package Tree;

import Util.*;
import java.net.*;

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

import Controller.*;

import Triangle.*;

import Postscript.*;
import interpreter.*;


import java.awt.*;
import java.awt.event.*;
import java.awt.geom.*;
import javax.swing.*;
import javax.swing.border.*;

import java.net.*;
import com.sun.jimi.core.*;
import java.awt.image.BufferedImage;
import com.sun.jimi.core.raster.*;

import sun.awt.image.codec.JPEGImageEncoderImpl;

import java.io.ByteArrayOutputStream;
import java.awt.Frame;
import java.awt.Graphics;
import java.awt.image.BufferedImage;
//import java.nio.file.StandardCopyOption.*;
import java.lang.String.*;

public class TreePlotManager extends JApplet implements ActionListener, Runnable {
//public class TreePlotManager {
	
    private StructureApp app;
    
    private String datafile; // the data file
    
    //private int popsize;
    private JComboBox[] palettelist;
    private Hashtable colormap;
    
    private Vector idVec;
   
    private int leftindex;  // the index to the bottom left corner
    private int rightindex; // the index to the bottom right corner
    private double[][] data;
    private int[] id;
    
    private File[] runlist;
    private String[] simlist;
    private Color[] colorlist;
 
    private int simlist_select;
    private int filelist_select;
    private int bleft_select;
    private int bright_select;

	private Frame frame;
	private int K;
	private Process proc; // the running process
	
	private String parameterSetName;
	private String plotFile;
	private String plotFileName;
	
	private String []pieces;
	
	static String postscriptFiles[] = {"test-parameter-set_run_5_f"};
	
    static JComboBox combo;
    static URL url;
    JPanel p1;
    Demo demo;
 	
    public TreePlotManager(StructureApp app,String[] simList,String plottingSimName,String plottingFilePath,String plotString){
		
		//System.out.println(plotString);
		
		//String plotFileName;
		
		plotString = plotString.replaceFirst(plottingSimName,"");
		plotString = plotString.replace("(","");
		plotString = plotString.replace(")","");
	
		plotFileName = plotString;
		
		//System.out.println(plotFileName);
		
		parameterSetName = plottingSimName;
		
		//System.out.println(parameterSetName);
		
		//pieces = plottingFilePath.split("/");
		
		//System.out.println(pieces[pieces.length-1]);
		//System.out.println(plottingFilePath);
		//System.out.println(simList[0]);
		
		//String fileSep = System.getProperty("file.separator");
		//pieces = plottingFilePath.split(fileSep);
		
		//could be a portability issue ##portable##
		//plotFile = "library/neighbor/plots/"+pieces[pieces.length-1];
		plotFile = "library/neighbor/plots/"+plotString;
		
		//plotFile = System.getProperty("user.dir")+fileSep+"library"+fileSep+"neighbor"+fileSep+"plots"+fileSep+pieces[pieces.length-1];
		
		
		//System.out.println(plotFile);
		
		this.app = app;
		if(simList==null || simList.length == 0)
			return;
		simlist = new String[simList.length+1];
		simlist[0] = "Select one";
		for(int i=0;i<simList.length;i++){
			//System.out.println("Simulation List: "+simList[i]);
			simlist[i+1] = simList[i];
		}
			
    }

    public TreePlotManager(){
    
	}
	
	public Integer getK(String paramset, String filename){		
		try{
			// Open the file that is the first 
			// command line parameter
			FileInputStream fINstream = new FileInputStream(filename);
			// Get the object of DataInputStream
			DataInputStream in = new DataInputStream(fINstream);
			BufferedReader br = new BufferedReader(new InputStreamReader(in));
			String strLine;
			//Read File Line By Line
			
			K=0;
						
			while ((strLine = br.readLine()) != null)   {	
				if (strLine.indexOf("populations assumed") >= 0){
					StringTokenizer st = new StringTokenizer(strLine);
					K = Integer.valueOf(st.nextToken());
					//return K;
				}
			} //end while loop
			
			//Close the input stream
			in.close();
			}catch (Exception e){
				System.err.println("Error: " + e.getMessage());
			}
			return K; 
	}//end getK

	public void parseDistanceMatrix(String paramset, String filename){
		//System.out.println(paramset);
		String userDir = System.getProperty("user.dir");
		//System.out.println(userDir);

		
		
		try{
			// Open the file that is the first 
			// command line parameter
			FileInputStream fINstream = new FileInputStream(filename);
			// Get the object of DataInputStream
			DataInputStream in = new DataInputStream(fINstream);
			BufferedReader br = new BufferedReader(new InputStreamReader(in));
			String strLine;
			//Read File Line By Line
			
			int matrixRow = 0;
			boolean flag = false;
			
			try{
				// Create file 
				//FileWriter fOUTstream = new FileWriter("./library/neighbor/plots/infile");
				//System.out.println(userDir+"/library/neighbor/plots/infile");
				FileWriter fOUTstream = new FileWriter(userDir+"/library/neighbor/plots/infile");
				
				BufferedWriter out = new BufferedWriter(fOUTstream);
				
				while ((strLine = br.readLine()) != null)   {
							
					if (strLine.indexOf("populations assumed") >= 0){
						StringTokenizer st = new StringTokenizer(strLine);
						K = Integer.valueOf(st.nextToken());
						//The phylip algorithm is very picky about the input file, hence the preprocessing. 
						out.write("    "+K);
						out.newLine();
					}
						
					if (strLine.indexOf("Net nucleotide distance") >= 0){ flag = true; }
	
					if (matrixRow > 3 && matrixRow < (3 + K + 1) ){
						//The phylip algorithm is very picky about the input file, hence the preprocessing. 
						strLine = strLine.replace("   -  ","0.0000");
						strLine = strLine.replace("   ","            ");
						out.write(strLine);
						out.newLine();
						//System.out.println(strLine);
					}
			
					if (flag){ matrixRow++; }
				} //end while loop
				
			//Close the output stream
			out.close();
			}catch (Exception e){
				System.err.println("Error: " + e.getMessage());
			}
			
		//Close the input stream
		in.close();
		}catch (Exception e){
			System.err.println("Error: " + e.getMessage());
		}
	}
		
	public void runNeighborAlgorithm(String paramset, String filename){

		//String userDir = System.getProperty("user.dir");
		//String fileSep = System.getProperty("file.separator");
		
		//String []pieces = filename.split("/");
		//System.out.println(userDir);
		//System.out.println(fileSep);
		//String []pieces = filename.split(fileSep);
		//String []pieces = filename.split("/");
		
		String paraSet = paramset;
		//String resultFile = pieces[pieces.length-1];

		try {
		    String str;
			//System.out.println(userDir+fileSep+"library"+fileSep+"neighbor"+fileSep+"neighbor "+resultFile);
			//System.out.println("library/neighbor/neighbor "+plotFileName);
			
			//String dataFolder = System.getProperty("user.dir") +
			//System.getProperty("file.separator") + "data";
			//System.out.println("Data Folder = " + dataFolder);
			
			
		    proc = Runtime.getRuntime().exec("library/neighbor/neighbor "+plotFileName);
		    //proc = Runtime.getRuntime().exec(userDir+fileSep+"library"+fileSep+"neighbor"+fileSep+"neighbor "+resultFile);
			
			BufferedReader proc_in = new BufferedReader( new InputStreamReader(proc.getInputStream())); 

		    try {
				while ((str = proc_in.readLine()) != null){
					//output from the c routines.  
				    //System.out.print(str+"\n");
				}
	        }
			catch (IOException e) {
                System.exit(0);
				return;
	        }                                        

		}
		catch (IOException e1) {
		    System.err.println(e1);
		}
	}
	
	public void createTreePlot(String paramset, String filename){
		//System.out.println("Creating Tree Plot Window");
		//String userDir = System.getProperty("user.dir");
				
		JLabel pname = new JLabel("Parameter set:");
		JLabel rname = new JLabel("    Result file:");
		
		//String fileSep = System.getProperty("file.separator");
		//String []pieces = filename.split(fileSep);
		//String []pieces = filename.split("/");
		
		String[] paraSet = {paramset};
		
		//String[] resultFile = {pieces[pieces.length-1]};
		String[] resultFile = {plotFileName};
		
		//final String resultFileStr = pieces[pieces.length-1];
		final String resultFileStr = plotFileName;
		
		JComboBox paraList = new JComboBox(paraSet);
		JComboBox resultFileList = new JComboBox(resultFile);
		
		paraList.disable();
		resultFileList.disable();
			
		JPanel ptop = new JPanel(new FlowLayout());
		
		ptop.setBackground(Color.gray);
		
		ptop.add(pname);
		ptop.add(paraList);
		ptop.add(rname);
		ptop.add(resultFileList);

		JPanel p1 = new JPanel(new FlowLayout());
		JPanel p2 = new JPanel(new BorderLayout());
		
        EmptyBorder eb = new EmptyBorder(5,20,10,20);
        p1.setBorder(eb);
        p1.setBackground(Color.gray);
		
        p1.setToolTipText("click to start/stop iterating");
        p1.addMouseListener(new MouseAdapter() {
            public void mouseClicked(MouseEvent e) {
                if (demo.thread == null) demo.start(); else demo.stop();
            }
        });

        getContentPane().add("South", p1);
		getContentPane().add("North", ptop);

        
        eb = new EmptyBorder(20,20,5,20);
        BevelBorder bb = new BevelBorder(BevelBorder.LOWERED);
        p2.setBorder(new CompoundBorder(eb,bb));
        p2.setBackground(Color.gray);
        p2.add(demo = new Demo());

        getContentPane().add("Center", p2);

		//System.out.println(resultFileStr);
		
		//System.out.println(plotFile);
		//System.out.println("../library/neighbor/plots/"+resultFileStr);
		//System.out.println(userDir+"/library/neighbor/plots/"+resultFileStr);
		
        //url = PostscriptViewer.class.getResource(userDir+"/library/neighbor/plots/"+resultFileStr);
		//url = PostscriptViewer.class.getResource(plotFile);
		
		//url = PostscriptViewer.class.getResource("../library/neighbor/plots/"+resultFileStr);
		//url = PostscriptViewer.xxxxxcc("../library/neighbor/plots/"+resultFileStr);
		//url = "file:"+plotFile;
		
		//System.out.println(url);
		File file = new File(plotFile);
		
		try {
	        url = file.toURL();          // file:/d:/almanac1.4/java.io/filename
	    } 
		catch (MalformedURLException e) {
	    
		}
	    
		
		
		JButton saveButton = new JButton("Save");
		JButton closeButton = new JButton("Close");
		
		saveButton.addActionListener(this);
		saveButton.setActionCommand("save");
		saveButton.setEnabled(true);
		
		
		closeButton.addActionListener(this);
		closeButton.setActionCommand("close");
		closeButton.setEnabled(true);
		
		p1.add(saveButton, BorderLayout.CENTER);
		
		frame = new Frame("Neighbor Joining Tree - Structure");
		
		WindowListener l = new WindowAdapter() {
			public void windowClosing(WindowEvent e) {
				frame.dispose();
				deletefile(plotFile);
			}	
		};
		
		frame.addWindowListener(l);
		frame.add("Center", this);
		
		frame.pack();
        
		int w = 400*2; 
        int h = 400*2;
		
		frame.setSize(new Dimension(w, h));
		
        Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
		
		frame.setLocation(screenSize.width/2 - w/2, screenSize.height/2 - h/2); //the position of the window
		frame.show();
				
	}

	public void actionPerformed(ActionEvent e) {
		
		String action = e.getActionCommand();
		
		//System.out.println(action);

		if(action.equals("save")){
			
		    JFileChooser fc = new JFileChooser();
		    GeneralFileFilter jpgFilter = new GeneralFileFilter("ps", "POSTSCRIPT image files");
		    fc.addChoosableFileFilter(jpgFilter);
		    int returnVal = fc.showDialog(frame,"Save");

		    if (returnVal == JFileChooser.APPROVE_OPTION){ 

				File file = fc.getSelectedFile();
				String fname = file.getAbsolutePath();
				if(!fname.endsWith(".jpg")&&!fname.endsWith(".ps"))
				    file = new File(new String(fname+".ps"));

				//check if file exists
				if(file.exists()){
				    Object[] options = {"Yes",
							"No "};

				    int n=JOptionPane.showOptionDialog(frame,
								       "Target file "+file.getName()+" already exists, Overwrite it?",
								       "Save image",
								       JOptionPane.YES_NO_OPTION,
								       JOptionPane.QUESTION_MESSAGE,
								       null,
								       options,
								       options[1]);
				    if(n==JOptionPane.NO_OPTION)
					return;
				}
				File fc_dir = file.getParentFile();
				if(!fc_dir.canWrite()){
				    JOptionPane.showMessageDialog(null,
								  "Can not write image file: permission denied",
								  "Error",
								  JOptionPane.ERROR_MESSAGE);
				    return;
				}
			
				demo.saveImagePlotFile(file.getAbsolutePath(),plotFile);
		    }
		}
		
		
		if(action.equals("close")){
			frame.dispose();
		}

	}

	public void deletefile(String file){
		File f1 = new File(file);
		boolean success = f1.delete();
		if (!success){
			System.out.println("Deletion failed.");
			System.exit(0);
		}else{
			//System.out.println("File deleted.");
		}
	}

	public void run() {
        demo.repaint();
    }
	
	static class Demo extends Canvas implements Runnable {

        Thread thread; 
		Graphics2D g2;
		BufferedImage image;
		Graphics fg;

        public Demo() {
            setBackground(Color.white);
        }
    
        public void paint(Graphics g) {			
            Dimension d = getSize();
            Graphics2D g2 = (Graphics2D) g;
			//System.out.println(d);
            //double s = Math.min(d.width, d.height) / 800.0;
			double s = Math.min(d.width, d.height) / 700.0;
			
            PAContext context = new PAContext(g2, d);

            if (s != 1.0){
                AffineTransform fitInPage = new AffineTransform();
                fitInPage.scale(s*(1.2),s*(0.9));
				//fitInPage.scale(s,s);
                g2.transform(fitInPage);
            }
            try {
                InputStream inputStream = url.openStream();
                context.draw(inputStream);	
                inputStream.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }

	    public void saveImage(String filename){	
			BufferedImage image = new BufferedImage(420,380,BufferedImage.TYPE_INT_RGB);	

			Graphics fg = (Graphics2D)image.getGraphics();
			this.paint(fg);

			try {
			    File f = new File(filename);
			    JimiRasterImage jrf = Jimi.createRasterImage(image.getSource());
			    FileOutputStream fos=null;
			    try { 
				fos =new FileOutputStream(f);
			    }catch (Exception ee) { };

			    if(fos != null)
				Jimi.putImage("image/jpeg",jrf,fos);
			}catch (JimiException je) {je.printStackTrace();}
			// end testing code
	    }
		
		public void saveImagePlotFile(String filename, String plotfile) {
			
			//System.out.println(filename);
			//String srFile = "library/neighbor/plots/plotfile";
			
			String dtFile = filename;
			String srFile = plotfile;
			
			try{
				File f1 = new File(srFile);
				File f2 = new File(dtFile);
				
				InputStream in = new FileInputStream(f1);

				//For Overwrite the file.
				OutputStream out = new FileOutputStream(f2);

				byte[] buf = new byte[1024];
				int len;
				
				while ((len = in.read(buf)) > 0){
					out.write(buf, 0, len);
				}
				in.close();
				out.close();

			}
			catch(FileNotFoundException ex){
				System.out.println(ex.getMessage() + " in the specified directory.");
				System.exit(0);
			}
			catch(IOException e){
				System.out.println(e.getMessage());      
			}
	  	}
		
        public void start() {
            if (thread != null) {
                return;
            }
            thread = new Thread(this);
            thread.setPriority(Thread.MIN_PRIORITY);
            thread.start();
        }
    
        public synchronized void stop() {
            if (thread != null) {
                thread.interrupt();
            }
            thread = null;
        }
    
        public void run() {
            Thread me = Thread.currentThread();
            while (thread == me) {
                for (int i = 0; i < postscriptFiles.length; i++) {
                    combo.setSelectedIndex(i);
                    try {
                        thread.sleep(6000);
                    } catch (InterruptedException e) { return; }
                }
            }
            thread = null;
        } 
    } // End Demo class
    
/*
	public static void main(String args[]){
		TreePlotManager tpm = new TreePlotManager();

	}
*/
}