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/*
* Copyright (c) 2015-2018, Fabian Klötzl <fabian-pfasta@kloetzl.info>
*
* Permission to use, copy, modify, and/or distribute this software for any
* purpose with or without fee is hereby granted, provided that the above
* copyright notice and this permission notice appear in all copies.
*
* THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
* WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
* MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
* ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
* WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
* ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
* OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*
*/
#ifndef PFASTA_H
#define PFASTA_H
#ifdef __cplusplus
extern "C" {
#endif
#include <stddef.h>
/**
* There is no magic to this structure. Its just a container of three strings.
* Feel free to duplicate or move them. But don't forget to free the data after
* usage!
*/
struct pfasta_record {
char *name, *comment, *sequence;
size_t name_length, comment_length, sequence_length;
};
/**
* This structure holds a number of members to represent the state of the FASTA
* parser. Please make sure that it is properly initialized before usage.
* Always free this structure when the parser is done.
*/
struct pfasta_parser {
const char *errstr;
int done;
/*< private -- do not touch! >*/
int file_descriptor;
char *buffer;
char *read_ptr, *fill_ptr;
size_t line_number;
};
/**
* This function initializes a `pfasta_parser` struct with a parser bound to a
* specific file descriptor. Iff an error occurred `errstr` is set to contain a
* suitable message. Otherwise you can read data from it as long as `done` isn't
* set. The parser should be freed after usage.
*
* Please note that the user is responsible for opening the file descriptor as
* readable and closing after usage.
*/
struct pfasta_parser pfasta_init(int file_descriptor);
/**
* Using a properly initialized parser, this function can read FASTA sequences.
* These are stored in the simple structure and returned. On error, the `errstr`
* property of the parser is set.
*/
struct pfasta_record pfasta_read(struct pfasta_parser *pp);
/**
* This function frees the resources held by a pfasta record.
*/
void pfasta_record_free(struct pfasta_record *pr);
/**
* This function frees the resources held by a pfasta parser.
*/
void pfasta_free(struct pfasta_parser *pp);
/**
* Get a string defining the version of the pfasta library.
*/
const char *pfasta_version(void);
#ifdef __STDC_NO_THREADS__
/** If the preprocessor macro `PFASTA_NO_THREADS` is defined, the parser is not
* fully thread safe. */
#define PFASTA_NO_THREADS
#endif
#ifdef __cplusplus
}
#endif
#endif /* PFASTA_H */
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