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

/**
 * Class that manages the program
 * @author Gard Thomassen
 * @see ProgramManager
 * @see PromoterSearcher
 * @see PromoterScoreManager
 * @see ScoreTable
 * @see PromoterSequenceScorer
 */

public class PromoterSearchManager {
       
    Vector score;   
    PrintWriter out;
    Vector promoCand;
    Threshold threshold;
    PromoterSearcher promoSearcher;
    
    /**
     * Constructor ,establishes the actual threshold values 
     * and the vector with the scoring info, and the vector for new candidates.
     * The construcot also creates a Printwriter for where
     * to print the Promoter Candidates
     * @param c is the vector with to store the candidates in
     * @param s is the vector containing info to score the sequences
     * @param thresholds an array with the user defined threhold percentages
    */
    
    protected PromoterSearchManager(Vector c, Vector s, double [] thresholds  ){
	promoCand = c;
	score = s;
	//get the Thresholds established
	threshold = new Threshold(score);
	threshold.setThreshold(thresholds);
   	//creating output stream
	try{
 	    out =  new PrintWriter(new BufferedWriter(new FileWriter("PromoterCandidates.txt")));
	}
	catch(IOException e){
	    System.err.println("Trouble with creating output file");
	}
    }

    /**
     *Method that runs the promoter search
     *Creates a PromoterSearcher object
     *Tells the PromoterSearcher to search for promoters
     *Then writes promoter candidates to the candidate vector
     *@param s is the sequence that is to be searched
     */
    
    public void startSearch(Sequence s)throws Exception{
	Sequence seq = s;	
	promoSearcher = new PromoterSearcher(score);
	promoSearcher.searchPromoter(seq);
        promoCand.addAll(promoSearcher.cleanAndStore());
    }
    /**
     * This method writes all promoter data to file 
     *
     */
    
    public void writePromoterCandidatesToFile(){
	//iterator help
	int i = 0;
	// a candidate pointer used in the iteration
	PromoterCandidate cand;
	
	//iterate through all candidates

	while(i < promoCand.size()){
	    cand = (PromoterCandidate)promoCand.elementAt(i);
	    //writing data to file
	    cand.writeCandidateToFile(out, i);
	 	    
	    i++;
	    
	}//end while
	System.out.println("");
	System.out.println("Located : " +promoCand.size()+ " promoter candidates" );
	out.close();	
    }//end write method


    //method for debugging (not used in the actual program)
    public void testName(){
	Vector names = new Vector();
	PromoterCandidate cand;
	int z = 0;
	System.out.print(promoCand.size()+"\n");
	while(z < promoCand.size()){
	    cand = (PromoterCandidate)promoCand.elementAt(z);
	    if(!names.contains(cand.seq_name)){
		names.addElement(cand.seq_name);
	    }
	    z++;
	}
	System.out.println("Number of different sigma factor names"+names.size());
    }

}//end Manager