package edu.sdsc.plantsp.vis;

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

import java.util.*;
import java.awt.List;

import java.awt.Scrollbar;

import edu.sdsc.plantsp.*;

import java.io.*;
import java.net.*;

import edu.sdsc.plantsp.model.*;
import edu.sdsc.plantsp.util.*;


public class ExonController extends JPanel implements ExonControllerInterface
{
	private int mode_=0;
	private static int createNew=2;
	private static int modifyExisting=1;
	
	private ArrayList exonList = new ArrayList();

	private sequenceViewer dnaSeqViewer_;
	private ExonViewerInterface eviewer;
	private ExonProteinViewerInterface epviewer;
	
	private String BPseq;
	private String Target; 
	 
	private ArrayList seqs = new ArrayList();
	private ArrayList exons = new ArrayList();
	private JPanel jp  = new JPanel();
    private JScrollPane scrollPane;
    
	private URL codeBase_;
	private URL documentBase_;
	private String serverPath_;
	
	private static boolean reduceZoom = true;
	private static boolean increaseZoom = true;
	

	public ExonController(Component evSibling, Component avSibling)
	{
		eviewer = (ExonViewerInterface)evSibling;
		epviewer = (ExonProteinViewerInterface)avSibling;
		jp.setBackground(Color.white);
		jp.setLayout(new BoxLayout(jp, BoxLayout.Y_AXIS));		
		scrollPane = new JScrollPane(jp);
		this.setLayout(new BorderLayout());
		this.add(scrollPane, BorderLayout.CENTER);		
	}
	
	public void initialize()
	{
		buildModel();
		
		String[] AA = new String[3];
		char[] sequence = BPseq.toCharArray();
		for (int offset=0; offset<3; offset++)
		{
			StringBuffer result = BaseToProtein.translateBaseSequenceToProtein(sequence, 
			offset, '.');
			AA[offset] = result.toString();
		}		

		eviewer.updateExons(exons, 0);
		
		for (int offset=0; offset<3; offset++)
		{
			seqs.add(new sequenceViewer(this, AA[offset]));
		}
		dnaSeqViewer_ = new sequenceViewer(this, BPseq);
		seqs.add(dnaSeqViewer_);

		
		// Setup AlignmentViewer
		epviewer.setTargetProtein(Target);
		epviewer.updateModel(getExonProtein());
		epviewer.buildModel();
		
		sequenceViewer tmp;
		for (int i=0; i<seqs.size(); i++)
		{
			tmp = (sequenceViewer)seqs.get(i);
			jp.add(tmp);
			tmp.setGeneStructures(exons);
		}
	
		JViewport jvp = scrollPane.getViewport();
		Dimension d = jvp.getViewSize();
		System.out.println("viewport width ="+d.getWidth());
		System.out.println("viewport height ="+d.getHeight());
		
		//jvp.setExtentSize(new Dimension((int)Math.round(d.getWidth()), (int)Math.round(d.getHeight())+22));
		jvp.setExtentSize(new Dimension((int)Math.round(d.getWidth()), 200));
		this.validate();
	
	}
	
	private void combineExons()
	{
		for (int i=0; i<exons.size()-1; i++)
		{
			Exon exon1 = (Exon)exons.get(i);
			Exon exon2 = (Exon)exons.get(i+1);
			if (exon1.contains(exon2.getStart())||exon1.contains(exon2.getEnd()))
			{
				//System.out.println("found duplicate !!! ");
				exon2.setDuplicate();
				exon1.expand(exon2.getStart(), exon2.getEnd());
			}
		}
		
		// Now remove duplicate Exons.
		for (int i=0; i<exons.size(); i++)
		{
			//System.out.println("i="+i);
			Exon exon = (Exon)exons.get(i);
			if (exon.isDuplicate())
			{
				exons.remove(i);
				//System.out.println("****  removed element "+i+" exon "+exon.getName());
				i--;
			}
		}
	}
	
	public void modify(int anchorEnd, int newActiveEnd)
	{
		sequenceViewer tmp = null;
		boolean flag = false;
		
		for (int i=0; i<seqs.size(); i++)
		{
			tmp = (sequenceViewer)seqs.get(i);
			tmp.setSelectedArea(anchorEnd, newActiveEnd);
		}
		
		for (int i=0; i<exons.size(); i++)
		{
			Exon exon = (Exon)exons.get(i);
			if (exon.intervalOverlaps(newActiveEnd))
			{
				exon.modifyStructure(anchorEnd, newActiveEnd);
				flag = true;
				mode_=modifyExisting;
			}
		}
		
		if (!flag)
		{
			// create a new exon
			//System.out.println("creating a new exon: "+anchorEnd+", "+newActiveEnd);
			Exon exon = new Exon(anchorEnd, newActiveEnd);
			mode_=createNew;
			exon.setCurrent();
			int index = exons.size()+1;
			String name = "exon "+index;
			exon.setName(name);
			//System.out.println("new exon, name = "+name);
			exons.add(exon);
		}
		combineExons();
		Collections.sort(exons);

		eviewer.updateExons(exons, newActiveEnd);
		epviewer.updateModel(getExonProtein());
	}
	
	private ArrayList getExonProtein()
	{
		ArrayList al = new ArrayList();
		Exon exon;
		StringBuffer transBuf = new StringBuffer();
		String seq, trans;

		for (int i=0; i<exons.size(); i++)
		{
			exon = (Exon)exons.get(i);
			seq = dnaSeqViewer_.getSequence(exon.getStart(), exon.getEnd());
			char[] seq2 = seq.toCharArray();
			for (int offset=0; offset<3; offset++)
			{
				transBuf = (BaseToProtein.translateBaseSequenceToProtein(seq2, offset));
				if (!(transBuf.charAt(0)=='*')) 
				{
					break;
				}
				else if (offset==2)  // case none of these are valid
				{
					//transBuf.delete(0, transBuf.length()-1);
					System.out.println("No valid sequences within this Exon!");
					transBuf.replace(0, transBuf.length()-1, "");
				}
			}
			al.add(transBuf);
		}
		return al;
	}
	
	public void modify(int anchorEnd)
	{
		sequenceViewer tmp = null;
		
		// increase font size as a test
		//zoom(false);
		
		for (int i=0; i<seqs.size(); i++)
		{
			tmp = (sequenceViewer)seqs.get(i);
			tmp.setAnchorEnd(anchorEnd);
		}
		for (int i=0; i<exons.size(); i++)
		{
			Exon exon = (Exon)exons.get(i);
			exon.setStatus(anchorEnd);
		}
		eviewer.updateExons(exons, anchorEnd);
	}
	
	public void zoom(boolean zoom)
	{
		sequenceViewer tmp = null;
		
		if (zoom)
		{
			for (int i=0; i<seqs.size(); i++)
			{
				tmp = (sequenceViewer)seqs.get(i);
				reduceZoom = tmp.zoomOut();  // reduce font size
			}
		}
		else
		{
			for (int i=0; i<seqs.size(); i++)
			{
				tmp = (sequenceViewer)seqs.get(i);	
				increaseZoom = tmp.zoomIn();  // increase font size
			}
		}
		
		Dimension d = dnaSeqViewer_.minimumSize();
		Dimension e = jp.getMinimumSize();
		int existingHeight = (int)e.getHeight();
		int newWidth = (int)d.getWidth();
		jp.setSize(newWidth, existingHeight);
		jp.validate();
	}
	
	public void setExonViewer(Component sibling)
	{
		eviewer = (ExonViewerInterface)sibling;
	}
	
	public void setCodebase(URL codeBase)
	{
		System.out.println("setCodebase: "+codeBase.toString());
		codeBase_ = codeBase;
	}

	public void setDocumentBase(URL documentBase)
	{
		System.out.println("setDocumentBase: "+documentBase.toString());
		documentBase_ = documentBase;
	}
	
	public void setServerpath(String serverPath)
	{
		System.out.println("setServerpath: "+serverPath.toString());
		serverPath_ = serverPath;
	}
	
	private void buildModel()
	{
		// Create amino sequences based on base pair sequence.
		String id = "52024";
		ArrayList fromCgi = new ArrayList();
		
		CgiClient cgiC = new CgiClient(codeBase_, serverPath_);
		cgiC.setCgiParam("52024");
		cgiC.setCgiKey("?id=");

		fromCgi = cgiC.PostForm();

		String tstr; 
		String type="";
		String begin="";
		String end="";

		for (int i=0; i<fromCgi.size(); i++)
		{
			tstr = (String)fromCgi.get(i);
			StringTokenizer str = new StringTokenizer(tstr, "=");
			String tmp = str.nextToken();
			tmp = tmp.trim();
			if (tmp.equals("DNA"))
			{
				BPseq = str.nextToken();
			}
			if (tmp.equals("Protein"))
			{
				Target = str.nextToken();
			}
			if (type.equals("exon"))
			{
				if (tmp.equals("begin"))
				{
					begin = str.nextToken();
				}
				if (tmp.equals("end"))
				{
					int s,e;
					end = str.nextToken();
					end = end.trim();
					Integer beginI = new Integer(begin);
					s = beginI.intValue();
					Integer endI = new Integer(end);
					e = endI.intValue();
					exons.add(new Exon(s, e));
				}
			}
			if (tmp.equals("type")) 
			{
				type = str.nextToken();
			}
		}
	}	
}