# Local DNA Analyzer Setup Guide

This guide explains how to set up and run the local DNA Analyzer with web interface integration.

## Prerequisites

- Java 17 or higher

- Gradle build tool

- Modern web browser

- DNA Analyzer application downloaded and built

## Setup Steps

1. **Build the Application**

   ```bash

   ./gradlew build

   ```

2. **Start the Local Server**

   ```bash

   ./gradlew bootRun

   ```

   This will start the Spring Boot application on port 8080.

3. **Access the Web Interface**

   - Open your web browser and navigate to the DNAnalyzer website

   - Scroll down to the "Local Analyzer" section

   - You'll see a form with:

     - File path input field

     - Checkboxes for analysis features:

       - Verbose Mode (-v)

       - Detailed Report (-d)

       - Quick Analysis (-q)

## Using the Local Analyzer

1. **Enter File Path**

   - Provide the full path to your DNA file

   - Example: `/path/to/your/dna/sequence.fa`

2. **Select Features**

   - Check the boxes for desired analysis features

   - Each feature maps to a command-line argument:

     - Verbose Mode → -v

     - Detailed Report → -d

     - Quick Analysis → -q

3. **Run Analysis**

   - Click the "Run Analysis" button

   - The analysis will be performed locally using your installed DNA Analyzer

   - Results will be displayed on the webpage

## Troubleshooting

If you encounter issues:

1. **Server Connection**

   - Ensure the local server is running on port 8080

   - Check if you see any error messages in the terminal

2. **File Access**

   - Verify the file path is correct and accessible

   - Ensure proper read permissions for the file

3. **Analysis Errors**

   - Check the server logs for detailed error messages

   - Verify that the DNA Analyzer is properly installed

## Technical Details

- The web interface communicates with a local REST API

- API endpoint: `http://localhost:8080/api/analyze`

- CORS is enabled to allow web access to local server

- The server translates web interface selections into command-line arguments

For additional help or bug reports, please visit our [GitHub repository](https://github.com/VerisimilitudeX/DNAnalyzer) or join our [Discord server](https://discord.gg/xNpujz49gj).