src/blast_interface.h File Reference

Header file for the interface between the Flex/Bison parser and this software. More...

#include <stdio.h>
#include "types.h"

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Defines

#define blastwarning(s)   (blastwarning_token(s, yytext))
 Defines a function to display flex warnings.
#define blasterror(s)   (blasterror_token(s, yytext))
 Defines a function to display flex error.

Functions

void blastrestart (FILE *f)
 Function used to start processing a file.
int blastparse ()
 Function used to start parsing a blast.
void blastwarning_token (const char *s, const char *token)
 Function used to display flex warnings.
void blasterror_token (const char *s, const char *token)
 Function used to display flex errors.

Variables

int blastlineno = 1
char * blasttext
FILE * blastin = (FILE *) 0
char * blast_file_name
int blast_nb_errors
p_alignment_infoblast_result

Detailed Description

Header file for the interface between the Flex/Bison parser and this software.

Author:
Benjamin Grenier-Boley <benjamin.grenier-boley@inria.fr>
Version:
1.02
Date:
September 2008
This file will define all functions and defines that will be used to communicate with the Flex/Bison blast tabular parser

Define Documentation

#define blasterror (  )     (blasterror_token(s, yytext))

Defines a function to display flex error.

Parameters:
[in] s : the error message
This function will be used to display flex error messages by calling the blasterror function

#define blastwarning (  )     (blastwarning_token(s, yytext))

Defines a function to display flex warnings.

Parameters:
[in] s : the warning message
This function will be used to display flex warning messages by calling the blastwarning function


Function Documentation

void blasterror_token ( const char *  s,
const char *  token 
)

Function used to display flex errors.

Parameters:
[in] s : the error message
[in] token : the token that has raised the error
This function will be used to display flex errors

References _ERROR, blast_file_name, blast_nb_errors, blasterror_token(), blastlineno, and ERROR_.

Referenced by blasterror_token().

blastparse (  ) 

Function used to start parsing a blast.

Returns:
an integer representing the parsing status
This function will be used to start parsing a blast by the parser

Referenced by read_alignments_files().

blastrestart ( FILE *  f  ) 

Function used to start processing a file.

Parameters:
[in] f : the file to process
This function will be used to start processing a file by the parser

Referenced by read_alignments_files().

void blastwarning_token ( const char *  s,
const char *  token 
)

Function used to display flex warnings.

Parameters:
[in] s : the warning message
[in] token : the token that has raised the warning
This function will be used to display flex warnings

References _ERROR, blast_file_name, blastlineno, blastwarning_token(), and ERROR_.

Referenced by blastwarning_token().


Variable Documentation

The file to read

The file to parse

Referenced by blasterror_token(), blastwarning_token(), and read_alignments_files().

Numbers of parser's error

The number of errors

Referenced by blasterror_token(), and read_alignments_files().

The result of the parser: the alignments

The result of the parsing : the alignments

Referenced by read_alignments_files().

FILE * blastin = (FILE *) 0

The file desriptor

int blastlineno = 1

Line number

Referenced by blasterror_token(), and blastwarning_token().

char * blasttext

Blast text


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