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esl_distance.h
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esl_distance.h
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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"
#ifdef __cplusplus // magic to make C++ compilers happy
extern "C" {
#endif
/* 1. Pairwise distances for aligned text sequences.
*/
extern int esl_dst_CPairId ( const char *as1, const char *as2, double *opt_pid, int *opt_nid, int *opt_n);
extern int esl_dst_CPairmatch ( const char *as1, const char *as2, double *opt_pm, int *opt_nm, 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_pm, int *opt_nm, int *opt_n);
extern int esl_dst_XJukesCantor(const ESL_ALPHABET *abc, const ESL_DSQ *ax1, const ESL_DSQ *ax2, double *opt_distance, double *opt_variance);
/* 3. Distance matrices for aligned text sequences.
*/
extern int esl_dst_CPairIdMx ( char **as, int N, ESL_DMATRIX **opt_S);
extern int esl_dst_CDiffMx ( char **as, int N, ESL_DMATRIX **opt_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 **opt_S);
extern int esl_dst_XDiffMx (const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, ESL_DMATRIX **opt_D);
extern int esl_dst_XJukesCantorMx(const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, ESL_DMATRIX **opt_D, ESL_DMATRIX **opt_V);
/* 5. Average pairwise identity for multiple alignments.
*/
extern int esl_dst_CAverageId (char **as, int N, int max_comparisons, double *ret_avgid);
extern int esl_dst_CAverageMatch(char **as, int N, int max_comparisons, double *ret_avgpm);
extern int esl_dst_XAverageId (const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, int max_comparisons, double *ret_avgid);
extern int esl_dst_XAverageMatch (const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, int max_comparisons, double *ret_avgpm);
extern int esl_dst_XAvgConnectivity(const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, int max_comparisons, double idthresh, double *opt_avgid, double *opt_avgconn);
extern int esl_dst_XAvgSubsetConnectivity(const ESL_ALPHABET *abc, ESL_DSQ **ax, int N, int *V, int nV, int max_comparisons, double idthresh, double *opt_avgid, double *opt_avgconn);
#ifdef __cplusplus // magic to make C++ compilers happy
}
#endif
#endif /*eslDISTANCE_INCLUDED*/