package Loader;

import java.io.*;
import java.util.*;

public class Decoder {

    
    // input files 
    private String rstFile;
    private String runtimeFile;

    // positioning Vector
    private Vector posVec;

    // data storage 
    private Vector fstVec;
    private Vector alphaVec;
    //private Vector lambdVec;
    
    private Vector   recVec;
    private Vector   llhdVec;  
    private Vector   lnpdVec;

    private int countFst=0;
    private int countAlpha=0;
    private int countLambd=0;
    private int countKLD=0;
    private int countRec=0;
    private int countLike=0;
    private int countLnpd=0;

    private int burnin=0;
    
    double[][] fst_array;
    double[][] alpha_array;
    double[][] llhd_array;
    double[][] rec_array;
    double[][] lnpd_array;

    // controlling bits
    boolean record = false;

    public Decoder(String rstFile, String runtimeFile){
	this.rstFile = rstFile;
	this.runtimeFile = runtimeFile;
    }

    
    public String getRstContent(){
	
	StringBuffer buffer = new StringBuffer();
	String content = "";
	
	try {
	    FileInputStream fis = new FileInputStream(rstFile);
	    InputStreamReader isr = new InputStreamReader(fis,"UTF8");
	    
	    Reader in = new BufferedReader(isr);
	    int ch;
	    while ((ch = in.read()) > -1) {
		buffer.append((char)ch);
	    }
	    in.close();
	    content = buffer.toString();
	} catch (IOException e) {
	    return null;
	}
	
	return content;
    }
	
 

    public void readRuntimeData(){
		
	StringBuffer buffer = new StringBuffer();
	String content = "";
	
	try {
	    FileInputStream fis = new FileInputStream(runtimeFile);
	    InputStreamReader isr = new InputStreamReader(fis,"UTF8");
	    
	    Reader in = new BufferedReader(isr);
	    int ch;
	    while ((ch = in.read()) > -1) {
		buffer.append((char)ch);
	    }
	    in.close();
	    content = buffer.toString();
	} catch (IOException e) {
	    return;
	}
	
	String str = new String();
	StringTokenizer file_st = new StringTokenizer(content,"\n");
	while(file_st.hasMoreTokens()){
	    
	    str = file_st.nextToken();
	    
	    if(str.startsWith("BURNIN completed")){
		if(countLike!=0)
		    burnin = llhdVec.size()/2;
		else if(countFst!=0){
		    Vector v = (Vector)fstVec.elementAt(0);
		    burnin = v.size()/2;
		}else if(countAlpha!=0){
		    Vector v = (Vector)alphaVec.elementAt(0);
		    burnin = v.size()/2;
		}else if(countRec!=0){
		    burnin = recVec.size()/2;
		}
	    }
	    if(str.indexOf("MCMC completed")>=0)
		break;
	    if(str.indexOf("Rep#")>=0){
		parseTitle(str);
		record = true;
		continue;
	    }
	    if(record){
		parseData(str);
	    }
	    
	}
	// System.out.println(countRec+" "+countLambd+" "+countAlpha+" "+countFst+" "+countKLD+" "+countLike+" "+countLnpd);
	/*
	Vector v = (Vector)alphaVec.elementAt(0);
	for(int i=0;i<v.size();i++)
	    System.out.println(v.elementAt(i));
	*/
	genPlotData();
	
    }

    private void parseTitle(String str){
	StringTokenizer st = new StringTokenizer(str);
	String key = new String();
	int fst=0;
	int alpha=0;
	int lnpd=0;
	int like=0;
	int kld=0;
	int rec=0;
	int lambd=0;
	while(st.hasMoreTokens()){
	    key = st.nextToken();
	    if(key.equals("r")){
		rec++;
		continue;
	    }
	    
	    if(key.startsWith("Lambda")){
		lambd++;
		continue;
	    }
	    if(key.startsWith("Alpha")){
		alpha++;
		continue;
	    }
	    if(key.startsWith("F")){
		fst++;
		continue;
	    }
	    if(key.startsWith("D")){
		kld++;
		continue;
	    }
	    if(key.equals("Like")){
		like++;
		continue;
	    }
	    if(key.equals("P(D)")){
		lnpd++;
		continue;
	    }
	}
	    
	//System.out.println("recomb:"+rec+" lambda:"+lambd+" alpha:"+alpha+" fst:"+fst+" KLD:"+kld+" Like:"+like+" LnPD:"+lnpd);
	// update the format counter then
	countRec=rec;
	if(rec>0 && recVec==null){
	    recVec = new Vector();
	}
	

	countFst = fst;
	if(fst>0 && fstVec==null){
	    fstVec = new Vector();
	    for(int i=0;i<fst;i++){
		fstVec.addElement(new Vector());
	    }
	}
	countAlpha=alpha;
	if(alpha>0 && alphaVec==null){
	    alphaVec = new Vector();
	    for(int i=0;i<alpha;i++){
		alphaVec.addElement(new Vector());
	    }
	}
	
	//recording and initialization
 
	countLambd=lambd;
	countKLD=kld;
	
	countLike=like;
	if(like>0 &&llhdVec==null){
	    llhdVec=new Vector();
	}
	countLnpd=lnpd;
	if(lnpd>0 &&lnpdVec==null){
	    lnpdVec=new Vector();
	}

	//arrange everthing in position
	posVec=null;
	posVec = new Vector();
	if(rec!=0)
	    posVec.addElement(recVec);
	for(int i=0;i<lambd;i++)   
	    posVec.addElement(null);
	for(int i=0;i<alpha;i++)   
	    posVec.addElement(alphaVec.elementAt(i));
	for(int i=0;i<fst;i++)   
	    posVec.addElement(fstVec.elementAt(i));
	for(int i=0;i<kld;i++)
	    posVec.addElement(null);
	if(like!=0)
	    posVec.addElement(llhdVec);
	if(lnpd!=0)
	    posVec.addElement(lnpdVec);
	
    }

    private void parseData(String str){
	if(str==null)
	    return;
	StringTokenizer st = new StringTokenizer(str);
	String key = new String();
	String round= new String();
	int token_count=0;
	int curr_rep=0;
	while(st.hasMoreTokens()){
	    key = st.nextToken();
	    if(token_count==0){
		// test if it is a valid data entry
		int index=key.indexOf(":");
		if(index<0){
		    record = false;
		    return;
		}
		round = key.substring(0,index);
		try{
		    curr_rep=Integer.parseInt(round);
		}catch (Exception e){
		    record=false;
		    return;
		}
	    }else{
		Vector targetVec = (Vector)posVec.elementAt(token_count-1);
		if(targetVec!=null){
		    targetVec.addElement(round);
		    targetVec.addElement(key);
		}
	    }
	    token_count++;
	}
    }
    
    private void genPlotData(){
	
	if(countFst!=0){    
	    fst_array = new double[countFst][];
	    for(int i=0;i<countFst;i++)
		fst_array[i] = vec2array((Vector)fstVec.elementAt(i));
	}
	   
	if( countAlpha!=0){	    
	    alpha_array = new double[countAlpha][];
	    for(int i=0;i<countAlpha;i++)
		alpha_array[i] = vec2logarray((Vector)alphaVec.elementAt(i));
	    
	}
	
	if(countLike !=0 ){
	    llhd_array = new double[1][];	    
	    llhd_array[0] = vec2array(llhdVec);
	}
	if(countRec !=0){
	    rec_array = new double[1][];	    
	    rec_array[0] = vec2array(recVec);
	}
	
	if(countLnpd !=0){	    
	    lnpd_array = new double[1][];	    
	    lnpd_array[0] = vec2array(lnpdVec);
	}
	
	recVec=llhdVec=lnpdVec=alphaVec=fstVec=null;

	/*
	if(fstHist!=null){
	    PlotData pd = new PlotData(fstHist);
	    pd.writeDataFile(saveDir, sim.getRstName()+"_fsthist");
	}
	if(alphaHist!=null){
	    PlotData pd = new PlotData(alphaHist);
	    pd.writeDataFile(saveDir, sim.getRstName()+"_alphahist");
	}
	
	if(lnpdHist != null){	    
	    double[][] lnpd_hist = new double[1][];	    
	    lnpd_hist[0] = lnpdHist;
	    PlotData pd = new PlotData(lnpd_hist);
	    pd.writeDataFile(saveDir, sim.getRstName()+"_lnpdhist");
	}
	
	if(recHist != null){
	    double[][] rec_hist = new double[1][];	    
	    rec_hist[0] = recHist;
	    PlotData pd = new PlotData(rec_hist);
	    pd.writeDataFile(saveDir, sim.getRstName()+"_recmbhist");
	}
	
	if(likHist != null){
	    
	    double[][] lik_hist = new double[1][];	    
	    lik_hist[0] = likHist;
	    PlotData pd = new PlotData(lik_hist);
	    pd.writeDataFile(saveDir, sim.getRstName()+"_lhdhist");
	}
	*/
	// System.out.println("Burnin = "+burnin);

    }

    

    private double[] vec2logarray(Vector v){
	
	if(v == null)
	    return null;
	double[] result = new double[v.size()];
	for(int i=0;i<v.size();i++){
	    try{		
		result[i] = Double.parseDouble((String)v.elementAt(i));
		if(i%2==1)
		    result[i] = Math.log(result[i])/Math.log(10) ;		    
	    }catch (Exception e){
		System.err.println(e);
	    }
	}
	
	return result;
    }
    
    private double[] vec2array(Vector v){
	if(v == null)
	    return null;
	double[] result = new double[v.size()];
	for(int i=0;i<v.size();i++){
	    try{
		result[i] = Double.parseDouble((String)v.elementAt(i));	
	    }catch (NumberFormatException e){
		System.err.println(e);
	    }
	}
	
	return result;
    }
    
    public double[][] getHistArray(int cat){
	
	double[][] hist=null;
	
	// for rec
	if(cat==1){
	    if(countRec==0)
		return null;
	    hist = new double[1][];
	    hist[0]= new double[rec_array[0].length/2-burnin];
	    int count=0;
	    for(int i=2*burnin+1;i<rec_array[0].length;i+=2){
		hist[0][count]=rec_array[0][i];
		count++;
	    }
	}
	if(cat==2){
	    if(countAlpha==0)
		return null;
	    hist = new double[countAlpha][];
	    for(int k=0;k<countAlpha;k++){
		hist[k]= new double[alpha_array[k].length/2-burnin];
		int count=0;
		for(int i=2*burnin+1;i<alpha_array[k].length;i+=2){
		    hist[k][count]=alpha_array[k][i];
		    count++;
		} 
	    }
	}
	if(cat==3){
	    if(countFst==0)
		return null;
	    hist = new double[countFst][];
	    for(int k=0;k<countFst;k++){
		hist[k]= new double[fst_array[k].length/2-burnin];
		int count=0;
		for(int i=2*burnin+1;i<fst_array[k].length;i+=2){
		    hist[k][count]=fst_array[k][i];
		    count++;
		} 
	    }
	}
	if(cat==4){
	    if(countLike==0)
		return null;
	    hist = new double[1][];
	    hist[0]= new double[llhd_array[0].length/2-burnin];
	    int count=0;
	    for(int i=2*burnin+1;i<llhd_array[0].length;i+=2){
		hist[0][count]=llhd_array[0][i];
		count++;
	    }
	}
	if(cat==5){
	    if(countLnpd==0)
		return null;
	    hist = new double[1][];
	    hist[0]= new double[lnpd_array[0].length/2];
	    int count=0;
	    for(int i=1;i<lnpd_array[0].length;i+=2){
		hist[0][count]=lnpd_array[0][i];
		count++;
	    }
	}
	
	
	return hist;
    }
    
}