ARB
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Go to the source code of this file.
Macros | |
#define | MAXEDGE 1.2 |
#define | ATOLPARAM 0.0001 |
#define | RTOLPARAM 0.001 |
Enumerations | |
enum | { T, C, A, G, N, N1, N2 } |
enum | { REV, TN93, HKY85 } |
Functions | |
char | encodeBase (char c) |
char | decodeBase (char c) |
void | normalizeBaseFreqs (double *F, double fT, double fC, double fA, double fG) |
void | normalizeRateParams (double *X, double a, double b, double c, double d, double e, double f) |
void | initTrnsprob (double ****PP) |
void | uninitTrnsprob (double ****PP) |
void | getTrnsprob (double **P, double ***PP, double d) |
void | updateTrnsprob (double ***PP, double *F, double *X, short M) |
#define MAXEDGE 1.2 |
Definition at line 15 of file trnsprob.h.
#define ATOLPARAM 0.0001 |
Definition at line 17 of file trnsprob.h.
Referenced by normalizeBaseFreqs(), and normalizeRateParams().
#define RTOLPARAM 0.001 |
Definition at line 18 of file trnsprob.h.
anonymous enum |
Enumerator | |
---|---|
T | |
C | |
A | |
G | |
N | |
N1 | |
N2 |
Definition at line 20 of file trnsprob.h.
anonymous enum |
Enumerator | |
---|---|
REV | |
TN93 | |
HKY85 |
Definition at line 21 of file trnsprob.h.
Definition at line 95 of file trnsprob.cxx.
Referenced by Align(), drawLowerPath(), and drawPath().
void normalizeBaseFreqs | ( | double * | F, |
double | fT, | ||
double | fC, | ||
double | fA, | ||
double | fG | ||
) |
void normalizeRateParams | ( | double * | X, |
double | a, | ||
double | b, | ||
double | c, | ||
double | d, | ||
double | e, | ||
double | f | ||
) |
void initTrnsprob | ( | double **** | PP | ) |
Definition at line 155 of file trnsprob.cxx.
References N, newMatrix(), newVector, and P.
Referenced by updateScore().
void uninitTrnsprob | ( | double **** | PP | ) |
Definition at line 167 of file trnsprob.cxx.
References freeBlock, freeMatrix, and P.
Referenced by updateScore().
void getTrnsprob | ( | double ** | P, |
double *** | PP, | ||
double | d | ||
) |