package Gui.Wizard;

import Obj.*;
import Util.*;

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


public class WizardController extends WindowAdapter implements ActionListener
{
    //The all 4 wizard windows

    private Wizard_1 w1; 
    private Wizard_2 w2;
    private Wizard_3 w3;
    private Wizard_4 w4;
    private JFrame main;
    private Point pos;
    
    
    private File dataFile;
    
    //window control varible
    private JDialog currDlg;
    private boolean isDone;

    // date member controlled
    private NProjObj projObj;
    private String[][] data;  // the data from source file


    // use to set up connection objects
    public WizardController(JFrame main){
	this.main = main;
	isDone = false;
    }

    
    public boolean isDone(){
	return isDone;
    }
    

    public void initWizard(){
	w1 = new Wizard_1(main, this);
	w2 = new Wizard_2(main, this);
	w3 = new Wizard_3(main, this);
	w4 = new Wizard_4(main, this);
	
	
	currDlg = w1;
	w1.setLocationRelativeTo(main);
	w1.showDialog();	
	return;

	
    }

    public void windowClosing(WindowEvent e){
	projObj = null;
	destroyAll();
	super.windowClosing(e);
    }

    public void actionPerformed(ActionEvent e) {
	String action = e.getActionCommand();
	
	if(action.compareTo("w1_next")==0){
	    pos = w1.getLocation();
	    
	    String filename = w1.getDataFile();
	    
	    dataFile = new File(filename);
	    if(!dataFile.exists()){
		dataFile = null;
		JOptionPane.showMessageDialog(null,
					      "Invalid data file",
					      "Error",
					      JOptionPane.ERROR_MESSAGE);
		return;
	    }
	    w1.dispose();
	    w2.setLocation(pos);
	    w2.showDialog();
	    currDlg = w2;
	    return;
	}

	if(action.compareTo("w2_next")==0){
	    pos = w2.getLocation();
	    w2.dispose();
	    w3.setLocation(pos);
	    w3.showDialog(w2.getPloidy());
	    currDlg = w3;
	    return;
	}

	if(action.compareTo("w3_next")==0){
	    pos = w3.getLocation();
	    w3.dispose();
	    w4.setLocation(pos);
	    w4.showDialog();
	    currDlg = w4;
	    return;
	}
	
	if(action.compareTo("w4_back")==0){
	    pos = w4.getLocation();
	    w4.dispose();
	    w3.setLocation(pos);
	    w3.showDialog(w2.getPloidy());
	    currDlg = w3;
	    return;
	}
	
	if(action.compareTo("w3_back")==0){
	    pos = w3.getLocation();
	    w3.dispose();
	    w2.setLocation(pos);
	    w2.showDialog();
	    currDlg = w2;
	    return;
	}

	
	if(action.compareTo("w2_back")==0){
	    pos = w2.getLocation();
	    w2.dispose();
	    w1.setLocation(pos);
	    w1.showDialog();
	    currDlg = w1;
	    return;
	}
	
	
	if(action.compareTo("w1_cancel")==0){
	    // destroy everything then return
	    w1.dispose();
	    destroyAll();
	    return;
	}
	
	if(action.compareTo("w2_cancel")==0){
	    // destroy everything then return
	    w2.dispose();
	    destroyAll();
	    return;
	}
	
	if(action.compareTo("w3_cancel")==0){
	    // destroy everything then return
	    w3.dispose();
	    destroyAll();
	    return;
	}
	
	if(action.compareTo("w4_cancel")==0){
	    // destroy everything then return
	    w4.dispose();
	    destroyAll();
	    return;
	}

	if(action.compareTo("finish")==0){
	    buildProjObj();
	    if(projObj!=null){
		w4.dispose();
		destroyAll();
	    }
	    return;
	}  
	
	if(action.equals("datainfo")){
	    if(dataFile == null){
		JOptionPane.showMessageDialog(null,
					      "No valid data file is specified",
					      "Error",
					      JOptionPane.ERROR_MESSAGE);
		return;
	    }
	    FileCounter fc = new FileCounter(dataFile);
	    fc.report();
	    return;
	}

    }
    

    private void destroyAll(){
	w1 = null;
	w2 = null;
	w3 = null;
	w4 = null;
	isDone = true;
    }

   
    

    private void buildProjObj(){

	//
	// check all user input when user trying to build the project
	// if errors found return the string containing error messages
	// and build nothing
	//
       
	String errString = "";
	
	
	String name = w1.getProjName();
	String path = w1.getProjDir();
	File projParent = new File(path);
	if(!projParent.exists())
	    errString += new String("\n* The directory to save project does not exist");
		
	boolean indlabel = w4.getIndLabel();
	boolean popId =  w4.getPopId();
	boolean popflag = w4.getPopFlag();
	boolean genename = w3.getGeneName();
	boolean locusname = w3.getLocusName();
	boolean phaseinfo = w3.getPhaseInfo();
	boolean onerow = w3.getOneRow();
	boolean phased =false;
	boolean phenotype = w4.getPheno();
	boolean recessiveAllele = w3.getRecessiveAllele();
	boolean locData = w4.getLocData();
	String extraStr= w4.getExtraCols();
	String notambiguous="";
	
	int extraCol = 0;
	if(extraStr == null )
	    extraCol = 0;
	else {
	    try {
		extraCol = Integer.parseInt(extraStr);
	    }catch (NumberFormatException e){
		errString += new String("\n* Input in \"Extra Column\" Field is not an Integer");
	    }
	}

       
	String numIndStr = w2.getNumInds();
	int numInds = 0;
	try {
	    numInds = Integer.parseInt(numIndStr);
	}catch (NumberFormatException e){
	    errString += new String("\n* Input in \"Number of Individuals\" Field is not an Integer");
	}
	
      

	String ploidyStr = w2.getPloidy();
	int ploidy = 0;
	try {
	    ploidy = Integer.parseInt(ploidyStr);
	}catch (NumberFormatException e){
	    errString += new String("\n* Input in \"Number of Ploidy\" Field is not an Integer");
	}

	String lociStr = w2.getNumLoci();
	int numLoci = 0;
	try {
	    numLoci = Integer.parseInt(lociStr);
	}catch (NumberFormatException e){
	    errString += new String("\n* Input in \"Number of Loci\" Field is not an Integer");
	}
		
	String missingVal = w2.getMissingVal();
       
	String dataFile = w1.getDataFile();
	if(dataFile != null){
	    File f = new File(dataFile);
	    if(!f.exists())
		errString += new String("\n* The Data Source does not exist");
	}
	// End of data validation
	
	// if some errors detected
  	if(errString.compareTo("")!=0){
	    String prefix = "Errors detected when building project:\n\n";
	    errString = prefix.concat(errString);
	    errString += new String("\n\n");
	    JOptionPane.showMessageDialog(w4,
					  errString,
					  "Input errors",
					  JOptionPane.ERROR_MESSAGE);
	    return;
	} else {
	    // show a confirm message board
	    String msg = "You are about to build a Structure project with following settings:\n\n";
	    msg += new String("Project Name:  " + name);
	    msg += new String("\nProject Path:  " + path);
	    if(dataFile != null)
		msg += new String("\nData Source:  " + dataFile + "\n\n");
	    else 
		msg += new String("\nData Source: Manually Input\n\n");
	    msg += new String("\n========================================\n");
	    msg += new String("\nNumber of Individuals:  "+ numInds);
	    msg += new String("\nNumber of Loci:  " + numLoci);
	    msg += new String("\nNumber of Ploidy:  " + ploidy);
	    msg += new String("\nMissing Value represented as:  " + missingVal+"\n");
	    msg += new String("\n========================================\n");
	    
	 
	    if(genename)
		msg += new String("\nData File Contains Row of Marker Names");
	    if(locusname)
		msg += new String("\nData File Contains Row of Map Distances between Loci");
	    if(phaseinfo)
		msg += new String("\nData File Contains Phase Information");
	    if(onerow)
		msg += new String("\nData File Stores Data for Individuals in a Single Line");
	    if(indlabel)
		msg += new String("\nData File Contains Individual Labels");
	    if(popId)
		msg += new String("\nData File Contains Population Identifiers");
	    if(locData)
		msg += new String("\nData File Contains Sampling Location Information");
	    if(popflag)
		msg += new String("\nData File Contains USEPOPINFO Selection Flagn");
	    if(phenotype)
		msg += new String("\nData File Contains Phenotpye Information");
	    msg += new String("\nNumber of Other Extra Columns:  " + extraCol + "\n");  
	    
	    msg += new String("\n========================================\n");
	   
	    Object[] options = {"Proceed", "Go back"};
	    int n = JOptionPane.showOptionDialog(w4,
						 msg,		 
						 "Comfirmation",
						 JOptionPane.YES_NO_OPTION,
						 JOptionPane.QUESTION_MESSAGE,
						 null,
						 options,
						 options[0]);
	    if (n == JOptionPane.NO_OPTION) {
		return;
	    }
	    
	    
	}

	// one last qustion

	if(ploidy == 1 ){
	    phased = true;
	}
	
	if((ploidy>=3&&locusname)||(ploidy==2&&!phaseinfo&&locusname)){
	    Object[] options = {" Yes ","  No " };
	    int n = JOptionPane.showOptionDialog(null,
						 "Are the data phased ?",
						 "One more question",
						 JOptionPane.YES_NO_OPTION,
						 JOptionPane.QUESTION_MESSAGE,
						 null,
						 options,
						 null);
	    if(n == JOptionPane.YES_OPTION)
		phased = true;
	    else
		phased = false;
	}
	
	
	if(ploidy>=3&&recessiveAllele){
	    
	    String sC = null;
	    while(sC==null){
		sC=JOptionPane.showInputDialog("Indicator code for locus without genotypic ambiguity");
		if(sC.equals(missingVal)){
		    JOptionPane.showMessageDialog(null,
						  "Indicator code must be different from missing value",
						  "Error",
						  JOptionPane.ERROR_MESSAGE);
		    sC = null;
		}
	    }
	    notambiguous = sC;
	}
	
	
	// if reaches here build the project 
	projObj = new NProjObj(name, path,
			      indlabel, popId,
			      extraCol, numInds,
			      ploidy, numLoci,
			      missingVal, dataFile,
			      popflag, genename,
			      locusname, phaseinfo,
			      onerow, phased, phenotype,recessiveAllele,locData);
	
	if(ploidy>=3&&recessiveAllele)
	    projObj.setNAMBCode(notambiguous);
	
	data = projObj.loadData();
	if(data == null){
	    // bad data format, discard this projObj
	    String expection = new String("The data file is expected to have following format:\n\n");
	    if(genename)
		expection += "1 row with "+numLoci+" entries (marker name) \n";
	    if(recessiveAllele)
		expection += "1 row with "+numLoci+" entries (recessive allele) \n";
	    if(locusname)
		expection += "1 row with "+numLoci+" entries (map distance) \n";
	    if(phaseinfo)
		expection += ""+numInds+" rows with "+ numLoci+ " entries (phase information)\n";
	    int rowcount = ploidy;
	    if(onerow)
		rowcount = 1;
	    int datarow = rowcount*numInds;
	    int colcount = numLoci;
	    if(onerow)
		colcount = numLoci*ploidy;
	    if(indlabel)	    
		colcount++;
	    if(popId)
		colcount++;
	    if(locData)
		colcount++;
	    if(popflag)
		colcount++;
	    colcount+= extraCol;
	    expection += ""+datarow+" rows with "+colcount+" entries (data)\n\n";
	    JOptionPane.showMessageDialog(null,
					  expection,
					  "Structure Wizard",
					  JOptionPane.INFORMATION_MESSAGE);
	    
	    projObj = null;
	}
    }
	    


    public File getDataFile(){
	return dataFile;
    }
    
    public String[][] getData(){
	return data;
    }
    
    public NProjObj getProjObj(){
	return projObj;
    }
  
    //           Utility   Method                             //

    /**********************************************************/
    /***** opens a file for reading, returning a file ref *****/
    private static InputStream OpenInputFile(String filename){
	
	InputStream  in;
	
	try {  // try to open input file so we can input data...
	    in = new FileInputStream(filename);
	} catch (FileNotFoundException e) {
	    System.err.println("**Error: unable to open input file.");
	    in = null;
	}//try-catch
	
	return in;
    }
    
    
    
}