Update Main.java

import edu.bu.ec504.project.Molecule;

import javax.imageio.ImageIO;

import javax.swing.*;

import java.awt.*;

import java.awt.event.*;

import java.io.*;

import java.net.ConnectException;

import java.net.ServerSocket;

import java.net.Socket;

import java.net.*;

import java.awt.image.BufferedImage;

import java.util.ArrayList;

public class Main {

public class GUI extends JFrame {

    private JTextArea outputTextArea;

    private JButton chooseFileButton;

    private JButton addMoleculeButton;

    private JButton findMoleculeButton;

    private JButton statisticsButton;

    private JButton displayMoleculeButton;

    private JButton findSubgraphButton;

    private JTextField filePathField;

    private static MDB moleculeDb;

    private Socket clientSocket;

    private PrintWriter writer;

    private BufferedReader reader;

    static MoleculeDatabase moleculeDb = null;

    static boolean verbose = false;

    /**

     * GUI constructor

     */

    public GUI() {

        // Set up the JFrame

        setTitle("Molecule Database");

        setDefaultCloseOperation(EXIT_ON_CLOSE);

        setLayout(new BorderLayout());

        getContentPane().setBackground(Color.BLACK);

    public static void initDb(String dbName) throws IOException {

        // Load the database

        moleculeDb = new MoleculeDatabase();

        File dbFile = new File(dbName);

        if (dbFile.exists()) {

            moleculeDb.load(dbName);

        }

    }

        // Create components

        outputTextArea = new JTextArea(20, 50); // the text area for all outputs

        outputTextArea.setBackground(Color.BLACK); // Set the background color of the text area

        outputTextArea.setForeground(Color.WHITE); // Set the text color

        JScrollPane scrollPane = new JScrollPane(outputTextArea);

        chooseFileButton = new JButton("Choose File");

        addMoleculeButton = new JButton("Add Molecule");

        findMoleculeButton = new JButton("Find Molecule");

        findSubgraphButton = new JButton("Find Subgraph");

        statisticsButton = new JButton("Database Statistics");

        displayMoleculeButton = new JButton("Display Molecule");

        filePathField = new JTextField(20); // to show the file path

        JLabel filePathLabel = new JLabel("File Path:");

        filePathLabel.setForeground(Color.WHITE); // Set the text color

        filePathField.setBackground(Color.WHITE); // Set the background color of the text field

        filePathField.setForeground(Color.BLACK); // Set the text color

    public static void printVerbose(String s) {

        if (verbose) {

            System.out.println(s);

        }

    }

        // Add components to the JFrame

        JPanel controlPanel = new JPanel();

        controlPanel.setBackground(Color.BLACK);

        controlPanel.add(chooseFileButton);

        controlPanel.add(addMoleculeButton);

        controlPanel.add(findMoleculeButton);

        controlPanel.add(findSubgraphButton);

        controlPanel.add(displayMoleculeButton);

        controlPanel.add(statisticsButton);

        controlPanel.add(filePathLabel);

        controlPanel.add(filePathField);

        add(controlPanel, BorderLayout.NORTH); // to show the control panel (e.g., buttons)

        add(scrollPane, BorderLayout.CENTER); // to show the printed output text area

    public static void commandHandler1(String cmd) {

        switch (cmd) {

            case "--printDb":

                moleculeDb.printDb();

                break;

            case "--verbose":

                if (verbose) {

                    System.out.println("verbose: true -> false");

                } else {

                    System.out.println("verbose: false -> true");

                }

                verbose = !verbose;

                moleculeDb.verbose = verbose;

                break;

            default:

                printVerbose("unrecognized command: " + cmd);

                break;

        // Initialize molecule database

        moleculeDb = new MDB(outputTextArea);

        // Action listener for Choose File button

        chooseFileButton.addActionListener(new ActionListener() {

            @Override

            public void actionPerformed(ActionEvent e) {

                // Create a file chooser

                JFileChooser fileChooser = new JFileChooser();

                fileChooser.setDialogTitle("Choose a file");

                int result = fileChooser.showOpenDialog(GUI.this);

                // If a file is selected, set its path in the molecule path field

                if (result == JFileChooser.APPROVE_OPTION) {

                    File selectedFile = fileChooser.getSelectedFile();

                    filePathField.setText(selectedFile.getAbsolutePath());

                }

            }

        });

    public static void commandHandler2(String cmd, String moleculePath) {

        switch (cmd) {

            case "--addMolecule":

        // Action listener for Add Molecule button

        addMoleculeButton.addActionListener(new ActionListener() {

            @Override

            public void actionPerformed(ActionEvent e) {

                // Get the molecule path from the text field

                String moleculePath = filePathField.getText();

                // Execute the addMolecule command

                moleculeDb.addMolecule(new Molecule(moleculePath));

                break;

            case "--findMolecule":

                // Display output

                outputTextArea.append("Molecule added: " + moleculePath + "\n\n");

            }

        });

        // Action listener for Find Molecule button

        findMoleculeButton.addActionListener(new ActionListener() {

            @Override

            public void actionPerformed(ActionEvent e) {

                // Get the molecule path from the text field

                String moleculePath = filePathField.getText();

                // Execute the findMolecule command

                Molecule molecule = moleculeDb.findMolecule(new Molecule(moleculePath));

                if (molecule == null) {

                    System.out.println("NO EXACT MATCH FOUND");

                    outputTextArea.append("NO EXACT MATCH FOUND" + "\n\n");

                    molecule= moleculeDb.similarMolecule(new Molecule(moleculePath));

                    if(molecule!=null)

                    {

                        System.out.println(molecule.moleculeName + " is the most similar");

                        // Perform most similar function

                        outputTextArea.append(molecule.moleculeName + " is the most similar" + "\n\n");

                    }

                } else {

                    printVerbose("FOUND");

                    outputTextArea.append("FOUND\n\n");

                }

                break;

            default:

                printVerbose("unrecognized command: " + cmd);

                break;

            }

        });

        // Action listener for Find Subgraph button

        findSubgraphButton.addActionListener(new ActionListener() {

            @Override

            public void actionPerformed(ActionEvent e) {

                String moleculePath = filePathField.getText();

                ArrayList<Molecule> mList = moleculeDb.findSubgraph(new Molecule(moleculePath));

                if (mList.isEmpty())

                    outputTextArea.append("No subraphs found" + "\n\n");

                else

                    for (Molecule m : mList)

                        outputTextArea.append("Subgraph found: " + m.moleculeName + "\n\n");

            }

        });

    /**

     * Method to run the client side of the program

     *

     * @param clientSocket

     * @param argument

     * @throws IOException

     */

    public static void runClient(Socket clientSocket, String argument) throws IOException {

        // Set up output stream to send data to the server

        OutputStream outStream = clientSocket.getOutputStream();

        PrintWriter writer = new PrintWriter(outStream);

        // Action listener for Display Molecule button

        displayMoleculeButton.addActionListener(new ActionListener() {

            @Override

            public void actionPerformed(ActionEvent e) {

        // Write the argument to the output stream

        writer.println(argument);

        writer.flush();

                // Get the API for the molecule

                String moleculePath = filePathField.getText();

                String moleculeName = null;

        // Close the streams

        writer.close();

        outStream.close();

                try (BufferedReader reader = new BufferedReader(new FileReader(moleculePath))) {

                    moleculeName = reader.readLine(); // Read the first line to get the molecule name

                } catch (IOException ex) {

                    System.err.println("Error reading the file: " + ex.getMessage());

                    outputTextArea.append("Error reading the file." + "\n\n");

                    return;

                }

    /**

     * Method to run the server side of the program

     */

    public static void runServer(ServerSocket serverSocket, String cmd, String moleculePath,

                                 String dbName) throws IOException {

        // Continue processing commands until "--quit" command is received

        while (!cmd.equals("--quit")) {

            // Perform actions based on the received command

            if (moleculePath.isEmpty()) {

                commandHandler1(cmd);

            } else {

                commandHandler2(cmd, moleculePath);

            }

                // https://cactus.nci.nih.gov/chemical/structure/isopropanol/image

                String imageURL = "https://cactus.nci.nih.gov/chemical/structure/" + moleculeName + "/image";

            // Accept incoming client connections

            Socket clientSocket;

                try {

                clientSocket = serverSocket.accept();

            } catch (IOException e) {

                System.out.println("connection timed out");

                break;

            }

            InputStream inStream = clientSocket.getInputStream();

            BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));

            String[] args = reader.readLine().split(" ");

                    // Download the image from the URL

                    URL url = new URL(imageURL);

                    BufferedImage image = ImageIO.read(url);

            // close the streams

            reader.close();

            inStream.close();

            clientSocket.close();

                    // Create a JLabel to display the image

                    JLabel imageLabel = new JLabel(new ImageIcon(image));

            // parse argument from client

            cmd = args[0];

            moleculePath = "";

            if (args.length > 1) {

                moleculePath = args[1];

                    // Create a new JFrame to display the image

                    JFrame imageFrame = new JFrame("Molecule Display");

                    imageFrame.getContentPane().add(imageLabel, BorderLayout.CENTER);

                    imageFrame.setSize(400, 400);

                    imageFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

                    imageFrame.setLocationRelativeTo(null); // Center the frame

                    imageFrame.setVisible(true); // Make the frame visible

                } catch (IOException ex) {

                    ex.printStackTrace();

                    outputTextArea.append("Molecule display failed. The provided molecule name may be incorrect or does not match any records in the PubChem database.\n\n");

                }

            }

        });

        // save the database before exiting

        moleculeDb.save(dbName);

        System.out.println("Database saved successfully.");

        System.out.println("Goodbye");

        // Action listener for Statistics button

        statisticsButton.addActionListener(new ActionListener() {

            @Override

            public void actionPerformed(ActionEvent e) {

                moleculeDb.printDb(); // print the content of database

            }

        });

    /**

     * Main method to start the program

     */

    public static void main(String[] args) throws IOException {

        final int ARG_COUNT = args.length;

        // Window listener to save the database before closing the GUI

        addWindowListener(new WindowAdapter() {

            @Override

            public void windowClosing(WindowEvent e) {

                try {

                    moleculeDb.save("molecule.db"); // save the database

                } catch (IOException ex) {

                    ex.printStackTrace();

                }

            }

        });

        // Connect to client or server

        connectToServerOrClient();

        // Get the port number from the command line arguments

        final int PORT_NUMBER = Integer.parseInt(args[0]);

        // Display the JFrame

        pack();

        setLocationRelativeTo(null);

        setVisible(true);

        // Load database on startup

        try {

            initDb("molecule.db");

        } catch (IOException e) {

            e.printStackTrace();

        }

        // get other command line arguments

        String cmd = args[1];

        String moleculePath = "";

        if (ARG_COUNT > 2) {

            moleculePath = args[2];

    }

        // run as client or server

        try (Socket clientSocket = new Socket("localhost", PORT_NUMBER)) {

            // If a client connection is successful, run the client side of the program

            runClient(clientSocket, cmd + " " + moleculePath);

    /**

     * Run as client or server

     */

    private void connectToServerOrClient() {

        try {

            // Run the client side

            clientSocket = new Socket("localhost", 5000);

            writer = new PrintWriter(clientSocket.getOutputStream(), true);

            reader = new BufferedReader(new InputStreamReader(clientSocket.getInputStream()));

        } catch (ConnectException e) {

            // If a client connection fails, run the server side of the program

            ServerSocket serverSocket = new ServerSocket(PORT_NUMBER);

            // Run the server side

            try {

                ServerSocket serverSocket = new ServerSocket(5000);

                serverSocket.setSoTimeout(60 * 1000);

            // Set the default filename for the database

            String dbName = "molecule.db";

                // Close the server socket after accepting the connection

                serverSocket.close();

            // Check if an alternative filename is provided as a command line argument

            if (ARG_COUNT > 3) {

                dbName = args[3];

            } catch (IOException ex) {

                ex.printStackTrace();

            }

        } catch (IOException ex) {

            ex.printStackTrace();

        }

    }

            // initialize database and start server

            initDb(dbName);

            runServer(serverSocket, cmd, moleculePath, dbName);

            serverSocket.close();

    /**

     * Initialize a database

     */

    public void initDb(String dbName) throws IOException {

        // Load the database

        moleculeDb = new MDB(outputTextArea);

        File dbFile = new File(dbName);

        if (dbFile.exists()) {

            moleculeDb.load(dbName);

        }

    }

    /**

     * Main function

     */

    public static void main(String[] args) {

        SwingUtilities.invokeLater(new Runnable() {

            @Override

            public void run() {

                GUI gui = new GUI();

            }

        });

    }

}