@nfdi4plants/arctrl 3.1.1 → 3.2.0

package/dist/ts/ts/Core/ArcTypes.d.ts

@@ -1,20 +1,21 @@
-import { Option } from '@fable-org/fable-library-js/Option.js';
-import { OntologyAnnotation } from './OntologyAnnotation.js';
-import { Datamap } from './Datamap.js';
-import { Person } from './Person.js';
-import { Remark, Comment$ } from './Comment.js';
-import { int32 } from '@fable-org/fable-library-js/Int32.js';
-import { ArcTable } from './Table/ArcTable.js';
-import { CompositeHeader_$union } from './Table/CompositeHeader.js';
-import { CompositeCell_$union } from './Table/CompositeCell.js';
-import { CompositeColumn } from './Table/CompositeColumn.js';
-import { ArcTables } from './Table/ArcTables.js';
-import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
-import { Publication } from './Publication.js';
-import { Component } from './Process/Component.js';
-import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.js';
-import { CWLParameterReference } from '../CWL/ParameterReference.js';
-import { OntologySourceReference } from './OntologySourceReference.js';
+import { Option } from '@fable-org/fable-library-ts/Option.ts';
+import { OntologyAnnotation } from './OntologyAnnotation.ts';
+import { Datamap } from './Datamap.ts';
+import { Person } from './Person.ts';
+import { Remark, Comment$ } from './Comment.ts';
+import { int32 } from '@fable-org/fable-library-ts/Int32.ts';
+import { ArcTable } from './Table/ArcTable.ts';
+import { MutableArray } from '@fable-org/fable-library-ts/Util.ts';
+import { CompositeHeader_$union } from './Table/CompositeHeader.ts';
+import { CompositeCell_$union } from './Table/CompositeCell.ts';
+import { CompositeColumn } from './Table/CompositeColumn.ts';
+import { ArcTables } from './Table/ArcTables.ts';
+import { TypeInfo } from '@fable-org/fable-library-ts/Reflection.ts';
+import { Publication } from './Publication.ts';
+import { Component } from './Process/Component.ts';
+import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.ts';
+import { CWLParameterReference } from '../CWL/ParameterReference.ts';
+import { OntologySourceReference } from './OntologySourceReference.ts';
 export declare class ArcAssay extends ArcTables implements Iterable<ArcTable> {
     "identifier@129": string;
     "title@133": Option<string>;
@@ -28,7 +29,13 @@ export declare class ArcAssay extends ArcTables implements Iterable<ArcTable> {
     "comments@141-1": Comment$[];
     staticHash: int32;
     constructor(identifier: string, title?: string, description?: string, measurementType?: OntologyAnnotation, technologyType?: OntologyAnnotation, technologyPlatform?: OntologyAnnotation, tables?: ArcTable[], datamap?: Datamap, performers?: Person[], comments?: Comment$[]);
+    /**
+     * Must be unique in one study
+     */
     get Identifier(): string;
+    /**
+     * Must be unique in one study
+     */
     set Identifier(i: string);
     get Investigation(): ArcInvestigation | undefined;
     set Investigation(i: Option<ArcInvestigation>);
@@ -54,12 +61,18 @@ export declare class ArcAssay extends ArcTables implements Iterable<ArcTable> {
     static create(identifier: string, title?: string, description?: string, measurementType?: OntologyAnnotation, technologyType?: OntologyAnnotation, technologyPlatform?: OntologyAnnotation, tables?: ArcTable[], datamap?: Datamap, performers?: Person[], comments?: Comment$[]): ArcAssay;
     static make(identifier: string, title: Option<string>, description: Option<string>, measurementType: Option<OntologyAnnotation>, technologyType: Option<OntologyAnnotation>, technologyPlatform: Option<OntologyAnnotation>, tables: ArcTable[], datamap: Option<Datamap>, performers: Person[], comments: Comment$[]): ArcAssay;
     static get FileName(): string;
-    get StudiesRegisteredIn(): ArcStudy[];
+    get StudiesRegisteredIn(): MutableArray<ArcStudy>;
     static addTable(table: ArcTable, index?: int32): ((arg0: ArcAssay) => ArcAssay);
     static addTables(tables: Iterable<ArcTable>, index?: int32): ((arg0: ArcAssay) => ArcAssay);
     static initTable(tableName: string, index?: int32): ((arg0: ArcAssay) => [ArcAssay, ArcTable]);
     static initTables(tableNames: Iterable<string>, index?: int32): ((arg0: ArcAssay) => ArcAssay);
+    /**
+     * Receive **copy** of table at `index`
+     */
     static getTableAt(index: int32): ((arg0: ArcAssay) => ArcTable);
+    /**
+     * Receive **copy** of table with `name` = `ArcTable.Name`
+     */
     static getTable(name: string): ((arg0: ArcAssay) => ArcTable);
     static updateTableAt(index: int32, table: ArcTable): ((arg0: ArcAssay) => ArcAssay);
     static updateTable(name: string, table: ArcTable): ((arg0: ArcAssay) => ArcAssay);
@@ -89,12 +102,23 @@ export declare class ArcAssay extends ArcTables implements Iterable<ArcTable> {
     static getRow(tableName: string, rowIndex: int32): ((arg0: ArcAssay) => CompositeCell_$union[]);
     static setPerformers(performers: Person[], assay: ArcAssay): ArcAssay;
     Copy(): ArcAssay;
+    /**
+     * Updates given assay with another assay, Identifier will never be updated. By default update is full replace. Optional Parameters can be used to specify update logic.
+     */
     UpdateBy(assay: ArcAssay, onlyReplaceExisting?: boolean, appendSequences?: boolean): void;
     toString(): string;
     AddToInvestigation(investigation: ArcInvestigation): void;
     RemoveFromInvestigation(): void;
+    /**
+     * Updates given assay stored in an study or investigation file with values from an assay file.
+     */
     UpdateReferenceByAssayFile(assay: ArcAssay, onlyReplaceExisting?: boolean): void;
     StructurallyEquals(other: ArcAssay): boolean;
+    /**
+     * Use this function to check if this ArcAssay and the input ArcAssay refer to the same object.
+     *
+     * If true, updating one will update the other due to mutability.
+     */
     ReferenceEquals(other: ArcAssay): boolean;
     Equals(other: any): boolean;
     GetLightHashCode(): int32;
@@ -103,21 +127,27 @@ export declare class ArcAssay extends ArcTables implements Iterable<ArcTable> {
 export declare function ArcAssay_$reflection(): TypeInfo;
 export declare function ArcAssay_$ctor_Z69B192EC(identifier: string, title?: string, description?: string, measurementType?: OntologyAnnotation, technologyType?: OntologyAnnotation, technologyPlatform?: OntologyAnnotation, tables?: ArcTable[], datamap?: Datamap, performers?: Person[], comments?: Comment$[]): ArcAssay;
 export declare class ArcStudy extends ArcTables implements Iterable<ArcTable> {
-    "identifier@579": string;
+    "identifier@582": string;
     investigation: Option<ArcInvestigation>;
-    "title@584": Option<string>;
-    "description@585": Option<string>;
-    "submissionDate@586": Option<string>;
-    "publicReleaseDate@587": Option<string>;
-    "publications@588-1": Publication[];
-    "contacts@589-1": Person[];
-    "studyDesignDescriptors@590-1": OntologyAnnotation[];
-    "datamap@591": Option<Datamap>;
-    "registeredAssayIdentifiers@592-1": string[];
-    "comments@593-1": Comment$[];
+    "title@587": Option<string>;
+    "description@588": Option<string>;
+    "submissionDate@589": Option<string>;
+    "publicReleaseDate@590": Option<string>;
+    "publications@591-1": Publication[];
+    "contacts@592-1": Person[];
+    "studyDesignDescriptors@593-1": OntologyAnnotation[];
+    "datamap@594": Option<Datamap>;
+    "registeredAssayIdentifiers@595-1": string[];
+    "comments@596-1": Comment$[];
     staticHash: int32;
     constructor(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, publications?: Publication[], contacts?: Person[], studyDesignDescriptors?: OntologyAnnotation[], tables?: ArcTable[], datamap?: Datamap, registeredAssayIdentifiers?: string[], comments?: Comment$[]);
+    /**
+     * Must be unique in one investigation
+     */
     get Identifier(): string;
+    /**
+     * Must be unique in one investigation
+     */
     set Identifier(i: string);
     get Investigation(): ArcInvestigation | undefined;
     set Investigation(i: Option<ArcInvestigation>);
@@ -146,12 +176,30 @@ export declare class ArcStudy extends ArcTables implements Iterable<ArcTable> {
     static init(identifier: string): ArcStudy;
     static create(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, publications?: Publication[], contacts?: Person[], studyDesignDescriptors?: OntologyAnnotation[], tables?: ArcTable[], datamap?: Datamap, registeredAssayIdentifiers?: string[], comments?: Comment$[]): ArcStudy;
     static make(identifier: string, title: Option<string>, description: Option<string>, submissionDate: Option<string>, publicReleaseDate: Option<string>, publications: Publication[], contacts: Person[], studyDesignDescriptors: OntologyAnnotation[], tables: ArcTable[], datamap: Option<Datamap>, registeredAssayIdentifiers: string[], comments: Comment$[]): ArcStudy;
+    /**
+     * Returns true if all fields are None/ empty sequences **except** Identifier.
+     */
     get isEmpty(): boolean;
     static get FileName(): string;
+    /**
+     * Returns the count of registered assay *identifiers*. This is not necessarily the same as the count of registered assays, as not all identifiers correspond to an existing assay.
+     */
     get RegisteredAssayIdentifierCount(): int32;
+    /**
+     * Returns the count of registered assays. This is not necessarily the same as the count of registered assay *identifiers*, as not all identifiers correspond to an existing assay.
+     */
     get RegisteredAssayCount(): int32;
+    /**
+     * Returns all assays registered in this study, that correspond to an existing assay object in the associated investigation.
+     */
     get RegisteredAssays(): ArcAssay[];
+    /**
+     * Returns all registered assay identifiers that do not correspond to an existing assay object in the associated investigation.
+     */
     get VacantAssayIdentifiers(): string[];
+    /**
+     * Add assay to investigation and register it to study.
+     */
     AddRegisteredAssay(assay: ArcAssay): void;
     static addRegisteredAssay(assay: ArcAssay): ((arg0: ArcStudy) => ArcStudy);
     InitRegisteredAssay(assayIdentifier: string): ArcAssay;
@@ -163,13 +211,25 @@ export declare class ArcStudy extends ArcTables implements Iterable<ArcTable> {
     GetRegisteredAssay(assayIdentifier: string): ArcAssay;
     static getRegisteredAssay(assayIdentifier: string): ((arg0: ArcStudy) => ArcAssay);
     static getRegisteredAssays(): ((arg0: ArcStudy) => ArcAssay[]);
+    /**
+     * Returns ArcAssays registered in study, or if no parent exists, initializies new ArcAssay from identifier.
+     */
     GetRegisteredAssaysOrIdentifier(): ArcAssay[];
+    /**
+     * Returns ArcAssays registered in study, or if no parent exists, initializies new ArcAssay from identifier.
+     */
     static getRegisteredAssaysOrIdentifier(): ((arg0: ArcStudy) => ArcAssay[]);
     static addTable(table: ArcTable, index?: int32): ((arg0: ArcStudy) => ArcStudy);
     static addTables(tables: Iterable<ArcTable>, index?: int32): ((arg0: ArcStudy) => ArcStudy);
     static initTable(tableName: string, index?: int32): ((arg0: ArcStudy) => [ArcStudy, ArcTable]);
     static initTables(tableNames: Iterable<string>, index?: int32): ((arg0: ArcStudy) => ArcStudy);
+    /**
+     * Receive **copy** of table at `index`
+     */
     static getTableAt(index: int32): ((arg0: ArcStudy) => ArcTable);
+    /**
+     * Receive **copy** of table with `name` = `ArcTable.Name`
+     */
     static getTable(name: string): ((arg0: ArcStudy) => ArcTable);
     static updateTableAt(index: int32, table: ArcTable): ((arg0: ArcStudy) => ArcStudy);
     static updateTable(name: string, table: ArcTable): ((arg0: ArcStudy) => ArcStudy);
@@ -199,9 +259,24 @@ export declare class ArcStudy extends ArcTables implements Iterable<ArcTable> {
     static getRow(tableName: string, rowIndex: int32): ((arg0: ArcStudy) => CompositeCell_$union[]);
     AddToInvestigation(investigation: ArcInvestigation): void;
     RemoveFromInvestigation(): void;
+    /**
+     * Copies ArcStudy object without the pointer to the parent ArcInvestigation
+     *
+     * This copy does only contain the identifiers of the registered ArcAssays and not the actual objects.
+     *
+     * In order to copy the ArcAssays as well, use the Copy() method of the ArcInvestigation.
+     */
     Copy(copyInvestigationRef?: boolean): ArcStudy;
+    /**
+     * Updates given study from an investigation file against a study from a study file. Identifier will never be updated.
+     */
     UpdateReferenceByStudyFile(study: ArcStudy, onlyReplaceExisting?: boolean, keepUnusedRefTables?: boolean): void;
     StructurallyEquals(other: ArcStudy): boolean;
+    /**
+     * Use this function to check if this ArcStudy and the input ArcStudy refer to the same object.
+     *
+     * If true, updating one will update the other due to mutability.
+     */
     ReferenceEquals(other: ArcStudy): boolean;
     toString(): string;
     Equals(other: any): boolean;
@@ -211,23 +286,29 @@ export declare class ArcStudy extends ArcTables implements Iterable<ArcTable> {
 export declare function ArcStudy_$reflection(): TypeInfo;
 export declare function ArcStudy_$ctor_Z273F64C5(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, publications?: Publication[], contacts?: Person[], studyDesignDescriptors?: OntologyAnnotation[], tables?: ArcTable[], datamap?: Datamap, registeredAssayIdentifiers?: string[], comments?: Comment$[]): ArcStudy;
 export declare class ArcWorkflow {
-    "identifier@1151": string;
+    "identifier@1157": string;
     investigation: Option<ArcInvestigation>;
-    "title@1156": Option<string>;
-    "description@1157": Option<string>;
-    "subWorkflowIdentifiers@1158": string[];
-    "workflowType@1159": Option<OntologyAnnotation>;
-    "uri@1160": Option<string>;
-    "version@1161": Option<string>;
-    "parameters@1162": OntologyAnnotation[];
-    "components@1163": Component[];
-    "datamap@1164": Option<Datamap>;
-    "contacts@1165": Person[];
-    "cwlDescription@1166": Option<CWLProcessingUnit_$union>;
-    "comments@1167": Comment$[];
+    "title@1162": Option<string>;
+    "description@1163": Option<string>;
+    "subWorkflowIdentifiers@1164": string[];
+    "workflowType@1165": Option<OntologyAnnotation>;
+    "uri@1166": Option<string>;
+    "version@1167": Option<string>;
+    "parameters@1168": OntologyAnnotation[];
+    "components@1169": Component[];
+    "datamap@1170": Option<Datamap>;
+    "contacts@1171": Person[];
+    "cwlDescription@1172": Option<CWLProcessingUnit_$union>;
+    "comments@1173": Comment$[];
     staticHash: int32;
     constructor(identifier: string, title?: string, description?: string, workflowType?: OntologyAnnotation, uri?: string, version?: string, subWorkflowIdentifiers?: string[], parameters?: OntologyAnnotation[], components?: Component[], datamap?: Datamap, contacts?: Person[], cwlDescription?: CWLProcessingUnit_$union, comments?: Comment$[]);
+    /**
+     * Must be unique in one study
+     */
     get Identifier(): string;
+    /**
+     * Must be unique in one study
+     */
     set Identifier(i: string);
     get Investigation(): ArcInvestigation | undefined;
     set Investigation(a: Option<ArcInvestigation>);
@@ -261,10 +342,25 @@ export declare class ArcWorkflow {
     static create(identifier: string, title?: string, description?: string, workflowType?: OntologyAnnotation, uri?: string, version?: string, subWorkflowIdentifiers?: string[], parameters?: OntologyAnnotation[], components?: Component[], datamap?: Datamap, contacts?: Person[], cwlDescription?: CWLProcessingUnit_$union, comments?: Comment$[]): ArcWorkflow;
     static make(identifier: string, title: Option<string>, description: Option<string>, workflowType: Option<OntologyAnnotation>, uri: Option<string>, version: Option<string>, subWorkflowIdentifiers: string[], parameters: OntologyAnnotation[], components: Component[], datamap: Option<Datamap>, contacts: Person[], cwlDescription: Option<CWLProcessingUnit_$union>, comments: Comment$[]): ArcWorkflow;
     static get FileName(): string;
+    /**
+     * Returns the count of registered subWorkflow *identifiers*. This is not necessarily the same as the count of registered subWorkflows, as not all identifiers correspond to an existing subWorkflow.
+     */
     get SubWorkflowIdentifiersCount(): int32;
+    /**
+     * Returns the count of registered subWorkflows. This is not necessarily the same as the count of registered subWorkflow *identifiers*, as not all identifiers correspond to an existing subWorkflow.
+     */
     get SubWorkflowCount(): int32;
+    /**
+     * Returns all subWorkflows registered in this workflow, that correspond to an existing subWorkflow object in the associated investigation.
+     */
     get SubWorkflows(): ArcWorkflow[];
+    /**
+     * Returns all registered subWorkflow identifiers that do not correspond to an existing subWorkflow object in the associated investigation.
+     */
     get VacantSubWorkflowIdentifiers(): string[];
+    /**
+     * Add subWorkflow to investigation and register it to workflow.
+     */
     AddSubWorkflow(subWorkflow: ArcWorkflow): void;
     static addSubWorkflow(subWorkflow: ArcWorkflow): ((arg0: ArcWorkflow) => ArcWorkflow);
     InitSubWorkflow(subWorkflowIdentifier: string): ArcWorkflow;
@@ -276,10 +372,28 @@ export declare class ArcWorkflow {
     GetRegisteredSubWorkflow(subWorkflowIdentifier: string): ArcWorkflow;
     static getRegisteredSubWorkflow(subWorkflowIdentifier: string): ((arg0: ArcWorkflow) => ArcWorkflow);
     static getRegisteredSubWorkflows(): ((arg0: ArcWorkflow) => ArcWorkflow[]);
+    /**
+     * Returns ArcSubWorkflows registered in workflow, or if no parent exists, initializies new ArcSubWorkflow from identifier.
+     */
     GetRegisteredSubWorkflowsOrIdentifier(): ArcWorkflow[];
+    /**
+     * Returns ArcSubWorkflows registered in workflow, or if no parent exists, initializies new ArcSubWorkflow from identifier.
+     */
     static getRegisteredSubWorkflowsOrIdentifier(): ((arg0: ArcWorkflow) => ArcWorkflow[]);
+    /**
+     * Copies ArcStudy object without the pointer to the parent ArcInvestigation
+     *
+     * This copy does only contain the identifiers of the registered ArcAssays and not the actual objects.
+     *
+     * In order to copy the ArcAssays as well, use the Copy() method of the ArcInvestigation.
+     */
     Copy(copyInvestigationRef?: boolean): ArcWorkflow;
     StructurallyEquals(other: ArcWorkflow): boolean;
+    /**
+     * Use this function to check if this ArcWorkflow and the input ArcWorkflow refer to the same object.
+     *
+     * If true, updating one will update the other due to mutability.
+     */
     ReferenceEquals(other: ArcStudy): boolean;
     toString(): string;
     Equals(other: any): boolean;
@@ -289,22 +403,28 @@ export declare class ArcWorkflow {
 export declare function ArcWorkflow_$reflection(): TypeInfo;
 export declare function ArcWorkflow_$ctor_Z5FF2D3D5(identifier: string, title?: string, description?: string, workflowType?: OntologyAnnotation, uri?: string, version?: string, subWorkflowIdentifiers?: string[], parameters?: OntologyAnnotation[], components?: Component[], datamap?: Datamap, contacts?: Person[], cwlDescription?: CWLProcessingUnit_$union, comments?: Comment$[]): ArcWorkflow;
 export declare class ArcRun extends ArcTables implements Iterable<ArcTable> {
-    "identifier@1453": string;
-    "title@1457": Option<string>;
-    "description@1458": Option<string>;
+    "identifier@1462": string;
+    "title@1466": Option<string>;
+    "description@1467": Option<string>;
     investigation: Option<ArcInvestigation>;
-    "measurementType@1460": Option<OntologyAnnotation>;
-    "technologyType@1461": Option<OntologyAnnotation>;
-    "technologyPlatform@1462": Option<OntologyAnnotation>;
-    "workflowIdentifiers@1463-1": string[];
-    "datamap@1464": Option<Datamap>;
-    "performers@1465-1": Person[];
-    "cwlDescription@1466": Option<CWLProcessingUnit_$union>;
-    "cwlInput@1467-1": CWLParameterReference[];
-    "comments@1468-1": Comment$[];
+    "measurementType@1469": Option<OntologyAnnotation>;
+    "technologyType@1470": Option<OntologyAnnotation>;
+    "technologyPlatform@1471": Option<OntologyAnnotation>;
+    "workflowIdentifiers@1472-1": string[];
+    "datamap@1473": Option<Datamap>;
+    "performers@1474-1": Person[];
+    "cwlDescription@1475": Option<CWLProcessingUnit_$union>;
+    "cwlInput@1476-1": CWLParameterReference[];
+    "comments@1477-1": Comment$[];
     staticHash: int32;
     constructor(identifier: string, title?: string, description?: string, measurementType?: OntologyAnnotation, technologyType?: OntologyAnnotation, technologyPlatform?: OntologyAnnotation, workflowIdentifiers?: string[], tables?: ArcTable[], datamap?: Datamap, performers?: Person[], cwlDescription?: CWLProcessingUnit_$union, cwlInput?: CWLParameterReference[], comments?: Comment$[]);
+    /**
+     * Must be unique in one study
+     */
     get Identifier(): string;
+    /**
+     * Must be unique in one study
+     */
     set Identifier(i: string);
     get Investigation(): ArcInvestigation | undefined;
     set Investigation(i: Option<ArcInvestigation>);
@@ -336,15 +456,30 @@ export declare class ArcRun extends ArcTables implements Iterable<ArcTable> {
     static create(identifier: string, title?: string, description?: string, measurementType?: OntologyAnnotation, technologyType?: OntologyAnnotation, technologyPlatform?: OntologyAnnotation, workflowIdentifiers?: string[], tables?: ArcTable[], datamap?: Datamap, performers?: Person[], cwlDescription?: CWLProcessingUnit_$union, cwlInput?: CWLParameterReference[], comments?: Comment$[]): ArcRun;
     static make(identifier: string, title: Option<string>, description: Option<string>, measurementType: Option<OntologyAnnotation>, technologyType: Option<OntologyAnnotation>, technologyPlatform: Option<OntologyAnnotation>, workflowIdentifiers: string[], tables: ArcTable[], datamap: Option<Datamap>, performers: Person[], cwlDescription: Option<CWLProcessingUnit_$union>, cwlInput: CWLParameterReference[], comments: Comment$[]): ArcRun;
     static get FileName(): string;
+    /**
+     * Returns the count of workflow *identifiers*. This is not necessarily the same as the count of workflows, as not all identifiers correspond to an existing workflow.
+     */
     get WorkflowIdentifierCount(): int32;
     get WorkflowCount(): int32;
+    /**
+     * Returns all workflows registered in this run, that correspond to an existing workflow object in the associated investigation.
+     */
     get Workflows(): ArcWorkflow[];
+    /**
+     * Returns all registered workflow identifiers that do not correspond to an existing workflow object in the associated investigation.
+     */
     get VacantWorkflowIdentifiers(): string[];
     static addTable(table: ArcTable, index?: int32): ((arg0: ArcRun) => ArcRun);
     static addTables(tables: Iterable<ArcTable>, index?: int32): ((arg0: ArcRun) => ArcRun);
     static initTable(tableName: string, index?: int32): ((arg0: ArcRun) => [ArcRun, ArcTable]);
     static initTables(tableNames: Iterable<string>, index?: int32): ((arg0: ArcRun) => ArcRun);
+    /**
+     * Receive **copy** of table at `index`
+     */
     static getTableAt(index: int32): ((arg0: ArcRun) => ArcTable);
+    /**
+     * Receive **copy** of table with `name` = `ArcTable.Name`
+     */
     static getTable(name: string): ((arg0: ArcRun) => ArcTable);
     static updateTableAt(index: int32, table: ArcTable): ((arg0: ArcRun) => ArcRun);
     static updateTable(name: string, table: ArcTable): ((arg0: ArcRun) => ArcRun);
@@ -374,11 +509,19 @@ export declare class ArcRun extends ArcTables implements Iterable<ArcTable> {
     static getRow(tableName: string, rowIndex: int32): ((arg0: ArcRun) => CompositeCell_$union[]);
     static setPerformers(performers: Person[], run: ArcRun): ArcRun;
     Copy(): ArcRun;
+    /**
+     * Updates given run with another run, Identifier will never be updated. By default update is full replace. Optional Parameters can be used to specify update logic.
+     */
     UpdateBy(run: ArcRun, onlyReplaceExisting?: boolean, appendSequences?: boolean): void;
     toString(): string;
     AddToInvestigation(investigation: ArcInvestigation): void;
     RemoveFromInvestigation(): void;
     StructurallyEquals(other: ArcRun): boolean;
+    /**
+     * Use this function to check if this ArcRun and the input ArcRun refer to the same object.
+     *
+     * If true, updating one will update the other due to mutability.
+     */
     ReferenceEquals(other: ArcRun): boolean;
     Equals(other: any): boolean;
     GetLightHashCode(): int32;
@@ -387,25 +530,31 @@ export declare class ArcRun extends ArcTables implements Iterable<ArcTable> {
 export declare function ArcRun_$reflection(): TypeInfo;
 export declare function ArcRun_$ctor_287C1303(identifier: string, title?: string, description?: string, measurementType?: OntologyAnnotation, technologyType?: OntologyAnnotation, technologyPlatform?: OntologyAnnotation, workflowIdentifiers?: string[], tables?: ArcTable[], datamap?: Datamap, performers?: Person[], cwlDescription?: CWLProcessingUnit_$union, cwlInput?: CWLParameterReference[], comments?: Comment$[]): ArcRun;
 export declare class ArcInvestigation {
-    "identifier@1951": string;
-    "title@1952": Option<string>;
-    "description@1953": Option<string>;
-    "submissionDate@1954": Option<string>;
-    "publicReleaseDate@1955": Option<string>;
-    "ontologySourceReferences@1956-1": OntologySourceReference[];
-    "publications@1957-1": Publication[];
-    "contacts@1958-1": Person[];
-    "assays@1959-1": ArcAssay[];
-    "studies@1960-1": ArcStudy[];
-    "workflows@1961-1": ArcWorkflow[];
-    "runs@1962-1": ArcRun[];
-    "registeredStudyIdentifiers@1963-1": string[];
-    "comments@1964-1": Comment$[];
-    "remarks@1965-1": Remark[];
+    "identifier@1963": string;
+    "title@1964": Option<string>;
+    "description@1965": Option<string>;
+    "submissionDate@1966": Option<string>;
+    "publicReleaseDate@1967": Option<string>;
+    "ontologySourceReferences@1968-1": OntologySourceReference[];
+    "publications@1969-1": Publication[];
+    "contacts@1970-1": Person[];
+    "assays@1971-1": ArcAssay[];
+    "studies@1972-1": ArcStudy[];
+    "workflows@1973-1": ArcWorkflow[];
+    "runs@1974-1": ArcRun[];
+    "registeredStudyIdentifiers@1975-1": string[];
+    "comments@1976-1": Comment$[];
+    "remarks@1977-1": Remark[];
     staticHash: int32;
-    "init@1922": int32;
+    "init@1934": int32;
     constructor(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, ontologySourceReferences?: OntologySourceReference[], publications?: Publication[], contacts?: Person[], assays?: ArcAssay[], studies?: ArcStudy[], workflows?: ArcWorkflow[], runs?: ArcRun[], registeredStudyIdentifiers?: string[], comments?: Comment$[], remarks?: Remark[]);
+    /**
+     * Must be unique in one investigation
+     */
     get Identifier(): string;
+    /**
+     * Must be unique in one investigation
+     */
     set Identifier(i: string);
     get Title(): string | undefined;
     set Title(n: Option<string>);
@@ -442,24 +591,57 @@ export declare class ArcInvestigation {
     static create(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, ontologySourceReferences?: OntologySourceReference[], publications?: Publication[], contacts?: Person[], assays?: ArcAssay[], studies?: ArcStudy[], workflows?: ArcWorkflow[], runs?: ArcRun[], registeredStudyIdentifiers?: string[], comments?: Comment$[], remarks?: Remark[]): ArcInvestigation;
     static make(identifier: string, title: Option<string>, description: Option<string>, submissionDate: Option<string>, publicReleaseDate: Option<string>, ontologySourceReferences: OntologySourceReference[], publications: Publication[], contacts: Person[], assays: ArcAssay[], studies: ArcStudy[], workflows: ArcWorkflow[], runs: ArcRun[], registeredStudyIdentifiers: string[], comments: Comment$[], remarks: Remark[]): ArcInvestigation;
     get AssayCount(): int32;
-    get AssayIdentifiers(): string[];
+    get AssayIdentifiers(): MutableArray<string>;
     get UnregisteredAssays(): ArcAssay[];
     AddAssay(assay: ArcAssay, registerIn?: ArcStudy[]): void;
     static addAssay(assay: ArcAssay, registerIn?: ArcStudy[]): ((arg0: ArcInvestigation) => ArcInvestigation);
     InitAssay(assayIdentifier: string, registerIn?: ArcStudy[]): ArcAssay;
     static initAssay(assayIdentifier: string, registerIn?: ArcStudy[]): ((arg0: ArcInvestigation) => ArcAssay);
+    /**
+     * Removes assay at specified index from ArcInvestigation without deregistering it from studies.
+     */
     DeleteAssayAt(index: int32): void;
+    /**
+     * Removes assay at specified index from ArcInvestigation without deregistering it from studies.
+     */
     static deleteAssayAt(index: int32): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Removes assay with given identifier from ArcInvestigation without deregistering it from studies.
+     */
     DeleteAssay(assayIdentifier: string): void;
+    /**
+     * Removes assay with given identifier from ArcInvestigation without deregistering it from studies.
+     */
     static deleteAssay(assayIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Removes assay at specified index from ArcInvestigation and deregisteres it from all studies.
+     */
     RemoveAssayAt(index: int32): void;
+    /**
+     * Removes assay at specified index from ArcInvestigation and deregisteres it from all studies.
+     */
     static removeAssayAt(index: int32): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Removes assay with specified identifier from ArcInvestigation and deregisteres it from all studies.
+     */
     RemoveAssay(assayIdentifier: string): void;
+    /**
+     * Removes assay with specified identifier from ArcInvestigation and deregisteres it from all studies.
+     */
     static removeAssay(assayIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Renames an assay in the whole investigation
+     */
     RenameAssay(oldIdentifier: string, newIdentifier: string): void;
     static renameAssay(oldIdentifier: string, newIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Renames an run in the whole investigation
+     */
     RenameRun(oldIdentifier: string, newIdentifier: string): void;
     static renameRun(oldIdentifier: string, newIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Renames an workflow in the whole investigation
+     */
     RenameWorkflow(oldIdentifier: string, newIdentifier: string): void;
     static renameWorkflow(oldIdentifier: string, newIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
     SetAssayAt(index: int32, assay: ArcAssay): void;
@@ -476,12 +658,24 @@ export declare class ArcInvestigation {
     static tryGetAssay(assayIdentifier: string): ((arg0: ArcInvestigation) => Option<ArcAssay>);
     ContainsAssay(assayIdentifier: string): boolean;
     static containsAssay(assayIdentifier: string): ((arg0: ArcInvestigation) => boolean);
+    /**
+     * Returns the count of registered study *identifiers*. This is not necessarily the same as the count of registered studies, as not all identifiers correspond to an existing study object.
+     */
     get RegisteredStudyIdentifierCount(): int32;
+    /**
+     * Returns all studies registered in this investigation, that correspond to an existing study object investigation.
+     */
     get RegisteredStudies(): ArcStudy[];
+    /**
+     * Returns the count of registered studies. This is not necessarily the same as the count of registered study *identifiers*, as not all identifiers correspond to an existing study object.
+     */
     get RegisteredStudyCount(): int32;
+    /**
+     * Returns all registered study identifiers that do not correspond to an existing study object in the investigation.
+     */
     get VacantStudyIdentifiers(): string[];
     get StudyCount(): int32;
-    get StudyIdentifiers(): string[];
+    get StudyIdentifiers(): MutableArray<string>;
     get UnregisteredStudies(): ArcStudy[];
     AddStudy(study: ArcStudy): void;
     static addStudy(study: ArcStudy): ((arg0: ArcInvestigation) => ArcInvestigation);
@@ -491,15 +685,45 @@ export declare class ArcInvestigation {
     static registerStudy(studyIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
     AddRegisteredStudy(study: ArcStudy): void;
     static addRegisteredStudy(study: ArcStudy): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Removes study at specified index from ArcInvestigation without deregistering it.
+     */
     DeleteStudyAt(index: int32): void;
+    /**
+     * Removes study at specified index from ArcInvestigation without deregistering it.
+     */
     static deleteStudyAt(index: int32): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Removes study with specified identifier from ArcInvestigation without deregistering it.
+     */
     DeleteStudy(studyIdentifier: string): void;
+    /**
+     * Removes study with specified identifier from ArcInvestigation without deregistering it.
+     */
     static deleteStudy(studyIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Removes study at specified index from ArcInvestigation and deregisteres it.
+     */
     RemoveStudyAt(index: int32): void;
+    /**
+     * Removes study at specified index from ArcInvestigation and deregisteres it.
+     */
     static removeStudyAt(index: int32): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Removes study with specified identifier from ArcInvestigation and deregisteres it.
+     */
     RemoveStudy(studyIdentifier: string): void;
+    /**
+     * Removes study with specified identifier from ArcInvestigation and deregisteres it.
+     */
     static removeStudy(studyIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Renames a study in the whole investigation
+     */
     RenameStudy(oldIdentifier: string, newIdentifier: string): void;
+    /**
+     * Renames a study in the whole investigation
+     */
     static renameStudy(oldIdentifier: string, newIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
     SetStudyAt(index: int32, study: ArcStudy): void;
     static setStudyAt(index: int32, study: ArcStudy): ((arg0: ArcInvestigation) => ArcInvestigation);
@@ -515,8 +739,14 @@ export declare class ArcInvestigation {
     static tryGetStudy(studyIdentifier: string): ((arg0: ArcInvestigation) => Option<ArcStudy>);
     ContainsStudy(studyIdentifier: string): boolean;
     static containsStudy(studyIdentifier: string): ((arg0: ArcInvestigation) => boolean);
+    /**
+     * Register an existing assay from ArcInvestigation.Assays to a existing study.
+     */
     RegisterAssayAt(studyIndex: int32, assayIdentifier: string): void;
     static registerAssayAt(studyIndex: int32, assayIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Register an existing assay from ArcInvestigation.Assays to a existing study.
+     */
     RegisterAssay(studyIdentifier: string, assayIdentifier: string): void;
     static registerAssay(studyIdentifier: string, assayIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
     DeregisterAssayAt(studyIndex: int32, assayIdentifier: string): void;
@@ -526,7 +756,7 @@ export declare class ArcInvestigation {
     DeregisterStudy(studyIdentifier: string): void;
     static deregisterStudy(studyIdentifier: string): ((arg0: ArcInvestigation) => ArcInvestigation);
     get WorkflowCount(): int32;
-    get WorkflowIdentifiers(): string[];
+    get WorkflowIdentifiers(): MutableArray<string>;
     GetWorkflowIndex(workflowIdentifier: string): int32;
     static getWorkflowIndex(workflowIdentifier: string): ((arg0: ArcInvestigation) => int32);
     AddWorkflow(workflow: ArcWorkflow): void;
@@ -550,7 +780,7 @@ export declare class ArcInvestigation {
     static setWorkflow(workflowIdentifier: string, workflow: ArcWorkflow): ((arg0: ArcInvestigation) => ArcInvestigation);
     static setWorkflowAt(index: int32, workflow: ArcWorkflow): ((arg0: ArcInvestigation) => ArcInvestigation);
     get RunCount(): int32;
-    get RunIdentifiers(): string[];
+    get RunIdentifiers(): MutableArray<string>;
     GetRunIndex(runIdentifier: string): int32;
     static getRunIndex(runIdentifier: string): ((arg0: ArcInvestigation) => int32);
     AddRun(run: ArcRun): void;
@@ -573,13 +803,38 @@ export declare class ArcInvestigation {
     SetRun(runIdentifier: string, run: ArcRun): void;
     static setRunAt(index: int32, run: ArcRun): ((arg0: ArcInvestigation) => ArcInvestigation);
     static setRun(runIdentifier: string, run: ArcRun): ((arg0: ArcInvestigation) => ArcInvestigation);
-    GetAllPersons(): Person[];
-    GetAllPublications(): Publication[];
+    /**
+     * Returns all fully distinct Contacts/Performers from assays/studies/investigation.
+     */
+    GetAllPersons(): MutableArray<Person>;
+    /**
+     * Returns all fully distinct Contacts/Performers from assays/studies/investigation unfiltered.
+     */
+    GetAllPublications(): MutableArray<Publication>;
+    /**
+     * Deregisters assays not found in ArcInvestigation.Assays from all studies.
+     */
     DeregisterMissingAssays(): void;
     static deregisterMissingAssays(): ((arg0: ArcInvestigation) => ArcInvestigation);
+    /**
+     * Updates the IOtypes of the IO columns (Input, Output) across all tables in the investigation if possible.
+     *
+     * If an entity (Row Value of IO Column) with the same name as an entity with a higher IOType specifity is found, the IOType of the entity with the lower IOType specificity is updated.
+     *
+     * E.g. In Table1, there is a column "Output [Sample Name]" with an entity "Sample1". In Table2, there is a column "Input [Source Name]" with the same entity "Sample1". By equality of the entities, the IOType of the Input column in Table2 is inferred to be Sample, resulting in "Input [Sample Name]".
+     *
+     * E.g. RawDataFile is more specific than Source, but less specific than DerivedDataFile.
+     *
+     * E.g. Sample is equally specific to RawDataFile.
+     */
     UpdateIOTypeByEntityID(): void;
     Copy(): ArcInvestigation;
     StructurallyEquals(other: ArcInvestigation): boolean;
+    /**
+     * Use this function to check if this ArcInvestigation and the input ArcInvestigation refer to the same object.
+     *
+     * If true, updating one will update the other due to mutability.
+     */
     ReferenceEquals(other: ArcInvestigation): boolean;
     toString(): string;
     Equals(other: any): boolean;