import java.io.*;
import java.util.*;

/**
 * This class creates a score matrix for the different positions a character
 * can have in a sequence of the same length as the input sequence.
 * <P>
 * This class creates an object of the class Matrix that holds the scoring
 * table of the bases
 * This class also holds a method to print the matrix
 * @author Gard Thomassen
 * @see ProgramManager
 * @see PromoterSequenceScorer
 * @see PromoterSearcher
 * @see PromoterSearchManager
*/

public class ScoreTable{

    double threshold;
    String promoter_name;
    int maxDistance, minDistance;
    double[] A_score;
    double[] T_score;
    double[] C_score;
    double[] G_score;
            
    /**
     * The method computes a scoring matrix.
     * The method produces an array for each of the DNA bases,
     * and holds the score for each base at every position i the sequence.
     * Creates a Matrix object which holds the matrix
     * @param seqv  a char array which holds a given sequence
     * @param inf_val a double array witch holds the different scores of
     *              the nucleotide at this position
     * @param name name of the sigma subunit to this promoter sequence
     * @param n an integer telling if it is a -10 or -35 region
     *
    */

   public void createTable(char [] seqv, double[] inf_val, String name, int n){

       promoter_name = name;
       A_score = new double [seqv.length];
       T_score = new double [seqv.length];
       C_score = new double [seqv.length];
       G_score = new double [seqv.length];	 

       if(n == 10 && name.equals("sigma 70(Dave)")){
	   
	   A_score[0] = inf_val[0]*40  ;
	   T_score[0] = inf_val[0]*40  ;
	   C_score[0] = inf_val[0]*10  ; 
	   G_score[0] = inf_val[0]*10  ;

	   A_score[1] = inf_val[1]*45.5   ;
	   T_score[1] = inf_val[1]*33.3   ;
	   C_score[1] = inf_val[1]*12.1  ; 
	   G_score[1] = inf_val[1]*9.1  ;

	   A_score[2] = inf_val[2]*33.3   ;
	   T_score[2] = inf_val[2]*33.3 ;
	   C_score[2] = inf_val[2]*16.7   ; 
	   G_score[2] = inf_val[2]*16.7   ;

	   A_score[3] = inf_val[3]*36.4   ;
	   T_score[3] = inf_val[3]*27.2   ;
	   C_score[3] = inf_val[3]*18.2   ; 
	   G_score[3] = inf_val[3]*18.2   ;

	   A_score[4] = inf_val[4]*22.6   ;
	   T_score[4] = inf_val[4]*51.2  ;
	   C_score[4] = inf_val[4]*12.9   ; 
	   G_score[4] = inf_val[4]*12.9   ;

	   A_score[5] = inf_val[5]*15.6  ;
	   T_score[5] = inf_val[5]*53.1   ;
	   C_score[5] = inf_val[5]*15.6   ; 
	   G_score[5] = inf_val[5]*15.6   ;
       
       }
       if(n == 35 && name.equals("sigma 70(Dave)")){
	   A_score[0] = inf_val[0]*18.2  ;
	   T_score[0] = inf_val[0]*45.5  ;
	   C_score[0] = inf_val[0]*18.2  ; 
	   G_score[0] = inf_val[0]*18.2  ;

	   A_score[1] = inf_val[1]*12.5  ;
	   T_score[1] = inf_val[1]*55.0  ;
	   C_score[1] = inf_val[1]*12.5  ; 
	   G_score[1] = inf_val[1]*18.0;

	   A_score[2] = inf_val[2]*11.5  ;
	   T_score[2] = inf_val[2]*53.8;
	   C_score[2] = inf_val[2]*11.5  ; 
	   G_score[2] = inf_val[2]*23.1  ;

	   A_score[3] = inf_val[3]*25.0  ;
	   T_score[3] = inf_val[3]*25.0  ;
	   C_score[3] = inf_val[3]*25.0  ; 
	   G_score[3] = inf_val[3]*25.0  ;

	   A_score[4] = inf_val[4]*33.3  ;
	   T_score[4] = inf_val[4]*33.3;
	   C_score[4] = inf_val[4]*16.7 ; 
	   G_score[4] = inf_val[4]*16.7  ;

	   A_score[5] = inf_val[5]*42.8  ;
	   T_score[5] = inf_val[5]*28.6  ;
	   C_score[5] = inf_val[5]*14.3  ; 
	   G_score[5] = inf_val[5]*14.3  ;
	  
       }
       if(n == 12 && name.equals("sigma 54(Dave)")){
	   
	   A_score[0] = inf_val[0]*20  ;
	   T_score[0] = inf_val[0]*40  ;
	   C_score[0] = inf_val[0]*40 ; 
	   G_score[0] = inf_val[0]*0  ;

	   A_score[1] = inf_val[1]* 0  ;
	   T_score[1] = inf_val[1]* 61.5  ;
	   C_score[1] = inf_val[1]* 30.8 ; 
	   G_score[1] = inf_val[1]* 7.7  ;

	   A_score[2] = inf_val[2]* 0.0  ;
	   T_score[2] = inf_val[2]* 37.0  ;
	   C_score[2] = inf_val[2]* 22.2; 
	   G_score[2] = inf_val[2]* 40.7 ;

	   A_score[3] = inf_val[3]* 2.3  ;
	   T_score[3] = inf_val[3]* 11.6  ;
	   C_score[3] = inf_val[3]* 39.6  ; 
	   G_score[3] = inf_val[3]* 46.5 ;

	   A_score[4] = inf_val[4]* 20  ;
	   T_score[4] = inf_val[4]* 15  ;
	   C_score[4] = inf_val[4]* 50  ; 
	   G_score[4] = inf_val[4]* 15 ;
       }
       
       if(n == 24 && name.equals("sigma 54(Dave)")){
       
	   A_score[0] = inf_val[0]*0;
	   T_score[0] = inf_val[0]*45.5;
	   C_score[0] = inf_val[0]*36.4;
	   G_score[0] = inf_val[0]*18.2;

	   A_score[1] = inf_val[1]*0;
	   T_score[1] = inf_val[1]*43.4;
	   C_score[1] = inf_val[1]*10.9;
	   G_score[1] = inf_val[1]*45.7;

	   A_score[2] = inf_val[2]*3.0;
	   T_score[2] = inf_val[2]*11.0;
	   C_score[2] = inf_val[2]*4;
	   G_score[2] = inf_val[2]*82;

	   A_score[3] = inf_val[3]*5.9;
	   T_score[3] = inf_val[3]*2.0;
	   C_score[3] = inf_val[3]*27.5;
	   G_score[3] = inf_val[3]*64.7;

	   A_score[4] = inf_val[4]*28.6;
	   T_score[4] = inf_val[4]*0;
	   C_score[4] = inf_val[4]*57.1;
	   G_score[4] = inf_val[4]*14.3;

	   A_score[5] = inf_val[5]*63.6;
	   T_score[5] = inf_val[5]*0;
	   C_score[5] = inf_val[5]*18.2;
	   G_score[5] = inf_val[5]*18.2;
       }
  
       if(n == 10 && name.equals("sigma 38(Dave)")){

	   A_score[0] = inf_val[0]*33.3;
	   T_score[0] = inf_val[0]*50;
	   C_score[0] = inf_val[0]*8.3;
	   G_score[0] = inf_val[0]*8.3;

	   A_score[1] = inf_val[1]*60.3;
	   T_score[1] = inf_val[1]*31.7;
	   C_score[1] = inf_val[1]*7.9;
	   G_score[1] = inf_val[1]*0;

	   A_score[2] = inf_val[2]*44.4;
	   T_score[2] = inf_val[2]*27.8;
	   C_score[2] = inf_val[2]*16.7;
	   G_score[2] = inf_val[2]*1.1;

	   A_score[3] = inf_val[3]*25;
	   T_score[3] = inf_val[3]*25;
	   C_score[3] = inf_val[3]*25;
	   G_score[3] = inf_val[3]*25;

	   A_score[4] = inf_val[4]*26.7;
	   T_score[4] = inf_val[4]*50;
	   C_score[4] = inf_val[4]*13.3;
	   G_score[4] = inf_val[4]*10;

	   A_score[5] = inf_val[5]*20.3;
	   T_score[5] = inf_val[5]*64.4;
	   C_score[5] = inf_val[5]*13.6;
	   G_score[5] = inf_val[5]*16.9;

	   A_score[6] = inf_val[6]*20.0;
	   T_score[6] = inf_val[6]*53.3;
	   C_score[6] = inf_val[6]*6.7;
	   G_score[6] = inf_val[6]*26.7;
       }

       if(n == 35 && name.equals("sigma 38(Dave)")){
  
	   A_score[0] = inf_val[0]*25;
	   T_score[0] = inf_val[0]*50;
	   C_score[0] = inf_val[0]*12.5;
	   G_score[0] = inf_val[0]*12.5;

	   A_score[1] = inf_val[1]*18.6;
	   T_score[1] = inf_val[1]*56.3;
	   C_score[1] = inf_val[1]*12.5;
	   G_score[1] = inf_val[1]*12.5;

	   A_score[2] = inf_val[2]*25;
	   T_score[2] = inf_val[2]*50;
	   C_score[2] = inf_val[2]*12.5;
	   G_score[2] = inf_val[2]*12.5;

	   A_score[3] = inf_val[3]*25;
	   T_score[3] = inf_val[3]*50;
	   C_score[3] = inf_val[3]*12.5;
	   G_score[3] = inf_val[3]*12.5;

	   A_score[4] = inf_val[4]*42.3;
	   T_score[4] = inf_val[4]*28.6;
	   C_score[4] = inf_val[4]*28.6;
	   G_score[4] = inf_val[4]*0;

	   A_score[5] = inf_val[5]*45.5;
	   T_score[5] = inf_val[5]*9.1;
	   C_score[5] = inf_val[5]*27.3;
	   G_score[5] = inf_val[5]*18.2;
	   
       }
       if(n == 15 && name.equals("sigma 32(Dave)")){
	   
	   A_score[0] = inf_val[0]*9.3;
	   T_score[0] = inf_val[0]*9.3;
	   C_score[0] = inf_val[0]*65.1;
	   G_score[0] = inf_val[0]*16.3;
	   
	   A_score[1] = inf_val[1]*4.7;
	   T_score[1] = inf_val[1]*5.8;
	   C_score[1] = inf_val[1]*79.1;
	   G_score[1] = inf_val[1]*10.5;

	   A_score[2] = inf_val[2]*13.7;
	   T_score[2] = inf_val[2]*8.2;
	   C_score[2] = inf_val[2]*72.6;
	   G_score[2] = inf_val[2]*5.5;
   	
	   A_score[3] = inf_val[3]*50;
	   T_score[3] = inf_val[3]*9.1;
	   C_score[3] = inf_val[3]*31.8;
	   G_score[3] = inf_val[3]*9.1;

	   A_score[4] = inf_val[4]*49;
	   T_score[4] = inf_val[4]*42.9;
	   C_score[4] = inf_val[4]*4.1;
	   G_score[4] = inf_val[4]*4.1;

	   A_score[5] = inf_val[5]*24.1;
	   T_score[5] = inf_val[5]*62.1;
	   C_score[5] = inf_val[5]*10.3;
	   G_score[5] = inf_val[5]*3.4;

	   A_score[6] = inf_val[6]*25;
	   T_score[6] = inf_val[6]*50;
	   C_score[6] = inf_val[6]*12.5;
	   G_score[6] = inf_val[6]*12.5;

	   A_score[7] = inf_val[7]*33.3;	    
	   T_score[7] = inf_val[7]*40;
	   C_score[7] = inf_val[7]*13.3;
	   G_score[7] = inf_val[7]*13.3;
       }

       if(n == 31 && name.equals("sigma 32(Dave)")){

	   A_score[0] = inf_val[0]*10.8;
	   T_score[0] = inf_val[0]*62.2;
	   C_score[0] = inf_val[0]*10.8;
	   G_score[0] = inf_val[0]*18.9;
	   
	   A_score[1] = inf_val[1]*9.3;
	   T_score[1] = inf_val[1]*60.5;
	   C_score[1] = inf_val[1]*16.3;
	   G_score[1] = inf_val[1]*14.0;

	   A_score[2] = inf_val[2]*31.3;
	   T_score[2] = inf_val[2]*31.3;
	   C_score[2] = inf_val[2]*6.1;
	   G_score[2] = inf_val[2]*31.3;

	   A_score[3] = inf_val[3]*44.4;
	   T_score[3] = inf_val[3]*37.0;
	   C_score[3] = inf_val[3]*3.7;
	   G_score[3] = inf_val[3]*14.8;
	   
	   A_score[4] = inf_val[4]*57.9;
	   T_score[4] = inf_val[4]*23.7;
	   C_score[4] = inf_val[4]*5.3;
	   G_score[4] = inf_val[4]*13.2;

	   A_score[5] = inf_val[5]*57.1;
	   T_score[5] = inf_val[5]*14.3;
	   C_score[5] = inf_val[5]*5.7;
	   G_score[5] = inf_val[5]*22.9;

	   A_score[6] = inf_val[6]*58.3;
	   T_score[6] = inf_val[6]*8.3;
	   C_score[6] = inf_val[6]*25;
	   G_score[6] = inf_val[6]*0;

           A_score[7] = inf_val[7]*58.3;
	   T_score[7] = inf_val[7]*8.3;
	   C_score[7] = inf_val[7]*0;
	   G_score[7] = inf_val[7]*25;
       }
       if(n == 10 && name.equals("sigma all")){
	   
	   A_score[0] = inf_val[0]*5;
	   T_score[0] = inf_val[0]*77;
	   C_score[0] = inf_val[0]*10;
	   G_score[0] = inf_val[0]*8;
	   
	   A_score[1] = inf_val[1]*76;
	   T_score[1] = inf_val[1]*12;
	   C_score[1] = inf_val[1]*6;
	   G_score[1] = inf_val[1]*6;

	   A_score[2] = inf_val[2]*15;
	   T_score[2] = inf_val[2]*60;
	   C_score[2] = inf_val[2]*11;
	   G_score[2] = inf_val[2]*14;

	   A_score[3] = inf_val[3]*61;
	   T_score[3] = inf_val[3]*12;
	   C_score[3] = inf_val[3]*13;
	   G_score[3] = inf_val[3]*14;

	   A_score[4] = inf_val[4]*56;
	   T_score[4] = inf_val[4]*15;
	   C_score[4] = inf_val[4]*20;
	   G_score[4] = inf_val[4]*8;

	   A_score[5] = inf_val[5]*6;
	   T_score[5] = inf_val[5]*82;
	   C_score[5] = inf_val[5]*7;
	   G_score[5] = inf_val[5]*5;

       }
       if(n == 35 && name.equals("sigma all")){

	   A_score[0] = inf_val[0]*10;
	   T_score[0] = inf_val[0]*69;
	   C_score[0] = inf_val[0]*10;
	   G_score[0] = inf_val[0]*10;
	   
	   A_score[1] = inf_val[1]*6;
	   T_score[1] = inf_val[1]*79;
	   C_score[1] = inf_val[1]*7;
	   G_score[1] = inf_val[1]*8;

	   A_score[2] = inf_val[2]*9;
	   T_score[2] = inf_val[2]*18;
	   C_score[2] = inf_val[2]*12;
	   G_score[2] = inf_val[2]*61;

	   A_score[3] = inf_val[3]*56;
	   T_score[3] = inf_val[3]*16;
	   C_score[3] = inf_val[3]*17;
	   G_score[3] = inf_val[3]*11;

	   A_score[4] = inf_val[4]*21;
	   T_score[4] = inf_val[4]*16;
	   C_score[4] = inf_val[4]*54;
	   G_score[4] = inf_val[4]*9;

	   A_score[5] = inf_val[5]*54;
	   T_score[5] = inf_val[5]*17;
	   C_score[5] = inf_val[5]*13;
	   G_score[5] = inf_val[5]*16;

       }

       
       if(n == 35 && name.equals("sigma_70_regulonDB")){
	   A_score[0] = inf_val[0]*24;
	   T_score[0] = inf_val[0]*31;
	   C_score[0] = inf_val[0]*22;
	   G_score[0] = inf_val[0]*24;
	   
	   A_score[1] = inf_val[1]*22;
	   T_score[1] = inf_val[1]*36;
	   C_score[1] = inf_val[1]*20;
	   G_score[1] = inf_val[1]*21;
	   
	   A_score[2] = inf_val[2]*27;
	   T_score[2] = inf_val[2]*47;
	   C_score[2] = inf_val[2]*17;
	   G_score[2] = inf_val[2]*19;
	   
	   A_score[3] = inf_val[3]*14;
	   T_score[3] = inf_val[3]*46;
	   C_score[3] = inf_val[3]*17;
	   G_score[3] = inf_val[3]*23;
	   
	   A_score[4] = inf_val[4]*17;
	   T_score[4] = inf_val[4]*36;
	   C_score[4] = inf_val[4]*19;
	   G_score[4] = inf_val[4]*27;
	   
	   A_score[5] = inf_val[5]*21;
	   T_score[5] = inf_val[5]*32;
	   C_score[5] = inf_val[5]*26;
	   G_score[5] = inf_val[5]*21;
       }
   
       
       if(n == 10 && name.equals("sigma_70_regulonDB")){
	   A_score[0] = inf_val[0]*22;
	   T_score[0] = inf_val[0]*51;
	   C_score[0] = inf_val[0]*16;
	   G_score[0] = inf_val[0]*12;
	   
	   A_score[1] = inf_val[1]*54;
	   T_score[1] = inf_val[1]*26;
	   C_score[1] = inf_val[1]*9;
	   G_score[1] = inf_val[1]*10;
	   
	   A_score[2] = inf_val[2]*45;
	   T_score[2] = inf_val[2]*32;
	   C_score[2] = inf_val[2]*12;
	   G_score[2] = inf_val[2]*11;
	   
	   A_score[3] = inf_val[3]*40;
	   T_score[3] = inf_val[3]*29;
	   C_score[3] = inf_val[3]*20;
	   G_score[3] = inf_val[3]*11;
	   
	   A_score[4] = inf_val[4]*41;
	   T_score[4] = inf_val[4]*26;
	   C_score[4] = inf_val[4]*21;
	   G_score[4] = inf_val[4]*13;
	   
	   A_score[5] = inf_val[5]*20;
	   T_score[5] = inf_val[5]*53;
	   C_score[5] = inf_val[5]*15;
	   G_score[5] = inf_val[5]*12;
       }
   
 
       if(n == 35 && name.equals("sigma_32_regulonDB")){
	   A_score[0] = inf_val[0]*31;
	   T_score[0] = inf_val[0]*37;
	   C_score[0] = inf_val[0]*12;
	   G_score[0] = inf_val[0]*23;
	   
	   A_score[1] = inf_val[1]*37;
	   T_score[1] = inf_val[1]*27;
	   C_score[1] = inf_val[1]*12;
	   G_score[1] = inf_val[1]*27;
	   
	   A_score[2] = inf_val[2]*44;
	   T_score[2] = inf_val[2]*25;
	   C_score[2] = inf_val[2]*10;
	   G_score[2] = inf_val[2]*23;
	   
	   A_score[3] = inf_val[3]*56;
	   T_score[3] = inf_val[3]*17;
	   C_score[3] = inf_val[3]*10;
	   G_score[3] = inf_val[3]*19;
	   
	   A_score[4] = inf_val[4]*50;
	   T_score[4] = inf_val[4]*21;
	   C_score[4] = inf_val[4]*15;
	   G_score[4] = inf_val[4]*15;
	   
	   A_score[5] = inf_val[5]*46;
	   T_score[5] = inf_val[5]*21;
	   C_score[5] = inf_val[5]*13;
	   G_score[5] = inf_val[5]*21;
       }
    
       if(n == 10 && name.equals("sigma_32_regulonDB")){
	   A_score[0] = inf_val[0]*27;
	   T_score[0] = inf_val[0]*12;
	   C_score[0] = inf_val[0]*52;
	   G_score[0] = inf_val[0]*12;
	   
	   A_score[1] = inf_val[1]*10;
	   T_score[1] = inf_val[1]*6;
	   C_score[1] = inf_val[1]*63;
	   G_score[1] = inf_val[1]*23;
	   
	   A_score[2] = inf_val[2]*12;
	   T_score[2] = inf_val[2]*6;
	   C_score[2] = inf_val[2]*71;
	   G_score[2] = inf_val[2]*13;
	   
	   A_score[3] = inf_val[3]*19;
	   T_score[3] = inf_val[3]*12;
	   C_score[3] = inf_val[3]*65;
	   G_score[3] = inf_val[3]*6;
	   
	   A_score[4] = inf_val[4]*54;
	   T_score[4] = inf_val[4]*15;
	   C_score[4] = inf_val[4]*21;
	   G_score[4] = inf_val[4]*12;
	   
	   A_score[5] = inf_val[5]*25;
	   T_score[5] = inf_val[5]*65;
	   C_score[5] = inf_val[5]*6;
	   G_score[5] = inf_val[5]*6;
    
	   A_score[6] = inf_val[6]*25;
	   T_score[6] = inf_val[6]*48;
	   C_score[6] = inf_val[6]*23;
	   G_score[6] = inf_val[6]*6;
       }
       
       
       if(n == 35 && name.equals("sigma_24_regulonDB")){
	   A_score[0] = inf_val[0]*19;
	   T_score[0] = inf_val[0]*11;
	   C_score[0] = inf_val[0]*27;
	   G_score[0] = inf_val[0]*43;
	   
	   A_score[1] = inf_val[1]*27;
	   T_score[1] = inf_val[1]*19;
	   C_score[1] = inf_val[1]*16;
	   G_score[1] = inf_val[1]*38;
	   
	   A_score[2] = inf_val[2]*43;
	   T_score[2] = inf_val[2]*5;
	   C_score[2] = inf_val[2]*11;
	   G_score[2] = inf_val[2]*41;
	   
	   A_score[3] = inf_val[3]*43;
	   T_score[3] = inf_val[3]*16;
	   C_score[3] = inf_val[3]*11;
	   G_score[3] = inf_val[3]*41;
	   
	   A_score[4] = inf_val[4]*49;
	   T_score[4] = inf_val[4]*27;
	   C_score[4] = inf_val[4]*16;
	   G_score[4] = inf_val[4]*8;
	   
	   A_score[5] = inf_val[5]*41;
	   T_score[5] = inf_val[5]*24;
	   C_score[5] = inf_val[5]*19;
	   G_score[5] = inf_val[5]*17;
       }
   
 
       if(n == 10 && name.equals("sigma_24_regulonDB")){
	   A_score[0] = inf_val[0]*57;
	   T_score[0] = inf_val[0]*3;
	   C_score[0] = inf_val[0]*11;
	   G_score[0] = inf_val[0]*30;
	   
	   A_score[1] = inf_val[1]*24;
	   T_score[1] = inf_val[1]*16;
	   C_score[1] = inf_val[1]*14;
	   G_score[1] = inf_val[1]*46;
	   
	   A_score[2] = inf_val[2]*19;
	   T_score[2] = inf_val[2]*57;
	   C_score[2] = inf_val[2]*16;
	   G_score[2] = inf_val[2]*8;
	   
	   A_score[3] = inf_val[3]*3;
	   T_score[3] = inf_val[3]*38;
	   C_score[3] = inf_val[3]*57;
	   G_score[3] = inf_val[3]*3;
	   
	   A_score[4] = inf_val[4]*3;
	   T_score[4] = inf_val[4]*57;
	   C_score[4] = inf_val[4]*24;
	   G_score[4] = inf_val[4]*16;
	   
	   A_score[5] = inf_val[5]*16;
	   T_score[5] = inf_val[5]*24;
	   C_score[5] = inf_val[5]*3;
	   G_score[5] = inf_val[5]*57;

	   A_score[6] = inf_val[6]*70;
	   T_score[6] = inf_val[6]*3;
	   C_score[6] = inf_val[6]*3;
	   G_score[6] = inf_val[6]*24;


	   A_score[7] = inf_val[7]*49;
	   T_score[7] = inf_val[7]*21;
	   C_score[7] = inf_val[7]*24;
	   G_score[7] = inf_val[7]*5;
       }
   
 
   }//end createTable
    
    /** 
     * Method to print the Scoretable, only used as debugging 
     * @param n the name of the sigma factor to this scoretable
     */
    

    public void printResultTable(String n){
	String name = n ;
	System.out.println(n);
	System.out.print("A_score : ");
	String tmp;
	for(int i=0; i<A_score.length; i++){
	    tmp= Double.toString(A_score[i]);
	    System.out.print(tmp.substring(0,3)+"\t");
	}
	System.out.println();
	System.out.print("T_score : ");
	for(int i=0; i<T_score.length; i++){
	    tmp= Double.toString(T_score[i]);
	    System.out.print(tmp.substring(0,3)+"\t");
	}
	System.out.println();
	System.out.print("C_score : ");
	for(int i=0; i<C_score.length; i++){
	    tmp= Double.toString(C_score[i]);
	    System.out.print(tmp.substring(0,3)+"\t");
	}
	System.out.println();
	System.out.print("G_score : ");
	for(int i=0; i<G_score.length; i++){
	    tmp= Double.toString(G_score[i]);
	    System.out.print(tmp.substring(0,3)+"\t");
	}
	System.out.println("");
    }//end printResultTable
    
    
    /**
     * Typical set method for the minDistance variable
     * @param min the minimum distance allowd 
     */
    public void setMinDistance(int min){
	minDistance = min;
    }
    /**
     * Typical get method for the minDistance variable
     * @return the minimin distance allowed 
    */
    public int getMinDistance(){
	return minDistance;
    }
    /**
     * Typical set method for the maxDistance variable
     * @param max the maximum distance allowed
     */
    public void setMaxDistance(int max){
	maxDistance = max;
    }
    /**
     * Typical get method for the maxDistance variable
     * @return the maximim distance allowed
     */
    public int getMaxDistance(){
	return maxDistance;
    }
    /**
     * Typical set method for the threshold to this sigma factor
     * @param thres the threshold in percent
     */
    public void setThreshold(double thres){
	threshold = thres;
    }
    /**
     * Typical get method for the threshold of this sigma factor
     * @return the threshold
     */
    public double getThreshold(){
	return threshold;
    }

    
}//end class ScoreMatrix