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

"""
Encoding Skill - Comprehensive encoding capability bundle.

Provides:
- Quaternary encoding
- Balanced GC encoding
- Run-length limited encoding
- Triplet encoding
- Streaming support
"""

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


@dataclass
class EncodingSkill:
    """
    VibeDNA Encoding Skill.

    Comprehensive skill for binary-to-DNA encoding operations.
    """

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

    capabilities: List[str] = field(default_factory=lambda: [
        "quaternary_encoding",
        "balanced_gc_encoding",
        "rll_encoding",
        "triplet_encoding",
        "streaming_encoding",
        "header_generation",
        "block_management",
    ])

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

## Encoding Fundamentals

### Quaternary Mapping
The foundation of VibeDNA encoding maps 2 bits to each nucleotide:
- 00 → A (Adenine)
- 01 → T (Thymine)
- 10 → C (Cytosine)
- 11 → G (Guanine)

### Encoding Process
1. **Input Validation**: Verify binary data integrity
2. **Binary Conversion**: Convert bytes to binary string
3. **Scheme Application**: Apply selected encoding scheme
4. **Block Formation**: Chunk into 1024-nucleotide blocks
5. **Header Addition**: Prepend 256-nucleotide header
6. **Footer Addition**: Append 32-nucleotide footer

### Scheme Selection Guide
| Use Case | Recommended Scheme |
|----------|-------------------|
| Maximum density | quaternary |
| DNA synthesis | balanced_gc |
| Sequencing accuracy | rll |
| Error tolerance | triplet |

## Code Templates

```python
# Basic encoding
from vibedna import DNAEncoder

encoder = DNAEncoder()
result = encoder.encode(data, scheme="quaternary")

# With custom config
from vibedna import EncodingConfig, EncodingScheme

config = EncodingConfig(
    scheme=EncodingScheme.BALANCED_GC,
    add_error_correction=True
)
encoder = DNAEncoder(config)
result = encoder.encode(data)
```

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

    @classmethod
    def get_scheme_info(cls) -> Dict[str, Dict[str, Any]]:
        """Get information about available encoding schemes."""
        return {
            "quaternary": {
                "name": "Quaternary",
                "density": 2.0,
                "description": "2 bits per nucleotide, maximum density",
                "mapping": {"00": "A", "01": "T", "10": "C", "11": "G"},
                "use_case": "Maximum storage density",
            },
            "balanced_gc": {
                "name": "Balanced GC",
                "density": 1.9,
                "description": "Rotating mapping to maintain 40-60% GC content",
                "use_case": "DNA synthesis compatibility",
            },
            "rll": {
                "name": "Run-Length Limited",
                "density": 1.7,
                "description": "Inserts spacers to prevent homopolymer runs > 3",
                "use_case": "Sequencing accuracy",
            },
            "triplet": {
                "name": "Redundant Triplet",
                "density": 0.67,
                "description": "Each bit encoded as 3 nucleotides for redundancy",
                "mapping": {"0": "ATC", "1": "GAC"},
                "use_case": "Maximum error tolerance",
            },
        }
