# SQLDNAEncoder Class

---

## Overview
The `SQLDNAEncoder` class provides a SQLite-based storage system for encoding, storing, and retrieving biological data (e.g., DNA sequences) in a structured manner. It supports various operations such as storing, retrieving, deleting, and copying data, as well as interfacing with different hardware protocols (Serial, IP, OPC UA, and USB) for DNA sequencing and CRISPR operations.

---

## Class Definition

```python
class SQLDNAEncoder:
    def __init__(self, db_name='dna_database.db'):
        """
        Initialize a new SQLDNAEncoder object.
        :param db_name: Name of the SQLite database file
        """
        ...
```

---

## Attributes

| Attribute | Type | Description |
|-----------|------|-------------|
| `db_name` | `str` | Name of the SQLite database file. |
| `conn` | `sqlite3.Connection` | SQLite database connection. |
| `cursor` | `sqlite3.Cursor` | Database cursor for executing SQL commands. |

---

## Methods

### Initialization and Database Management
- **`__init__(self, db_name='dna_database.db')`**
  Initializes a new `SQLDNAEncoder` instance with the specified database name.

- **`_connect(self) -> sqlite3.Connection`**
  Establishes a connection to the SQLite database.

- **`create_table(self)`**
  Creates the `dna_data` table if it does not already exist.

- **`close(self)`**
  Closes the database connection.

- **`__enter__(self)`**
  Enables the use of the class as a context manager.

- **`__exit__(self, exc_type, exc_val, exc_tb)`**
  Ensures the database connection is closed when exiting the context.

---

### Data Encoding and Decoding
- **`_text_to_base64(self, text: str) -> str`**
  Converts a text string to a Base64-encoded string.

- **`_base64_to_text(self, base64_data: str) -> str`**
  Converts a Base64-encoded string back to the original text.

- **`generate_unique_key(self) -> str`**
  Generates a unique key using UUID.

---

### Data Storage and Retrieval
- **`store_data(self, data_name: str, data: dict)`**
  Stores data in the database after encoding it into a DNA sequence.

- **`retrieve_data(self, data_name: str) -> dict`
  Retrieves and decodes data from the database.

- **`retrieve_dna(self, data_name: str) -> str`**
  Retrieves the raw DNA sequence associated with a data name.

- **`list_stored_data(self) -> List[str]`**
  Lists all stored data names in the database.

- **`delete_data(self, data_name: str)`**
  Deletes data from the database.

---

### Database Operations
- **`copy(self, new_db_name: str)`**
  Copies the current database to a new SQLite database file.

---

### Hardware Interface Methods

#### Serial Interface
- **`serial_insert_dna_data(self, data_name: str, dna: DNA, port: str, baudrate: int, timeout: int, guide_rna: str, occurrence: int = 1)`**
  Inserts new DNA data using a serial CRISPR device.

- **`serial_delete_dna_data(self, data_name: str, port: str, baudrate: int, timeout: int, guide_rna: str, occurrence: int = 1)`**
  Deletes DNA data using a serial CRISPR device.

- **`serial_replace_dna_data(self, data_name: str, new_dna: DNA, port: str, baudrate: int, timeout: int, guide_rna: str, occurrence: int = 1)`**
  Replaces DNA data using a serial CRISPR device.

- **`serial_analyze_dna_data(self, data_name: str, port: str)`**
  Analyzes DNA data using a serial DNA sequencer.

---

#### IP Interface
- **`ip_analyze_dna_data(self, data_name: str, ip_address: str)`**
  Analyzes DNA data using an IP-based DNA sequencer.

- **`ip_replace_dna_data(self, data_name: str, new_dna: DNA, ip_address: str, guide_rna: str)`**
  Replaces DNA data using an IP-based CRISPR device.

- **`ip_delete_dna_data(self, data_name: str, ip_address: str, guide_rna: str)`**
  Deletes DNA data using an IP-based CRISPR device.

- **`ip_insert_dna_data(self, data_name: str, new_dna: DNA, ip_address: str, guide_rna: str)`**
  Inserts DNA data using an IP-based CRISPR device.

---

#### OPC UA Interface
- **`opcua_analyze_dna_data(self, data_name: str, ip_address: str)`**
  Analyzes DNA data using an OPC UA-based DNA sequencer.

- **`opcua_replace_dna_data(self, data_name: str, new_dna: DNA, ip_address: str, guide_rna: str)`**
  Replaces DNA data using an OPC UA-based CRISPR device.

- **`opcua_delete_dna_data(self, data_name: str, ip_address: str, guide_rna: str)`**
  Deletes DNA data using an OPC UA-based CRISPR device.

- **`opcua_insert_dna_data(self, data_name: str, new_dna: DNA, ip_address: str, guide_rna: str)`**
  Inserts DNA data using an OPC UA-based CRISPR device.

---

#### USB Interface
- **`usb_analyze_dna_data(self, data_name: str, product_id: int, vendor_id: int)`**
  Analyzes DNA data using a USB-based DNA sequencer.

- **`usb_replace_dna_data(self, data_name: str, new_dna: DNA, product_id: int, vendor_id: int, guide_rna: str)`**
  Replaces DNA data using a USB-based CRISPR device.

- **`usb_delete_dna_data(self, data_name: str, product_id: int, vendor_id: int, guide_rna: str)`**
  Deletes DNA data using a USB-based CRISPR device.

- **`usb_insert_dna_data(self, data_name: str, new_dna: DNA, product_id: int, vendor_id: int, guide_rna: str)`**
  Inserts DNA data using a USB-based CRISPR device.

---

## Example Usage

```python
# Initialize the SQLDNAEncoder
encoder = SQLDNAEncoder(db_name='example.db')

# Store data
data = {"sequence": "ATGCGATCG", "description": "Example DNA sequence"}
encoder.store_data("example_dna", data)

# Retrieve data
retrieved_data = encoder.retrieve_data("example_dna")
print(retrieved_data)

# List stored data
stored_data = encoder.list_stored_data()
print(stored_data)

# Delete data
encoder.delete_data("example_dna")

# Copy database
encoder.copy("example_copy.db")

# Serial interface example
dna = DNA("ATGCGATCG")
encoder.serial_insert_dna_data("serial_dna", dna, port="/dev/ttyUSB0", baudrate=9600, timeout=1, guide_rna="GUIDE")

# IP interface example
encoder.ip_analyze_dna_data("ip_dna", ip_address="192.168.1.1")

# Close the encoder
encoder.close()
```

---

## Dependencies
- **`sqlite3`**: For SQLite database operations.
- **`json`**: For JSON serialization and deserialization.
- **`uuid`**: For generating unique keys.
- **`base64`**: For encoding and decoding data.
- **`DNA`**: Class representing DNA sequences.
- **`SerialDNASequencer`, `SerialCRISPR`**: Classes for serial communication with DNA sequencers and CRISPR devices.
- **`IpDNASequencer`, `IpCRISPR`**: Classes for IP-based communication with DNA sequencers and CRISPR devices.
- **`DNASequencerOpcua`, `OpcuaCRISPR`**: Classes for OPC UA-based communication with DNA sequencers and CRISPR devices.
- **`UsbDNASequencer`, `UsbCRISPR`**: Classes for USB-based communication with DNA sequencers and CRISPR devices.

---

## Error Handling
- **Database Errors**: Errors during database operations are propagated to the caller.
- **Data Integrity**: The class checks for data integrity using unique keys.
- **Connection Errors**: Errors during hardware communication are caught and logged.

---

## Notes
- The `SQLDNAEncoder` class is designed to be used as a context manager, ensuring that database connections are properly closed.
- The class supports multiple hardware interfaces for DNA sequencing and CRISPR operations, making it versatile for different experimental setups.
