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/* Routines for manipulating sequence alignment score matrices.
#include "esl_config.h"
#include "esl_alphabet.h"
#include "esl_fileparser.h"
#include "esl_dmatrix.h"
* allocation is in one array in s[0].
* i,j can range from 0..Kp-1, including all characters valid in the alphabet.
* Only values for 0..K-1 (canonical alphabet) are mandatory.
typedef struct {
int **s; /* s[i][j] is the score of aligning residue i,j; i,j range 0..Kp-1 */
int K; /* size of base alphabet (duplicate of S->abc_r->K) */
int Kp; /* full size of s[][], including degeneracies (duplicate of S->abc_r->Kp) */
/* bookkeeping for degenerate residues */
char *isval; /* array 0..Kp-1: which residues of alphabet have valid scores in S. */
const ESL_ALPHABET *abc_r; /* reference to the alphabet: includes K, Kp, and sym order */
/* bookkeeping that lets us output exactly the residue order we read in a matrix file */
int nc; /* number of residues with scores (inclusive of *, if present) */
char *outorder; /* NUL-terminated string giving order of residues in col/row labels */
char *name; /* optional: name of score matrix; or NULL */
char *path; /* optional: full path to file that score matrix was read from; or NULL */
/* 1. The ESL_SCOREMATRIX object. */
extern ESL_SCOREMATRIX *esl_scorematrix_Create(const ESL_ALPHABET *abc);
extern int esl_scorematrix_Copy(const ESL_SCOREMATRIX *src, ESL_SCOREMATRIX *dest);
extern ESL_SCOREMATRIX *esl_scorematrix_Clone(const ESL_SCOREMATRIX *S);
extern int esl_scorematrix_Compare(const ESL_SCOREMATRIX *S1, const ESL_SCOREMATRIX *S2);
extern int esl_scorematrix_CompareCanon(const ESL_SCOREMATRIX *S1, const ESL_SCOREMATRIX *S2);
extern int esl_scorematrix_Max(const ESL_SCOREMATRIX *S);
extern int esl_scorematrix_Min(const ESL_SCOREMATRIX *S);
extern int esl_scorematrix_IsSymmetric(const ESL_SCOREMATRIX *S);
extern int esl_scorematrix_ExpectedScore(ESL_SCOREMATRIX *S, double *fi, double *fj, double *ret_E);
extern int esl_scorematrix_RelEntropy(const ESL_SCOREMATRIX *S, const double *fi, const double *fj,
double lambda, double *ret_D);
extern int esl_scorematrix_JointToConditionalOnQuery(const ESL_ALPHABET *abc, ESL_DMATRIX *P);
extern void esl_scorematrix_Destroy(ESL_SCOREMATRIX *S);
/* 2. Some classic score matrices */
extern int esl_scorematrix_Set(const char *name, ESL_SCOREMATRIX *S);
extern int esl_scorematrix_SetIdentity(ESL_SCOREMATRIX *S);
/* 3. Deriving a score matrix probabilistically */
extern int esl_scorematrix_SetFromProbs(ESL_SCOREMATRIX *S, double lambda, const ESL_DMATRIX *P,
const double *fi, const double *fj);
extern int esl_scorematrix_SetWAG(ESL_SCOREMATRIX *S, double lambda, double t);
/* 4. Reading/writing score matrices. */
extern int esl_scorematrix_Read(ESL_FILEPARSER *efp, const ESL_ALPHABET *abc, ESL_SCOREMATRIX **ret_S);
extern int esl_scorematrix_Write(FILE *fp, const ESL_SCOREMATRIX *S);
/* 5. Implicit probabilistic basis, I: given bg. */
extern int esl_scorematrix_ProbifyGivenBG(const ESL_SCOREMATRIX *S, const double *fi, const double *fj,
double *opt_lambda, ESL_DMATRIX **opt_P);
/* 6. Implicit probabilistic basis, II: bg unknown. */
extern int esl_scorematrix_Probify(const ESL_SCOREMATRIX *S, ESL_DMATRIX **opt_P,
double **opt_fi, double **opt_fj, double *opt_lambda);
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