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

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Define Documentation

#define PAIRDIST_KTUPLE   1

#define PAIRDIST_SQUIDID   2

#define PAIRDIST_SQUIDID_KIMURA   3

#define PAIRDIST_UNKNOWN   0

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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