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Functions | Variables
SWcommon.c File Reference
#include "SWcommon.h"
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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
 

Detailed Description

Common definitions and utilities for the Smith-Waterman algorihtm.

Author
Javier Fresno
Date
Jun 2013

Definition in file SWcommon.c.

Function Documentation

void closeProtein ( ProteinFile fprotein)

Close the protein file.

Definition at line 255 of file SWcommon.c.

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void exit_error ( const char *  s)

Exit printing the given error.

Definition at line 263 of file SWcommon.c.

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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.

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void input_parameters ( int  argc,
char *  argv[] 
)

Process the input parameters

Definition at line 75 of file SWcommon.c.

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void openProtein ( ProteinFile fprotein,
char *  filename 
)

Open a protein file.

Definition at line 241 of file SWcommon.c.

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Variable Documentation

AAName aa_names

Variable for the PAM Matrix.

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.