src/clustal/ktuple_pair.c File Reference

#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <math.h>
#include <assert.h>
#include "squid/squid.h"
#include "util.h"
#include "symmatrix.h"
#include "ktuple_pair.h"
#include "seq.h"
#include "progress.h"
#include <stdarg.h>

Include dependency graph for ktuple_pair.c:

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Data Structures
struct	two_ints_t
Defines
#define	END_MARK   -3
#define	NUMRES   32
Functions
void	KTuplePairDist (symmatrix_t *tmat, mseq_t *mseq, int istart, int iend, int jstart, int jend, ktuple_param_t *param_override, progress_t *prProgress, unsigned long int *ulStepNo, unsigned long int ulTotalStepNo)
Variables
const ktuple_param_t	default_protein_param
const ktuple_param_t	default_dna_param

---

Define Documentation

#define END_MARK   -3

#define NUMRES   32

---

Function Documentation

void KTuplePairDist	(	symmatrix_t *	tmat,
		mseq_t *	mseq,
		int	istart,
		int	iend,
		int	jstart,
		int	jend,
		ktuple_param_t *	param_override,
		progress_t *	prProgress,
		unsigned long int *	ulStepNo,
		unsigned long int	ulTotalStepNo
	)

Will compute ktuple scores and store in tmat Following values will be set: tmat[i][j], where istart <= i <iend and jstart <= j < jend i.e. zero-offset tmat data members have to be preallocated

if ktuple_param_t *aln_param == NULL defaults will be used

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Variable Documentation

const ktuple_param_t default_dna_param

Initial value:

 {
    .ktup = 2,
    .wind_gap = 5,
    .signif = 4,
    .window = 4,
}

const ktuple_param_t default_protein_param

Initial value:

 {
     .ktup = 1,
     .wind_gap = 3,
     .signif = 5,
     .window = 5,
}