edit GUI + add new buttons (44747db1) · Commits · EC504 Spring 2024 Group Projects / Group4

src/GUI.java

+137 −20

Original line number	Diff line number	Diff line
		@@ -7,18 +7,23 @@ import java.awt.event.*;
		import java.io.*;
		import java.net.*;
		import java.awt.image.BufferedImage;
		import java.nio.file.*;
		import java.nio.file.attribute.BasicFileAttributes;
		import java.util.ArrayList;
		import java.util.Arrays;

		public class GUI extends JFrame {
		private JTextArea outputTextArea;
		private JButton chooseFileButton;
		private JButton chooseButton;
		private JButton addMoleculeButton;
		private JButton findMoleculeButton;
		private JButton statisticsButton;
		private JButton displayMoleculeButton;
		private JButton findSubgraphButton;
		private JButton downloadPubChemButton;
		private JButton makeSimpleButton;
		private JButton makeComplexButton;
		private JButton addProteinsButton;
		private JButton addMultipleMoleculesButton;
		private JTextField filePathField;
		private static MDB moleculeDb;
		private Socket clientSocket;
		@@ -40,49 +45,71 @@ public class GUI extends JFrame {
		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");
		chooseButton = new JButton("Choose File/Folder");
		downloadPubChemButton = new JButton("Download PubChem");
		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");
		addProteinsButton = new JButton("Add Proteins");
		makeSimpleButton = new JButton("Make Simple Molecules");
		makeComplexButton = new JButton("Make Complex Molecules");
		addMultipleMoleculesButton = new JButton("Add Multiple Molecules");
		filePathField = new JTextField(20); // to show the file path
		JLabel filePathLabel = new JLabel("File Path:");
		JLabel filePathLabel = new JLabel("File/Folder 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

		// Add components to the JFrame
		// Create panels
		JPanel firstRowPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
		firstRowPanel.setBackground(Color.BLACK);
		firstRowPanel.add(chooseButton);
		firstRowPanel.add(addMoleculeButton);
		firstRowPanel.add(findMoleculeButton);
		firstRowPanel.add(findSubgraphButton);
		firstRowPanel.add(displayMoleculeButton);
		firstRowPanel.add(filePathLabel);
		firstRowPanel.add(filePathField);

		JPanel secondRowPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
		secondRowPanel.setBackground(Color.BLACK);
		secondRowPanel.add(addMultipleMoleculesButton);
		secondRowPanel.add(addProteinsButton);
		secondRowPanel.add(makeSimpleButton);
		secondRowPanel.add(makeComplexButton);
		secondRowPanel.add(statisticsButton);

		JPanel controlPanel = new JPanel();
		controlPanel.setLayout(new BoxLayout(controlPanel, BoxLayout.Y_AXIS));
		controlPanel.setBackground(Color.BLACK);
		controlPanel.add(chooseFileButton);
		controlPanel.add(downloadPubChemButton);
		controlPanel.add(addMoleculeButton);
		controlPanel.add(findMoleculeButton);
		controlPanel.add(findSubgraphButton);
		controlPanel.add(displayMoleculeButton);
		controlPanel.add(statisticsButton);
		controlPanel.add(filePathLabel);
		controlPanel.add(filePathField);
		controlPanel.add(firstRowPanel);
		controlPanel.add(secondRowPanel);

		add(controlPanel, BorderLayout.NORTH); // to show the control panel (e.g., buttons)
		add(scrollPane, BorderLayout.CENTER); // to show the printed output text area


		// Initialize molecule database
		moleculeDb = new MDB(outputTextArea);

		// Action listener for Choose File button
		chooseFileButton.addActionListener(new ActionListener() {
		// Action listener for Choose File/Folder button
		final File[] lastOpenedDirectory = {new File(System.getProperty("user.home"))};
		chooseButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		// Create a file chooser
		JFileChooser fileChooser = new JFileChooser();
		fileChooser.setDialogTitle("Choose a file");
		fileChooser.setCurrentDirectory(lastOpenedDirectory[0]);
		fileChooser.setDialogTitle("Choose File/Folder");
		fileChooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
		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());
		lastOpenedDirectory[0] = selectedFile.getParentFile();
		}
		}
		});
		@@ -103,6 +130,7 @@ public class GUI extends JFrame {
		String start = indexes[0];
		String end = indexes[1];
		moleculeDb.downloadPubChem(start, end);
		outputTextArea.append("Download complete!" + "\n\n");
		} else {
		outputTextArea.append("Invalid Input" + "\n\n");
		}
		@@ -171,8 +199,8 @@ public class GUI extends JFrame {
		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:" + ex.getMessage() + "\n\n");
		System.err.println("File reading error. Please check file format.");
		outputTextArea.append("File reading error. Please check file format." + "\n\n");
		return;
		}

		@@ -196,7 +224,7 @@ public class GUI extends JFrame {
		imageFrame.setVisible(true); // Make the frame visible

		} catch (IOException ex) {
		ex.printStackTrace();
		System.err.println("Molecule display failed. The provided molecule name may be incorrect or does not match any records in the PubChem database.");
		outputTextArea.append("Molecule display failed. The provided molecule name may be incorrect or does not match any records in the PubChem database.\n\n");
		}
		}
		@@ -210,6 +238,82 @@ public class GUI extends JFrame {
		}
		});

		// Action listener for the Add Proteins button
		addProteinsButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		String moleculePath = filePathField.getText();
		try {
		addProteins(moleculePath);
		} catch (Exception ex) {
		System.err.println("Adding proteins failed.");
		outputTextArea.append("Adding proteins failed." + "\n\n");
		}
		}
		});

		// Action listener for Make Simple Molecules button
		makeSimpleButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		outputTextArea.append("Generating 10 million molecule files, each containing 52 to 136 atoms." + "\n");
		outputTextArea.append("To follow the progress, please observe the terminal output." + "\n");
		outputTextArea.append("Generating..." + "\n");
		SwingWorker<Void, Void> worker = new SwingWorker<Void, Void>() {
		@Override
		protected Void doInBackground() throws Exception {
		try {
		ProteinFactory.manySimpleProteins();
		} catch (IOException ex) {
		throw new RuntimeException(ex);
		}
		return null;
		}
		@Override
		protected void done() {
		outputTextArea.append("Complete!" + "\n\n");
		}
		};
		worker.execute(); // Start the background task
		}
		});


		// Action listener for Make Complex Molecules button
		makeComplexButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		outputTextArea.append("Generating 10,000 million molecule files, each containing over 10,000 atoms." + "\n");
		outputTextArea.append("To follow the progress, please observe the terminal output." + "\n");
		outputTextArea.append("Generating..." + "\n");
		SwingWorker<Void, Void> worker = new SwingWorker<Void, Void>() {
		@Override
		protected Void doInBackground() throws Exception {
		try {
		ProteinFactory.fewComplexProteins();
		} catch (IOException ex) {
		throw new RuntimeException(ex);
		}
		return null;
		}
		@Override
		protected void done() {
		outputTextArea.append("Complete!" + "\n\n");
		}
		};
		worker.execute(); // Start the background task
		}
		});

		// Action listener for Add Multiple Molecules button
		addMultipleMoleculesButton.addActionListener(new ActionListener() {
		@Override
		public void actionPerformed(ActionEvent e) {
		String moleculePath = filePathField.getText();
		moleculeDb.addMultipleMolecules(moleculePath);
		}
		});

		// Window listener to save the database before closing the GUI
		addWindowListener(new WindowAdapter() {
		@Override
		@@ -277,6 +381,19 @@ public class GUI extends JFrame {
		}
		}

		public static void addProteins(String proteinPath) throws IOException {
		Files.walkFileTree(Paths.get(proteinPath), new SimpleFileVisitor<>() {
		@Override
		public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
		if (!Files.isDirectory(file)) {
		moleculeDb.addMolecule(new Molecule(proteinPath + "/" +
		file.getParent().toString() + "/" + file.getFileName().toString()));
		}
		return FileVisitResult.CONTINUE;
		}
		});
		}

		/**
		* Main function
		*/

src/MDB.java

+28 −4

Original line number	Diff line number	Diff line
		@@ -187,20 +187,44 @@ public class MDB {
		filenames.add(file);
		}

		int exitCode = process.waitFor();
		outputTextArea.append("Exited with code: " + exitCode + "\n\n");

		// add created files to the database
		for (String filename : filenames) {
		this.addMolecule(new Molecule(filename));
		}

		outputTextArea.append("Download complete!" + "\n\n");

		} catch (Exception e) {
		outputTextArea.append("Error downloading from PubChem" + "\n\n");
		e.printStackTrace();
		}
		}

		/**
		* Add all molecules from a specified folder
		*/
		public void addMultipleMolecules(String path) {
		File directory = new File(path);
		// Check if the directory exists
		if (!directory.exists() \|\| !directory.isDirectory()) {
		outputTextArea.append("Invalid directory: " + path + "\n\n");
		return;
		}
		// Get list of files in the directory
		File[] files = directory.listFiles();
		if (files == null) {
		outputTextArea.append("No files found inside directory: " + path + "\n\n");
		return;
		}
		// Iterate over the files in the directory
		for (File file : files) {
		// Check if the file is a text file
		if (file.isFile() && file.getName().endsWith(".txt")) {
		addMolecule(new Molecule(file.getAbsolutePath()));
		}
		}
		outputTextArea.append("Complete adding all molecules from directory!" + "\n\n");
		}

		/**
		* Save database to file system
		*/

src/Main.java

+4 −0

Original line number	Diff line number	Diff line
		@@ -118,10 +118,14 @@ public class Main {
		String start = indexes[0];
		String end = indexes[1];
		moleculeDb.downloadPubChem(start, end);
		System.out.println("Download Complete!");
		} else {
		printVerbose("invalid Input");
		}
		break;
		case "--addBulk":
		moleculeDb.addMultipleMolecules(moleculePath);
		break;
		default:
		printVerbose("unrecognized command: " + cmd);
		break;

src/MoleculeDatabase.java

+29 −52

Original line number	Diff line number	Diff line
		@@ -141,19 +141,44 @@ public class MoleculeDatabase {
		filenames.add(file);
		}

		int exitCode = process.waitFor();
		printVerbose("Exited with code: " + exitCode);

		// add created files to the database
		for (String filename : filenames) {
		this.addMolecule(new Molecule(filename));
		}

		System.out.println("Download complete!");

		} catch (Exception e) {
		e.printStackTrace();
		System.out.println("Error downloading from PubChem.");
		}
		}

		/**
		* Add all molecules from a specified folder
		*/
		public void addMultipleMolecules(String path) {
		File directory = new File(path);
		// Check if the directory exists
		if (!directory.exists() \|\| !directory.isDirectory()) {
		System.out.println("Invalid directory: " + path);
		return;
		}
		// Get list of files in the directory
		File[] files = directory.listFiles();
		if (files == null) {
		System.out.println("No files found inside directory: " + path);
		return;
		}
		// Iterate over the files in the directory
		for (File file : files) {
		// Check if the file is a text file
		if (file.isFile() && file.getName().endsWith(".txt")) {
		addMolecule(new Molecule(file.getAbsolutePath()));
		}
		}
		System.out.println("Complete adding all molecules from directory!");
		}


		/**
		* Find all molecules that contain the @param subgraph
		@@ -203,52 +228,4 @@ public class MoleculeDatabase {
		fileInStream.close();
		}

		/**
		* Get database statistics as a string
		* Note: this method is designed to work with the webpage
		*/
		public String showDb() {
		StringBuilder stringBuilder = new StringBuilder();

		// Print number of molecules
		int size = 0;
		for (ArrayList<Molecule> molecules : db.values()) {
		size += molecules.size();
		}
		stringBuilder.append("# of molecules: ").append(size).append("\n\n");

		if (size == 0)
		return stringBuilder.toString(); // if database is empty, return early

		// Print the list of molecules
		stringBuilder.append("List of molecules: ").append("\n\n");
		for (Integer atomCount : this.db.keySet()) {
		ArrayList<Molecule> moleculesWithSameNumAtoms = this.db.get(atomCount);
		for (Molecule molecule : moleculesWithSameNumAtoms) {
		stringBuilder.append("Molecule name: ").append(molecule.moleculeName).append("\n");
		stringBuilder.append("# of atoms: ").append(atomCount.toString()).append("\n\n");
		}
		}

		// Print the largest and smallest molecules
		int maxAtoms = Integer.MIN_VALUE;
		int minAtoms = Integer.MAX_VALUE;
		Molecule largestMolecule = null;
		Molecule smallestMolecule = null;
		for (Map.Entry<Integer, ArrayList<Molecule>> entry : db.entrySet()) {
		int numAtoms = entry.getKey();
		if (numAtoms > maxAtoms) {
		maxAtoms = numAtoms;
		largestMolecule = entry.getValue().get(0); // only print 1 representative molecule
		}
		if (numAtoms < minAtoms) {
		minAtoms = numAtoms;
		smallestMolecule = entry.getValue().get(0); // only print 1 representative molecule
		}
		}
		stringBuilder.append("Smallest molecule: ").append(smallestMolecule.moleculeName).append("\n");
		stringBuilder.append("Largest molecule: ").append(largestMolecule.moleculeName).append("\n\n");

		return stringBuilder.toString();
		}
		}