scoredialog.java

Sequence alignement using different algorithms

            wholeMatrix.setScore('M', 'Q', -1);
            wholeMatrix.setScore('M', 'E', -2);
            wholeMatrix.setScore('M', 'G', -3);
            wholeMatrix.setScore('M', 'H', -2);
            wholeMatrix.setScore('M', 'I', 2);
            wholeMatrix.setScore('M', 'L', 4);
            wholeMatrix.setScore('M', 'K', 0);
            wholeMatrix.setScore('M', 'M', 6);
            wholeMatrix.setScore('F', 'A', -3);
            wholeMatrix.setScore('F', 'R', -4);
            wholeMatrix.setScore('F', 'N', -3);
            wholeMatrix.setScore('F', 'D', -6);
            wholeMatrix.setScore('F', 'C', -4);
            wholeMatrix.setScore('F', 'Q', -5);
            wholeMatrix.setScore('F', 'E', -5);
            wholeMatrix.setScore('F', 'G', -5);
            wholeMatrix.setScore('F', 'H', -2);
            wholeMatrix.setScore('F', 'I', 1);
            wholeMatrix.setScore('F', 'L', 2);
            wholeMatrix.setScore('F', 'K', -5);
            wholeMatrix.setScore('F', 'M', 0);
            wholeMatrix.setScore('F', 'F', 9);
            wholeMatrix.setScore('P', 'A', 1);
            wholeMatrix.setScore('P', 'R', 0);
            wholeMatrix.setScore('P', 'N', 0);
            wholeMatrix.setScore('P', 'D', -1);
            wholeMatrix.setScore('P', 'C', -3);
            wholeMatrix.setScore('P', 'Q', 0);
            wholeMatrix.setScore('P', 'E', -1);
            wholeMatrix.setScore('P', 'G', 0);
            wholeMatrix.setScore('P', 'H', 0);
            wholeMatrix.setScore('P', 'I', -2);
            wholeMatrix.setScore('P', 'L', -3);
            wholeMatrix.setScore('P', 'K', -1);
            wholeMatrix.setScore('P', 'M', -2);
            wholeMatrix.setScore('P', 'F', -5);
            wholeMatrix.setScore('P', 'P', 6);
            wholeMatrix.setScore('S', 'A', 1);
            wholeMatrix.setScore('S', 'R', 0);
            wholeMatrix.setScore('S', 'N', 1);
            wholeMatrix.setScore('S', 'D', 0);
            wholeMatrix.setScore('S', 'C', 0);
            wholeMatrix.setScore('S', 'Q', -1);
            wholeMatrix.setScore('S', 'E', 0);
            wholeMatrix.setScore('S', 'G', 1);
            wholeMatrix.setScore('S', 'H', -1);
            wholeMatrix.setScore('S', 'I', -1);
            wholeMatrix.setScore('S', 'L', -3);
            wholeMatrix.setScore('S', 'K', 0);
            wholeMatrix.setScore('S', 'M', -2);
            wholeMatrix.setScore('S', 'F', -3);
            wholeMatrix.setScore('S', 'P', 1);
            wholeMatrix.setScore('S', 'S', 2);
            wholeMatrix.setScore('T', 'A', 1);
            wholeMatrix.setScore('T', 'R', -1);
            wholeMatrix.setScore('T', 'N', 0);
            wholeMatrix.setScore('T', 'D', 0);
            wholeMatrix.setScore('T', 'C', -2);
            wholeMatrix.setScore('T', 'Q', -1);
            wholeMatrix.setScore('T', 'E', 0);
            wholeMatrix.setScore('T', 'G', 0);
            wholeMatrix.setScore('T', 'H', -1);
            wholeMatrix.setScore('T', 'I', 0);
            wholeMatrix.setScore('T', 'L', -2);
            wholeMatrix.setScore('T', 'K', 0);
            wholeMatrix.setScore('T', 'M', -1);
            wholeMatrix.setScore('T', 'F', -3);
            wholeMatrix.setScore('T', 'P', 0);
            wholeMatrix.setScore('T', 'S', 1);
            wholeMatrix.setScore('T', 'T', 3);
            wholeMatrix.setScore('W', 'A', -6);
            wholeMatrix.setScore('W', 'R', 2);
            wholeMatrix.setScore('W', 'N', -4);
            wholeMatrix.setScore('W', 'D', -7);
            wholeMatrix.setScore('W', 'C', -8);
            wholeMatrix.setScore('W', 'Q', -5);
            wholeMatrix.setScore('W', 'E', -7);
            wholeMatrix.setScore('W', 'G', -7);
            wholeMatrix.setScore('W', 'H', -3);
            wholeMatrix.setScore('W', 'I', -5);
            wholeMatrix.setScore('W', 'L', -2);
            wholeMatrix.setScore('W', 'K', -3);
            wholeMatrix.setScore('W', 'M', -4);
            wholeMatrix.setScore('W', 'F', 0);
            wholeMatrix.setScore('W', 'P', -6);
            wholeMatrix.setScore('W', 'S', -2);
            wholeMatrix.setScore('W', 'T', -5);
            wholeMatrix.setScore('W', 'W', 17);
            wholeMatrix.setScore('Y', 'A', -3);
            wholeMatrix.setScore('Y', 'R', -4);
            wholeMatrix.setScore('Y', 'N', -2);
            wholeMatrix.setScore('Y', 'D', -4);
            wholeMatrix.setScore('Y', 'C', 0);
            wholeMatrix.setScore('Y', 'Q', -4);
            wholeMatrix.setScore('Y', 'E', -4);
            wholeMatrix.setScore('Y', 'G', -5);
            wholeMatrix.setScore('Y', 'H', 0);
            wholeMatrix.setScore('Y', 'I', -1);
            wholeMatrix.setScore('Y', 'L', -1);
            wholeMatrix.setScore('Y', 'K', -4);
            wholeMatrix.setScore('Y', 'M', -2);
            wholeMatrix.setScore('Y', 'F', 7);
            wholeMatrix.setScore('Y', 'P', -5);
            wholeMatrix.setScore('Y', 'S', -3);
            wholeMatrix.setScore('Y', 'T', -3);
            wholeMatrix.setScore('Y', 'W', 0);
            wholeMatrix.setScore('Y', 'Y', 10);
            wholeMatrix.setScore('V', 'A', 0);
            wholeMatrix.setScore('V', 'R', -2);
            wholeMatrix.setScore('V', 'N', -2);
            wholeMatrix.setScore('V', 'D', -2);
            wholeMatrix.setScore('V', 'C', -2);
            wholeMatrix.setScore('V', 'Q', -2);
            wholeMatrix.setScore('V', 'E', -2);
            wholeMatrix.setScore('V', 'G', -1);
            wholeMatrix.setScore('V', 'H', -2);
            wholeMatrix.setScore('V', 'I', 4);
            wholeMatrix.setScore('V', 'L', 2);
            wholeMatrix.setScore('V', 'K', -2);
            wholeMatrix.setScore('V', 'M', 2);
            wholeMatrix.setScore('V', 'F', -1);
            wholeMatrix.setScore('V', 'P', -1);
            wholeMatrix.setScore('V', 'S', -1);
            wholeMatrix.setScore('V', 'T', 0);
            wholeMatrix.setScore('V', 'W', -6);
            wholeMatrix.setScore('V', 'Y', -2);
            wholeMatrix.setScore('V', 'V', 4);
            wholeMatrix.setScore('B', 'A', 0);
            wholeMatrix.setScore('B', 'R', -1);
            wholeMatrix.setScore('B', 'N', 2);
            wholeMatrix.setScore('B', 'D', 3);
            wholeMatrix.setScore('B', 'C', -4);
            wholeMatrix.setScore('B', 'Q', 1);
            wholeMatrix.setScore('B', 'E', 3);
            wholeMatrix.setScore('B', 'G', 0);
            wholeMatrix.setScore('B', 'H', 1);
            wholeMatrix.setScore('B', 'I', -2);
            wholeMatrix.setScore('B', 'L', -3);
            wholeMatrix.setScore('B', 'K', 1);
            wholeMatrix.setScore('B', 'M', -2);
            wholeMatrix.setScore('B', 'F', -4);
            wholeMatrix.setScore('B', 'P', -1);
            wholeMatrix.setScore('B', 'S', 0);
            wholeMatrix.setScore('B', 'T', 0);
            wholeMatrix.setScore('B', 'W', -5);
            wholeMatrix.setScore('B', 'Y', -3);
            wholeMatrix.setScore('B', 'V', -2);
            wholeMatrix.setScore('B', 'B', 3);
            wholeMatrix.setScore('Z', 'A', 0);
            wholeMatrix.setScore('Z', 'R', 0);
            wholeMatrix.setScore('Z', 'N', 1);
            wholeMatrix.setScore('Z', 'D', 3);
            wholeMatrix.setScore('Z', 'C', -5);
            wholeMatrix.setScore('Z', 'Q', 3);
            wholeMatrix.setScore('Z', 'E', 3);
            wholeMatrix.setScore('Z', 'G', 0);
            wholeMatrix.setScore('Z', 'H', 2);
            wholeMatrix.setScore('Z', 'I', -2);
            wholeMatrix.setScore('Z', 'L', -3);
            wholeMatrix.setScore('Z', 'K', 0);
            wholeMatrix.setScore('Z', 'M', -2);
            wholeMatrix.setScore('Z', 'F', -5);
            wholeMatrix.setScore('Z', 'P', 0);
            wholeMatrix.setScore('Z', 'S', 0);
            wholeMatrix.setScore('Z', 'T', -1);
            wholeMatrix.setScore('Z', 'W', -6);
            wholeMatrix.setScore('Z', 'Y', -4);
            wholeMatrix.setScore('Z', 'V', -2);
            wholeMatrix.setScore('Z', 'B', 2);
            wholeMatrix.setScore('Z', 'Z', 3);
            wholeMatrix.setScore('X', 'A', 0);
            wholeMatrix.setScore('X', 'R', -1);
            wholeMatrix.setScore('X', 'N', 0);
            wholeMatrix.setScore('X', 'D', -1);
            wholeMatrix.setScore('X', 'C', -3);
            wholeMatrix.setScore('X', 'Q', -1);
            wholeMatrix.setScore('X', 'E', -1);
            wholeMatrix.setScore('X', 'G', -1);
            wholeMatrix.setScore('X', 'H', -1);
            wholeMatrix.setScore('X', 'I', -1);
            wholeMatrix.setScore('X', 'L', -1);
            wholeMatrix.setScore('X', 'K', -1);
            wholeMatrix.setScore('X', 'M', -1);
            wholeMatrix.setScore('X', 'F', -2);
            wholeMatrix.setScore('X', 'P', -1);
            wholeMatrix.setScore('X', 'S', 0);
            wholeMatrix.setScore('X', 'T', 0);
            wholeMatrix.setScore('X', 'W', -4);
            wholeMatrix.setScore('X', 'Y', -2);
            wholeMatrix.setScore('X', 'V', -1);
            wholeMatrix.setScore('X', 'B', -1);
            wholeMatrix.setScore('X', 'Z', -1);
            wholeMatrix.setScore('X', 'X', -1);

            break;

         case SCOREMATRIX_BLOSUM62:

            wholeMatrix = new ScoreHash();
            wholeMatrix.setScore('A', 'A', 4);
            wholeMatrix.setScore('R', 'A', -1);
            wholeMatrix.setScore('R', 'R', 5);
            wholeMatrix.setScore('N', 'A', -2);
            wholeMatrix.setScore('N', 'R', 0);
            wholeMatrix.setScore('N', 'N', 6);
            wholeMatrix.setScore('D', 'A', -2);
            wholeMatrix.setScore('D', 'R', -2);
            wholeMatrix.setScore('D', 'N', 1);
            wholeMatrix.setScore('D', 'D', 6);
            wholeMatrix.setScore('C', 'A', 0);
            wholeMatrix.setScore('C', 'R', -3);
            wholeMatrix.setScore('C', 'N', -3);
            wholeMatrix.setScore('C', 'D', -3);
            wholeMatrix.setScore('C', 'C', 9);
            wholeMatrix.setScore('Q', 'A', -1);
            wholeMatrix.setScore('Q', 'R', 1);
            wholeMatrix.setScore('Q', 'N', 0);
            wholeMatrix.setScore('Q', 'D', 0);
            wholeMatrix.setScore('Q', 'C', -3);
            wholeMatrix.setScore('Q', 'Q', 5);
            wholeMatrix.setScore('E', 'A', -1);
            wholeMatrix.setScore('E', 'R', 0);
            wholeMatrix.setScore('E', 'N', 0);
            wholeMatrix.setScore('E', 'D', 2);
            wholeMatrix.setScore('E', 'C', -4);
            wholeMatrix.setScore('E', 'Q', 2);
            wholeMatrix.setScore('E', 'E', 5);
            wholeMatrix.setScore('G', 'A', 0);
            wholeMatrix.setScore('G', 'R', -2);
            wholeMatrix.setScore('G', 'N', 0);
            wholeMatrix.setScore('G', 'D', -1);
            wholeMatrix.setScore('G', 'C', -3);
            wholeMatrix.setScore('G', 'Q', -2);
            wholeMatrix.setScore('G', 'E', -2);
            wholeMatrix.setScore('G', 'G', 6);
            wholeMatrix.setScore('H', 'A', -2);
            wholeMatrix.setScore('H', 'R', 0);
            wholeMatrix.setScore('H', 'N', 1);
            wholeMatrix.setScore('H', 'D', -1);
            wholeMatrix.setScore('H', 'C', -3);
            wholeMatrix.setScore('H', 'Q', 0);
            wholeMatrix.setScore('H', 'E', 0);
            wholeMatrix.setScore('H', 'G', -2);
            wholeMatrix.setScore('H', 'H', 8);
            wholeMatrix.setScore('I', 'A', -1);
            wholeMatrix.setScore('I', 'R', -3);
            wholeMatrix.setScore('I', 'N', -3);
            wholeMatrix.setScore('I', 'D', -3);
            wholeMatrix.setScore('I', 'C', -1);
            wholeMatrix.setScore('I', 'Q', -3);
            wholeMatrix.setScore('I', 'E', -3);
            wholeMatrix.setScore('I', 'G', -4);
            wholeMatrix.setScore('I', 'H', -3);
            wholeMatrix.setScore('I', 'I', 4);
            wholeMatrix.setScore('L', 'A', -1);
            wholeMatrix.setScore('L', 'R', -2);
            wholeMatrix.setScore('L', 'N', -3);
            wholeMatrix.setScore('L', 'D', -4);
            wholeMatrix.setScore('L', 'C', -1);
            wholeMatrix.setScore('L', 'Q', -2);
            wholeMatrix.setScore('L', 'E', -3);
            wholeMatrix.setScore('L', 'G', -4);
            wholeMatrix.setScore('L', 'H', -3);
            wholeMatrix.setScore('L', 'I', 2);
            wholeMatrix.setScore('L', 'L', 4);
            wholeMatrix.setScore('K', 'A', -1);
            wholeMatrix.setScore('K', 'R', 2);
            wholeMatrix.setScore('K', 'N', 0);
            wholeMatrix.setScore('K', 'D', -1);
            wholeMatrix.setScore('K', 'C', -3);
            wholeMatrix.setScore('K', 'Q', 1);
            wholeMatrix.setScore('K', 'E', 1);
            wholeMatrix.setScore('K', 'G', -2);
            wholeMatrix.setScore('K', 'H', -1);
            wholeMatrix.setScore('K', 'I', -3);
            wholeMatrix.setScore('K', 'L', -2);
            wholeMatrix.setScore('K', 'K', 5);