/*
* DNA sequence characters {‘A’,’C’,’G’,’T’} are indexed by {0, 1, 2, 3} respectively.
*
* The Replace costs are defined in replaceMatrix.
* For example, replaceMatrix[1][0] is the cost when ‘C’ is replaced by ‘A’.
*
* The Insert costs are defined in insertMatrix.
* For example, insertMatrix[1] is the cost when ‘C’ is inserted.
*
* The Delete costs are defined in deleteMatrix.
* For example, deleteMatrix[1] is the cost when ‘C’ is deleted.
*/
public class EditCost {
// The values of edit costs may be changed in marking.
private static int[][] replaceMatrix = {{0,3,2,1,0},{3,0,1,2,0},{2,1,0,3,0},{1,2,3,0,0},{0,0,0,0,0}};
private static int[] insertMatrix = {1,1,2,3,99};
private static int[] deleteMatrix = {2,2,1,1,99};
private static char[] DNASequence = {‘A’,’C’,’G’,’T’,’?’};
public static int convertToIndex(char c){
switch(c){
case ‘A’:
return 0;
case ‘C’:
return 1;
case ‘G’:
return 2;
case ‘T’:
return 3;
case ‘?’:
return 4;
}
return -1;
}
public static int getReplaceCost(int indexX, int indexY){
return replaceMatrix[indexX][indexY];
}
public static int getInsertCost(int indexX){
return insertMatrix[indexX];
}
public static int getDeleteCost(int indexX){
return deleteMatrix[indexX];
}
}