src/sequence_interface.h File Reference

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

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

Include dependency graph for sequence_interface.h:

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Defines

#define INPUT_BUFFER   20000
 Defines the buffer size.
#define sequencewarning(s)   (sequencewarning_token(s, yytext))
 Defines a function to display flex warnings.
#define sequenceerror(s)   (sequenceerror_token(s, yytext))
 Defines a function to display flex error.

Functions

void sequencerestart (FILE *f)
 Function used to start processing a file.
int sequenceparse ()
 Function used to start parsing a sequence.
int sequencelex ()
 Function used to start parsing a sequence.
void sequenceerror_token (const char *s, const char *token)
 Function used to display flex errors.
void free_flex_mem ()
 Function used to free all memory allocated by the parser.

Variables

int sequencelineno = 1
char * sequencetext
FILE * sequencein = (FILE *) 0
char * sequence_file_name
int sequence_nb_errors
p_sequencesequence_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 fasta parser

Define Documentation

#define INPUT_BUFFER   20000

Defines the buffer size.

This definition defines the buffer size that will be used by the parser

#define sequenceerror (  )     (sequenceerror_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 sequenceerror function

#define sequencewarning (  )     (sequencewarning_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 sequencewarning function


Function Documentation

free_flex_mem (  ) 

Function used to free all memory allocated by the parser.

This function will be used to free all pointers declared by the parser that have not been destroyed

Referenced by get_sequences().

void sequenceerror_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, ERROR_, sequence_file_name, sequence_nb_errors, sequenceerror_token(), and sequencelineno.

Referenced by sequenceerror_token().

sequencelex ( void   ) 

Function used to start parsing a sequence.

This function will be used to start parsing a sequence by the parser

sequenceparse (  ) 

Function used to start parsing a sequence.

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

Referenced by get_sequences().

sequencerestart ( 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 get_sequences().


Variable Documentation

The file to read

The file to parse

Referenced by get_sequences(), and sequenceerror_token().

Numbers of parser's error

The number of errors

Referenced by get_sequences(), and sequenceerror_token().

The result of the parser: the sequences

The result of the parsing : the sequences

Referenced by get_sequences().

FILE * sequencein = (FILE *) 0

The file desriptor

int sequencelineno = 1

Line number

Referenced by sequenceerror_token().

char * sequencetext

Sequence nucleotides


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