import java.util.*;

/**
 * Class that calculates thresholds for every chosen promoter
 * sequence. Also calculates threshold for a user defined 
 * consensus sequence.
 * @author Gard Thomassen
 * @see Interaction
 * @see Control
 * @see Invoke
 * @see ProgramManager
 * @see PromoterScoreManager
 * @see ScoreTable
*/

public class Threshold{

    public Vector score;

    /**
     * Constructor, establishes a pointer to the score Vector
     * @param s vector containing score tables
     */    
    public Threshold(Vector s){
	score = s;
    }    
    /** 
     * Method that iterates through all given sequences and
     * sets a threshold for this sequences
     * @param thresholds an array holding all the user defined thresholds
     */
    public void setThreshold(double [] thresholds){
	boolean more = true;
	int i = 0;
	double max;
	double threshold;
	ScoreTable table = (ScoreTable)score.elementAt(i);
	int counter = 0;
	

	//iterating through all objects in score vector
	while(more){
	    max = 0;
	    for(int n=0; n<table.A_score.length; n++){
		
		if(table.A_score[n] >=
		   table.T_score[n] &&
		   table.A_score[n] >=
		   table.C_score[n] &&
		   table.A_score[n] >=
		   table.G_score[n])
		    max += (double)table.A_score[n];
		
		else if (table.T_score[n] >=
			 table.A_score[n] &&
			 table.T_score[n] >=
			 table.C_score[n] &&
			 table.T_score[n] >=
			 table.G_score[n])
		    max += (double)table.T_score[n];
		
		else if (table.C_score[n] >=
			 table.T_score[n] &&
			 table.C_score[n] >=
			 table.A_score[n] &&
			 table.C_score[n] >=
			 table.G_score[n])
		    max += (double)table.C_score[n];
		
		
		else 
		    max += (double)table.G_score[n];
	    }//end for
	    //set threshold as  product of threshold and max score
	    table.setThreshold(max*(thresholds[counter]/100));
	    //for debugging
	    //System.out.println("threshold% :"+ thresholds[counter]);
	    //System.out.println("threshold set to: "+ table.getThreshold());
	    i += 1;
	    //takes care of iteration
	    if(i < score.size()){
		table = (ScoreTable)score.elementAt(i);
		counter ++;
	    }
	    else{
		more = false;
	    }
	}//end while
    }//end setThreshold
} //end class Threshold