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#if !defined(SP_ALIGNMENT_H)
#define SP_ALIGNMENT_H
#include <stdio.h> /* For FILE structure */
namespace sp {
#define SP_ALIGNMENT_RETURN_SEQ 1
#define SP_ALIGNMENT_RETURN_EDIT_BUFFERS 2
#define SP_ALIGNMENT_RETURN_EDIT_BUFFER 4
#define SP_ALIGNMENT_RETURN_NEW_PADS 8
#define SP_ALIGNMENT_LEFT_EDGE_GAPS_COUNT 1
#define SP_ALIGNMENT_BEST_RIGHT_EDGE 2
#define EDGE_GAPS_COUNT 1
#define EDGE_GAPS_ZERO 2
#define FULL_LENGTH_TRACE 4
#define BEST_EDGE_TRACE 8
#define HASH_JOB_DIAG 1
#define HASH_JOB_HIST 2
#define HASH_JOB_EXPD 4
#define HASH_JOB_DMTCH 8
#define HASH_JOB_BLKS 16
void init_DNA_lookup(void);
#ifdef DYNMAT
int get_alignment_matrix( int** score_matrix, char *fn, char *base_order);
#else
int get_alignment_matrix (int score_matrix[128][128], char *fn, char *base_order);
#endif
void print_128(int matrix_128[128][128]);
OVERLAP *create_overlap(void);
void init_overlap (OVERLAP *overlap, char *seq1, char *seq2, int seq1_len, int seq2_len);
void destroy_overlap (OVERLAP *overlap);
void free_overlap (OVERLAP *overlap);
int set_overlap_seq1(OVERLAP *overlap, char *seq, int seq_len);
int set_overlap_seq2(OVERLAP *overlap, char *seq, int seq_len);
ALIGN_PARAMS *create_align_params(void);
void destroy_align_params (ALIGN_PARAMS *params);
#ifdef DYNMAT
int set_align_params (ALIGN_PARAMS *params, int band, int gap_open,
int gap_extend, int return_job,
int seq1_start, int seq2_start,
char old_pad_sym, char new_pad_sym,
int seq1_end, int seq2_end,
int algorithm, int word_length, int min_match,
int user_edge_mode,
double max_prob, int** score_matrix );
#else
int set_align_params (ALIGN_PARAMS *params, int band, int gap_open,
int gap_extend, int return_job,
int seq1_start, int seq2_start,
char old_pad_sym, char new_pad_sym,
int seq1_end, int seq2_end,
int algorithm, int word_length, int min_match,
int user_edge_mode,
double max_prob, int (*score_matrix)[128][128]);
#endif
int prepare_for_aligner(ALIGN_PARAMS *params, OVERLAP *overlap);
int aligner(ALIGN_PARAMS *params, OVERLAP *overlap);
int set_align_params_band_size (ALIGN_PARAMS *params, int band);
int set_align_params_banding (ALIGN_PARAMS *params, int band, int seq1_start,
int seq2_start);
int set_align_params_range (ALIGN_PARAMS *params, OVERLAP *overlap,
int seq1_start, int seq1_end,
int seq2_start, int seq2_end);
int init_align_params_hashing(ALIGN_PARAMS *params, int max_seq1, int max_seq2);
int set_align_params_edge_mode (ALIGN_PARAMS *params, int user_edge_mode);
int affine_align(OVERLAP *overlap, ALIGN_PARAMS *params);
int print_overlap(OVERLAP *overlap, FILE *fpt);
void print_edit_buffers(OVERLAP *overlap);
void print_overlap_posn(OVERLAP *overlap);
void print_overlap_struct(OVERLAP *overlap);
void print_align_params(ALIGN_PARAMS *params);
void set_hash8_lookupn(void);
int init_hash8n (int max_seq, int max_diagonal, int word_length,
int max_matches,
int min_match,
int job,
Hash **h);
void destroy_hash8n ( Hash *h );
void free_hash8n1 ( Hash *h );
void store_hashn ( Hash *h );
void p_comp(double comp[], char *seq, int seq_len);
int poisson_diagonals(int min_diag, int max_diag, int word_length,
double max_prob_in, int *expected_scores,
double comp[]);
int hash_seqn (Hash *h, int job);
int hash_seq1(ALIGN_PARAMS *params, char *seq, int seq_len);
int hash_seq2(ALIGN_PARAMS *params, char *seq, int seq_len);
}
#endif
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