Hitmap 1.3
|
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <time.h>
Go to the source code of this file.
Data Structures | |
struct | PAM |
struct | ProteinFile |
struct | AAName |
Macros | |
#define | DEBUG |
#define | MAX_NUM_AA 30 |
#define | DEFAULT_SIZE 8 |
#define | DEFAULT_GAPPENALTY -1.0 |
#define | DEFAULT_ITERATIONS 1 |
#define | is_root() (1) |
#define | printfroot(...) if( is_root() ) { printf(__VA_ARGS__); } |
#define | fprintfroot(...) if( is_root() ) { fprintf(__VA_ARGS__); } |
#define | pam(a, b) (pam_matrix.data[(a)*(pam_matrix.num_aa)+(b)]) |
#define | NOTFOUND_AA -2 |
#define | NOTFOUND_CHAR '!' |
#define | GAP_AA MAX_NUM_AA |
#define | GAP_CHAR '-' |
#define | NOT_USED(p) ((void)(p)) |
#define | CHECK_NULL(check) |
Typedefs | |
typedef short | aa_t |
typedef double | h_t |
typedef short | trace_t |
Functions | |
void | initPAM (char *file) |
void | openProtein (ProteinFile *fprotein, char *filename) |
void | closeProtein (ProteinFile *fprotein) |
void | exit_error (const char *s) |
void | input_parameters (int argc, char *argv[]) |
Variables | |
PAM | pam_matrix |
AAName | aa_names |
char * | prot_name1 |
char * | prot_name2 |
char * | pam_name |
double | gapPenalty |
int | size [2] |
int | iterations |
ProteinFile | pfile1 |
ProteinFile | pfile2 |
Common definitions and utilities for the Smith-Waterman algorihtm.
Definition in file SWcommon.h.
#define CHECK_NULL | ( | check | ) |
Check NULL pointers
Definition at line 275 of file SWcommon.h.
#define DEBUG |
Flag to see the debug messages.
Definition at line 48 of file SWcommon.h.
#define DEFAULT_GAPPENALTY -1.0 |
Default Gap Penalty.
Definition at line 91 of file SWcommon.h.
#define DEFAULT_ITERATIONS 1 |
Default number of iterations
Definition at line 93 of file SWcommon.h.
#define DEFAULT_SIZE 8 |
Default protein size.
Definition at line 89 of file SWcommon.h.
#define fprintfroot | ( | ... | ) | if( is_root() ) { fprintf(__VA_ARGS__); } |
fprintf function for the root processor.
Definition at line 140 of file SWcommon.h.
#define GAP_AA MAX_NUM_AA |
Value for the gap AA code.
Definition at line 243 of file SWcommon.h.
#define GAP_CHAR '-' |
Value for the gap char name.
Definition at line 245 of file SWcommon.h.
#define is_root | ( | ) | (1) |
In sequential there is only one processor.
Definition at line 123 of file SWcommon.h.
#define MAX_NUM_AA 30 |
Max number of amino acids.
Definition at line 87 of file SWcommon.h.
#define NOT_USED | ( | p | ) | ((void)(p)) |
Hides the not used warning
Definition at line 271 of file SWcommon.h.
#define NOTFOUND_AA -2 |
Value for not found AA code.
Definition at line 239 of file SWcommon.h.
#define NOTFOUND_CHAR '!' |
Value for not found char name.
Definition at line 241 of file SWcommon.h.
#define pam | ( | a, | |
b | |||
) | (pam_matrix.data[(a)*(pam_matrix.num_aa)+(b)]) |
Macro to access the PAM Matrix.
Definition at line 181 of file SWcommon.h.
#define printfroot | ( | ... | ) | if( is_root() ) { printf(__VA_ARGS__); } |
printf function for the root processor.
Definition at line 135 of file SWcommon.h.
typedef short aa_t |
Typedef for the amino acid.
Definition at line 59 of file SWcommon.h.
typedef double h_t |
Typedef of the H and PAM matrices
Definition at line 61 of file SWcommon.h.
typedef short trace_t |
Typedef for the traceback matrix.
Definition at line 63 of file SWcommon.h.
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 |
Definition at line 54 of file SWcommon.c.
int 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] |
Definition at line 57 of file SWcommon.c.