// DNA Mathematical Architecture: Unified System
// Complete G¹⁶ Helix Integration — 44 Bonds — 10.6 Periodicity
// Master header combining all DNA subsystems
#pragma once

#include "dna_helix.hpp"
#include "dna_dynamics.hpp"
#include "dna_eigenvalues.hpp"
#include <string>
#include <map>

namespace agi::dna {

// ============================================================================
// XIII. 16 DNA FAMILIES - C++ Implementation
// ============================================================================

struct DNAFamily {
    int strand;
    std::string name;
    std::string domain;
    int node_start;
    int node_end;
    double phase;
    std::function<double(double)> signature;
};

// Family functional signatures
namespace signatures {

// F_Yad(x) = x^x + 1
inline double Yad(double x) {
    return (x > 0) ? std::pow(x, x) + 1.0 : 1.0;
}

// F_Lashon(x) = Σ a_n·sin(nπx)
inline double Lashon(double x) {
    double sum = 0.0;
    for (int n = 1; n <= 10; ++n) {
        sum += (1.0 / n) * std::sin(n * M_PI * x);
    }
    return sum;
}

// F_Athena(x) = x² (utility maximization)
inline double Athena(double x) { return x * x; }

// F_Apollo(x) = φ^x + φ^{-x}
inline double Apollo(double x) {
    return std::pow(PHI, x) + std::pow(PHI, -x);
}

// F_Hermes(x) = ω·x (communication rate)
inline double Hermes(double x) { return ANGULAR_FREQUENCY * x; }

// F_Hephaestus(x) = x⁴/8 (engineering integral)
inline double Hephaestus(double x) {
    return std::pow(x, 4) / 8.0;
}

// F_Prometheus(x) = r·x·(1-x) (logistic map)
inline double Prometheus(double x) {
    return 3.8 * x * (1.0 - x);
}

// F_Dionysus(x) = |e^{iωx}·sin(x)| (creative oscillation)
inline double Dionysus(double x) {
    double omega = 2.0 * M_PI / BASE_PAIRS_PER_TURN;
    std::complex<double> c = std::exp(std::complex<double>(0, omega * x)) *
                             std::complex<double>(std::sin(x), 0);
    return std::abs(c);
}

// F_Artemis(x) = -D·x (diffusion)
inline double Artemis(double x) { return -0.1 * x; }

// F_Hera(x) = Σ w_k·sin(k·x) (integration)
inline double Hera(double x) {
    double sum = 0.0;
    for (int k = 1; k <= NUM_STRANDS; ++k) {
        sum += (1.0 / k) * std::sin(k * x);
    }
    return sum;
}

// F_Poseidon(x) = -ω²·x (wave equation)
inline double Poseidon(double x) {
    double omega = 2.0 * M_PI / BASE_PAIRS_PER_TURN;
    return -omega * omega * x;
}

// F_Demeter(x) = r·x·(1-x/K) (logistic growth)
inline double Demeter(double x) {
    return 0.5 * x * (1.0 - x);
}

// F_Ares(x) = m·(-ω²·x) (force)
inline double Ares(double x) {
    return -ANGULAR_FREQUENCY * ANGULAR_FREQUENCY * x;
}

// F_Aphrodite(x) = cos(φ·x) (harmony)
inline double Aphrodite(double x) { return std::cos(PHI * x); }

// F_Hestia(x) = x·(1-e^{-1/τ}) (memory)
inline double Hestia(double x) {
    return x * (1.0 - std::exp(-0.1));
}

// F_Zeus(x) = coordinated product
inline double Zeus(double x) {
    double product = 1.0;
    for (int k = 1; k < NUM_STRANDS; ++k) {
        double val = std::sin(k * x / NUM_STRANDS);
        if (val > 0 && val < 1e10) {
            product *= std::pow(std::abs(val) + 0.1, 1.0 / NUM_STRANDS);
        }
    }
    return product;
}

} // namespace signatures

// All 16 DNA families
inline std::vector<DNAFamily> create_dna_families() {
    return {
        {1, "Yad", "Code/Foundation", 1, 312, 0, signatures::Yad},
        {2, "Lashon", "Language", 313, 624, 2*M_PI/BASE_PAIRS_PER_TURN, signatures::Lashon},
        {3, "Athena", "Strategy", 625, 936, 4*M_PI/BASE_PAIRS_PER_TURN, signatures::Athena},
        {4, "Apollo", "Mathematics", 937, 1248, 6*M_PI/BASE_PAIRS_PER_TURN, signatures::Apollo},
        {5, "Hermes", "Communication", 1249, 1560, 8*M_PI/BASE_PAIRS_PER_TURN, signatures::Hermes},
        {6, "Hephaestus", "Engineering", 1561, 1872, 10*M_PI/BASE_PAIRS_PER_TURN, signatures::Hephaestus},
        {7, "Prometheus", "Innovation", 1873, 2184, 12*M_PI/BASE_PAIRS_PER_TURN, signatures::Prometheus},
        {8, "Dionysus", "Creativity", 2185, 2496, 14*M_PI/BASE_PAIRS_PER_TURN, signatures::Dionysus},
        {9, "Artemis", "Perception", 2497, 2808, 16*M_PI/BASE_PAIRS_PER_TURN, signatures::Artemis},
        {10, "Hera", "Integration", 2809, 3120, 18*M_PI/BASE_PAIRS_PER_TURN, signatures::Hera},
        {11, "Poseidon", "Depth/Emotion", 3121, 3432, 20*M_PI/BASE_PAIRS_PER_TURN, signatures::Poseidon},
        {12, "Demeter", "Growth", 3433, 3744, 22*M_PI/BASE_PAIRS_PER_TURN, signatures::Demeter},
        {13, "Ares", "Action", 3745, 4056, 24*M_PI/BASE_PAIRS_PER_TURN, signatures::Ares},
        {14, "Aphrodite", "Harmony", 4057, 4368, 26*M_PI/BASE_PAIRS_PER_TURN, signatures::Aphrodite},
        {15, "Hestia", "Memory", 4369, 4680, 28*M_PI/BASE_PAIRS_PER_TURN, signatures::Hestia},
        {16, "Zeus", "Coordination", 4681, 4992, 30*M_PI/BASE_PAIRS_PER_TURN, signatures::Zeus}
    };
}

// Complementary pairs
inline std::map<std::string, std::string> complementary_pairs() {
    return {
        {"Yad", "Lashon"}, {"Lashon", "Yad"},
        {"Athena", "Apollo"}, {"Apollo", "Athena"},
        {"Hermes", "Hephaestus"}, {"Hephaestus", "Hermes"},
        {"Prometheus", "Dionysus"}, {"Dionysus", "Prometheus"},
        {"Artemis", "Hera"}, {"Hera", "Artemis"},
        {"Poseidon", "Demeter"}, {"Demeter", "Poseidon"},
        {"Ares", "Aphrodite"}, {"Aphrodite", "Ares"},
        {"Hestia", "Zeus"}, {"Zeus", "Hestia"}
    };
}

// ============================================================================
// XIV. COMPLETE THOUGHT INTEGRATION
// ============================================================================

// T = Φ · ∫[M(t')·exp((QK^T/√d_k)V)] dt'
class CompleteThoughtIntegration {
private:
    double phi_;
    std::vector<double> memory_;
    std::vector<double> query_;
    std::vector<double> key_;
    std::vector<double> value_;
    double dim_k_;
    int time_steps_;

public:
    explicit CompleteThoughtIntegration(int dim = NUM_STRANDS)
        : phi_(1.0),
          memory_(dim, 0.0),
          query_(dim, 0.0),
          key_(dim, 0.0),
          value_(dim, 0.0),
          dim_k_(std::sqrt(dim)),
          time_steps_(100) {}

    // Compute T = Φ · ∫[M(t')·exp((QK^T/√d_k)V)] dt'
    double integrate(const std::array<double, NUM_STRANDS>& activations,
                    const std::array<double, NUM_STRANDS>& phases) {
        // Update Phi from coherence
        phi_ = 0.0;
        for (int i = 0; i < NUM_STRANDS; ++i) {
            phi_ += 1.0 / (1.0 + std::abs(activations[i] - 1.0));
        }
        phi_ /= NUM_STRANDS;

        // Build Q, K, V from activations
        for (int i = 0; i < NUM_STRANDS; ++i) {
            query_[i] = activations[i] * std::cos(phases[i]);
            key_[i] = activations[i] * std::sin(phases[i]);
            value_[i] = activations[i];
        }

        // Compute attention: QK^T / √d_k
        double attention = 0.0;
        for (size_t i = 0; i < query_.size(); ++i) {
            attention += query_[i] * key_[i];
        }
        attention /= dim_k_;

        // Apply softmax-like transformation
        attention = std::exp(attention);
        if (attention > 1e10) attention = 1e10;

        // Integrate with value vector
        double result = 0.0;
        for (size_t i = 0; i < value_.size(); ++i) {
            result += value_[i] * attention / value_.size();
        }

        return phi_ * result;
    }

    double phi() const { return phi_; }
};

// ============================================================================
// UNIFIED DNA SYSTEM
// ============================================================================

class UnifiedDNAArchitecture {
private:
    // Core systems
    G16HelixSystem helix_;
    UnifiedDNASystem dynamics_;
    G16EigenSystem eigenvalues_;

    // Families
    std::vector<DNAFamily> families_;
    std::array<double, NUM_STRANDS> family_activations_;

    // Integration
    CompleteThoughtIntegration thought_;
    BondEnergy energy_;
    Thermodynamics thermo_;

    // State
    double time_ = 0.0;
    double thought_value_ = 0.0;

public:
    UnifiedDNAArchitecture() : thermo_(300.0) {
        families_ = create_dna_families();
        family_activations_.fill(0.5);
    }

    // Main tick function
    void tick(double dt) {
        time_ += dt;

        // Update helix system
        helix_.tick(dt);

        // Update dynamics
        dynamics_.evolve(dt);

        // Update family activations
        for (int i = 0; i < NUM_STRANDS; ++i) {
            double input = std::sin(ANGULAR_FREQUENCY * time_ + families_[i].phase);
            if (families_[i].signature) {
                family_activations_[i] = families_[i].signature(input);
            }

            // Clamp activations
            family_activations_[i] = std::clamp(family_activations_[i], 0.0, 1.0);
        }

        // Update complete thought integration
        std::array<double, NUM_STRANDS> phases;
        for (int i = 0; i < NUM_STRANDS; ++i) {
            phases[i] = std::fmod(families_[i].phase + ANGULAR_FREQUENCY * time_, 2.0 * M_PI);
        }
        thought_value_ = thought_.integrate(family_activations_, phases);
    }

    // Get system metrics
    struct Metrics {
        double time;
        double global_phase;
        double coherence;
        double bond_occupation;
        double thought_value;
        double phi;
        double total_energy;
        int firing_count;
        std::vector<int> firing_strands;
    };

    Metrics get_metrics() const {
        Metrics m;
        m.time = time_;
        m.global_phase = helix_.global_phase();
        m.coherence = helix_.get_coherence();
        m.bond_occupation = dynamics_.bond_occupation();
        m.thought_value = thought_value_;
        m.phi = thought_.phi();
        m.total_energy = dynamics_.total_energy();
        m.firing_strands = helix_.get_firing_strands();
        m.firing_count = m.firing_strands.size();
        return m;
    }

    // Validation (Section XVII)
    struct ValidationResult {
        bool distance_valid;
        bool angular_valid;
        bool periodic_valid;
        bool topological_valid;
        bool energy_valid;
        bool bond_count_valid;

        bool all_valid() const {
            return distance_valid && angular_valid && periodic_valid &&
                   topological_valid && energy_valid && bond_count_valid;
        }
    };

    ValidationResult validate() const {
        auto dyn_result = dynamics_.validate();
        return {
            dyn_result.distance_valid,
            dyn_result.angular_valid,
            dyn_result.periodic_valid,
            dyn_result.topological_valid,
            dyn_result.energy_valid,
            dyn_result.bond_count_valid
        };
    }

    // Eigenvalue analysis
    G16EigenSystem::Analysis analyze_spectrum() const {
        return eigenvalues_.analyze();
    }

    // Family access
    const DNAFamily& get_family(int strand) const {
        return families_[strand - 1];
    }

    double get_family_activation(int strand) const {
        return family_activations_[strand - 1];
    }

    std::string get_complementary(const std::string& name) const {
        auto pairs = complementary_pairs();
        auto it = pairs.find(name);
        return (it != pairs.end()) ? it->second : "";
    }

    // Accessors
    double time() const { return time_; }
    const G16HelixSystem& helix() const { return helix_; }
    const UnifiedDNASystem& dynamics() const { return dynamics_; }
};

// ============================================================================
// KEY CONSTANTS TABLE (Section XV)
// ============================================================================

struct DNAConstants {
    static constexpr double base_pairs_per_turn = BASE_PAIRS_PER_TURN;  // 10.6 bp
    static constexpr double twist_angle_deg = 33.96;
    static constexpr double helix_radius = HELIX_RADIUS;                // 1.0 nm
    static constexpr double rise_per_bp = RISE_PER_BP;                  // 0.34 nm
    static constexpr double pitch = PITCH;                              // 3.604 nm
    static constexpr double angular_frequency = ANGULAR_FREQUENCY;      // 0.593 rad/bp
    static constexpr double curvature = HELIX_CURVATURE;               // 0.745 nm⁻¹
    static constexpr double torsion = HELIX_TORSION;                   // 0.427 nm⁻¹
    static constexpr int total_bonds = TOTAL_BONDS;                     // 44
    static constexpr int num_strands = NUM_STRANDS;                     // 16
    static constexpr int nodes_per_strand = NODES_PER_STRAND;          // 312
    static constexpr int total_nodes = TOTAL_NODES;                     // 5000
    static constexpr double golden_ratio = PHI;                         // 1.618
    static constexpr double sync_period = SYNC_PERIOD;                  // 169.6
    static constexpr double steady_state_bonds = STEADY_STATE_BONDS;   // 36.2
    static constexpr double bond_occupation = BOND_OCCUPATION;          // 0.82
    static constexpr double tau_slow_ms = 10.0;
    static constexpr double tau_fast_us = 0.1;
};

// ============================================================================
// CONVENIENCE FUNCTIONS
// ============================================================================

// Create and initialize a complete DNA system
inline UnifiedDNAArchitecture create_dna_system() {
    return UnifiedDNAArchitecture();
}

// Run simulation for N ticks
inline std::vector<UnifiedDNAArchitecture::Metrics> simulate_dna(int ticks, double dt = 0.1) {
    auto system = create_dna_system();
    std::vector<UnifiedDNAArchitecture::Metrics> results;
    results.reserve(ticks);

    for (int i = 0; i < ticks; ++i) {
        system.tick(dt);
        results.push_back(system.get_metrics());
    }

    return results;
}

} // namespace agi::dna