DNA.java

// takes input of DNA and converts to complementary strand (or RNA output)
// A pairs with T (or U for RNA), & C with G
// handles errors from input in the GUI

import java.awt.BorderLayout;
import java.awt.Container;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Scanner;
import javax.swing.JButton;
import javax.swing.JFrame;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSplitPane;
import javax.swing.JTextArea;

public class DNA extends JFrame implements ActionListener{
  
  // GUI elements
  private JButton translate;
  private JButton rna;
  private JTextArea inputText;
  private JTextArea outputText;
  private Container frame;
  private char[][] table;
  
  // main method, calls the DNA object
  public static void main(String[] args){
    DNA dna = new DNA();
  }
  
  // creates the main GUI window and creates the DNA sequence array
  public DNA(){
    this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    this.setSize(800,600);
    this.setTitle("DNA Sequencer");
    this.setVisible(true);
    inputText = new JTextArea();
    outputText = new JTextArea();
    JScrollPane scrollerLeft = new JScrollPane(inputText);
    JScrollPane scrollerRight = new JScrollPane(outputText);
    frame = this.getContentPane();
    JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, scrollerLeft,scrollerRight);
    splitPane.setOneTouchExpandable(true);
    splitPane.setDividerLocation(400);
    translate = new JButton("Sequence");
    translate.addActionListener((ActionListener) this);
    translate.setActionCommand("translate");
    rna = new JButton("RNA Transcription");
    rna.addActionListener((ActionListener) this);
    rna.setActionCommand("transcription");
    JPanel buttons = new JPanel();
    buttons.add(translate);buttons.add(rna);
    frame.add(splitPane,BorderLayout.CENTER);
    frame.add(buttons,BorderLayout.NORTH);
    this.validate();
    this.makeArray();
  }
  
  // creates an array for the sequencing (0 is for input, 1 & 2 is for output)
  private void makeArray(){
    table = new char[4][3];
    table[0][0] = 'A';
    table[0][1] = 'T';
    table[0][2] = 'U';
    table[1][0] = 'G';
    table[1][1] = 'C';
    table[1][2] = 'C';
    table[2][0] = 'C';
    table[2][1] = 'G';
    table[2][2] = 'G';
    table[3][0] = 'T';
    table[3][1] = 'A';
    table[3][2] = 'A';
  }
  
  // for translating or transcribing the DNA
  public void actionPerformed(ActionEvent evt){
    if(evt.getActionCommand().equals("translate"))
      readInput(1);
    if(evt.getActionCommand().equals("transcription"))
      readInput(2);
  }
  
  // reads the input DNA strand and converts it to the appropriate strand
  // x = 1: convert to complementary DNA strand   x = 2: RNA transcription
  private void readInput(int x){
    Scanner inputStream = null;
    Scanner outputStream = null;
    outputText.setText("");
    try{
      inputStream = new Scanner(inputText.getText());
      String parse = "";
      String sequence = "";
      String out = "";
      boolean error = false;
      
      // processes user input, first to make sure input is proper
      // and then to replace any unneeded characters for the sequencing
      while(inputStream.hasNext()){
        parse = inputStream.nextLine();
        parse = parse.toUpperCase();
        parse = parse.replace(" ", "");
        String test = parse.replaceAll("[A||G||C||T]", "");
        if(!test.isEmpty())
          error = true;
        parse = parse.replaceAll("[^A||G||C||T]", "");
        sequence = this.sequencer(parse, x);
        outputText.append(sequence + "\n");
      }
      
      // processes the output and if the input was empty or the input
      // was incorrectly typed then an error box is displayed
      outputStream = new Scanner(outputText.getText());
      while(outputStream.hasNext())
        out = out + outputStream.nextLine();
      if(out.equals("") || error)
        JOptionPane.showMessageDialog(frame, "Please type a proper DNA sequence in the pane on the left.", "Input Error", JOptionPane.ERROR_MESSAGE);
      
    //closes stream
    }finally{
      if(inputStream != null)
        inputStream.close();
      if(outputStream != null)
        outputStream.close();
    }
  }
  
  // sequencer takes the input string and outputs the correct sequence
  private String sequencer(String in, int x){
    String out = "";
    int length = in.length();
    for(int i = 0; i < length; i++)
      out = out + this.getChar(in.charAt(i), x);
    return out;
  }
  
  // takes some character and finds its complementary letter (or U for RNA)
  private char getChar(char a, int x){
    char b='q';
    for(int i = 0; i < 4; i++){
      if(a==table[i][0])
        b = table[i][x];
    }
    return b;
  }
}