import { SampleClass, SampleClassKind } from '../../types/auto-group';
export interface ClassVocab {
    blankPattern: RegExp;
    iqcPattern: RegExp;
    eqcPattern: RegExp;
    standardPattern: RegExp;
    standardAllow: Set<string>;
    spikeInPattern: RegExp;
    stockPattern: RegExp;
    /**
     * Matrix lookup: lowercase token → canonical display name. Matching is
     * case-insensitive, and several aliases can collapse to one display name
     * (cell → Cells, medium → Medium).
     */
    matrixVocab: Map<string, string>;
    /** Lowercase polarity tokens → POS / NEG. */
    ionizationModes: Map<string, 'POS' | 'NEG'>;
    /** Lowercase tokens that flag the next token as the organ subKind. */
    tissueParentTokens: Set<string>;
}
export declare const classVocab: ClassVocab;
export interface DetectClassOptions {
    vocab?: Partial<ClassVocab>;
    /** Per-sample explicit `sample_type` hint (e.g. from experiment design data). */
    sampleTypeHints?: (string | undefined)[];
    /** Number of leading tokens that all samples share (`TokenizedBatch.sharedPrefix`). */
    sharedPrefix?: number;
}
/** A token that names a QC-type class (blank, QC, standard, spike-in, stock). */
export declare function isClassMarker(token: string, vocab?: ClassVocab): boolean;
/** Kinds that form experimental groups; all other kinds are QC-type overlay classes. */
export declare function isExperimentalKind(kind: SampleClassKind): boolean;
/** Classify each tokenized sample into a SampleClass. */
export declare function detectClass(tokenizedSamples: string[][], options: DetectClassOptions): SampleClass[];