#ifndef COMPLETE_STRIPED_SMITH_WATERMAN_CPP_H_
#define COMPLETE_STRIPED_SMITH_WATERMAN_CPP_H_

#include <stdint.h>
#include <string>
#include <vector>

namespace StripedSmithWaterman {

struct Alignment {
  uint16_t sw_score;           // The best alignment score 
  uint16_t sw_score_next_best; // The next best alignment score
  int32_t  ref_begin;          // Reference begin position of the best alignment
  int32_t  ref_end;            // Reference end position of the best alignment
  int32_t  query_begin;        // Query begin position of the best alignment
  int32_t  query_end;          // Query end position of the best alignment
  int32_t  ref_end_next_best;  // Reference end position of the next best alignment
  int32_t  mismatches;         // Number of mismatches of the alignment
  std::string cigar_string;    // Cigar string of the best alignment
  std::vector<uint32_t> cigar; // Cigar stored in the BAM format
                               //   high 28 bits: length
			       //   low 4 bits: M/I/D/S/X (0/1/2/4/8);
  // the following fields are used by scissors only.
  bool is_reverse;
  bool is_complement;
  int ref_id;
  void Clear() {
    sw_score           = 0;
    sw_score_next_best = 0;
    ref_begin          = 0;
    ref_end            = 0;
    query_begin        = 0;
    query_end          = 0;
    ref_end_next_best  = 0;
    mismatches         = 0;
    is_reverse         = false;
    is_complement      = false;
    ref_id             = -1;

    cigar_string.clear();
    cigar.clear();
  };
};

struct Filter {
  // NOTE: No matter the filter, those five fields will be given anyway.
  //       sw_score; sw_score_next_best; ref_end; query_end; ref_end_next_best.
  
  bool report_begin_position;    // Give ref_begin and query_begin. 
                                 //   If it is not set, ref_begin and query_begin are -1.
  bool report_cigar;             // Give cigar_string and cigar.
                                 //   report_begin_position is automatically TRUE.
  
  // When *report_cigar* is true and alignment passes these two filters,
  //   cigar_string and cigar will be given.
  uint16_t score_filter;         // score >= score_filter
  uint16_t distance_filter;      // ((ref_end - ref_begin) < distance_filter) &&
                                 // ((query_end - read_begin) < distance_filter)

  Filter()
    : report_begin_position(true)
    , report_cigar(true)
    , score_filter(0)
    , distance_filter(32767)
  {};
};

class Aligner {
 public:
  // =========
  // @function Construct an Aligner on default values.
  //             The function will build the {A.C,G,T,N} aligner.
  //             If you target for other character aligners, then please
  //             use the other constructor and pass the corresponding matrix in.
  // =========
  Aligner(void);
  
  // =========
  // @function Construct an Aligner by assigning scores.
  //             The function will build the {A.C,G,T,N} aligner.
  //             If you target for other character aligners, then please
  //             use the other constructor and pass the corresponding matrix in.
  // =========
  Aligner(const uint8_t& match_score,
          const uint8_t& mismatch_penalty,
	  const uint8_t& gap_opening_penalty,
	  const uint8_t& gap_extending_penalty);
  
  // =========
  // @function Construct an Aligner by the specific matrixs.
  // =========
  Aligner(const int8_t* score_matrix, 
          const int&    score_matrix_size,
          const int8_t* translation_matrix,
	  const int&    translation_matrix_size);
  
  ~Aligner(void);

  // =========
  // @function Build the reference sequence and thus make 
  //             Align(const char* query, s_align* alignment) function;
  //             otherwise the reference should be given when aligning.
  //           [NOTICE] If there exists a sequence, that one will be deleted 
  //                    and replaced.
  // @param    seq    The reference bases;
  //                  [NOTICE] It is not necessary null terminated.
  // @param    length The length of bases will be be built.
  // @return   The length of the built bases.
  // =========
  int SetReferenceSequence(const char* seq, const int& length);

  void CleanReferenceSequence(void);

  // =========
  // @function Set penalties for opening and extending gaps
  //           [NOTICE] The defaults are 3 and 1 respectively.
  // =========
  void SetGapPenalty(const uint8_t& opening, const uint8_t& extending) {
    gap_opening_penalty_ = opening;
    gap_extending_penalty_ = extending;
  };

  // =========
  // @function Align the query againt the reference that is set by 
  //             SetReferenceSequence.
  // @param    query     The query sequence.
  // @param    filter    The filter for the alignment.
  // @param    alignment The container contains the result.
  // @return   True: succeed; false: fail.
  // =========
  bool Align(const char* query, const Filter& filter, Alignment* alignment) const;

  // =========
  // @function Align the query againt the reference.
  //           [NOTICE] The reference won't replace the reference 
  //                      set by SetReferenceSequence.
  // @param    query     The query sequence.
  // @param    ref       The reference sequence.
  //                     [NOTICE] It is not necessary null terminated.
  // @param    ref_len   The length of the reference sequence.
  // @param    filter    The filter for the alignment.
  // @param    alignment The container contains the result.
  // @return   True: succeed; false: fail.
  // =========
  bool Align(const char* query, const char* ref, const int& ref_len, 
             const Filter& filter, Alignment* alignment) const;

  // @function Clear up all containers and thus the aligner is disabled.
  //             To rebuild the aligner please use Build functions.
  void Clear(void);

  // =========
  // @function Rebuild the aligner's ability on default values.
  //           [NOTICE] If the aligner is not cleaned, rebuilding will fail.
  // @return   True: succeed; false: fail.
  // =========
  bool ReBuild(void);

  // =========
  // @function Rebuild the aligner's ability by the specific matrixs.
  //           [NOTICE] If the aligner is not cleaned, rebuilding will fail.
  // @return   True: succeed; false: fail.
  // =========
  bool ReBuild(
          const uint8_t& match_score,
          const uint8_t& mismatch_penalty,
	  const uint8_t& gap_opening_penalty,
	  const uint8_t& gap_extending_penalty);
  
  // =========
  // @function Construct an Aligner by the specific matrixs.
  //           [NOTICE] If the aligner is not cleaned, rebuilding will fail.
  // @return   True: succeed; false: fail.
  // =========
  bool ReBuild(
          const int8_t* score_matrix, 
          const int&    score_matrix_size,
          const int8_t* translation_matrix,
	  const int&    translation_matrix_size);
  
 private:
  int8_t* score_matrix_;
  int     score_matrix_size_;
  int8_t* translation_matrix_;
  bool    default_matrix_;
  bool    matrix_built_;

  uint8_t match_score_;           // default: 2
  uint8_t mismatch_penalty_;      // default: 2
  uint8_t gap_opening_penalty_;   // default: 3
  uint8_t gap_extending_penalty_; // default: 1

  int8_t* translated_reference_;
  int32_t reference_length_;

  int TranslateBase(const char* bases, const int& length, int8_t* translated) const;
  void SetAllDefault(void);
  void BuildDefaultMatrix(void);
  
  Aligner& operator= (const Aligner&);
  Aligner (const Aligner&); 
}; // class Aligner


// ================
// inline functions
// ================
inline void Aligner::CleanReferenceSequence(void) {
  if (reference_length_ == 0) return;
  
  // delete the current buffer
  if (reference_length_ > 1) delete [] translated_reference_;
  else delete translated_reference_;
  
  reference_length_ = 0;
}
} // namespace StripedSmithWaterman

#endif // COMPLETE_STRIPED_SMITH_WATERMAN_CPP_H_
