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Implementation Plan for Enhancing Scientific Rigor and Web-based Local Launch for DNA Analyzer

1. Enhancing Scientific Rigor in the Codebase

1.1. Code Review and Algorithm Validation

  • Review all scientific algorithms, focusing especially on reading frame analysis and Poisson calculations.
  • Validate mathematical formulas and add inline documentation with references to relevant literature.
  • Integrate assertions and input validations in critical scientific functions to ensure reliable outputs.

1.2. Documentation and Testing

  • Improve inline documentation within source files (e.g., PoissonCalculator.java, ReadingFrameAnalyzer.java).
  • Update research and architecture documentation under docs/research and docs/architecture to detail the implemented algorithms and their theoretical basis.
  • Enhance unit tests (in src/test) to cover edge cases and verify the robustness of scientific processing.

1.3. Error Handling and Logging

  • Incorporate robust error handling for invalid or unexpected parameters.
  • Add detailed logging in scientific modules to aid in troubleshooting and validating the analysis process.

2. Updating the Website for Local DNA Analyzer Integration

2.1. UI Updates

  • Modify web/index.html to include:
    • An input field for the user to provide the file path of the DNA file to analyze.
    • A set of checkboxes for selecting command line features (e.g., "Verbose Mode", "Detailed Report", "Quick Analysis").
    • A "Run Analysis" button to initiate the process.

2.2. JavaScript Connector Implementation

  • Create a new JavaScript file (e.g., web/index.js) that will:
    • Capture the user’s input and selected options.
    • Send an AJAX/WebSocket request to the local DNA Analyzer service, assumed to be running on http://localhost:8080.
    • Process and display the results or errors returned from the local service.

2.3. Integration Details

  • Assume that the local DNA Analyzer application exposes an HTTP API endpoint to handle analysis requests.
  • Update web/style.css if necessary to style the new form elements.
  • Ensure that the website interface seamlessly connects to the local application by properly handling CORS or other local network restrictions.

3. Next Steps and Testing

  • Implement the above changes in a local development environment.
  • Perform integration testing to confirm that the scientific enhancements and website functionality work as expected.
  • Update user documentation to guide end users on how to operate the new local connection feature.

This plan incorporates necessary assumptions to enhance the scientific rigor of the current codebase and integrate the full DNA Analyzer application into the website. The next logical step is to proceed with implementing these changes.