import { SampleGroup } from './components';
import { TreeNode } from './componentLabTypes';
export type OutlierAction = 'include' | 'exclude' | 'qc';
export type InputMode = 'paste' | 'csv' | 'experiment';
export interface OutlierInfo {
    sample: string;
    index: number;
    fieldCount: number;
    action: OutlierAction;
}
export interface MetadataRow {
    sampleName: string;
    fields: Record<string, string>;
    group: string;
}
export interface ParsedCsvData {
    columns: string[];
    rows: Record<string, string>[];
    sampleColumn: string;
    delimiter: string;
}
export type SampleClassKind = 'biological' | 'iqc' | 'eqc' | 'standard' | 'spike-in' | 'stock' | 'blank' | 'unknown';
export type ClassDisposition = 'group' | 'overlay' | 'exclude';
export interface SampleClass {
    kind: SampleClassKind;
    label: string;
    subKind?: string;
    members: number[];
    classTagPositions: number[];
    disposition: ClassDisposition;
    /**
     * Token count shared by every member of this class. Set by `splitByTokenLength`
     * after type classification so that samples with different field counts never
     * share a schema — column index N then means the same field for every member.
     */
    tokenLength?: number;
}
export type ColumnRole = 'constant' | 'factor' | 'replicate' | 'run-order' | 'id' | 'numeric' | 'class-tag' | 'ignore';
export interface NumericParse {
    value: number;
    unit: string;
    raw: string;
}
export interface NumericBinning {
    mode: 'discrete' | 'binned';
    edges?: number[];
    labels?: string[];
}
export interface ValueOps {
    alias?: Record<string, string>;
    exclude?: string[];
}
export interface ColumnInfo {
    index: number;
    name: string;
    sourceIndices: number[];
    uniqueValues: string[];
    cardinality: number;
    /** Legacy field, retained alongside `role` during the shim window. */
    type?: 'prefix' | 'suffix';
    role?: ColumnRole;
    numeric?: {
        byValue: Record<string, NumericParse>;
    };
    binning?: NumericBinning;
    ops?: ValueOps;
    /** Original CSV column header — used for row lookups when name is renamed */
    originalName?: string;
    displayName?: string;
}
export interface ClassSchema {
    classKind: SampleClassKind;
    subKind?: string;
    /** Token count of the class this schema describes. Distinguishes schemas that
     *  share a (kind, subKind) but were split apart by token-length. */
    tokenLength?: number;
    columns: ColumnInfo[];
    groupBy: number[];
    replicateColumn?: number;
}
export interface MergeSuggestion {
    classKind: SampleClassKind;
    subKind?: string;
    columnIndices: number[];
    proposedName: string;
    confidence: number;
}
export interface AutoGroupResult {
    /** All emitted groups, experimental + overlay concatenated for source compat. */
    groups: SampleGroup[];
    /** Class disposition === 'group' only. */
    experimentalGroups?: SampleGroup[];
    /** Class disposition === 'overlay' only. */
    qcGroups?: SampleGroup[];
    metadata: MetadataRow[];
    excludedSamples: string[];
    schemas?: ClassSchema[];
    fingerprint?: SchemaFingerprint;
    /**
     * Experimental (disposition === 'group') classes as a nested hierarchy:
     * one root per class, then one level per enabled groupBy column, then the
     * sample leaves. Parent nodes carry a sample-count `badge`; leaves carry the
     * sample name plus the detected injection number (`metadata.injection` and as
     * the leaf badge). Renders directly in `SampleHierarchyTree`.
     */
    groupTree?: TreeNode[];
}
export interface SchemaFingerprint {
    version: 1;
    classes: Array<{
        kind: SampleClassKind;
        subKind?: string;
        tokenLength?: number;
        columns: Array<{
            name: string;
            role: ColumnRole;
            sourceIndices: number[];
            binning?: NumericBinning;
            ops?: ValueOps;
        }>;
        groupBy: number[];
    }>;
}