package Gui.Param;

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

import Obj.*;

public class AncestryPanel extends JPanel implements ActionListener {
    
    // controls
    private JRadioButton admixBox;
    private JRadioButton noadmixBox;
    private JRadioButton linkageBox;
    private JRadioButton popinfoBox;

    private  ButtonGroup bp;

    private JButton admixButton;
    private JButton noadmixButton;
    private JButton linkageButton;
    private JButton popinfoButton;

    private JButton defaultButton;

        
    private RecombineDlg recombineDlg;
    private PopinfoDlg popinfoDlg;
    private AdmixDlg admixDlg;
    

    // v2.3 new features
    private JCheckBox noadmixPriorBox;
    private JCheckBox admixPriorBox;

    
    // data members
    private boolean noadmix = false;
    private boolean admix = true;
    private boolean popinfo = false;
    private boolean recomb = false;
    private boolean locationprior = false;
    
    // data model
    private NSimObj sim;
    
    public AncestryPanel(NSimObj sim){
	
	this.sim = sim;
	
	bp = new ButtonGroup();
	admixBox      = new JRadioButton("Use Admixture Model");
	bp.add(admixBox);
	admixBox.setActionCommand("admixbox");
	admixBox.addActionListener(this);
	
	noadmixBox    = new JRadioButton("Use No Admixture Model");
	bp.add(noadmixBox);
	noadmixBox.setActionCommand("noadmixbox");
	noadmixBox.addActionListener(this);
	
	noadmixPriorBox = new JCheckBox("Use sampling locations as prior (LOCPRIOR)");
	noadmixPriorBox.setActionCommand("locationprior");
	noadmixPriorBox.addActionListener(this);
	admixPriorBox   = new JCheckBox("Use sampling locations as prior (LOCPRIOR)");
	admixPriorBox.setActionCommand("locationprior");
	admixPriorBox.addActionListener(this);
	
	JPanel boxpane1 = new JPanel();
	boxpane1.add(new JLabel());
	boxpane1.add(noadmixPriorBox);
	
	JPanel boxpane2 = new JPanel();
	boxpane2.add(new JLabel());
	boxpane2.add(admixPriorBox);

	linkageBox    = new JRadioButton("Use Linkage Model");
	bp.add(linkageBox);
	linkageBox.setActionCommand("linkagebox");
	linkageBox.addActionListener(this);
	
	popinfoBox = new JRadioButton("Use Population Information to test for migrants");
	bp.add(popinfoBox);
	popinfoBox.setActionCommand("popinfobox");
	popinfoBox.addActionListener(this);
	
	admixButton = new JButton("Advanced ...");
	admixButton.setActionCommand("admixbutton");
	admixButton.addActionListener(this);

	noadmixButton = new JButton("Advanced ...");
	noadmixButton.setVisible(false);
	
	linkageButton = new JButton("Advanced ...");
	linkageButton.setActionCommand("linkagebutton");
	linkageButton.addActionListener(this);
	
	popinfoButton = new JButton("Advanced ...");
	popinfoButton.setActionCommand("popinfobutton");
	popinfoButton.addActionListener(this);
	
	JPanel pt1 = new JPanel();
	pt1.add(noadmixButton);

	JPanel pt2 = new JPanel();
	pt2.add(admixButton);
	
	JPanel pt3 = new JPanel();
	pt3.add(linkageButton);
	
	JPanel pt4 = new JPanel();
	pt4.add(popinfoButton);

	
	JPanel p1 = new JPanel();
	p1.setLayout(new GridLayout(0,1));
	p1.add(noadmixBox);
	p1.add(boxpane1);
	p1.add(admixBox);
	p1.add(boxpane2);
	p1.add(linkageBox);
	p1.add(popinfoBox);

	JPanel p2 = new JPanel();
	p2.setLayout(new GridLayout(0,1));
	p2.add(pt1);
	p2.add(new JLabel());
	p2.add(pt2);
	p2.add(new JLabel());
	p2.add(pt3);
	p2.add(pt4);
	

	JPanel topPane = new JPanel();
	JLabel title = new JLabel("Select ONE from the following:");
	topPane.add(title, BorderLayout.CENTER);
	topPane.setPreferredSize(new Dimension(500,30));
	JPanel bottomPane = new JPanel();
	defaultButton = new JButton ("Default Setting");
	defaultButton.setActionCommand("default");
	defaultButton.addActionListener(this);
	
	bottomPane.add(defaultButton);
	bottomPane.setPreferredSize(new Dimension(500,30));

	JPanel mainPane = new JPanel();
	GridBagLayout gridbag = new GridBagLayout();
        GridBagConstraints c = new GridBagConstraints();
	mainPane.setLayout(gridbag);
	c.fill = GridBagConstraints.BOTH;
	c.gridx = 0;
	c.gridy = 0;
	c.weightx = 1;
		
	gridbag.setConstraints(topPane, c);
	mainPane.add(topPane);
	
	c.gridx = 0;
	c.gridy = 1;
	c.weightx = 0.5;
	c.insets = new Insets(10,70,10,0);
	gridbag.setConstraints(p1, c);
	mainPane.add(p1);
	c.gridx = 1;
	c.gridy = 1;
	c.weightx = 0.5;
	c.insets = new Insets(10,0,10,70);
	gridbag.setConstraints(p2, c);
	mainPane.add(p2);
	
	c.gridx = 0;
	c.gridy = 2;
	c.weightx = 1;
	c.insets = new Insets(10,175,10,0);
	gridbag.setConstraints(bottomPane, c);
	mainPane.add(bottomPane);
	
	
	mainPane.setPreferredSize(new Dimension(500,225));
	
	
	this.setLayout(new BorderLayout());
	
	
	add(mainPane,BorderLayout.CENTER);
	

	if(!sim.isNew()){
	    if(sim.USEPOPINFO){
		popinfo = true;
		noadmix = false;
		admix = false;
		recomb = false;
		popinfoDlg = new PopinfoDlg(this,sim,false);
	    }else if(sim.RECOMBINE){
		popinfo = false;
		noadmix = false;
		admix = false;
		recomb = true;
		recombineDlg = new RecombineDlg(this, sim, false);
	    }else if(!sim.NOADMIX){
		popinfo = false;
		noadmix = false;
		admix = true;
		recomb = false;
		admixDlg = new AdmixDlg(this, sim, false);
	    }else{
		popinfo = false;
		noadmix = true;
		admix = false;
		recomb = false;
	    }
	    locationprior = sim.LOCPRIOR;
	}
	
	NProjObj proj = sim.getProjObj();
	if(!proj.getMapDistance()){
	    linkageBox.setEnabled(false);
	    recomb = false;
	} else if(proj.getPloidy()>2&&!proj.getPhased()){
	    linkageBox.setEnabled(false);
	    recomb = false;
	}

	if(!proj.getLocData()&&!proj.getPopId()){
	    admixPriorBox.setEnabled(false);
	    noadmixPriorBox.setEnabled(false);
	    locationprior = false;
	}
		
	updatePanelUI();
	
    }
    

    private void updatePanelUI(){
	
	noadmixBox.setSelected(noadmix);
	noadmixPriorBox.setEnabled(noadmix);
	noadmixPriorBox.setSelected(noadmix&&locationprior&&!recomb);
	admixBox.setSelected(admix);
	admixPriorBox.setEnabled(admix);
	admixPriorBox.setSelected(admix&&locationprior&&!recomb);
	admixButton.setEnabled(admix);
	linkageBox.setSelected(recomb);
	linkageButton.setEnabled(recomb);
	popinfoBox.setSelected(popinfo);
	popinfoButton.setEnabled(popinfo);
	
    }
    
    
    private void reset(){
	noadmix = false;
	admix = true;
	recomb = false;
	locationprior = false;
	popinfo = false;
	popinfoDlg = null;
	admixDlg = null;
	recombineDlg = null;
	updatePanelUI();
    }
    
    
    public void updateData(){
	

	if(noadmix){
	    sim.NOADMIX = true;
	    sim.RECOMBINE = false;
	    sim.USEPOPINFO = false;
            // bug fixed by William 05012009 
	    //return;
	}
	
	if(admix){
	    sim.NOADMIX = false;
	    sim.USEPOPINFO = false;
	    sim.RECOMBINE = false;
	    
	    if(admixDlg == null){
		sim.INFERALPHA = true;
		sim.ALPHA = 1.0f;
		sim.POPALPHAS = false;
		sim.UNIFPRIORALPHA = true;
		sim.ALPHAMAX = 10.0f;
		sim.ALPHAPROPSD = 0.025f;
	    } else {
		admixDlg.updateData();
	    }
	}
	
	sim.LOCPRIOR = locationprior;
	
	if(popinfo){
	    
	    sim.NOADMIX = true;
	    sim.USEPOPINFO = true;
	    sim.RECOMBINE = false;
	    
	    if(popinfoDlg == null){
		sim.GENSBACK = 2;
		sim.MIGRPRIOR = 0.05f;
		
		sim.POPNOADMIX = false;
		sim.INFERALPHA = true;
		sim.ALPHA = 1.0f;
		sim.POPALPHAS = false;
		sim.UNIFPRIORALPHA = true;
		sim.ALPHAMAX = 10.0f;
		sim.ALPHAPROPSD = 0.025f;
		sim.MARKOVPHASE = false;
	    } else {
		popinfoDlg.updateData();
	    }
	}
	
	if(recomb){
	    sim.NOADMIX = true;
	    sim.USEPOPINFO = false;
	    sim.RECOMBINE = true;
	    
	    if(recombineDlg == null){
		sim.USEDEFAULTADMBURNIN = true;
		sim.SITEBYSITE = false;
		sim.RSTART = -2f;
		sim.RMAX = 2f;
		sim.RSTD = 0.1f;
		sim.RMIN = -4f;
	    } else {
		recombineDlg.updateData();
	    }
	}
	    
    }

    public void actionPerformed(ActionEvent e){
	String cmd = e.getActionCommand();
	if(cmd.equals("noadmixbox")){
	    noadmix = true;
	    admix = false;
	    recomb = false;
	    popinfo = false;
	    popinfoDlg = null;
	    admixDlg = null;
	    recombineDlg = null;
	    updatePanelUI();
	    return;
	}

	if(cmd.equals("admixbox")){
	    noadmix = false;
	    admix = true;
	    recomb = false;
	    popinfo = false;
	    popinfoDlg = null;
	    recombineDlg = null;
	    updatePanelUI();
	    return;
	    
	}
	
	if(cmd.equals("linkagebox")){
	    noadmix = false;
	    admix = false;
	    recomb = true;
	    popinfo = false;
	    popinfoDlg = null;
	    admixDlg = null;
	    updatePanelUI();
	    return;
	    
	}
	
	if(cmd.equals("popinfobox")){
	    noadmix = false;
	    admix = false;
	    recomb = false;
	    popinfo = true;
	    admixDlg = null;
	    recombineDlg = null;
	    updatePanelUI();
	    return;
	}
	
	if(cmd.equals("admixbutton")){
	    if(admixDlg == null){
		admixDlg = new AdmixDlg(this,sim,true);
	    }
	    admixDlg.showDialog();
	    
	    return;
	}
	
	if(cmd.equals("locationprior"))
	    locationprior = admixPriorBox.isSelected() || noadmixPriorBox.isSelected();
	
	if(cmd.equals("linkagebutton")){
	    if(recombineDlg == null){
		recombineDlg = new RecombineDlg(this,sim,true);
	    }
	    
	    recombineDlg.showDialog();
	    return;
	}
	    
	if(cmd.equals("popinfobutton")){
	    if(popinfoDlg == null){
		popinfoDlg = new PopinfoDlg(this,sim,true);
	    }
	    
	    popinfoDlg.showDialog();
	    return;
	}
	
	if(cmd.equals("default")){
	    reset();
	    return;
	}

	
    }


}