import java.io.*;
import java.util.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;


/**
 * Class that holds methods for printing final result
 * data to file and to standard output
 * @author Gard Thomassen
 * @see ProgramManager
 */

public class ResultPrinter{

    Vector geneCandidates;
    int i=0;
    RNACandidate cand;
    PrintWriter candOut, fastaOut;
    SequenceIterator fastaReader;
    String fileName;
    int en, to, tre , fire, fem, seks, syv, otte;
    /**
     * Constructor for the ResultPrinter
     * holds one vector with RNA candidates
     * Creates a target file for the output, and 
     * establishes a printWriter
     * @param v Vector with the RNACandidates
     */

    public ResultPrinter(Vector v, String n){

	fileName = n;
	geneCandidates = v;

	try{
	    candOut =  new PrintWriter(new BufferedWriter(new FileWriter("ncRNACandidateGenes.txt")));
	}
	catch(IOException e){
	    System.err.println("Trouble while creating final output file");
	}
	try{
	    fastaOut =  new PrintWriter(new BufferedWriter(new FileWriter("ncRNAfasta.txt")));
	}
	catch(IOException e){
	    System.err.println("Trouble while creating FASTA output file");
	}

    }
    
    /**
     * Method that iterates through the RNACandidates
     * and calls methods to print them to file and std.out.
     */

    public void printAllncRNACandidates(){
	candOut.write("Number of ncRNA gene candidates " +geneCandidates.size()+"\n");
	while(i < geneCandidates.size()){
	    cand = (RNACandidate)geneCandidates.elementAt(i);
	    //debug
	    if(cand.promoter_name.equals("sigma 70(Dave)"))
		en++;
	    else if(cand.promoter_name.equals("sigma 32(Dave)"))
		to++;
	    else if(cand.promoter_name.equals("sigma 54(Dave)"))
		tre++;
            else if(cand.promoter_name.equals("sigma 38(Dave)"))
		fire++;
	    else if(cand.promoter_name.equals("sigma all"))
		fem++;
	    else if(cand.promoter_name.equals("sigma_70_regulonDB"))
		seks++;
	    else if(cand.promoter_name.equals("sigma_32_regulonDB"))
		syv++;
	    else 
		otte++;
	    
	    printCandidateToFile(cand, (i+1));
	    //printCandidateToScreen(cand); 
	    printCandidateToFASTAfile(cand); 
	    i++;    
	}
	fastaOut.close();
	candOut.close();
	System.out.println("Located : " + geneCandidates.size() + " ncRNA gene candidates");
	//debugging
	//	System.out.println("1= "+ en+ "\n 2= "+to+"\n 3= "+tre+"\n 4= "+fire+"\n 5= "+fem+ "\n 6= "+seks + "\n 7="+syv+ "\n 8= "+otte);  
    }

    /**
     * Method that prints all RNACandidates data to file
     */
    
    protected void printCandidateToFile(RNACandidate c, int n){
	
	//printing gene data of this candidate
	candOut.write("Gene data for this candidate: \n");
		
	//printing name of sequence wher ecandidate is located
	candOut.write("Seq name : "+c.sequenceName+"\n");
	candOut.write("Candidate number = " + n + "\n");
	candOut.write("Candidate length = " +(c.relativeStart - c.finish)+ "\n");
	//printing promoter data of this Candidate
	candOut.write("Promoter data for this candidate: \n");
	candOut.write("Promoter name :" + c.promoter_name+"\n");
	candOut.write("-35 Threshold =" +c.threshold35+"\n");
	candOut.write("-35 score = "+c.score35+"\n");
	candOut.write("Distance between -35 and -10 :" + c.distance+"\n");
	candOut.write("-10 Threshold =" +c.threshold10+"\n");
	candOut.write("-10 score = "+c.score10 +"\n");
	candOut.write("Relative start of promoter: " + c.start+"\n");
	candOut.write("Relative finish of promoter: " + c.finish+"\n");
	candOut.write("-35 region : " + c.seq2 +"\n");
	candOut.write("-10 region : " + c.seq1 +"\n");
	candOut.write("\n");
		
	//printing terminator data of this candidate
	candOut.write("Terminator data for this candidate: \n");
	candOut.write("Hairpin Energy score: " + c.hairpinEnergy +"\n");
	candOut.write("U_tail score : "+ c.u_Score+"\n");
	candOut.write("Rightleg = " + c.rightleg +"\n");
	candOut.write("Leftleg = "+ c.leftleg +"\n");
	candOut.write("Loop =" + c.loop + "\n");
	candOut.write("U_tail = " + c.u_sequence +"\n");
	candOut.write("Relative start of terminator= " + c.relativeStart +"\n");
	candOut.write("Relative end of terminator= " + c.relativeEnd +"\n");
	candOut.write("Numbers of nucleotides in terminator = " + (c.relativeEnd - c.relativeStart +1) +"\n");
	candOut.write("\n \n");
    }//end printCandidatesToFile
    
    /**
    * Method that prints all RNACandidates data to std out.
    */
        
    protected void printCandidateToScreen(RNACandidate c){
	//printing gene data of this candidate
	System.out.println("Gene data for this candidate: ");
	
	//printing name of sequence where candidate is located
	System.out.println("Seq name :"+c.sequenceName);
	
	//printing promoter data of this Candidate
	System.out.println("Promoter data for this candidate: ");
	System.out.println("Promoter name :" + c.promoter_name);
	System.out.println("-35 Threshold =" +c.threshold35);
	System.out.println("-35 score = "+c.score35);
	System.out.println("Distance between -35 and -10 :" + c.distance);
	System.out.println("-10 Threshold =" +c.threshold10);
	System.out.println("-10 score = "+c.score10 );
	System.out.println("Relative start of promoter :" + c.start);
	System.out.println("Relative finish of promoter:" + c.finish);
	System.out.println("-35 region : " + c.seq2 +"\n");
	System.out.println("-10 region : " + c.seq1 +"\n");	
	System.out.println("\n");
	//printing terminator data of this candidate
	System.out.println("Terminator data for this candidate: ");
	System.out.println("Hairpin Energy score: " + c.hairpinEnergy );
	System.out.println("U_tail score : "+ c.u_Score);
	System.out.println("Rightleg = " + c.rightleg );
	System.out.println("Leftleg = "+ c.leftleg );
	System.out.println("Loop =" + c.loop );
	System.out.println("U_tail = " + c.u_sequence );
	System.out.println("Relative start of terminator= " + c.relativeStart );
	System.out.println("Relative end of terminator= " + c.relativeEnd );
	System.out.println("Numbers of nucleotides in terminator = " + (c.relativeEnd - c.relativeStart +1) );
    }//end printCandidatesToScreen

    protected void printCandidateToFASTAfile(RNACandidate c){
	
	int promoterEnd = c.start;
	int terminatorStart = c.relativeEnd;
	String name = c.sequenceName;
	Sequence sequence;
	Sequence tmpSeq = null;
	SeqTools seqTool = new SeqTools();
	String altName;
	StringTokenizer tok;
	int numTok = 0;
	int s = 0, f = 0;

	try{
	    FASTA_Reader fileReader = new FASTA_Reader();
	    fastaReader = fileReader.readFASTA(fileName);
	    while(fastaReader.hasNext()){
		sequence = fastaReader.nextSequence();
				
		if(sequence.getName().equals(name)){
		    promoterEnd = promoterEnd + c.seq2.length() + c.seq1.length() + c.distance;
		    terminatorStart = terminatorStart - (c.relativeEnd - c.relativeStart);
		    try {
			tok = new StringTokenizer(sequence.getName(), "_");
			numTok = tok.countTokens();
			altName = tok.nextToken();
			int i = 0;
			while(i <= (numTok - 4)){
			    altName = altName.concat("_");
			    altName = altName.concat(tok.nextToken());
			    i++;
			}
			s = Integer.parseInt(tok.nextToken());
			f = Integer.parseInt(tok.nextToken());
			fastaOut.write(">"+altName+" "+(s+promoterEnd-1)+" "+(s+terminatorStart)+ "\n");
		
		    }
		    catch(Exception e){
			fastaOut.write(">"+name+"\n");	
		    }
		    printSeq(sequence, promoterEnd, terminatorStart);
			 
		}
		
		else if(sequence.getName().concat(".reversed").equals(name)){
		    tmpSeq = seqTool.reverseCompliment(sequence);
		    promoterEnd = promoterEnd + c.seq2.length() + c.seq1.length() + c.distance;
		    terminatorStart = terminatorStart - (c.relativeEnd - c.relativeStart);
		    try{
			tok = new StringTokenizer(sequence.getName(), "_");
			numTok = tok.countTokens();
			altName = tok.nextToken();
			int i = 0;
			while(i <= (numTok - 4)){
			    altName = altName.concat("_");
			    altName = altName.concat(tok.nextToken());
			    i++;
			}
			altName = altName.concat(".reversed");
			s = Integer.parseInt(tok.nextToken());
			tok = new StringTokenizer(tok.nextToken(), ".");
			f = Integer.parseInt(tok.nextToken());
			fastaOut.write(">"+altName+" "+(f-terminatorStart-1)+" "+(f-promoterEnd+2)+ "\n");
		    }
		    catch(Exception e){
			fastaOut.write(">"+name+"\n");
		    }
		    //System.out.println(s +" " + f);
		    //System.out.println(promoterEnd +"\t"+ terminatorStart);
		    printSeq(tmpSeq, promoterEnd, terminatorStart);
		}		
	    }
	}
	catch(Exception e){
	    System.out.println("Something wrong while printing result FASTA file" );
	    System.out.println("name ="+ name +" pstart = " + promoterEnd + " tEnd = "+ terminatorStart);
	}
    }
    
    protected void printSeq(Sequence seq, int pStart, int tEnd){

	int z = 59;
	boolean more = true;
	while(more){
	    if((pStart + z)< tEnd ) {
		fastaOut.write(seq.subStr(pStart, (pStart + z))+"\n"); 
		pStart += 60;
	    }
	    else{
		more = false;
		fastaOut.write(seq.subStr(pStart, tEnd)+"\n");
	    } 
	}
    }
    
}//end class ResultPrinter