1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
|
// Copyright 2010, 2011 Martin C. Frith
// These definitions are for manipulating a score matrix, or a PSSM,
// as a 2-dimensional array. The hope is that 2D arrays are extremely
// fast. But arrays are "evil", so this may not be the best way...
#ifndef SCORE_MATRIX_ROW_HH
#define SCORE_MATRIX_ROW_HH
#include <limits.h>
namespace cbrc{
enum { scoreMatrixRowSize = ALPHABET_CAPACITY };
typedef int ScoreMatrixRow[scoreMatrixRowSize];
// Substitution score for delimiter symbols at the ends of sequences.
// It should be highly negative, to terminate alignments immediately,
// but not so negative that it causes overflow errors.
// The delimiter score when using short ints:
const int shortDelimiterScore = SHRT_MIN/2 + SCHAR_MIN;
// We want: short(delimiterScore) = shortDelimiterScore
const int delimiterScore = INT_MIN/2 + (unsigned short)shortDelimiterScore;
enum { INF = -delimiterScore };
}
#endif
|
