oxirs_core/molecular/

replication.rs

//! DNA replication machinery for data copying and validation

use super::dna_structures::{NucleotideData, SpecialMarker};
use crate::error::OxirsResult;
use serde::{Deserialize, Serialize};
use std::time::{Duration, Instant};

/// Replication machinery for data copying
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct ReplicationMachinery {
    /// DNA polymerase for strand synthesis
    pub polymerase: DnaPolymerase,
    /// Helicase for strand unwinding
    pub helicase: Helicase,
    /// Ligase for strand joining
    pub ligase: Ligase,
    /// Primase for primer synthesis
    pub primase: Primase,
    /// Proofreading system
    pub proofreading: ProofreadingSystem,
}

/// DNA polymerase for data synthesis
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct DnaPolymerase {
    /// Synthesis rate (nucleotides per second)
    pub synthesis_rate: f64,
    /// Error rate (errors per nucleotide)
    pub error_rate: f64,
    /// Processivity (nucleotides before dissociation)
    pub processivity: usize,
    /// Current position
    pub position: usize,
}

/// Helicase for strand unwinding
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct Helicase {
    /// Unwinding rate (base pairs per second)
    pub unwinding_rate: f64,
    /// Energy consumption (ATP per base pair)
    pub energy_consumption: f64,
    /// Current position
    pub position: usize,
}

/// Ligase for joining DNA fragments
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct Ligase {
    /// Ligation efficiency
    pub efficiency: f64,
    /// Energy requirement
    pub energy_requirement: f64,
}

/// Primase for primer synthesis
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct Primase {
    /// Primer length
    pub primer_length: usize,
    /// Synthesis rate
    pub synthesis_rate: f64,
}

/// Proofreading system for error detection and correction
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct ProofreadingSystem {
    /// Exonuclease activity for error removal
    pub exonuclease: ExonucleaseActivity,
    /// Mismatch detector
    pub mismatch_detector: MismatchDetector,
    /// Error correction efficiency
    pub correction_efficiency: f64,
    /// Detection threshold
    pub detection_threshold: f64,
}

/// Exonuclease activity for error correction
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct ExonucleaseActivity {
    /// Activity level (0.0 - 1.0)
    pub activity_level: f64,
    /// Direction (3' to 5' or 5' to 3')
    pub direction: ExonucleaseDirection,
}

/// Exonuclease direction
#[derive(Debug, Clone, Serialize, Deserialize)]
pub enum ExonucleaseDirection {
    ThreePrimeToFivePrime,
    FivePrimeToThreePrime,
}

/// Mismatch detector for finding replication errors
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct MismatchDetector {
    /// Detection accuracy
    pub accuracy: f64,
    /// Scanning speed
    pub scanning_speed: f64,
    /// False positive rate
    pub false_positive_rate: f64,
    /// Last scan time
    #[serde(skip)]
    pub last_scan: Option<Instant>,
}

impl Default for MismatchDetector {
    fn default() -> Self {
        Self {
            accuracy: 0.95,
            scanning_speed: 1000.0,
            false_positive_rate: 0.01,
            last_scan: None,
        }
    }
}

impl ReplicationMachinery {
    /// Create new replication machinery with default settings
    pub fn new() -> Self {
        Self {
            polymerase: DnaPolymerase::new(),
            helicase: Helicase::new(),
            ligase: Ligase::new(),
            primase: Primase::new(),
            proofreading: ProofreadingSystem::new(),
        }
    }

    /// Replicate a DNA strand
    pub fn replicate_strand(
        &mut self,
        template: &[NucleotideData],
    ) -> OxirsResult<Vec<NucleotideData>> {
        let mut new_strand = Vec::with_capacity(template.len());

        // Initialize replication
        self.helicase.unwind_start()?;

        // Synthesize primer
        let primer = self.primase.synthesize_primer()?;
        new_strand.extend(primer);

        // Main synthesis loop
        for (i, nucleotide) in template.iter().enumerate() {
            self.helicase.advance_position(i)?;

            // Synthesize complementary nucleotide
            let complement = self.polymerase.synthesize_complement(nucleotide)?;

            // Proofreading check
            if self.proofreading.should_proofread(i) {
                if let Some(corrected) = self
                    .proofreading
                    .check_and_correct(&complement, nucleotide)?
                {
                    new_strand.push(corrected);
                } else {
                    new_strand.push(complement);
                }
            } else {
                new_strand.push(complement);
            }

            // Update polymerase position
            self.polymerase.advance()?;
        }

        // Join any fragments
        self.ligase.join_fragments(&mut new_strand)?;

        Ok(new_strand)
    }

    /// Get replication statistics
    pub fn get_statistics(&self) -> ReplicationStatistics {
        ReplicationStatistics {
            polymerase_errors: self.polymerase.error_count(),
            proofreading_corrections: self.proofreading.correction_count(),
            total_nucleotides_synthesized: self.polymerase.nucleotides_synthesized(),
            replication_time: self.polymerase.total_time(),
            efficiency: self.calculate_efficiency(),
        }
    }

    /// Calculate overall replication efficiency
    fn calculate_efficiency(&self) -> f64 {
        let error_rate = self.polymerase.error_rate;
        let correction_efficiency = self.proofreading.correction_efficiency;

        (1.0 - error_rate) * correction_efficiency
    }
}

impl DnaPolymerase {
    /// Create new polymerase with high-fidelity settings
    pub fn new() -> Self {
        Self {
            synthesis_rate: 1000.0, // nucleotides per second
            error_rate: 1e-6,       // very low error rate
            processivity: 10000,    // high processivity
            position: 0,
        }
    }

    /// Synthesize complement of a nucleotide
    pub fn synthesize_complement(&self, template: &NucleotideData) -> OxirsResult<NucleotideData> {
        // Simulate synthesis time
        std::thread::sleep(Duration::from_nanos(
            (1_000_000_000.0 / self.synthesis_rate) as u64,
        ));

        let complement = match template {
            NucleotideData::Adenine(term) => NucleotideData::Thymine(term.clone()),
            NucleotideData::Thymine(term) => NucleotideData::Adenine(term.clone()),
            NucleotideData::Guanine(term) => {
                NucleotideData::Cytosine(SpecialMarker::Enhancer(term.to_string()))
            }
            NucleotideData::Cytosine(marker) => {
                // Handle special markers appropriately
                match marker {
                    SpecialMarker::StartCodon => NucleotideData::Cytosine(SpecialMarker::StopCodon),
                    SpecialMarker::StopCodon => NucleotideData::Cytosine(SpecialMarker::StartCodon),
                    _ => template.clone(), // Pass through other markers
                }
            }
        };

        Ok(complement)
    }

    /// Advance polymerase position
    pub fn advance(&mut self) -> OxirsResult<()> {
        self.position += 1;
        Ok(())
    }

    /// Get error count (simulation)
    pub fn error_count(&self) -> u64 {
        (self.position as f64 * self.error_rate) as u64
    }

    /// Get total nucleotides synthesized
    pub fn nucleotides_synthesized(&self) -> usize {
        self.position
    }

    /// Get total synthesis time
    pub fn total_time(&self) -> Duration {
        Duration::from_nanos((self.position as f64 / self.synthesis_rate * 1_000_000_000.0) as u64)
    }
}

impl Helicase {
    /// Create new helicase
    pub fn new() -> Self {
        Self {
            unwinding_rate: 500.0,   // base pairs per second
            energy_consumption: 2.0, // ATP per base pair
            position: 0,
        }
    }

    /// Start unwinding process
    pub fn unwind_start(&mut self) -> OxirsResult<()> {
        self.position = 0;
        Ok(())
    }

    /// Advance helicase position
    pub fn advance_position(&mut self, new_position: usize) -> OxirsResult<()> {
        // Simulate unwinding time
        let distance = new_position.saturating_sub(self.position);
        let unwind_time = distance as f64 / self.unwinding_rate;
        std::thread::sleep(Duration::from_nanos((unwind_time * 1_000_000_000.0) as u64));

        self.position = new_position;
        Ok(())
    }
}

impl Ligase {
    /// Create new ligase
    pub fn new() -> Self {
        Self {
            efficiency: 0.99,
            energy_requirement: 1.0,
        }
    }

    /// Join DNA fragments
    pub fn join_fragments(&self, _strand: &mut [NucleotideData]) -> OxirsResult<()> {
        // Simulate ligation process
        // In this simplified model, we just ensure strand continuity
        Ok(())
    }
}

impl Primase {
    /// Create new primase
    pub fn new() -> Self {
        Self {
            primer_length: 10,
            synthesis_rate: 100.0,
        }
    }

    /// Synthesize RNA primer
    pub fn synthesize_primer(&self) -> OxirsResult<Vec<NucleotideData>> {
        let mut primer = Vec::with_capacity(self.primer_length);

        // Create simple primer sequence
        for i in 0..self.primer_length {
            let nucleotide = match i % 4 {
                0 => NucleotideData::Cytosine(SpecialMarker::StartCodon),
                1 => NucleotideData::Adenine(crate::model::Term::NamedNode(
                    crate::model::NamedNode::new(format!("primer:{i}"))
                        .expect("primer IRI is valid"),
                )),
                2 => NucleotideData::Thymine(crate::model::Term::NamedNode(
                    crate::model::NamedNode::new(format!("primer:{i}"))
                        .expect("primer IRI is valid"),
                )),
                3 => NucleotideData::Guanine(crate::model::Term::NamedNode(
                    crate::model::NamedNode::new(format!("primer:{i}"))
                        .expect("primer IRI is valid"),
                )),
                _ => unreachable!(),
            };
            primer.push(nucleotide);
        }

        Ok(primer)
    }
}

impl ProofreadingSystem {
    /// Create new proofreading system
    pub fn new() -> Self {
        Self {
            exonuclease: ExonucleaseActivity::new(),
            mismatch_detector: MismatchDetector::new(),
            correction_efficiency: 0.99,
            detection_threshold: 0.95,
        }
    }

    /// Check if proofreading should be performed at this position
    pub fn should_proofread(&self, position: usize) -> bool {
        // Perform proofreading every 100 nucleotides or at random intervals
        position % 100 == 0 || fastrand::f64() < 0.01
    }

    /// Check for errors and correct if found
    pub fn check_and_correct(
        &self,
        synthesized: &NucleotideData,
        template: &NucleotideData,
    ) -> OxirsResult<Option<NucleotideData>> {
        if self
            .mismatch_detector
            .detect_mismatch(synthesized, template)?
        {
            // Attempt correction
            if fastrand::f64() < self.correction_efficiency {
                return self.correct_nucleotide(template).map(Some);
            }
        }
        Ok(None)
    }

    /// Correct a nucleotide based on template
    fn correct_nucleotide(&self, template: &NucleotideData) -> OxirsResult<NucleotideData> {
        // Generate correct complement
        match template {
            NucleotideData::Adenine(term) => Ok(NucleotideData::Thymine(term.clone())),
            NucleotideData::Thymine(term) => Ok(NucleotideData::Adenine(term.clone())),
            NucleotideData::Guanine(term) => Ok(NucleotideData::Cytosine(SpecialMarker::Enhancer(
                term.to_string(),
            ))),
            NucleotideData::Cytosine(_marker) => Ok(template.clone()),
        }
    }

    /// Get correction count (simulation)
    pub fn correction_count(&self) -> u64 {
        // Simplified simulation
        42
    }
}

impl Default for ExonucleaseActivity {
    fn default() -> Self {
        Self::new()
    }
}

impl ExonucleaseActivity {
    /// Create new exonuclease activity
    pub fn new() -> Self {
        Self {
            activity_level: 0.95,
            direction: ExonucleaseDirection::ThreePrimeToFivePrime,
        }
    }
}

impl MismatchDetector {
    /// Create new mismatch detector
    pub fn new() -> Self {
        Self {
            accuracy: 0.99,
            scanning_speed: 1000.0,
            false_positive_rate: 0.001,
            last_scan: None,
        }
    }

    /// Detect mismatch between two nucleotides
    pub fn detect_mismatch(
        &self,
        nucleotide1: &NucleotideData,
        nucleotide2: &NucleotideData,
    ) -> OxirsResult<bool> {
        // Simplified mismatch detection logic
        let is_mismatch = !self.is_valid_pair(nucleotide1, nucleotide2);

        // Apply detection accuracy and false positive rate
        if is_mismatch {
            Ok(fastrand::f64() < self.accuracy)
        } else {
            Ok(fastrand::f64() < self.false_positive_rate)
        }
    }

    /// Check if two nucleotides form a valid base pair
    fn is_valid_pair(&self, n1: &NucleotideData, n2: &NucleotideData) -> bool {
        matches!(
            (n1, n2),
            (NucleotideData::Adenine(_), NucleotideData::Thymine(_))
                | (NucleotideData::Thymine(_), NucleotideData::Adenine(_))
                | (NucleotideData::Guanine(_), NucleotideData::Cytosine(_))
                | (NucleotideData::Cytosine(_), NucleotideData::Guanine(_))
        )
    }
}

/// Replication statistics
#[derive(Debug, Clone)]
pub struct ReplicationStatistics {
    pub polymerase_errors: u64,
    pub proofreading_corrections: u64,
    pub total_nucleotides_synthesized: usize,
    pub replication_time: Duration,
    pub efficiency: f64,
}

impl Default for ReplicationMachinery {
    fn default() -> Self {
        Self::new()
    }
}

impl Default for DnaPolymerase {
    fn default() -> Self {
        Self::new()
    }
}

impl Default for Helicase {
    fn default() -> Self {
        Self::new()
    }
}

impl Default for Ligase {
    fn default() -> Self {
        Self::new()
    }
}

impl Default for Primase {
    fn default() -> Self {
        Self::new()
    }
}

impl Default for ProofreadingSystem {
    fn default() -> Self {
        Self::new()
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::model::Term;
    use crate::NamedNode;

    #[test]
    fn test_replication_machinery_creation() {
        let machinery = ReplicationMachinery::new();
        assert_eq!(machinery.polymerase.position, 0);
        assert_eq!(machinery.helicase.position, 0);
    }

    #[test]
    fn test_polymerase_complement_synthesis() {
        let polymerase = DnaPolymerase::new();
        let adenine = NucleotideData::Adenine(Term::NamedNode(
            NamedNode::new("http://example.org/test").expect("valid IRI"),
        ));

        if let Ok(NucleotideData::Thymine(_)) = polymerase.synthesize_complement(&adenine) {
            // Test passed
        } else {
            panic!("Expected Thymine complement for Adenine");
        }
    }

    #[test]
    fn test_mismatch_detection() {
        let detector = MismatchDetector::new();
        let adenine = NucleotideData::Adenine(Term::NamedNode(
            NamedNode::new("http://example.org/test1").expect("valid IRI"),
        ));
        let thymine = NucleotideData::Thymine(Term::NamedNode(
            NamedNode::new("http://example.org/test2").expect("valid IRI"),
        ));

        // This should generally not be detected as a mismatch (valid pair)
        let result = detector
            .detect_mismatch(&adenine, &thymine)
            .expect("operation should succeed");
        // Due to false positive rate, we can't assert exact result, but it should be boolean
        // Result is already boolean type, no need for tautology assertion
        let _ = result; // Confirm result is used
    }
}