package Obj;
import java.io.*;
import java.util.*;

public class ObjIO {

public static NProjObj loadProjObj(File f){
 	NProjObj proj = readProjObj(f);
  if(proj == null){
  	proj = new NProjObj(ProjObj.loadProjObj(f));
  	
  	File dir = new File(f.getParent());
	  proj.setWorkingPath(dir.getAbsolutePath());
	  File df = new File(f.getParent(), "project_data");
	  proj.setDataFile(df.getAbsolutePath());
    proj.setSimVector();
  	writeProjFile(proj);
  }
  
  return proj;

}


    public static NSimObj loadSimObj(NProjObj proj, String simName){
    
	NSimObj sim = readSimObj(proj, simName);
	
	return sim;
    }
	    
	
	
    private static NProjObj readProjObj(File f){

	String projName=""; 
	boolean useIndLabel = false;
	boolean usePopId = false;
	boolean usePopFlag = false;
	boolean useGeneName = false;
	boolean useLocusName = false;
	boolean usePhaseInfo = false;
	boolean usePhenoType = false;
	boolean oneRow = false;
	boolean phased = false;
	boolean recessiveAllele = false;
	boolean locData = false;
	
	int extraCol = 0;
	int numInds = 0;
	int ploidy = 2;
	int numloci = 0;
	String missingVal = "-9";
	String notambiguous = "-939";
	String dataFile;
	
	
	
	// load data to memory
	StringBuffer buffer = new StringBuffer();
	String content = "";	
	try {
	    FileInputStream fis = new FileInputStream(f);
	    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;
	}
	
	if(content.indexOf("PROJNAME")==-1)
	  return null;
	  
	// parse the data file
	String str = new String();
	StringTokenizer file_st = new StringTokenizer(content,"\n");
	while(file_st.hasMoreTokens()){
	    
	    str = file_st.nextToken();
	    StringTokenizer st = new StringTokenizer(str);
	    String key = st.nextToken();
	    String val = st.nextToken();
	    
	    if(key.equals("PROJNAME"))
		projName = val;
	    
	    // general info
	    
	    if(key.equals("NUMINDS")){
	 	   try{ 
		       numInds = Integer.parseInt(val);
		   }catch (Exception e){
		       return null;
		   }
	    }
	    
	    
	    if(key.equals("NUMLOCI")){
		try{ 
		    numloci = Integer.parseInt(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("PLOIDY")){
		try{ 
		    ploidy = Integer.parseInt(val);
		}catch (Exception e){
		    return null;
		}
	    }

	    if(key.equals("MISSINGVAL")){
		missingVal = val;
	    }
	    
	    if(key.equals("ONEROW")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			oneRow = true;
		    
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("INDLABEL")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			useIndLabel = true;
		    
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    if(key.equals("POPID")){
	 	   try{ 
		       int bv = Integer.parseInt(val);
		    if(bv==1)
			usePopId = true;
		    
		   }catch (Exception e){
		       return null;
		   }
	    }
	    
	    if(key.equals("LOCDATA")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			locData = true;
		    
		   }catch (Exception e){
		       return null;
		   }
	    }

	    if(key.equals("POPFLAG")){
	 	   try{ 
		       int bv = Integer.parseInt(val);
		       if(bv==1)
			   usePopFlag = true;
		       
		   }catch (Exception e){
		       return null;
		   }
	    }
	    
	    if(key.equals("PHENOTYPE")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			usePhenoType = true;
		    
		}catch (Exception e){
		    return null;
		}
	    }
	    

	    if(key.equals("EXTRACOL")){
		try{ 
		    extraCol = Integer.parseInt(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    // rows	     
	    if(key.equals("GENENAME")||key.equals("MARKERNAME")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			useGeneName = true;
		    
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("RECESSIVEALLELE")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			recessiveAllele = true;
		    
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    // set when ploidy > 3 and recessive alleles model specified
	    if(key.equals("NOTAMBIGUOUS")){
		notambiguous = val;
	    }
	    
	    if(key.equals("LOCUSNAME")||key.equals("MAPDISTANCE")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			useLocusName = true;
		    
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("PHASED")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			phased = true;
		    
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    if(key.equals("PHASEINFO")){
		try{ 
		    int bv = Integer.parseInt(val);
		    if(bv==1)
			usePhaseInfo = true;
		    
		}catch (Exception e){
		    return null;
		}
	    }
	     
	    
	  }
	  
	  NProjObj proj= new NProjObj(projName, null,
				      useIndLabel, usePopId,
				      extraCol, numInds,
				      ploidy, numloci,
				      missingVal, null,
				      usePopFlag, useGeneName,
				      useLocusName,usePhaseInfo, 
				      oneRow,phased,usePhenoType,recessiveAllele,locData);
	  
	  if(ploidy>=3 && recessiveAllele){
	      proj.setNAMBCode(notambiguous);
	  }
	  
	  File dir = new File(f.getParent());
	  proj.setWorkingPath(dir.getAbsolutePath());
	  File df = new File(f.getParent(), "project_data");
	  proj.setDataFile(df.getAbsolutePath());
	  proj.setSimVector();
	  
	  
	  return proj;
	  
    }
    
    
    private static NSimObj readSimObj(NProjObj proj, String simName){
	if(proj==null)
	    return null;
	
	NSimObj sim = new NSimObj(proj);
	
	boolean confirm=false;

	File simDir = new File(proj.getWorkingPath(), simName);
	File simFile = new File(simDir.getAbsolutePath(), ".sim");
	
	// reset sim path everytime open the sim.
	
	sim.setSimPath(simDir.getAbsolutePath());
	sim.setSimName(simName);
	
	// load data to memory
	StringBuffer buffer = new StringBuffer();
	String content = "";	
	try {
	    FileInputStream fis = new FileInputStream(simFile);
	    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;
	}
	
	// parse the data file
	String str = new String();
	StringTokenizer file_st = new StringTokenizer(content,"\n");
	while(file_st.hasMoreTokens()){
	    
	    str = file_st.nextToken();
	    StringTokenizer st = new StringTokenizer(str);
	   
	    String key = st.nextToken();
	    String val = st.nextToken();
	    
	    // run parameter
	    
	    if(key.equals("BURNIN")){
		try{ 
		    sim.BURNIN = Integer.parseInt(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("NUMREPS")){
		try{ 
		    sim.NUMREPS = Integer.parseInt(val);
		    confirm = true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    // model params
	    

	     if(key.equals("NOADMIX")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.NOADMIX=false;
		    else        sim.NOADMIX=true;
		}catch (Exception e){
		    return null;
		}
	     }
	     
	     if(key.equals("LOCPRIOR")){
		 try{ 
		     int  temp = Integer.parseInt(val);
		     if(temp==1) sim.LOCPRIOR = true;
		     else        sim.LOCPRIOR = false;
		 }catch (Exception e){
		     return null;
		 }
	     }
	    
	     if(key.equals("RECOMBINE")||key.equals("LINKAGE")){
		 try{ 
		     int  temp = Integer.parseInt(val);
		     if(temp==0) sim.RECOMBINE=false;
		     else        sim.RECOMBINE=true;
		 }catch (Exception e){
		     return null;
		 }
	     }
	     
	     if(key.equals("USEPOPINFO")){
		 try{ 
		     int  temp = Integer.parseInt(val);
		     if(temp==0) sim.USEPOPINFO=false;
		     else        sim.USEPOPINFO=true;
		 }catch (Exception e){
		     return null;
		 }
	     }
	     
	     

	     if(key.equals("FREQSCORR")){
		 try{ 
		     int  temp = Integer.parseInt(val);
		     if(temp==0) sim.FREQSCORR=false;
		     else        sim.FREQSCORR=true;
		 }catch (Exception e){
		     return null;
		 }
	     }
	     
	    if(key.equals("ONEFST")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.ONEFST=false;
		    else        sim.ONEFST=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("INFERALPHA")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.INFERALPHA=false;
		    else        sim.INFERALPHA=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    if(key.equals("POPALPHAS")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.POPALPHAS=false;
		    else 
			sim.POPALPHAS=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("ALPHA")){
		try{ 
		    sim.ALPHA = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }

	    if(key.equals("INFERLAMBDA")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.INFERLAMBDA=false;
		    else        sim.INFERLAMBDA=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("POPSPECIFICLAMBDA")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.POPSPECIFICLAMBDA=false;
		    else        sim.POPSPECIFICLAMBDA=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("LAMBDA")){
		try{ 
		    sim.LAMBDA = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    // leftover from proj
	    	    
	    if(key.equals("MARKOVPHASE")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.MARKOVPHASE=false;
		    else        sim.MARKOVPHASE=true;
		}catch (Exception e){
		    return null;
		}
	    }	    
	    
	    // priors
	    
	    if(key.equals("FPRIORMEAN")){
		try{ 
		    sim.FPRIORMEAN = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }

	    if(key.equals("FPRIORSD")){
		try{ 
		    sim.FPRIORSD = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("UNIFPRIORALPHA")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.UNIFPRIORALPHA=false;
		    else        
			sim.UNIFPRIORALPHA=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("ALPHAMAX")){
		try{ 
		    sim.ALPHAMAX = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("ALPHAPRIORA")){
		try{ 
		    sim.ALPHAPRIORA = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("ALPHAPRIORB")){
		try{ 
		    sim.ALPHAPRIORB = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    


	    
	    if(key.equals("RMIN")){
		try{ 
		    sim.RMIN = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("RMAX")){
		try{ 
		    sim.RMAX = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("RSTD")){
		try{ 
		    sim.RSTD = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    if(key.equals("RSTART")){
		try{ 
		    sim.RSTART = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    	    
	    if(key.equals("RSTEP")){
		try{ 
		    sim.RSTEP = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    	    
	    
	    if(key.equals("GENSBACK")){
		try{ 
		    sim.GENSBACK = Integer.parseInt(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    	    	    
	    if(key.equals("MIGRPRIOR")){
		try{ 
		    sim.MIGRPRIOR = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("PFROMPOPFLAGONLY")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.PFROMPOPFLAGONLY=false;
		    else
			sim.PFROMPOPFLAGONLY=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    // sub model for popinfo 
	    
	    if(key.equals("POPNOADMIX")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.POPNOADMIX=false;
		    else        sim.POPNOADMIX=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("POPRECOMBINE")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.POPRECOMBINE=false;
		    else        sim.POPRECOMBINE=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    

	    // output option
	    
	    
	    if(key.equals("PRINTQ")){
		try{ 
		    int temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.PRINTQ=false;
		    else   
			sim.PRINTQ=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    if(key.equals("SITEBYSITE")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.SITEBYSITE=false;
		    else
			sim.SITEBYSITE=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    // miscellaneous
	    
	    if(key.equals("COMPUTEPROB")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) sim.COMPUTEPROB=false;
		    else        sim.COMPUTEPROB=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    

	    
	    if(key.equals("ADMBURNIN")){
		try{ 
		    sim.ADMBURNIN = Integer.parseInt(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	   	    
	    if(key.equals("USEDEFAULTADMBURNIN")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.USEDEFAULTADMBURNIN=false;
		    else        
			sim.USEDEFAULTADMBURNIN=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    if(key.equals("ALPHAPROPSD")){
		try{ 
		    sim.ALPHAPROPSD = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("STARTPOPINFO")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.STARTPOPINFO=false;
		    else 
			sim.STARTPOPINFO=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    	    
	    if(key.equals("METROFREQ")){
		try{ 
		    sim.METROFREQ = Integer.parseInt(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    ///////////////////////////////////////////////////////////////////////////////////////////////
	    
	    // not shown
	    if(key.equals("ANCESTDIST")){
		try{ 
		    int temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.ANCESTDIST=false;
		    else   
			sim.ANCESTDIST=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("NUMBOXES")){
		try{ 
		    sim.NUMBOXES = Integer.parseInt(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("ANCESTPINT")){
		try{ 
		    sim.ANCESTPINT = Float.parseFloat(val);
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    if(key.equals("FQSETLAMBDA")){
		try{ 
		    int temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.FQSETLAMBDA=false;
		    else        
			sim.FQSETLAMBDA=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("FQINFERLAMBDA")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.FQINFERLAMBDA=false;
		    else 
			sim.FQINFERLAMBDA=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("INDIFQSETLAMBDA")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.INDIFQSETLAMBDA=false;
		    else
			sim.INDIFQSETLAMBDA=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    if(key.equals("INDIFQINFERLAMBDA")){
		try{ 
		    int  temp = Integer.parseInt(val);
		    if(temp==0) 
			sim.INDIFQINFERLAMBDA=false;
		    else  
			sim.INDIFQINFERLAMBDA=true;
		}catch (Exception e){
		    return null;
		}
	    }
	    
	    
	    
	    

	    
	    
	}
	sim.isNew = false;
	if(confirm)
	    return sim;
	else 
	    return null;
    }
    
    
    
    public static void writeProjFile(NProjObj proj){
    	File f= new File ( proj.workingPath,proj.projName+".spj");
	PrintStream out = OpenOutputFile(f);
	
	out.println("PROJNAME"+"  "+proj.projName);
	
	// general
	
	out.println("NUMINDS"+"  "+proj.numInds);
	out.println("NUMLOCI"+"  "+proj.numloci);
	out.println("PLOIDY"+"  "+proj.ploidy);	
	out.println("MISSINGVAL"+"  "+proj.missingVal);

	if(proj.oneRow==true) 
	    out.println("ONEROW"+"   1");
	else               
	    out.println("ONEROW"+"   0");


	// columns

	if(proj.useIndLabel==true) 
	    out.println("INDLABEL"+"   1");
	else               
	    out.println("INDLABEL"+"   0");
	
	if(proj.usePopId==true) 
	    out.println("POPID"+"   1");
	else               
	    out.println("POPID"+"   0");
	
	if(proj.usePopFlag==true) 
	    out.println("POPFLAG"+"   1");
	else               
	    out.println("POPFLAG"+"   0");
	
	if(proj.locData==true) 
	    out.println("LOCDATA"+"   1");
	else               
	    out.println("LOCDATA"+"   0");
	
	if(proj.usePhenoType==true) 
	    out.println("PHENOTYPE"+"   1");
	else               
	    out.println("PHENOTYPE"+"   0");
	
	out.println("EXTRACOL"+"  "+proj.extraCol);
	
	
	
	// rows
	
	if(proj.useGeneName==true) 
	    out.println("MARKERNAME"+"   1");
	else               
	    out.println("MARKERNAME"+"   0");
	
		
	if(proj.recessiveAllele==true) {
	    out.println("RECESSIVEALLELE"+"   1");
	    if(proj.ploidy>=3)
		out.println("NOTAMBIGUOUS"+"  "+proj.notambiguous);
	}
	else               
	    out.println("RECESSIVEALLELE"+"   0");

	if(proj.useLocusName==true) 
	    out.println("MAPDISTANCE"+"   1");
	else               
	    out.println("MAPDISTANCE"+"   0");
	
	// additional row info
	if(proj.phased==true) 
	    out.println("PHASED"+"   1");
	else               
	    out.println("PHASED"+"   0");

	if(proj.usePhaseInfo==true) 
	    out.println("PHASEINFO"+"   1");
	else               
	    out.println("PHASEINFO"+"   0");
			
	out.close();
    }
   
    
    
    
    
    public static void writeSimFile(NSimObj sim){	
	File f= new File (sim.getSimPath(), ".sim");
	PrintStream out = OpenOutputFile(f);
	out.println("BURNIN"+"  "+sim.BURNIN);
	out.println("NUMREPS"+"  "+sim.NUMREPS);
	if(sim.FREQSCORR==true) out.println("FREQSCORR"+"   1");
	else               out.println("FREQSCORR"+"   0");
	if(sim.ONEFST==true) out.println("ONEFST"+"   1");
	else               out.println("ONEFST"+"   0");
	out.println("FPRIORMEAN"+"  "+sim.FPRIORMEAN);
	out.println("FPRIORSD"+"  "+sim.FPRIORSD);
	if(sim.FQSETLAMBDA==true) out.println("FQSETLAMBDA"+"   1");
	else               out.println("FQSETLAMBDA"+"   0");
	if(sim.FQINFERLAMBDA==true) out.println("FQINFERLAMBDA"+"   1");
	else               out.println("FQINFERLAMBDA"+"   0");
	if(sim.INDIFQSETLAMBDA==true) out.println("INDIFQSETLAMBDA"+"   1");
	else               out.println("INDIFQSETLAMBDA"+"   0");
	if(sim.INDIFQINFERLAMBDA==true) out.println("INDIFQINFERLAMBDA"+"   1");
	else               out.println("INDIFQINFERLAMBDA"+"   0");
	if(sim.NOADMIX==true) out.println("NOADMIX"+"   1");
	else               out.println("NOADMIX"+"   0");
	if(sim.LOCPRIOR==true) out.println("LOCPRIOR"+"   1");
	else               out.println("LOCPRIOR"+"   0");
	if(sim.USEDEFAULTADMBURNIN==true) out.println("USEDEFAULTADMBURNIN"+"   1");
	else               out.println("USEDEFAULTADMBURNIN"+"   0");
	out.println("ADMBURNIN"+"  "+sim.ADMBURNIN);
	if(sim.INFERALPHA==true) out.println("INFERALPHA"+"   1");
	else               out.println("INFERALPHA"+"   0");
	out.println("ALPHA"+"  "+sim.ALPHA);
	if(sim.POPALPHAS==true) out.println("POPALPHAS"+"   1");
	else               out.println("POPALPHAS"+"   0");
	if(sim.UNIFPRIORALPHA==true) out.println("UNIFPRIORALPHA"+"   1");
	else               out.println("UNIFPRIORALPHA"+"   0");
	out.println("ALPHAMAX"+"  "+sim.ALPHAMAX);
	out.println("ALPHAPROPSD"+"  "+sim.ALPHAPROPSD);
	out.println("ALPHAPRIORA"+"  "+sim.ALPHAPRIORA);
	out.println("ALPHAPRIORB"+"  "+sim.ALPHAPRIORB);
	if(sim.RECOMBINE==true) out.println("RECOMBINE"+"   1");
	else               out.println("RECOMBINE"+"   0");
	if(sim.SITEBYSITE==true) out.println("SITEBYSITE"+"   1");
	else               out.println("SITEBYSITE"+"   0");
	out.println("RSTART"+"  "+sim.RSTART);
	out.println("RSTEP"+"  "+sim.RSTEP);
	out.println("RMAX"+"  "+sim.RMAX);
	out.println("RMIN"+"  "+sim.RMIN);
	out.println("RSTD"+"  "+sim.RSTD);
	if(sim.MARKOVPHASE==true) out.println("MARKOVPHASE"+"   1");
	else               out.println("MARKOVPHASE"+"   0");
	if(sim.USEPOPINFO==true) out.println("USEPOPINFO"+"   1");
	else               out.println("USEPOPINFO"+"   0");
	out.println("GENSBACK"+"  "+sim.GENSBACK);
	out.println("MIGRPRIOR"+"  "+sim.MIGRPRIOR);
	if(sim.POPNOADMIX==true) out.println("POPNOADMIX"+"   1");
	else               out.println("POPNOADMIX"+"   0");
	if(sim.POPRECOMBINE==true) out.println("POPRECOMBINE"+"   1");
	else               out.println("POPRECOMBINE"+"   0");
	if(sim.INFERLAMBDA==true) out.println("INFERLAMBDA"+"   1");
	else               out.println("INFERLAMBDA"+"   0");
	if(sim.POPSPECIFICLAMBDA==true) out.println("POPSPECIFICLAMBDA"+"   1");
	else               out.println("POPSPECIFICLAMBDA"+"   0");
	out.println("LAMBDA"+"  "+sim.LAMBDA);
	if(sim.COMPUTEPROB==true) out.println("COMPUTEPROB"+"   1");
	else               out.println("COMPUTEPROB"+"   0");
	if(sim.ANCESTDIST==true) out.println("ANCESTDIST"+"   1");
	else               out.println("ANCESTDIST"+"   0");
	if(sim.PRINTQ==true) out.println("PRINTQ"+"   1");
	else               out.println("PRINTQ"+"   0");
	out.println("NUMBOXES"+"  "+sim.NUMBOXES);
	out.println("ANCESTPINT"+"  "+sim.ANCESTPINT);
	if(sim.STARTPOPINFO==true) out.println("STARTPOPINFO"+"   1");
	else               out.println("STARTPOPINFO"+"   0");
	if(sim.PFROMPOPFLAGONLY==true) out.println("PFROMPOPFLAGONLY"+"   1");
	else               out.println("PFROMPOPFLAGONLY"+"   0");
	out.println("METROFREQ"+"  "+sim.METROFREQ);
	out.close();
    }
    
    private static PrintStream OpenOutputFile(File file){
	
	PrintStream  out;
	try {  // try to open output file as well...	    
	    out = new PrintStream(new FileOutputStream(file));
	} 
	catch (FileNotFoundException e) {
	    System.err.println("**Error: unable to open output file.");
	    out = null;
	}//try-catch
	catch (SecurityException e) {
	    System.err.println("**Error: no permission to write output file.");
	    out = null;
	}//try-catch
	catch (IOException e) {
	    System.err.println("**Error: unknown error opening output file.");
	    out = null;
	}//try-catch
	
	return out;
    }
    
}