#if !defined(ALIGN_LIB_H)
#define ALIGN_LIB_H


namespace sp {


typedef struct Mseg {
  char *seq;
  int length;
  int offset;
} MSEG;

typedef struct Contigl {
  MSEG *mseg;
  struct Contigl *next;
}CONTIGL;

CONTIGL *create_contig_link(void);

void print_contig_links(CONTIGL *contigl);

typedef struct Malign {
  char *charset;
  int charset_size;
  int  nseqs;
  int  length;
  int  **matrix;
  CONTIGL *contigl;
  MSEG **msegs;
  char *consensus;
  int **scores;
} MALIGN;

typedef struct Moverlap {
    double  percent;
    int     length;
    int  direction;
    int     lo, ro; /* Left and right offsets */
    int     left1, left2, left, right1, right2, right;
    double  score;
    double  qual;
    int  *S; /* Alignment edit buffer */
    int     s_len;
    int  *S1, *S2; /* Sequence edit buffers for seq1 and seq2 */
    int     s1_len, s2_len; /* lengths of sequence edit buffers */
    int     malign_len, seq2_len; /* lengths of the original sequences */
  MALIGN *malign;
  MALIGN *malign_out;
    char        *seq2; /* the original sequence */
    char        *seq1_out, *seq2_out; 
    int    seq_out_len;
    /*
     * example overlap: 
     *
     * 01234567890123456
     * AACGTAAT**CGCT***
     * ****TATTGCCGCTAAG
     *
     * left1, right1, left2, right2, left, right are all positions in the alignment
     * left1  = first non-pad in seq1 (0)
     * right1 = last non-pad in seq1 (13)
     * left2  = first non-pad in seq2 (4)
     * right2 = last non-pad in seq2 (16)
     * left   = position to right of left overhang ie max(left1,left2) (4)
     * right  = position to left of right overhang ie min(right1,right2) (13)
     * length = length of overlapping section of the overlap = right - left + 1 (10)
     *
     *left1       right1
     *    AACGTAAT**CGCT***
     *    01234567890123456
     *    ****TATTGCCGCTAAG
     *    left2      right2
     *        <-length->
     *     left    right
     *
     * direction = describes the type of overlap:
     * 0 - suffix of seq1 overlaps with prefix of seq2
     * 11111111
     *     2222222
     * 1 - suffix of seq2 overlaps with prefix of seq1
     *     111111111
     * 22222222
     * 2 - seq1 contains seq2
     * 11111111111  111111111111  11111111111
     *     2222     222222        22222222222
     * 3 - seq2 contains seq1
     *     11111     11111111111
     * 22222222222   2222222222222
     *
     * for example overlap direction (0)
     * if(overlap->left1 == overlap->left2)
     *   overlap->direction = (overlap->right1 >= overlap->right2) ? 2 : 3;
     * else if(overlap->left1 < overlap->left2)
     *   overlap->direction = (overlap->right1 >= overlap->right2) ? 2 : 0;
     * else
     *   overlap->direction = (overlap->right1 <= overlap->right2) ? 3 : 1;
     *
     * lo and ro (left and right offsets): the lengths of the overhangs at each end:
     * depends on the direction and can be +ve or -ve:
     * a containment overlap will have +ve left_offset and -ve right_offset, 
     * a non-containment overlap will have +ve left_offset and +ve right_offset
     * 
     * 11111111
     *     2222222
     * lo (4) ro (3)
     *     111111111
     * 22222222
     * lo (4) ro (5)
     * 11111111111  lo (4) ro (3)  111111111111 lo (0) ro (-6) 11111111111 lo (0) ro (0)
     *     2222                    222222                      22222222222
     *
     *     11111  lo (4) ro (-2)   11111111111    lo (0) ro (-2)
     * 22222222222                  2222222222222
     *
     * switch(overlap->direction) {
     *  case 0: case 2:
     *    overlap->lo = overlap->left2 - overlap->left1;
     *    overlap->ro = overlap->right2 - overlap->right1;
     *    break;
     *  case 1: case 3:
     *    overlap->lo = overlap->left1 - overlap->left2;
     *    overlap->ro = overlap->right1 - overlap->right2;
     *    break;
     *  default:
     *    break;
     *
     * The formats of the edit buffers are as follows, using this
     * alignment as an example:
     *
     * AACGTAAT**CGCT***
     * ****TATTGCCGCTAAG
     *
     *    There are two sequence edit buffers, one for each sequence
     *    in the alignment. A sequence edit buffer contains +n for
     *    n bases from the sequence, and -n for n pads in the sequence.
     *    This would give S1 = {+8, -2, +4, -3} and S2 = {-4, 13} for
     *    the example alignment.
     *
     *    The alignment edit buffer contains '0' when two bases are
     *    aligned, +n for n pads in seq1, and -n for n pads in seq2.
     *    This would give S[] = {-4, 0, 0, 0, 0, +2, 0, 0, 0, 0, +3}
     *    for the example alignment. They are included only for
     *    compatibility with other programs in the package and are not
     *    used (or created).
     *
     */
} MOVERLAP;


#define RETURN_SEQ 1
#define RETURN_EDIT_BUFFERS 2
#define RETURN_EDIT_BUFFER  4
#define RETURN_NEW_PADS 8

#define EDGE_GAPS_COUNT   1
#define EDGE_GAPS_ZERO    2
#define FULL_LENGTH_TRACE 4
#define BEST_EDGE_TRACE   8

typedef struct Seg {
    int length;
    char *seq;
} SEG;

void init_malign_matrix(MALIGN *malign);

int set_alignment_matrix (char *fn, char *base_order);

int set_malign_charset(MALIGN *malign, char *charset);

void print_malign_matrix(MALIGN *malign);

int set_band(int seq1_len, int seq2_len);

SEG *create_seg(void);

void destroy_seg (SEG *seg);

MSEG *create_mseg(void);

void destroy_mseg (MSEG *mseg);

void init_mseg (MSEG *mseg, char *seq, int length, int offset);

CONTIGL *create_contig_link(void);

MALIGN *create_malign(void);

void destroy_malign (MALIGN *malign);

void free_malign (MALIGN *malign);

void set_malign_lookup(int charset_size);

int **create_malign_counts(int length, int depth);
 
void get_malign_counts (MALIGN *malign);

void get_malign_consensus(MALIGN *malign);

void print_malign_scores(MALIGN *malign);

void scale_malign_scores(MALIGN *malign, int gap_open, int gap_extend);

void print_contig_links (CONTIGL *contigl);

int contigl_length (CONTIGL *contigl);

int contigl_elements (CONTIGL *contigl);

MSEG **get_malign_segs(CONTIGL *contigl);

void print_malign_seqs(MALIGN *malign);

MALIGN *contigl_to_malign(CONTIGL *contigl_in);

MOVERLAP *create_moverlap(void);

void init_moverlap (MOVERLAP *moverlap, MALIGN *malign, char *seq2, int malign_len,
         int seq2_len);
void destroy_moverlap (MOVERLAP *moverlap);

void free_moverlap (MOVERLAP *moverlap);


void seq_expand(char   *seq,
      char    *seq_align,
      int     *seq_align_len,
      int *S,
      int       s_len,
      int       mode,
      char PAD_SYM);

#ifdef DYNMAT
int overlap_score (OVERLAP *overlap, int** score_matrix );
#else
int overlap_score (OVERLAP *overlap, W128_P score_matrix);
#endif

int overlap_score_old (OVERLAP *overlap);

int get_segment( OVERLAP *overlap, SEG *seg, int job);

int print_alignment(char   *seq1,
          char *seq2,
          int     seq1_len,
          int     seq2_len,
          int  *S1,
          int  *S2,
          int     s1_len,
          int     s2_len,
          double  score,
          FILE *fpt);

int print_overlap(OVERLAP *overlap, FILE *fpt);

void print_fasta(char *description, char *seq, FILE *fpt);

int overlap_ends ( char *seq, int seq_len, char PAD_SYM, int *left, int *right);

void to_internal_edges(int user, int *edge_mode);

#ifdef DYNMAT
void to_128( int** matrix_128, int **input_matrix, char *base_order, int unknown);
#else
void to_128( int matrix_128[128][128], int **input_matrix, char *base_order, int unknown);
#endif

void old_pads_for_new ( char *seq, int seq_len, char OLD_PAD_SYM, char NEW_PAD_SYM);

int seq_to_overlap ( OVERLAP *overlap, char OLD_PAD_SYM, char NEW_PAD_SYM);

int seq_to_moverlap ( MOVERLAP *overlap, char OLD_PAD_SYM, char NEW_PAD_SYM);

void shrink_edit_buffer(int *S, int *s_len);

void shrink_edit_buffers(OVERLAP *overlap);

int seq_to_edit ( char *seq, int seq_len, int **S_out, int *S_len, char PAD_SYM);

int do_trace_back_bits ( unsigned char *bit_trace, char *seq1, char *seq2,
         int seq1_len, int seq2_len, char **seq1_out_ret, char **seq2_out_ret,
         int *seq_out_len, int b_r, int b_c, int b_e,
         int band, int first_band_left, int first_row, 
         int band_length, char PAD_SYM);

int do_trace_back ( unsigned char *bit_trace, char *seq1, char *seq2,
         int seq1_len, int seq2_len, char **seq1_out_ret, char **seq2_out_ret,
         int *seq_out_len, int b_r, int b_c, int b_e,
         int band, int first_band_left, int first_row, 
         int band_length, char PAD_SYM);

void destroy_af_mem ( int *F1, int *F2, int *G1, int *G2, int *H1, int *H2,
            unsigned char *bit_trace, char *seq1_out, char *seq2_out );

int affine_align(OVERLAP *overlap, ALIGN_PARAMS *params);

int affine_align3(OVERLAP *overlap, ALIGN_PARAMS *params);

int affine_align_bits(OVERLAP *overlap, ALIGN_PARAMS *params);

int affine_align_big(OVERLAP *overlap, ALIGN_PARAMS *params);

int affine_align2_bits(OVERLAP *overlap, ALIGN_PARAMS *params);

int affine_align2_big(OVERLAP *overlap, ALIGN_PARAMS *params);

int affine_malign(MOVERLAP *moverlap, ALIGN_PARAMS *params);


}


#endif