Clustal Omega 1.2.4
Data Structures | Macros | Functions | Variables
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 "log.h"
#include "progress.h"
Include dependency graph for ktuple_pair.c:

Data Structures

struct  two_ints_t
 

Macros

#define END_MARK   -3 /* see interface.c in 1.83 */
 
#define NUMRES   32 /* max size of comparison matrix */
 

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
 

Macro Definition Documentation

◆ END_MARK

#define END_MARK   -3 /* see interface.c in 1.83 */

◆ NUMRES

#define NUMRES   32 /* max size of comparison matrix */

Function Documentation

◆ KTuplePairDist()

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

Variable Documentation

◆ default_dna_param

const ktuple_param_t default_dna_param
Initial value:
= {
.ktup = 2,
.wind_gap = 5,
.signif = 4,
.window = 4,
}

◆ default_protein_param

const ktuple_param_t default_protein_param
Initial value:
= {
.ktup = 1,
.wind_gap = 3,
.signif = 5,
.window = 5,
}