Clustal Omega  1.2.1
Macros | Functions
pair_dist.h File Reference
#include "seq.h"
#include "symmatrix.h"
Include dependency graph for pair_dist.h:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Macros

#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, bool bPercID, 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 More...
 

Macro Definition 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,
bool  bPercID,
int  istart,
int  iend,
int  jstart,
int  jend,
char *  fdist_in,
char *  fdist_out 
)

compute or read precomputed distances for given sequences

Parameters
[out]distmatDistances will be written to this matrix. will be allocated here as well. Caller must free with FreeSymMatrix()
[in]mseqDistances will be computed for these sequences
[in]pairdist_typeType of pairwise distance comparison
[in]fdist_inIf not NULL, sequences will be written from this file instead of computing them
[in]istartCompute distances for sequences i:j, i>=istart, i<j. Usually 0.
[in]iendCompute distances for sequences i:j, i<iend, i<j usually="" mseq->="">nseqs.
[in]jstartCompute distances for sequences i:j, j>=jstart, i<j Usually 0.
[in]jendCompute distances for sequences i:j, j<iend, i<j usually="" mseq->="">nseqs.
[in]fdist_outIf not NULL, distances will be written to this files