import javax.swing.*;
import java.awt.*;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
public class GeneGuiApp {
private JFrame frame;
private JTextField inputField;
private JLabel fileStatusLabel;
private JEditorPane outputDisplay;
private File selectedFile;
public GeneGuiApp() {
createAndShowGUI();
}
private void createAndShowGUI() {
frame = new JFrame("Central Dogma Bio-Processor");
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.setSize(1000, 650);
JPanel mainPanel = new JPanel(new BorderLayout(10, 10));
mainPanel.setBorder(BorderFactory.createEmptyBorder(15, 15, 15, 15));
mainPanel.setBackground(new Color(245, 247, 250));
// Control Header Row Panel
JPanel controlPanel = new JPanel();
controlPanel.setLayout(new BoxLayout(controlPanel, BoxLayout.X_AXIS));
controlPanel.setOpaque(false);
inputField = new JTextField();
inputField.setFont(new Font("Monospaced", Font.PLAIN, 14));
inputField.setMaximumSize(new Dimension(300, 35));
inputField.setPreferredSize(new Dimension(200, 35));
JButton processTextButton = new JButton("Process Text");
styleButton(processTextButton, new Color(70, 130, 180));
fileStatusLabel = new JLabel("No file selected ");
fileStatusLabel.setFont(new Font("SansSerif", Font.ITALIC, 12));
fileStatusLabel.setForeground(Color.GRAY);
JButton fileChooserButton = new JButton("Choose File");
styleButton(fileChooserButton, new Color(108, 117, 125));
JButton processFileButton = new JButton("Process File");
styleButton(processFileButton, new Color(40, 167, 69));
controlPanel.add(inputField);
controlPanel.add(Box.createHorizontalStrut(8));
controlPanel.add(processTextButton);
controlPanel.add(Box.createHorizontalStrut(20));
controlPanel.add(fileStatusLabel);
controlPanel.add(Box.createHorizontalStrut(8));
controlPanel.add(fileChooserButton);
controlPanel.add(Box.createHorizontalStrut(8));
controlPanel.add(processFileButton);
// Main Display Engine
outputDisplay = new JEditorPane();
outputDisplay.setContentType("text/html");
outputDisplay.setEditable(false);
outputDisplay.setBackground(Color.WHITE);
JScrollPane scrollPane = new JScrollPane(outputDisplay);
scrollPane.setBorder(BorderFactory.createLineBorder(new Color(210, 215, 225)));
mainPanel.add(controlPanel, BorderLayout.NORTH);
mainPanel.add(scrollPane, BorderLayout.CENTER);
processTextButton.addActionListener(e -> executeProcessingPipeline(inputField.getText().trim()));
fileChooserButton.addActionListener(e -> {
// Instantiate at current working project directory context path "."
JFileChooser fileChooser = new JFileChooser(".");
if (fileChooser.showOpenDialog(frame) == JFileChooser.APPROVE_OPTION) {
selectedFile = fileChooser.getSelectedFile();
fileStatusLabel.setText(selectedFile.getName() + " ");
fileStatusLabel.setForeground(new Color(40, 167, 69));
}
});
processFileButton.addActionListener(e -> {
if (selectedFile == null) {
outputDisplay.setText("Error: Choose a file first!");
return;
}
String extracted = parseFastaFile(selectedFile);
if (!extracted.isEmpty()) {
inputField.setText(extracted);
executeProcessingPipeline(extracted);
}
});
frame.add(mainPanel);
frame.setLocationRelativeTo(null);
frame.setVisible(true);
renderWelcomeScreen();
}
private void styleButton(JButton button, Color bg) {
button.setFont(new Font("SansSerif", Font.BOLD, 12));
button.setBackground(bg);
button.setForeground(Color.WHITE);
button.setOpaque(true);
button.setBorderPainted(false);
button.setFocusPainted(false);
button.setContentAreaFilled(true);
}
private String parseFastaFile(File file) {
StringBuilder sb = new StringBuilder();
try (BufferedReader br = new BufferedReader(new FileReader(file))) {
String line;
while ((line = br.readLine()) != null) {
line = line.trim();
if (line.startsWith(">") || line.isEmpty()) continue;
sb.append(line.replaceAll("\\s|\\d", ""));
}
} catch (IOException ex) { return ""; }
return sb.toString().toUpperCase();
}
private void executeProcessingPipeline(String rawDna) {
if (rawDna == null || rawDna.isEmpty()) return;
// GURANTEES absolute sanitization for manual text box entry/copy-pastes
rawDna = rawDna.replaceAll("\\s|\\d", "").toUpperCase();
// Invoke student business operations layers
String mrna = GeneUtils.transcribeToMrna(rawDna);
int startIndex = GeneUtils.findStartCodonIndex(mrna);
String aminoAcids = GeneUtils.translateMrna(mrna, startIndex);
// Find stop index independently for layout visualization highlights
int stopIndex = -1;
if (startIndex != -1) {
for (int i = startIndex; i <= mrna.length() - 3; i += 3) {
String codon = mrna.substring(i, i + 3);
if (codon.equals("UAA") || codon.equals("UAG") || codon.equals("UGA")) {
stopIndex = i;
break;
}
}
}
// Generate dot-separated tracking view for mRNA codons
StringBuilder mrnaFormatted = new StringBuilder();
if (startIndex == -1) {
mrnaFormatted.append(mrna);
} else {
mrnaFormatted.append(mrna, 0, startIndex);
int current = startIndex;
boolean insideCodingRegion = true;
while (current <= mrna.length() - 3) {
String codon = mrna.substring(current, current + 3);
if (current == startIndex) {
mrnaFormatted.append("AUG");
} else if (codon.equals("UAA") || codon.equals("UAG") || codon.equals("UGA")) {
mrnaFormatted.append("").append(codon).append("");
insideCodingRegion = false;
current += 3;
if (current < mrna.length()) mrnaFormatted.append(".");
break;
} else {
if (insideCodingRegion) {
mrnaFormatted.append("").append(codon).append("");
} else {
mrnaFormatted.append(codon);
}
}
current += 3;
if (current <= mrna.length() - 3) {
mrnaFormatted.append(".");
}
}
if (current < mrna.length()) {
if (current > startIndex) mrnaFormatted.append(".");
mrnaFormatted.append(mrna.substring(current));
}
}
StringBuilder html = new StringBuilder();
html.append("");
html.append("Genetics Pipeline Trace Analysis
");
html.append("
");
// 1. DNA panel with precise block dimension and scrolling constraints
html.append("Original 3' → 5' DNA Template Strand:
");
html.append("")
.append(rawDna).append("
");
// 2. mRNA panel with precise block dimension and scrolling constraints
html.append("Transcribed 5' → 3' mRNA Strand (Triplet Track):
");
html.append("")
.append(mrnaFormatted).append("
");
// Status Messaging Output Logs
if (startIndex == -1) {
html.append("⚠️ Warning: findStartCodonIndex returned -1. Translation step skipped.
");
} else if (stopIndex == -1) {
html.append("⚠️ Warning: No structural STOP codon encountered in reading frame. translateMrna returned null.
");
} else {
html.append("✔ Valid transcription and translation parameters mapped cleanly.
");
}
// 3. Polypeptide Panel: ONLY rendered and shown if the translation was successful (!= null)
if (aminoAcids != null) {
html.append("Translated Polypeptide Chain:
");
html.append("");
html.append(" [N-Terminus] ⇒ ").append(aminoAcids).append(" ⇒ [C-Terminus]");
html.append("
");
}
html.append("");
outputDisplay.setText(html.toString());
}
private void renderWelcomeScreen() {
outputDisplay.setText("Bio-Processor Workspace Ready
");
}
public static void main(String[] args) {
SwingUtilities.invokeLater(() -> new GeneGuiApp());
}
}