, RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
-                                        first: state.first,
-                                        after: state.after.toString()
-                                    }, excludeLogo: true }));
-                                break;
-                            case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
-                                uniprotCallback(elementId, pfv, RcsbFvUniprotBuilder.buildUniprotAlignmentFv, [groupId], Object.assign(Object.assign({}, additionalConfig), { page: {
-                                        first: state.first,
-                                        after: state.after.toString()
-                                    } }));
-                                break;
-                        }
-                    }
-                }
-            };
-            GroupPfvUI.fvUI(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;
-        });
-    }
-}

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

@@ -1,6 +0,0 @@
-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/RcsbFvWeb/RcsbFvBuilder/RcsbFvGroupBuilder.js

@@ -1,53 +0,0 @@
-import { __awaiter } from "tslib";
-import { RcsbFvCoreBuilder } from "./RcsbFvCoreBuilder";
-import { RcsbFvGroupAnnotation } from "../RcsbFvModule/RcsbFvGroupAnnotation";
-import { RcsbFvGroupAlignment } from "../RcsbFvModule/RcsbFvGroupAlignment";
-export 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 __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                try {
-                    RcsbFvCoreBuilder.createFv({
-                        elementId: elementId,
-                        fvModuleI: 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 __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                try {
-                    RcsbFvCoreBuilder.createFv({
-                        elementId: elementId,
-                        fvModuleI: RcsbFvGroupAlignment,
-                        config: {
-                            group: group,
-                            groupId: groupId,
-                            from: from,
-                            to: to,
-                            additionalConfig: Object.assign({}, additionalConfig),
-                            resolve: resolve
-                        }
-                    });
-                }
-                catch (e) {
-                    reject(e);
-                }
-            });
-        });
-    }
-}

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

@@ -1,24 +0,0 @@
-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/RcsbFvWeb/RcsbFvBuilder/RcsbFvInstanceBuilder.js

@@ -1,110 +0,0 @@
-import { __awaiter } from "tslib";
-import { RcsbFvInstance } from "../RcsbFvModule/RcsbFvInstance";
-import { RcsbFvCoreBuilder } from "./RcsbFvCoreBuilder";
-import { RcsbFvInterface } from "../RcsbFvModule/RcsbFvInterface";
-import { rcsbRequestCtxManager } from "../../RcsbRequest/RcsbRequestContextManager";
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-//TODO Find a better structure for change callbacks
-export class RcsbFvInstanceBuilder {
-    static buildMultipleInstanceSequenceFv(elementFvId_1, elementEntrySelectId_1, elementInstanceSelectId_1, entryIdList_1) {
-        return __awaiter(this, arguments, void 0, function* (elementFvId, elementEntrySelectId, elementInstanceSelectId, entryIdList, config = {}, additionalConfig) {
-            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 __awaiter(this, void 0, void 0, function* () {
-            const entityInstanceTranslator = yield rcsbRequestCtxManager.getEntityToInstance(entryId);
-            const result = entityInstanceTranslator.getData();
-            if (result.length == 0) {
-                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) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            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: () => __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.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 __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                try {
-                    const entryId = instanceId.split(TagDelimiter.instance)[0];
-                    const asymId = instanceId.split(TagDelimiter.instance)[1];
-                    RcsbFvCoreBuilder.getPolymerEntityInstanceMapAndBuildFv(elementId, entryId, module === "interface" ? RcsbFvInterface : 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);
-                }
-            });
-        });
-    }
-}

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

@@ -1,5 +0,0 @@
-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/RcsbFvWeb/RcsbFvBuilder/RcsbFvPairwiseAligmentBuilder.js

@@ -1,28 +0,0 @@
-import { __awaiter } from "tslib";
-import { RcsbFvCoreBuilder } from "./RcsbFvCoreBuilder";
-import { RcsbFvPairwiseAlignment } from "../RcsbFvModule/RcsbFvPairwiseAlignment";
-export class RcsbFvPairwiseAligmentBuilder {
-    static buildPairwiseAlignment(elementId, psa, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                try {
-                    RcsbFvCoreBuilder.createFv({
-                        elementId: elementId,
-                        fvModuleI: RcsbFvPairwiseAlignment,
-                        config: {
-                            psa: psa,
-                            additionalConfig: Object.assign({ rcsbContext: {
-                                    queryId: psa.queryId,
-                                    targetId: psa.targetId
-                                } }, additionalConfig),
-                            resolve: resolve
-                        }
-                    });
-                }
-                catch (e) {
-                    reject(e);
-                }
-            });
-        });
-    }
-}

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

@@ -1,12 +0,0 @@
-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/RcsbFvWeb/RcsbFvBuilder/RcsbFvProteinSequenceBuilder.js

@@ -1,42 +0,0 @@
-import { __awaiter } from "tslib";
-import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvProteinSequence } from "../RcsbFvModule/RcsbFvProteinSequence";
-import { RcsbFvCoreBuilder } from "./RcsbFvCoreBuilder";
-export class RcsbFvProteinSequenceBuilder {
-    static buildPfv(elementId, config) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            const alignmentSource = (_a = config.alignmentSource) !== null && _a !== void 0 ? _a : config.reference;
-            const sources = [Source.Uniprot];
-            if (config.reference == SequenceReference.PdbEntity)
-                sources.unshift(Source.PdbEntity);
-            if (config.reference == SequenceReference.PdbInstance)
-                sources.unshift(Source.PdbInstance);
-            return new Promise((resolve, reject) => {
-                try {
-                    RcsbFvCoreBuilder.createFv({
-                        elementId: elementId,
-                        fvModuleI: 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);
-                }
-            });
-        });
-    }
-}

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

@@ -1,17 +0,0 @@
-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>;
-}

package/lib/RcsbFvWeb/RcsbFvBuilder/RcsbFvUniprotBuilder.js

@@ -1,159 +0,0 @@
-import { __awaiter } from "tslib";
-import { RcsbFvUniprotEntity } from "../RcsbFvModule/RcsbFvUniprotEntity";
-import { RcsbFvUniprotInstance } from "../RcsbFvModule/RcsbFvUniprotInstance";
-import { RcsbFvUniprot } from "../RcsbFvModule/RcsbFvUniprot";
-import { RcsbFvCoreBuilder } from "./RcsbFvCoreBuilder";
-import { rcsbRequestCtxManager } from "../../RcsbRequest/RcsbRequestContextManager";
-import { RcsbFvUniprotAlignment } from "../RcsbFvModule/RcsbFvUniprotAlignment";
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-const ALL = "ALL";
-//TODO Find a better structure for change callbacks
-export class RcsbFvUniprotBuilder {
-    static buildUniprotMultipleEntitySequenceFv(elementFvId_1, elementSelectId_1, upAcc_1) {
-        return __awaiter(this, arguments, void 0, function* (elementFvId, elementSelectId, upAcc, config = {}, additionalConfig) {
-            return new Promise((resolve, reject) => __awaiter(this, void 0, void 0, function* () {
-                let externalContext;
-                if (typeof config.beforeChangeCallback === "function")
-                    externalContext = config.beforeChangeCallback({
-                        upAcc
-                    }, undefined);
-                const rcsbFvUniprot = yield RcsbFvUniprotBuilder.buildUniprotFv(elementFvId, upAcc, Object.assign(Object.assign({}, additionalConfig), { rcsbContext: Object.assign(Object.assign({}, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.rcsbContext), externalContext) }));
-                if (typeof config.onChangeCallback === "function")
-                    config.onChangeCallback({
-                        upAcc
-                    }, rcsbFvUniprot);
-                resolve(rcsbFvUniprot);
-                const targets = yield rcsbFvUniprot.getTargets();
-                RcsbFvCoreBuilder.buildSelectButton(elementFvId, elementSelectId, [ALL].concat(targets).map(entityId => {
-                    return {
-                        label: entityId === ALL ? entityId + " (" + targets.length + ")" : entityId,
-                        onChange: () => __awaiter(this, void 0, void 0, function* () {
-                            RcsbFvCoreBuilder.clearAdditionalSelectButton(elementFvId, elementSelectId);
-                            if (entityId === ALL) {
-                                let externalContext;
-                                if (typeof config.beforeChangeCallback === "function")
-                                    externalContext = config.beforeChangeCallback({
-                                        upAcc
-                                    }, rcsbFvUniprot);
-                                yield RcsbFvUniprotBuilder.buildUniprotFv(elementFvId, upAcc, Object.assign(Object.assign({}, additionalConfig), { rcsbContext: Object.assign(Object.assign({}, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.rcsbContext), externalContext) }));
-                                if (typeof config.onChangeCallback === "function")
-                                    config.onChangeCallback({
-                                        upAcc
-                                    }, rcsbFvUniprot);
-                            }
-                            else {
-                                const entryId = TagDelimiter.parseEntity(entityId).entryId;
-                                const entityInstanceTranslator = yield rcsbRequestCtxManager.getEntityToInstance(entryId);
-                                const result = entityInstanceTranslator.getData().filter(r => {
-                                    return r.entityId === TagDelimiter.parseEntity(entityId).entityId;
-                                });
-                                let externalContext;
-                                if (typeof config.beforeChangeCallback === "function")
-                                    externalContext = config.beforeChangeCallback(Object.assign(Object.assign({}, result[0]), { upAcc }), rcsbFvUniprot);
-                                yield RcsbFvUniprotBuilder.buildUniprotEntityInstanceFv(elementFvId, upAcc, result[0].entryId + TagDelimiter.entity + result[0].entityId, result[0].entryId + TagDelimiter.instance + result[0].asymId, Object.assign(Object.assign({}, additionalConfig), { rcsbContext: Object.assign(Object.assign({}, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.rcsbContext), externalContext) }));
-                                if (typeof config.onChangeCallback === "function")
-                                    config.onChangeCallback(Object.assign(Object.assign({}, result[0]), { upAcc }), rcsbFvUniprot);
-                                RcsbFvCoreBuilder.addSelectButton(elementFvId, elementSelectId, result.map(instance => {
-                                    return {
-                                        name: instance.taxNames.length > 0 ? instance.name + " - " + instance.taxNames.join(", ") : instance.name,
-                                        label: (instance.authId === instance.asymId ? instance.authId : `${instance.asymId} [auth ${instance.authId}]`) + " - " + instance.name,
-                                        shortLabel: (instance.authId === instance.asymId ? instance.authId : `${instance.asymId} [auth ${instance.authId}]`),
-                                        onChange: () => __awaiter(this, void 0, void 0, function* () {
-                                            let externalContext;
-                                            if (typeof config.beforeChangeCallback === "function")
-                                                externalContext = config.beforeChangeCallback(Object.assign(Object.assign({}, instance), { upAcc }), rcsbFvUniprot);
-                                            yield RcsbFvUniprotBuilder.buildUniprotEntityInstanceFv(elementFvId, upAcc, instance.entryId + TagDelimiter.entity + instance.entityId, instance.entryId + TagDelimiter.instance + instance.asymId, Object.assign(Object.assign({}, additionalConfig), { rcsbContext: Object.assign(Object.assign({}, additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.rcsbContext), externalContext) }));
-                                            if (typeof config.onChangeCallback === "function")
-                                                config.onChangeCallback(Object.assign(Object.assign({}, instance), { upAcc }), rcsbFvUniprot);
-                                        })
-                                    };
-                                }), { addTitle: true });
-                            }
-                        })
-                    };
-                }));
-            }));
-        });
-    }
-    static buildUniprotFv(elementId, upAcc, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                try {
-                    RcsbFvCoreBuilder.createFv({
-                        elementId: elementId,
-                        fvModuleI: RcsbFvUniprot,
-                        config: {
-                            upAcc: upAcc,
-                            additionalConfig: Object.assign({ rcsbContext: {
-                                    upAcc: upAcc
-                                } }, additionalConfig),
-                            resolve: resolve
-                        }
-                    });
-                }
-                catch (e) {
-                    reject(e);
-                }
-            });
-        });
-    }
-    static buildUniprotEntityFv(elementId, upAcc, entityId, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => __awaiter(this, void 0, void 0, function* () {
-                try {
-                    const entryId = TagDelimiter.parseEntity(entityId).entryId;
-                    yield RcsbFvCoreBuilder.getPolymerEntityInstanceMapAndBuildFv(elementId, entryId, RcsbFvUniprotEntity, {
-                        upAcc: upAcc,
-                        entityId: entityId,
-                        additionalConfig: Object.assign({ rcsbContext: Object.assign(Object.assign({}, TagDelimiter.parseEntity(entityId)), { upAcc: upAcc }) }, additionalConfig),
-                        resolve: resolve
-                    });
-                }
-                catch (e) {
-                    reject(e);
-                }
-            }));
-        });
-    }
-    static buildUniprotEntityInstanceFv(elementId, upAcc, entityId, instanceId, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => __awaiter(this, void 0, void 0, function* () {
-                try {
-                    const entryId = TagDelimiter.parseEntity(entityId).entryId;
-                    yield RcsbFvCoreBuilder.getPolymerEntityInstanceMapAndBuildFv(elementId, entryId, RcsbFvUniprotInstance, {
-                        upAcc: upAcc,
-                        entityId: entityId,
-                        instanceId: instanceId,
-                        additionalConfig: Object.assign({ rcsbContext: Object.assign(Object.assign({}, TagDelimiter.parseEntity(entityId)), { asymId: instanceId, upAcc: upAcc }) }, additionalConfig),
-                        resolve: resolve
-                    });
-                }
-                catch (e) {
-                    reject(e);
-                }
-            }));
-        });
-    }
-    static buildUniprotAlignmentFv(elementId, upAcc, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return new Promise((resolve, reject) => {
-                try {
-                    RcsbFvCoreBuilder.createFv({
-                        elementId: elementId,
-                        fvModuleI: RcsbFvUniprotAlignment,
-                        config: {
-                            upAcc: upAcc,
-                            additionalConfig: Object.assign({ rcsbContext: {
-                                    upAcc: upAcc
-                                } }, additionalConfig),
-                            resolve: resolve
-                        }
-                    });
-                }
-                catch (e) {
-                    reject(e);
-                }
-            });
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvBuilder.d.ts

@@ -1,30 +0,0 @@
-import { RcsbFvAdditionalConfig, RcsbFvModulePublicInterface, RcsbModuleDataProviderInterface } from "./RcsbFvModule/RcsbFvModuleInterface";
-import { UniprotSequenceConfig } from "./RcsbFvBuilder/RcsbFvUniprotBuilder";
-import { InstanceSequenceConfig, InstanceSequenceOnchangeInterface } from "./RcsbFvBuilder/RcsbFvInstanceBuilder";
-import { PfvBuilderInterface } from "./RcsbFvBuilder/RcsbFvProteinSequenceBuilder";
-import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { PairwiseAlignmentInterface } from "../RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder";
-import { ActionMethods } from "../RcsbFvUI/Helper/ActionMethods";
-export declare function unmount(elementId: string): void;
-export declare function buildMultipleAlignmentSequenceFv(elementFvId: string, elementSelectId: string, upAcc: string, config?: UniprotSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildEntitySummaryFv(elementFvId: string, elementSelectId: string, entityId: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildSingleEntitySummaryFv(elementId: string, entityId: string): Promise<RcsbFvModulePublicInterface>;
-export declare function buildInstanceSequenceFv(elementFvId: string, elementSelectId: string, entryId: string, config?: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildMultipleInstanceSequenceFv(elementFvId: string, elementEntrySelectId: string, elementInstanceSelectId: string, entryIdList: Array<string>, config?: InstanceSequenceConfig, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildAssemblySequenceFv(elementFvId: string, elementSelectAssemblyId: string, elementSelectInstanceId: string, entryId: string, onAsseblyChangeCallback?: (x: string) => void, onInstanceChangeCallback?: (x: InstanceSequenceOnchangeInterface) => void): Promise<RcsbFvModulePublicInterface>;
-export declare function buildUniprotFv(elementId: string, upAcc: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildEntityFv(elementId: string, entityId: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildInstanceFv(elementId: string, instanceId: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildUniprotEntityFv(elementId: string, upAcc: string, entityId: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildUniprotEntityInstanceFv(elementId: string, upAcc: string, entityId: string, instanceId: string, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildPfv(elementId: string, config: PfvBuilderInterface): Promise<RcsbFvModulePublicInterface>;
-export declare function buildPairwiseAlignment(elementId: string, psa: PairwiseAlignmentInterface, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;
-export declare function buildFullChromosome(elementFvId: string, chrId: string): Promise<RcsbFvModulePublicInterface>;
-export declare function buildEntryChromosome(elementFvId: string, entitySelectId: string, chromosomeSelectId: string, entryId: string): Promise<RcsbFvModulePublicInterface>;
-export declare function buildEntityChromosome(elementFvId: string, elementSelectId: string, entityId: string): Promise<RcsbFvModulePublicInterface>;
-export declare function buildChromosome(elementFvId: string, entityId: string, chrId: string, elementSelectId?: string): Promise<RcsbFvModulePublicInterface>;
-export declare function buildGroupFv(elementId: string, groupProvenanceId: GroupProvenanceId, groupId: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig): void;
-export declare function buildSequenceIdentityAlignmentFv(elementId: string, groupId: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig & ActionMethods.FvChangeConfigInterface): Promise<RcsbFvModulePublicInterface>;
-export declare function buildUniprotAlignmentFv(elementId: string, upAcc: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig & ActionMethods.FvChangeConfigInterface): Promise<RcsbFvModulePublicInterface>;
-export declare function buildDataProviderFv(elementId: string, dataProvider: RcsbModuleDataProviderInterface, additionalConfig?: RcsbFvAdditionalConfig): Promise<RcsbFvModulePublicInterface>;