import { PlateMap, ProtocolStep, Reagent, SampleType, Well } from '../types';
import { QpcrPlateTemplate } from './templateQpcrTypes';
export type TemplateKind = 'experiment-design';
export type TemplateId = 'plate-map' | 'sample-sheet' | 'sample-prep' | 'dose-response' | 'calibration-curve' | 'time-course' | 'protocol-steps' | 'assay-matrix' | 'reagent-list' | 'flow-cytometry-panel' | 'instrument-run' | 'qpcr-plate';
export type TemplatePresetId = 'wellplate-screen' | 'qpcr-expression' | 'lcms-batch' | 'targeted-metabolomics' | 'elisa-assay' | 'flow-cytometry-assay' | 'western-blot-assay';
export type TemplatePackId = 'cell-culture-screen' | 'omics-assay' | 'longitudinal-study' | 'molecular-assay';
export interface BioTemplateEnvelope<TData = Record<string, unknown>> {
    template_id: TemplateId | string;
    template_version: string;
    kind: TemplateKind | string;
    data: TData;
    metadata: Record<string, unknown>;
}
export type TemplateCollection = Record<string, BioTemplateEnvelope<unknown>>;
export interface TemplateCollectionEnvelope {
    templates: TemplateCollection;
    metadata?: Record<string, unknown>;
}
export type TemplateWell = Well;
export type TemplatePlateMap = PlateMap;
export type TemplateSample = SampleType;
export interface PlateMapTemplateData {
    plates: TemplatePlateMap[];
    samples: TemplateSample[];
    activePlateId?: string;
    selectedWells?: string[];
    activeSampleId?: string;
}
export type PlateMapTemplate = BioTemplateEnvelope<PlateMapTemplateData>;
export type SampleColumnType = 'string' | 'number' | 'integer' | 'boolean' | 'date' | 'category' | 'unknown';
export interface SampleColumn {
    id: string;
    label: string;
    type: SampleColumnType;
    required: boolean;
    groupable: boolean;
}
export interface SampleRecord {
    sampleId: string;
    name?: string;
    group?: string;
    batch?: string;
    replicate?: number | string;
    plateId?: string;
    wellId?: string;
    metadata?: Record<string, unknown>;
}
export interface SampleGroupDefinition {
    name: string;
    color: string;
    samples: string[];
}
export interface SampleSheetTemplateData {
    samples: SampleRecord[];
    columns: SampleColumn[];
    groups: SampleGroupDefinition[];
}
export type SampleSheetTemplate = BioTemplateEnvelope<SampleSheetTemplateData>;
export type SamplePrepStepType = 'extraction' | 'dilution' | 'normalization' | 'transfer' | 'incubation' | 'centrifugation' | 'cleanup' | 'digestion' | 'labeling' | 'other';
export type SamplePrepStatus = 'planned' | 'in-progress' | 'completed' | 'failed' | 'skipped';
export interface SamplePrepStep {
    id: string;
    order: number;
    type: SamplePrepStepType;
    name: string;
    sourceSampleId?: string;
    sourcePlateId?: string;
    sourceWellId?: string;
    destinationSampleId?: string;
    destinationPlateId?: string;
    destinationWellId?: string;
    reagentId?: string;
    inputVolume?: number;
    outputVolume?: number;
    volumeUnit: string;
    durationMin?: number;
    status: SamplePrepStatus;
    metadata?: Record<string, unknown>;
}
export interface SamplePrepTemplateData {
    protocolName: string;
    steps: SamplePrepStep[];
    metadata: Record<string, unknown>;
}
export type SamplePrepTemplate = BioTemplateEnvelope<SamplePrepTemplateData>;
export type SamplePrepStepInput = Partial<SamplePrepStep> & {
    name?: string;
    sourceSampleId?: string;
};
export interface CompoundDoseSeries {
    id: string;
    name: string;
    concentrations: number[];
    metadata?: Record<string, unknown>;
}
export type ControlRole = 'vehicle' | 'positive' | 'negative' | 'blank' | 'baseline' | 'other';
export interface ControlDefinition {
    id: string;
    name: string;
    role: ControlRole;
    vehicle?: string;
    metadata?: Record<string, unknown>;
}
export interface DoseResponseTemplateData {
    compounds: CompoundDoseSeries[];
    unit: string;
    replicates: number;
    controls: ControlDefinition[];
    layout?: PlateMapTemplateData;
    metadata: Record<string, unknown>;
}
export type DoseResponseTemplate = BioTemplateEnvelope<DoseResponseTemplateData>;
export type CalibrationModel = 'linear' | 'linear-weighted-1-x' | 'linear-weighted-1-x2' | 'quadratic' | 'four-parameter-logistic';
export type CalibrationPointRole = 'blank' | 'standard' | 'qc' | 'unknown';
export type CalibrationPointStatus = 'planned' | 'accepted' | 'rejected' | 'warning';
export interface CalibrationAcceptance {
    minRSquared: number;
    standardTolerancePercent: number;
    qcTolerancePercent: number;
    requireBlank: boolean;
    metadata?: Record<string, unknown>;
}
export interface CalibrationPoint {
    id: string;
    order: number;
    role: CalibrationPointRole;
    level: string;
    concentration: number;
    unit: string;
    expectedResponse?: number;
    response?: number;
    replicate: number;
    include: boolean;
    status: CalibrationPointStatus;
    metadata?: Record<string, unknown>;
}
export interface CalibrationCurveTemplateData {
    analyte: string;
    model: CalibrationModel;
    xUnit: string;
    responseUnit: string;
    points: CalibrationPoint[];
    acceptance: CalibrationAcceptance;
    metadata: Record<string, unknown>;
}
export type CalibrationCurveTemplate = BioTemplateEnvelope<CalibrationCurveTemplateData>;
export type CalibrationAcceptanceInput = Partial<CalibrationAcceptance>;
export type CalibrationPointInput = Partial<CalibrationPoint> & {
    concentration?: number;
    level?: string;
};
export type TimeUnit = 'second' | 'minute' | 'hour' | 'day' | 'week';
export interface TimePoint {
    id: string;
    label: string;
    value: number;
    unit: TimeUnit;
    metadata?: Record<string, unknown>;
}
export interface TimeCourseCondition {
    id: string;
    name: string;
    color?: string;
    description?: string;
    metadata?: Record<string, unknown>;
}
export interface TimeCourseSample {
    sampleId: string;
    conditionId: string;
    timepointId: string;
    replicate: number;
    metadata?: Record<string, unknown>;
}
export interface TimeCourseTemplateData {
    timepoints: TimePoint[];
    conditions: TimeCourseCondition[];
    samples: TimeCourseSample[];
    metadata: Record<string, unknown>;
}
export type TimeCourseTemplate = BioTemplateEnvelope<TimeCourseTemplateData>;
export type AssayFeatureType = 'metabolite' | 'protein' | 'gene' | 'cell' | 'compound' | 'readout' | 'other';
export interface AssaySample {
    sampleId: string;
    name?: string;
    group?: string;
    metadata?: Record<string, unknown>;
}
export interface AssayFeature {
    id: string;
    name: string;
    type: AssayFeatureType;
    unit?: string;
    metadata?: Record<string, unknown>;
}
export interface AssayMeasurement {
    sampleId: string;
    featureId: string;
    value?: number | null;
    metadata?: Record<string, unknown>;
}
export interface AssayMatrixTemplateData {
    samples: AssaySample[];
    features: AssayFeature[];
    measurements: AssayMeasurement[];
    metadata: Record<string, unknown>;
}
export type AssayMatrixTemplate = BioTemplateEnvelope<AssayMatrixTemplateData>;
export type ProtocolStepRecord = ProtocolStep & {
    metadata?: Record<string, unknown>;
};
export interface ProtocolStepsTemplateData {
    steps: ProtocolStepRecord[];
    metadata: Record<string, unknown>;
}
export type ProtocolStepsTemplate = BioTemplateEnvelope<ProtocolStepsTemplateData>;
export type ReagentKind = 'compound' | 'antibody' | 'primer' | 'enzyme' | 'buffer' | 'media' | 'kit' | 'reagent' | 'other';
export type ReagentTemplateInput = Omit<Reagent, 'expiryDate'> & {
    expiryDate?: Date | string | null;
    kind?: ReagentKind;
    concentration?: string;
    metadata?: Record<string, unknown>;
};
export interface ReagentRecord extends Omit<Reagent, 'expiryDate'> {
    expiryDate?: string;
    kind?: ReagentKind;
    concentration?: string;
    metadata?: Record<string, unknown>;
}
export interface ReagentListTemplateData {
    reagents: ReagentRecord[];
    metadata: Record<string, unknown>;
}
export type ReagentListTemplate = BioTemplateEnvelope<ReagentListTemplateData>;
export type FlowMarkerPurpose = 'phenotype' | 'viability' | 'activation' | 'sorting' | 'control' | 'other';
export type FlowControlKind = 'unstained' | 'single-stain' | 'fmo' | 'isotype' | 'viability' | 'beads' | 'other';
export interface FlowPanelMarker {
    id: string;
    marker: string;
    fluorophore: string;
    detector?: string;
    clone?: string;
    reagentId?: string;
    purpose: FlowMarkerPurpose;
    compensationRequired: boolean;
    metadata?: Record<string, unknown>;
}
export interface FlowPanelControl {
    id: string;
    name: string;
    kind: FlowControlKind;
    markerId?: string;
    required: boolean;
    metadata?: Record<string, unknown>;
}
export interface FlowCytometryPanelTemplateData {
    markers: FlowPanelMarker[];
    controls: FlowPanelControl[];
    instrument?: string;
    metadata: Record<string, unknown>;
}
export type FlowCytometryPanelTemplate = BioTemplateEnvelope<FlowCytometryPanelTemplateData>;
export type InstrumentRunItemKind = 'sample' | 'blank' | 'qc' | 'standard' | 'calibration' | 'wash' | 'other';
export type InstrumentRunStatus = 'planned' | 'queued' | 'running' | 'completed' | 'failed' | 'skipped';
export interface InstrumentMethod {
    id: string;
    name: string;
    instrument?: string;
    acquisitionMode?: string;
    metadata?: Record<string, unknown>;
}
export interface InstrumentRunItem {
    id: string;
    order: number;
    kind: InstrumentRunItemKind;
    sampleId?: string;
    name?: string;
    methodId: string;
    vial?: string;
    plateId?: string;
    wellId?: string;
    injectionVolume?: number;
    expectedDurationMin?: number;
    status: InstrumentRunStatus;
    metadata?: Record<string, unknown>;
}
export interface InstrumentRunTemplateData {
    runId: string;
    instrument?: string;
    methods: InstrumentMethod[];
    items: InstrumentRunItem[];
    metadata: Record<string, unknown>;
}
export type InstrumentRunTemplate = BioTemplateEnvelope<InstrumentRunTemplateData>;
export type InstrumentMethodInput = Partial<InstrumentMethod> & {
    name?: string;
};
export type InstrumentRunItemInput = Partial<InstrumentRunItem> & {
    name?: string;
    sampleId?: string;
};
export type DataFrameTemplate = SampleSheetTemplate | SamplePrepTemplate | CalibrationCurveTemplate | TimeCourseTemplate | ProtocolStepsTemplate | AssayMatrixTemplate | ReagentListTemplate | FlowCytometryPanelTemplate | InstrumentRunTemplate | QpcrPlateTemplate;
export type { QpcrChemistry, QpcrControlKind, QpcrPlateTemplate, QpcrPlateTemplateData, QpcrReaction, QpcrSample, QpcrTarget, } from './templateQpcrTypes';
export type { CreateAssayMatrixTemplateOptions, CreateBioTemplatePackCollectionOptions, CreateCalibrationCurveTemplateOptions, CreateDoseResponseTemplateOptions, CreateElisaAssayCollectionOptions, CreateFlowCytometryAssayCollectionOptions, CreateFlowCytometryPanelTemplateOptions, CreateInstrumentRunTemplateOptions, CreateLcmsBatchCollectionOptions, CreatePlateMapTemplateOptions, CreateProtocolStepsTemplateOptions, CreateQpcrExpressionCollectionOptions, CreateQpcrPlateTemplateOptions, CreateReagentListTemplateOptions, CreateSamplePrepTemplateOptions, CreateSampleSheetTemplateOptions, CreateTargetedMetabolomicsCollectionOptions, CreateTimeCourseTemplateOptions, CreateWellPlateScreenCollectionOptions, CreateWesternBlotAssayCollectionOptions, } from './templateCreateOptions';
export type { AssayMatrixColumnsAdapterResult, AssayMatrixDataFrameAdapterResult, AssayMatrixRowsAdapterResult, AssayMatrixSampleOptionsAdapterResult, CalibrationCurveColumnsAdapterResult, CalibrationCurveDataFrameAdapterResult, CalibrationCurveRowsAdapterResult, DataFrameAdapterResult, DoseConditionsAdapterResult, FlowPanelColumnsAdapterResult, FlowPanelDataFrameAdapterResult, FlowPanelRowsAdapterResult, InstrumentRunColumnsAdapterResult, InstrumentRunDataFrameAdapterResult, InstrumentRunRowsAdapterResult, InstrumentRunScheduleEventsAdapterResult, InstrumentRunStepsAdapterResult, PlateMapEditorAdapterResult, ProtocolColumnsAdapterResult, ProtocolDataFrameAdapterResult, ProtocolRowsAdapterResult, ProtocolStepsAdapterResult, QpcrColumnsAdapterResult, QpcrDataFrameAdapterResult, QpcrRowsAdapterResult, QpcrWellMapAdapterResult, ReagentColumnsAdapterResult, ReagentDataFrameAdapterResult, ReagentListItemsAdapterResult, ReagentRowsAdapterResult, SampleColumnsAdapterResult, SampleDataFrameAdapterResult, SampleOptionsAdapterResult, SamplePrepColumnsAdapterResult, SamplePrepDataFrameAdapterResult, SamplePrepRowsAdapterResult, SampleRowsAdapterResult, TemplateDataFrameAdapterResult, TimeCourseColumnsAdapterResult, TimeCourseDataFrameAdapterResult, TimeCourseRowsAdapterResult, TimeCourseStepsAdapterResult, WellMapAdapterResult, } from './templateAdapterTypes';