src/clustal/pair_dist.h File Reference

#include "seq.h"
#include "symmatrix.h"
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Defines

#define PAIRDIST_UNKNOWN   0
#define PAIRDIST_KTUPLE   1
#define PAIRDIST_SQUIDID   2
#define PAIRDIST_SQUIDID_KIMURA   3

Functions

int PairDistances (symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type, const int istart, const int iend, const int jstart, const int jend, char *fdist_in, char *fdist_out)
 compute or read precomputed distances for given sequences

Define Documentation

#define PAIRDIST_KTUPLE   1
#define PAIRDIST_SQUIDID   2
#define PAIRDIST_SQUIDID_KIMURA   3
#define PAIRDIST_UNKNOWN   0

Function Documentation

int PairDistances ( symmatrix_t **  distmat,
mseq_t mseq,
int  pairdist_type,
int  istart,
int  iend,
int  jstart,
int  jend,
char *  fdist_in,
char *  fdist_out 
)

compute or read precomputed distances for given sequences

Parameters:
[out] distmat Distances will be written to this matrix. will be allocated here as well. Caller must free with FreeSymMatrix()
[in] mseq Distances will be computed for these sequences
[in] pairdist_type Type of pairwise distance comparison
[in] fdist_in If not NULL, sequences will be written from this file instead of computing them
[in] istart Compute distances for sequences i:j, i>=istart, i<j. Usually 0.
[in] iend Compute distances for sequences i:j, i<iend, i<j Usually mseq->nseqs.
[in] jstart Compute distances for sequences i:j, j>=jstart, i<j Usually 0.
[in] jend Compute distances for sequences i:j, j<iend, i<j Usually mseq->nseqs.
[in] fdist_out If not NULL, distances will be written to this files
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