# VibeDNA Error Correction Skill
# © 2026 VibeDNA powered by VibeCaaS.com a division of NeuralQuantum.ai LLC. All rights reserved.

"""
Error Correction Skill - Reed-Solomon error correction for DNA.

Provides:
- Reed-Solomon encoding in GF(4)
- Error detection and localization
- Mutation modeling
- Sequence repair
"""

from dataclasses import dataclass, field
from typing import Any, Dict, List


@dataclass
class ErrorCorrectionSkill:
    """
    VibeDNA Error Correction Skill.

    Comprehensive skill for DNA error detection and correction
    using Reed-Solomon codes adapted for quaternary encoding.
    """

    name: str = "vibedna-error-correction"
    version: str = "1.0.0"
    location: str = "/mnt/skills/vibedna/error-correction/SKILL.md"

    capabilities: List[str] = field(default_factory=lambda: [
        "reed_solomon_encoding",
        "reed_solomon_decoding",
        "syndrome_computation",
        "error_localization",
        "mutation_modeling",
    ])

    @staticmethod
    def get_skill_content() -> str:
        """Get the skill documentation content."""
        return """# VibeDNA Error Correction Skill

## Reed-Solomon for DNA

### GF(4) Field
DNA naturally operates in GF(4):
- Elements: {0, 1, α, α+1} = {A, T, C, G}
- Addition: XOR operation
- Multiplication: Defined by primitive polynomial

### Correction Capacity
With 16 parity nucleotides per block:
- Can detect up to 16 errors
- Can correct up to 8 errors

### Mutation Model
DNA has specific mutation patterns:
- Transitions (A↔G, T↔C): 70% probability
- Transversions (purine↔pyrimidine): 30% probability

## Implementation

```python
from vibedna.error_correction import DNAReedSolomon

# Initialize with 16 parity symbols (can correct 8 errors)
rs = DNAReedSolomon(nsym=16)

# Encoding: Add parity
protected = rs.encode(sequence)

# Decoding: Detect and correct errors
result = rs.decode(corrupted)
print(f"Corrected {result.errors_corrected} errors")
print(f"Positions: {result.error_positions}")
```

## Error Correction Workflow

1. Receive sequence with suspected errors
2. Compute Reed-Solomon syndromes
3. If syndromes all zero → no errors, return
4. Find error locator polynomial (Berlekamp-Massey)
5. Locate error positions (Chien search)
6. If errors > correction capacity:
   a. Apply mutation model for soft correction
   b. Flag as partially corrected
7. Apply Forney correction
8. Verify corrected sequence
9. Return with correction report

© 2026 VibeDNA powered by VibeCaaS.com a division of NeuralQuantum.ai LLC."""

    @classmethod
    def get_gf4_info(cls) -> Dict[str, Any]:
        """Get information about GF(4) arithmetic."""
        return {
            "field": "GF(4)",
            "elements": {
                "A": 0,
                "T": 1,
                "C": 2,  # α
                "G": 3,  # α + 1
            },
            "addition_table": [
                [0, 1, 2, 3],
                [1, 0, 3, 2],
                [2, 3, 0, 1],
                [3, 2, 1, 0],
            ],
            "multiplication_table": [
                [0, 0, 0, 0],
                [0, 1, 2, 3],
                [0, 2, 3, 1],
                [0, 3, 1, 2],
            ],
        }

    @classmethod
    def get_mutation_probabilities(cls) -> Dict[str, Dict[str, float]]:
        """Get mutation probability matrix."""
        return {
            "A": {"G": 0.7, "T": 0.15, "C": 0.15},
            "G": {"A": 0.7, "T": 0.15, "C": 0.15},
            "T": {"C": 0.7, "A": 0.15, "G": 0.15},
            "C": {"T": 0.7, "A": 0.15, "G": 0.15},
        }
