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/* Distances between aligned sequences, including both
* probabilistic evolutionary models and ad hoc measures.
*
* SRE, Fri Apr 28 06:41:13 2006 [New York]
*/
#ifndef eslDISTANCE_INCLUDED
#define eslDISTANCE_INCLUDED
#include "esl_config.h"
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_dmatrix.h"
#include "esl_random.h"
/* 1. Pairwise distances for aligned text sequences.
*/
extern int esl_dst_CPairId(const char *asq1, const char *asq2,
double *opt_pid, int *opt_nid, int *opt_n);
extern int esl_dst_CPairmatch(const char *asq1, const char *asq2,
double *opt_pmatch, int *opt_nmatch, int *opt_n);
extern int esl_dst_CJukesCantor(int K, const char *as1, const char *as2,
double *opt_distance, double *opt_variance);
/* 2. Pairwise distances for aligned digital seqs.
*/
extern int esl_dst_XPairId(const ESL_ALPHABET *abc, const ESL_DSQ *ax1, const ESL_DSQ *ax2,
double *opt_pid, int *opt_nid, int *opt_n);
extern int esl_dst_XPairMatch(const ESL_ALPHABET *abc, const ESL_DSQ *ax1, const ESL_DSQ *ax2,
double *opt_distance, int *opt_nmatch, int *opt_n);
extern int esl_dst_XJukesCantor(const ESL_ALPHABET *abc, const ESL_DSQ *ax, const ESL_DSQ *ay,
double *opt_distance, double *opt_variance);
/* 3. Distance matrices for aligned text sequences.
*/
extern int esl_dst_CPairIdMx (char **as, int N, ESL_DMATRIX **ret_S);
extern int esl_dst_CDiffMx (char **as, int N, ESL_DMATRIX **ret_D);
extern int esl_dst_CJukesCantorMx(int K, char **as, int N, ESL_DMATRIX **opt_D, ESL_DMATRIX **opt_V);
/* 4. Distance matrices for aligned digital sequences.
*/
extern int esl_dst_XPairIdMx(const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, ESL_DMATRIX **ret_S);
extern int esl_dst_XDiffMx (const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, ESL_DMATRIX **ret_D);
extern int esl_dst_XJukesCantorMx(const ESL_ALPHABET *abc, ESL_DSQ **ax, int nseq,
ESL_DMATRIX **opt_D, ESL_DMATRIX **opt_V);
/* 5. Average pairwise identity for multiple alignments.
*/
extern int esl_dst_CAverageId (char **as, int nseq, int max_comparisons, double *ret_id);
extern int esl_dst_CAverageMatch(char **as, int N, int max_comparisons, double *ret_match);
extern int esl_dst_XAverageId (const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, int max_comparisons, double *ret_id);
extern int esl_dst_XAverageMatch(const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, int max_comparisons, double *ret_match);
#endif /*eslDISTANCE_INCLUDED*/
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