import javax.swing.*;
import java.awt.*;
import java.awt.geom.*;
import java.awt.event.*;
import java.io.*;
import java.util.*;;

public class Graphing_tool extends JFrame implements ActionListener{
	JFrame Error_message_enter_file_name = new JFrame("Error message");
	JFrame Error_message_file_not_present = new JFrame("Error message");
	private JFrame Graph_Frame = new JFrame();
	private Draw_line graph_constructor = new Draw_line();
	
	JLabel enter_file_name_error = new JLabel("Enter the file name please.");
	JLabel file_not_present_error = new JLabel("The file does not exits");
	
	JLabel Protein_name = new JLabel("Protein name");
	JTextField display = new JTextField("Enter file location here.",40);
	JCheckBox Disorderness = new JCheckBox("Disorderness");
	JCheckBox Secondary_structures = new JCheckBox("Secondary_structures");
	JCheckBox Sequence_conservation = new JCheckBox("Sequence_conservation");
	JCheckBox Antigenicity = new JCheckBox("Antigenicity");
	JCheckBox Hydrophilicity = new JCheckBox("Hydrophilicity");
	JCheckBox Concensus = new JCheckBox("Concensus");
	JCheckBox Window_sliding = new JCheckBox("Window_sliding");
	JButton Draw = new JButton("Draw");
		
	public Graphing_tool(){
		Panel panel_text = new Panel();
		Panel panel_options_1 = new Panel();
		Panel panel_options_2 = new Panel();
		panel_text.add(Protein_name);
		panel_text.add(display);
		panel_options_1.add(Disorderness);
		panel_options_1.add(Secondary_structures);
		panel_options_1.add(Sequence_conservation);
		panel_options_2.add(Antigenicity);
		panel_options_2.add(Hydrophilicity);
		panel_options_2.add(Concensus);
		panel_options_2.add(Window_sliding);
		
		setTitle("Fateh's Graphing Tool");
		
		
		getContentPane().setLayout(null);
		getContentPane().setBackground(Color.white);
		getContentPane().add(panel_text);
		getContentPane().add(panel_options_1);
		getContentPane().add(panel_options_2);
		getContentPane().add(Draw);
		
		panel_text.setBounds(0,50,800,40);
		panel_options_1.setBounds(100,100,600,40);
		panel_options_2.setBounds(100,150,600,40);
		Draw.setBounds(350,200,75,40);
		
		Draw.addActionListener(this);

		Graph_Frame.getContentPane().add(graph_constructor);
		Graph_Frame.setBackground(Color.white);
		Graph_Frame.pack();
		Graph_Frame.setTitle("Graph of the requested items");
	}
	
	public void actionPerformed(ActionEvent Click){
		System.out.println("Button was Clicked!!");
		if(Click.getSource() == Draw){
			String File_name = display.getText();
			System.out.println("File name - "+File_name);
			File final_out_file = new File(File_name);
			if (File_name.equals("Enter file location here.")){
				display_error_enter_file_name();
			}else if(!final_out_file.exists()){
				display_error_file_does_not_exist();
			}else{
				try {
					parse_file(File_name);
				} catch (IOException e) {}
			}
		}
	}
	
	public void parse_file(String File_name) throws IOException {
		BufferedReader infile = null;
		String line;
		int number_of_lines = count_lines(File_name);
		double[] Disorder_array = new double[number_of_lines];
		double[] Sec_str_array = new double[number_of_lines];
		double[] Seq_cons_array = new double[number_of_lines];
		double[] Antigene_array = new double[number_of_lines];
		double[] Hydro_array = new double[number_of_lines];
		double[] Sum_array = new double[number_of_lines];
		double[] Window_array = new double[number_of_lines];
		
		int number_of_options_selected = 0;
		int array_of_bools [] = new int[7];
		boolean Disorder = false,Sec_str = false,Seq_cons = false,Antigene = false,Hydro = false,Sum = false,Window = false;
		if(Disorderness.isSelected()){
			Disorder = true;
			number_of_options_selected++;
			array_of_bools[0] = 1;
		}if(Secondary_structures.isSelected()){
			Sec_str = true;
			number_of_options_selected++;
			array_of_bools[1] = 1;
		}if(Sequence_conservation.isSelected()){
			Seq_cons = true;
			number_of_options_selected++;
			array_of_bools[2] = 1;
		}if(Antigenicity.isSelected()){
			Antigene = true;
			number_of_options_selected++;
			array_of_bools[3] = 1;
		}if(Hydrophilicity.isSelected()){
			Hydro = true;
			number_of_options_selected++;
			array_of_bools[4] = 1;
		}if(Concensus.isSelected()){
			Sum = true;
			number_of_options_selected++;
			array_of_bools[5] = 1;
		}if(Window_sliding.isSelected()){
			Window = true;
			number_of_options_selected++;
			array_of_bools[6] = 1;
		}		
		System.out.println(Disorder  + " " + Sec_str + " " + 
				Seq_cons + " " + Antigene + " " + Hydro + " " + Sum + " " + Window);
		
		int counter = 0;
		infile = new BufferedReader(new FileReader(File_name));
		while((line = infile.readLine()) != null){
			String nums[] = line.split(" ");
			Disorder_array[counter] = Double.parseDouble(nums[3]);
			Sec_str_array[counter] = Double.parseDouble(nums[4]);
			Seq_cons_array[counter] = Double.parseDouble(nums[5]);
			Antigene_array[counter] = Double.parseDouble(nums[6]);
			Hydro_array[counter] = Double.parseDouble(nums[7]);
			Sum_array[counter] = Double.parseDouble(nums[9]);
			if (counter<number_of_lines-9)
				Window_array[counter] = Double.parseDouble(nums[10]);
			counter++;
		}
		int temp_counter = 0;
/*		while(temp_counter < counter){
			if(Disorderness.isSelected())
				System.out.print(Disorder_array[temp_counter]+ " ");
			if(Secondary_structures.isSelected())
				System.out.print(Sec_str_array[temp_counter]+ " ");
			if(Sequence_conservation.isSelected())
				System.out.print(Seq_cons_array[temp_counter]+ " ");
			if(Antigenicity.isSelected())
				System.out.print(Antigene_array[temp_counter]+ " ");			
			if(Hydrophilicity.isSelected())
				System.out.print(Hydro_array[temp_counter]+ " ");			
			if(Concensus.isSelected())
				System.out.print(Sum_array[temp_counter]+ " ");			
			if(Window_sliding.isSelected())
				System.out.print(Window_array[temp_counter]+ " ");	
			System.out.println();
			temp_counter++;
		}
*/		
		Graph_Frame.setBounds(0,0,counter+200,number_of_options_selected*140+100);
		graph_constructor.draw_line(Disorder_array,Sec_str_array,Seq_cons_array,
				Antigene_array,Hydro_array,Sum_array,Window_array, array_of_bools);
		Graph_Frame.setVisible(true);
	}

	public int count_lines(String filename) throws IOException {
	    InputStream is = new BufferedInputStream(new FileInputStream(filename));
	    try {
	        byte[] c = new byte[1024];
	        int count = 0;
	        int readChars = 0;
	        while ((readChars = is.read(c)) != -1) {
	            for (int i = 0; i < readChars; ++i) {
	                if (c[i] == '\n')
	                    ++count;
	            }
	        }
	        return count;
	    } finally {
	        is.close();
	    }
	}

	public void display_error_enter_file_name(){
		Error_message_enter_file_name.setLayout(null);
		Error_message_enter_file_name.add(enter_file_name_error);
		Error_message_enter_file_name.setBackground(Color.white);
		Error_message_enter_file_name.setBounds(500,500,250,100);
		enter_file_name_error.setBounds(25,25,250,40);
		Error_message_enter_file_name.setVisible(true);
	}
	
	public void display_error_file_does_not_exist(){
		Error_message_file_not_present.setLayout(null);
		Error_message_file_not_present.add(file_not_present_error);
		Error_message_file_not_present.setBackground(Color.white);
		Error_message_file_not_present.setBounds(500,500,250,100);
		file_not_present_error.setBounds(25,25,250,40);
		Error_message_file_not_present.setVisible(true);
	}
	
	public static void main(String[] args) {
		Graphing_tool TopTitle = new Graphing_tool();
		TopTitle.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
		TopTitle.setBounds(500,500,800,300);
		TopTitle.setVisible(true);
	}
}

class Draw_line extends JPanel{
	double[] Disorder_array;
	double[] Sec_str_array;
	double[] Seq_cons_array;
	double[] Antigene_array;
	double[] Hydro_array;
	double[] Sum_array ;
	double[] Window_array;
	int[] array_of_bools;
	public void draw_line(double [] diso, double [] psi,double [] conv, double [] anti,
			double [] hmoment, double [] sum,double [] sliding, int [] draw_what) {
		this.Disorder_array = diso;
		this.Sec_str_array = psi;
		this.Seq_cons_array = conv;
		this.Antigene_array = anti;
		this.Hydro_array = hmoment;
		this.Sum_array = sum;
		this.Window_array = sliding;
		this.array_of_bools = draw_what;
		repaint();
	}
	public void paintComponent(Graphics g){
		int valid_check = 0,line_position_y=0,length=0;
		for(int counter=0;counter<=6;counter++){
			if (array_of_bools[counter] == 1) 
				valid_check++;
		}
		if(valid_check == 0)
			return;
//		super.paintComponent(g);
		if(array_of_bools[0] == 1){
			System.out.println("Disorderness graph is being printed!!");
			length=Disorder_array.length;
			line_position_y+=75;
			g.drawLine(50,line_position_y-50,50,line_position_y);  //vertical
			g.drawLine(50,line_position_y,length+100,line_position_y);   //horizontal
			g.drawLine(48, line_position_y-25, 52, line_position_y-25);
			g.drawLine(48, line_position_y-50, 52, line_position_y-50);
			g.drawString("1", 40, line_position_y-21);
			g.drawString("2", 40, line_position_y-46);
			g.drawString("Disorderness", 100, line_position_y+30);
			int counter = 0;
			for(counter=0;counter<length;counter++){
//				System.out.print(Disorder_array[counter]+ " ");
				g.setColor(Color.red);
				g.drawLine(counter+50, line_position_y, counter+50,line_position_y-(int)(Disorder_array[counter]*31.25));
			}for(counter=0;counter<length;counter+=50){
				g.setColor(Color.black);
				g.drawLine(50+counter, line_position_y-2, 50+counter, line_position_y+2);
				String num = Integer.toString(counter);
				g.drawString(num,46+counter, line_position_y+15);
			}
			
//			System.out.println();
		}if(array_of_bools[1] == 1){
			System.out.println("Secondary structure graph is being printed!!");
			length=Sec_str_array.length;
			line_position_y+=100;
			g.drawLine(50,line_position_y-50,50,line_position_y);  //vertical
			g.drawLine(50,line_position_y,length+100,line_position_y);   //horizontal
			g.drawLine(48, line_position_y-25, 52, line_position_y-25);
			g.drawLine(48, line_position_y-50, 52, line_position_y-50);
			g.drawString("1", 40, line_position_y-21);
			g.drawString("2", 40, line_position_y-46);
			g.drawString("Secondary Structure Presence", 100, line_position_y+30);
			int counter = 0;
			for(counter=0;counter<length;counter++){
//				System.out.print(Sec_str_array[counter]+ " ");
				g.setColor(Color.red);
				g.drawLine(counter+50, line_position_y, counter+50,line_position_y-(int)(Sec_str_array[counter]*(double)25));
			}for(counter=0;counter<length;counter+=50){
				g.setColor(Color.black);
				g.drawLine(50+counter, line_position_y-2, 50+counter, line_position_y+2);
				String num = Integer.toString(counter);
				g.drawString(num,46+counter, line_position_y+15);
			}
			
//			System.out.println();
		}if(array_of_bools[2] == 1){
			System.out.println("Sequence conservation graph is being printed!!");
			length=Seq_cons_array.length;
			line_position_y+=100;
			g.drawLine(50,line_position_y-50,50,line_position_y);  //vertical
			g.drawLine(50,line_position_y,length+100,line_position_y);   //horizontal
			g.drawLine(48, line_position_y-25, 52, line_position_y-25);
			g.drawLine(48, line_position_y-50, 52, line_position_y-50);
			g.drawString("1", 40, line_position_y-21);
			g.drawString("2", 40, line_position_y-46);
			g.drawString("Sequence Conservation Score", 100, line_position_y+30);
			int counter = 0;
			for(counter=0;counter<length;counter++){
//				System.out.print(Seq_cons_array[counter]+ " ");
				g.setColor(Color.red);
				g.drawLine(counter+50, line_position_y, counter+50,line_position_y-(int)(Seq_cons_array[counter]*41.677));
			}for(counter=0;counter<length;counter+=50){
				g.setColor(Color.black);
				g.drawLine(50+counter, line_position_y-2, 50+counter, line_position_y+2);
				String num = Integer.toString(counter);
				g.drawString(num,46+counter, line_position_y+15);
			}
			
//			System.out.println();
		}if(array_of_bools[3] == 1){
			System.out.println("Antigene graph is being printed!!");
			length=Antigene_array.length;
			line_position_y+=100;
			g.drawLine(50,line_position_y-50,50,line_position_y);  //vertical
			g.drawLine(50,line_position_y,length+100,line_position_y);   //horizontal
			g.drawLine(48, line_position_y-25, 52, line_position_y-25);
			g.drawLine(48, line_position_y-50, 52, line_position_y-50);
			g.drawString("1", 40, line_position_y-21);
			g.drawString("2", 40, line_position_y-46);
			g.drawString("Antigenecity Score", 100, line_position_y+30);
			int counter = 0;
			for(counter=0;counter<length;counter++){
//				System.out.print(Antigene_array[counter]+ " ");
				g.setColor(Color.red);
				g.drawLine(counter+50, line_position_y, counter+50,line_position_y-(int)(Antigene_array[counter]*(double)25));
			}for(counter=0;counter<length;counter+=50){
				g.setColor(Color.black);
				g.drawLine(50+counter, line_position_y-2, 50+counter, line_position_y+2);
				String num = Integer.toString(counter);
				g.drawString(num,46+counter, line_position_y+15);
			}
			
//			System.out.println();
		}if(array_of_bools[4] == 1){
			System.out.println("Hydrophilicity graph is being printed!!");
			length=Hydro_array.length;
			line_position_y+=100;
			g.drawLine(50,line_position_y-50,50,line_position_y);  //vertical
			g.drawLine(50,line_position_y,length+100,line_position_y);   //horizontal
			g.drawLine(48, line_position_y-25, 52, line_position_y-25);
			g.drawLine(48, line_position_y-50, 52, line_position_y-50);
			g.drawString("1", 40, line_position_y-21);
			g.drawString("2", 40, line_position_y-46);
			g.drawString("Hydrophilicity Score", 100, line_position_y+30);
			int counter = 0;
			for(counter=0;counter<length;counter++){
//				System.out.print(Hydro_array[counter]+ " ");
				g.setColor(Color.red);
				g.drawLine(counter+50, line_position_y, counter+50,line_position_y-(int)(Hydro_array[counter]*(double)50));
			}for(counter=0;counter<length;counter+=50){
				g.setColor(Color.black);
				g.drawLine(50+counter, line_position_y-2, 50+counter, line_position_y+2);
				String num = Integer.toString(counter);
				g.drawString(num,46+counter, line_position_y+15);
			}
			
//			System.out.println();
		}if(array_of_bools[5] == 1){
			System.out.println("Sum graph is being printed!!");
			length=Sum_array.length;
			line_position_y+=150;
			g.drawLine(50,line_position_y-75,50,line_position_y);  //vertical
			g.drawLine(50,line_position_y,length+100,line_position_y);   //horizontal
			g.drawLine(48, line_position_y-25, 52, line_position_y-25);
			g.drawLine(48, line_position_y-50, 52, line_position_y-50);
			g.drawLine(48, line_position_y-75, 52, line_position_y-75);
			g.drawString("1", 40, line_position_y-21);
			g.drawString("2", 40, line_position_y-46);
			g.drawString("3", 40, line_position_y-71);
			g.drawString("Consensus Score", 100, line_position_y+30);
			int counter = 0;
			for(counter=0;counter<length;counter++){
//				System.out.print(Sum_array[counter]+ " ");
				g.setColor(Color.red);
				g.drawLine(counter+50, line_position_y, counter+50,line_position_y-(int)(Sum_array[counter]*(double)25));
			}for(counter=0;counter<length;counter+=50){
				g.setColor(Color.black);
				g.drawLine(50+counter, line_position_y-2, 50+counter, line_position_y+2);
				String num = Integer.toString(counter);
				g.drawString(num,46+counter, line_position_y+15);
			}
			
//			System.out.println();
		}if(array_of_bools[6] == 1){
			System.out.println("Window sliding graph is being printed!!");
			length=Window_array.length;
			line_position_y+=150;
			g.drawLine(50,line_position_y-75,50,line_position_y);  //vertical
			g.drawLine(50,line_position_y,length+100,line_position_y);   //horizontal
			g.drawLine(48, line_position_y-25, 52, line_position_y-25);
			g.drawLine(48, line_position_y-75, 52, line_position_y-75);
			g.drawString("1", 40, line_position_y-21);
			g.drawString("2", 40, line_position_y-46);
			g.drawString("3", 40, line_position_y-71);
			g.drawString("Window Sliding Score", 100, line_position_y+30);
			int counter = 0;
			for(counter=0;counter<length;counter++){
//				System.out.print(Window_array[counter]+ " ");
				g.setColor(Color.red);
				g.drawLine(counter+50, line_position_y, counter+50,line_position_y-(int)(Window_array[counter]*(double)25));
			}for(counter=0;counter<length;counter+=50){
				g.setColor(Color.black);
				g.drawLine(50+counter, line_position_y-2, 50+counter, line_position_y+2);
				String num = Integer.toString(counter);
				g.drawString(num,46+counter, line_position_y+15);
			}
			
//			System.out.println();
		}
	}
	
	
}