src/clustal/pair_dist.c File Reference

#include <stdlib.h>
#include <ctype.h>
#include <assert.h>
#include <time.h>
#include "clustal-omega.h"
#include "ktuple_pair.h"
#include "pair_dist.h"
#include "progress.h"
#include "util.h"

Include dependency graph for pair_dist.c:

Functions
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

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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