// Copyright 2008, 2009, 2011, 2014 Martin C. Frith

// This struct holds a score matrix for aligning pairs of residues,
// e.g. blosum62.  The delimiter symbol (space) aligned to anything
// gets a score of -INF.

// Maybe split this struct into two: ScoreMatrixEasy and ScoreMatrixFast?

#ifndef SCOREMATRIX_HH
#define SCOREMATRIX_HH
#include <string>
#include <vector>
#include <iosfwd>
#include <climits>  // INT_MAX

namespace cbrc{

typedef unsigned char uchar;

struct ScoreMatrix{
  enum { INF = INT_MAX / 2 };  // big, but try to avoid overflow
  enum { MAT = 64 };           // matrix size = MAT x MAT

  static const char *canonicalName( const std::string& name );
  static std::string stringFromName( const std::string& name );

  void setMatchMismatch(int matchScore,  // usually > 0
			int mismatchCost,  // usually > 0
			const std::string& symbols);  // case is preserved

  void fromString( const std::string& s );

  void init(const uchar symbolToIndex[]);  // unspecified letters get minScore

  // add scores for e.g. "W" meaning A or T
  void addAmbiguousScores(const uchar symbolToIndex[],
			  double scale,  // "lambda" for getting probabilities
			  const double rowSymbolProbs[],
			  const double colSymbolProbs[]);

  void writeCommented( std::ostream& stream ) const;  // write preceded by "#"

  std::string rowSymbols;  // row headings (letters)
  std::string colSymbols;  // column headings (letters)
  std::vector< std::vector<int> > cells;  // scores
  int caseSensitive[MAT][MAT];
  int caseInsensitive[MAT][MAT];
  int minScore;
  int maxScore;
};

std::istream& operator>>( std::istream& stream, ScoreMatrix& mat );
std::ostream& operator<<( std::ostream& stream, const ScoreMatrix& mat );

}

#endif