Hitmap 1.3
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#include "SWcommon.h"
Go to the source code of this file.
Functions | |
void | input_parameters (int argc, char *argv[]) |
void | initPAM (char *filename) |
void | openProtein (ProteinFile *fprotein, char *filename) |
void | closeProtein (ProteinFile *fprotein) |
void | exit_error (const char *s) |
Variables | |
char * | prot_name1 |
char * | prot_name2 |
char * | pam_name |
double | gapPenalty = DEFAULT_GAPPENALTY |
int | size [2] = {DEFAULT_SIZE,DEFAULT_SIZE} |
int | iterations = DEFAULT_ITERATIONS |
ProteinFile | pfile1 |
ProteinFile | pfile2 |
PAM | pam_matrix |
AAName | aa_names |
Common definitions and utilities for the Smith-Waterman algorihtm.
Definition in file SWcommon.c.
void closeProtein | ( | ProteinFile * | fprotein | ) |
Close the protein file.
Definition at line 255 of file SWcommon.c.
void exit_error | ( | const char * | s | ) |
Exit printing the given error.
Definition at line 263 of file SWcommon.c.
void initPAM | ( | char * | filename | ) |
Inits the PAM Matrix with the content of this file and also the AAName conversion structure.
Definition at line 128 of file SWcommon.c.
void input_parameters | ( | int | argc, |
char * | argv[] | ||
) |
Process the input parameters
Definition at line 75 of file SWcommon.c.
void openProtein | ( | ProteinFile * | fprotein, |
char * | filename | ||
) |
Open a protein file.
Definition at line 241 of file SWcommon.c.
AAName aa_names |
Definition at line 69 of file SWcommon.c.
double gapPenalty = DEFAULT_GAPPENALTY |
Definition at line 54 of file SWcommon.c.
int iterations = DEFAULT_ITERATIONS |
Definition at line 60 of file SWcommon.c.
PAM pam_matrix |
The PAM matrix.
Definition at line 67 of file SWcommon.c.
char* pam_name |
Definition at line 51 of file SWcommon.c.
ProteinFile pfile1 |
Definition at line 63 of file SWcommon.c.
ProteinFile pfile2 |
Definition at line 64 of file SWcommon.c.
char* prot_name1 |
Definition at line 49 of file SWcommon.c.
char* prot_name2 |
Definition at line 50 of file SWcommon.c.
int size[2] = {DEFAULT_SIZE,DEFAULT_SIZE} |
Definition at line 57 of file SWcommon.c.