import { Command } from 'commander';
/**
 * DNALang Ultimate Runtime
 * The core engine for multi-agent evolution and phase-conjugate intelligence
 */
export declare class DNALangRuntime {
    private agents;
    private genes;
    private organisms;
    constructor();
    /**
     * Create a new genetic agent
     */
    createAgent(name: string, config: AgentConfig): Agent;
    /**
     * Evolve an agent through mutation
     */
    evolveAgent(agentName: string, mutations: Mutation[]): EvolutionResult;
    /**
     * Create a new organism from agents
     */
    createOrganism(name: string, agents: Agent[]): Organism;
    /**
     * Apply phase conjugation to reverse evolution
     */
    phaseConjugate(organismName: string, steps?: number): ConjugationResult;
    /**
     * Get runtime statistics
     */
    getStats(): RuntimeStats;
}
/**
 * Agent class representing an individual AI entity
 */
export declare class Agent {
    name: string;
    config: AgentConfig;
    genes: Gene[];
    constructor(name: string, config: AgentConfig, genes?: Gene[]);
    evolve(mutations: Mutation[]): EvolutionResult;
    private applyMutation;
}
/**
 * Gene class representing hereditable traits
 */
export declare class Gene {
    name: string;
    sequence: string;
    traits: GeneTraits;
    constructor(name: string, sequence: string, traits: GeneTraits);
    mutate(): Gene;
    conjugate(): Gene;
    private applyRandomMutation;
    private reverseSequence;
}
/**
 * Organism class representing a collection of cooperating agents
 */
export declare class Organism {
    name: string;
    agents: Agent[];
    genome: Genome;
    constructor(name: string, agents: Agent[], genome?: Genome);
    conjugate(steps: number): ConjugationResult;
}
/**
 * Genome class representing the complete genetic makeup
 */
export declare class Genome {
    genes: Gene[];
    constructor(genes?: Gene[]);
}
export interface AgentConfig {
    type: string;
    capabilities: string[];
    learningRate: number;
}
export interface Mutation {
    type: 'insertion' | 'deletion' | 'substitution';
    position: number;
    value?: string;
}
export interface EvolutionResult {
    success: boolean;
    mutationsApplied: number;
    newGeneration: number;
}
export interface ConjugationResult {
    success: boolean;
    stepsReversed: number;
    agentsAffected: number;
}
export interface RuntimeStats {
    agents: number;
    genes: number;
    organisms: number;
    timestamp: string;
}
export interface GeneTraits {
    stability: number;
    expressiveness: number;
    adaptability: number;
}
export declare function createCLI(): Command;
export default DNALangRuntime;