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/**
* @file
* @brief Functions and structures for DNA sequences
*
*/
#ifndef _SEQUENCE_H_
#define _SEQUENCE_H_
#include <err.h>
#include <errno.h>
#include <stdlib.h>
/**
* @brief A structure for sequences.
*
* This structure is used to represent a DNA sequence of some kind.
*/
typedef struct seq_s {
/** This is the DNAs forward strand as a string. */
char *S;
/** The length of the forward strand. */
size_t len;
/** A name for this sequence */
char *name;
} seq_t;
/**
* @brief This structure enhances the usual sequence with its reverse
* complement.
*/
typedef struct seq_subject {
/** This member contains first the reverse strand and then the
forward strand. */
char *RS;
/** Corresponds to strlen(RS) */
size_t RSlen;
/**
* @brief GC-Content
*
* The relative amount of G or C in the DNA.
*/
double gc;
/** The minimum length for an anchor. */
size_t threshold;
} seq_subject;
void seq_free(seq_t *S);
int seq_subject_init(seq_subject *S, const seq_t *);
void seq_subject_free(seq_subject *S);
int seq_init(seq_t *S, const char *seq, const char *name);
/**
* @brief A dynamically growing structure for sequences.
*/
typedef struct dsa_s {
seq_t *data;
size_t capacity, size;
} dsa_t;
int dsa_init(dsa_t *A);
void dsa_push(dsa_t *A, seq_t S);
void dsa_free(dsa_t *A);
size_t dsa_size(const dsa_t *A);
seq_t *dsa_data(dsa_t *A);
seq_t dsa_join(dsa_t *dsa);
#endif
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