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Macros | Enumerations | Functions
trnsprob.h File Reference
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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)
 

Macro Definition Documentation

#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.

Enumeration Type Documentation

anonymous enum
Enumerator
N1 
N2 

Definition at line 20 of file trnsprob.h.

anonymous enum
Enumerator
REV 
TN93 
HKY85 

Definition at line 21 of file trnsprob.h.

Function Documentation

char encodeBase ( char  c)

Definition at line 80 of file trnsprob.cxx.

References A, C, G, N, and T.

Referenced by Align().

char decodeBase ( char  c)

Definition at line 95 of file trnsprob.cxx.

References A, C, G, N, and T.

Referenced by Align(), drawLowerPath(), and drawPath().

void normalizeBaseFreqs ( double *  F,
double  fT,
double  fC,
double  fA,
double  fG 
)

Definition at line 110 of file trnsprob.cxx.

References A, ATOLPARAM, C, G, REAL_MIN, s, and T.

Referenced by Align().

void normalizeRateParams ( double *  X,
double  a,
double  b,
double  c,
double  d,
double  e,
double  f 
)

Definition at line 132 of file trnsprob.cxx.

References ATOLPARAM, REAL_MIN, and s.

Referenced by Align().

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 
)

Definition at line 179 of file trnsprob.cxx.

References A, C, copy(), dot(), EPS, G, I, ipol(), J, long, N, T, and Z.

Referenced by updateScore().

void updateTrnsprob ( double ***  PP,
double *  F,
double *  X,
short  M 
)

Definition at line 226 of file trnsprob.cxx.

References A, addmul(), C, dot(), EPS, G, HKY85, identity(), ih_assert, N, REV, s, T, and TN93.

Referenced by updateScore().