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

/** 
 * Class that does the promoter search.
 * @author Gard Thomassen
 * @see PromoterSearchManager
 * @see PromoterSequenceScorer
 * @see PromoterCandidate
 */

public class PromoterSearcher{

    PromoterSearcher m = this;
    Vector score;
    PromoterSequenceScorer promoSequenceScorer;
    int s,f;
    Sequence seq;
    Vector tmpCand = new Vector(10,10);
    
    /** 
     * Constructor, recieves the needed scoring and candidate vectors,
     * creates a PromoterSequenceScorer object.
     * @param s A vector that holds the scoring tables
     */
    
    public PromoterSearcher(Vector s){
	score = s;
	promoSequenceScorer = new PromoterSequenceScorer(score);
    }

    /**
     * Method that searches through the parameter sequence for 
     * possible promoter sites, according to the user-chosen
     * promoters to search for.
     * Candidates are put into the candidates Vector of the Manager.
     * @param se the sequence that is to be searched in
     */

    public void searchPromoter(Sequence se){
	
	seq = se;
	int i = 0;
	ScoreTable table = (ScoreTable)score.elementAt(i);
	boolean t = true;
		
	while(t){
	    s = 1 ;
	    f = table.A_score.length;
	    boolean more = true;
	    
	    while(more){
		if(f <= seq.length()){
		    promoSequenceScorer.scoreSequence(seq.subStr(s,f),i,tmpCand, m);
		    s++;
		    f++;
		}
		else{
		    more = false;
		}
	    }
	    //takes care of iteration
	    i = i+2;
	    if(i < score.size())
		table = (ScoreTable)score.elementAt(i);
	    else
		t = false;
	}
    }//end searchPromoter
    
    /**
     * Method that is called from the PromoterSequenceScorer object
     * that this object has created
     * Method returns the given string where the promoSequenceScorer
     * wants to search for the -10 region
     * @param d the distance from the -35 to the -10 region
     * @param i the index of the right scoretable object in the score Vector
     * @return string the string that is wanted or EOF if OutOfBounds          
     */

    public String getSeqv(int d, int i){
		
	int score_length;
	ScoreTable m = (ScoreTable)score.elementAt(i);
	score_length = m.A_score.length;
	int s2,f2;	
	f2 = s-d-1;
	s2 = f2-score_length+1; 
	String tmp;
	
	//used for debugging
	//System.err.println("s2 = " +s2 + " f = "+ f);
	//System.err.println("Seq_length= " +seq.length());
	
	if(s2 >= 1){
	    promoSequenceScorer.setName(seq.getName());	    
	    promoSequenceScorer.setStart(s2);
	    promoSequenceScorer.setFinish(f);
	    return( seq.subStr(s2,f2));
	   
	}
	//handling errors
	else
	    return "OOB";
	
    }//end getSeqv

    /**
     * Method that looks at almost similar candidates.
     * Almost similar is if both the start and the stop of two sequences 
     * are no more than +/- 10 positions apart.
     * The method computes the best candidate and deletes the rest.
     * The method is called from the PromtoerSearchManager
     * @return a vector with the remaining candidates after the cleaning. 
    */

    public Vector cleanAndStore(){
		
	String name, pName;
	int start = 0, stop = 0 ;
	double candScore = 0;
	PromoterCandidate cand,tmp;
	int k;
	for(int i = 0; i < tmpCand.size(); i ++){
	    cand = (PromoterCandidate)tmpCand.elementAt(i);
	    name = cand.seq_name;
	    pName = cand.promoter_name;
	    start = cand.start;
	    stop = cand.finish;
	    k = i+1;
	    candScore = cand.score35 + cand.score10  ;
	    
	    if(k < tmpCand.size()){
		tmp = (PromoterCandidate)tmpCand.elementAt(k);
		
		while(k < tmpCand.size() && tmp.seq_name.equals(name) && pName.equals(tmp.promoter_name)){
		    tmp = (PromoterCandidate)tmpCand.elementAt(k);
		    if(((((start-tmp.start) <= 10) && (start-tmp.start) >= 0 ) ||
			(((tmp.start - start) <= 10) && ((tmp.start - start) >= 0)))
		       && ((((stop-tmp.finish) <= 10) && (stop-tmp.finish) >= 0) ||
			   (((tmp.finish - stop) <= 10) && ((tmp.finish - stop) >= 0)))
		       &&(cand.promoter_name.equals(tmp.promoter_name)))
			{
			    if((tmp.score35 + tmp.score10) <= candScore){
				tmp = (PromoterCandidate)tmpCand.remove(k);
				k--;
				
			    }
			    else{
				tmp = (PromoterCandidate)tmpCand.remove(i);
				k =  tmpCand.size();
				i--;
			    }
			}
		    k++;
		}
	    }
	}
	return tmpCand;
    }
}//end class