/**
 * Pure cohort logic for SmartGroupManual (the "manual" grouping mode).
 *
 * Mirrors the design prototype's selection-first model: a flat list of samples,
 * each optionally assigned to a group / subgroup / sub-subgroup, derived into a
 * three-level cohort tree for the right rail. Framework-free for unit testing.
 */
/** A sample with its (optional) manual cohort assignment. */
export interface ManualSample {
    name: string;
    group: string | null;
    sub: string | null;
    sub2: string | null;
    color: string | null;
}
/** Which slice of the sample list is shown. */
export type ManualFilter = 'all' | 'unassigned' | 'assigned';
/** A sample paired with its index in the source list (so the UI can toggle it). */
export interface ManualMatch {
    sample: ManualSample;
    index: number;
}
/** Second-level subgroup node: a sub-subgroup name → count map. */
export interface CohortSubNode {
    total: number;
    subs2: Map<string, number>;
}
/** Top-level cohort node: colour, total, and its subgroups. */
export interface CohortNode {
    color: string | null;
    total: number;
    subs: Map<string, CohortSubNode>;
}
/** The assignment values applied to a selection. */
export interface CohortAssignment {
    grp: string;
    sub: string;
    sub2: string;
    color: string;
}
/**
 * Build the group → subgroup → sub-subgroup tree from assigned samples.
 * Unassigned samples are ignored. Missing sub/sub2 values collapse to `—`.
 */
export declare function buildCohortTree(samples: ManualSample[]): Map<string, CohortNode>;
/** Filter the sample list by a case-insensitive name query and assignment state. */
export declare function filterSamples(samples: ManualSample[], query: string, filter: ManualFilter): ManualMatch[];
/**
 * Apply a cohort assignment to the selected sample indices, returning a new list.
 * Blank subgroup / sub-subgroup values become `null`.
 */
export declare function assignSamples(samples: ManualSample[], selected: ReadonlySet<number>, assignment: CohortAssignment): ManualSample[];