private:  Score m_s; public:  double empty() const {return 0.0;};  double replace(RNA_Alphabet_Profile a,double down, RNA_Alphabet_Profile b, double over) const  {    if(a.p[ALPHA_PRO_BASEPAIR]>0 && b.p[ALPHA_PRO_BASEPAIR]>0)      {	// pair replacement	return a.p[ALPHA_PRO_BASEPAIR]*b.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_rep_score +	       down+over;      }    else      {	if(a.p[ALPHA_PRO_BASE]>0 && b.p[ALPHA_PRO_BASE]>0)	  {		double s=0;	    // base replacement  		for(int i=ALPHA_PRO_BASE_A;i<=ALPHA_PRO_BASE_U;i++)			for(int j=ALPHA_PRO_BASE_A;j<=ALPHA_PRO_BASE_U;j++)				s+= i==j ? a.p[i]*b.p[j]*m_s.m_b_match_score : a.p[i]*b.p[j]*m_s.m_b_rep_score;		if(s==0) // no sequence information			s=a.p[ALPHA_PRO_BASE]*b.p[ALPHA_PRO_BASE]*m_s.m_b_rep_score;		return s+down+over;	  }	else	  {	    // undefined operation (replace base by basepair ??)	    return DBL_NEG/4;	  }	        }	       };  double del(RNA_Alphabet_Profile a,double down, double over) const  {    if(a.p[ALPHA_PRO_BASEPAIR]>0)      return a.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_del_score+down+over;    else      return a.p[ALPHA_PRO_BASE]*m_s.m_b_del_score+down+over;  };  double insert(double down,RNA_Alphabet_Profile b,double over) const  {    if(b.p[ALPHA_PRO_BASEPAIR]>0)      return b.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_del_score+down+over;    else      return b.p[ALPHA_PRO_BASE]*m_s.m_b_del_score+down+over;  };  double choice(double a, double  b) const  {    return max(a,b);  };  double worst_score() const  {    return DBL_NEG;  };  DoubleSimiProfileAlgebra(const Score &s)    : m_s(s) {};};/** Distance algebra for RNA profile forests */class DoubleDistProfileAlgebra : public DoubleScoreProfileAlgebraType{ private:  Score m_s; public:  double empty() const {return 0.0;};  double replace(RNA_Alphabet_Profile a,double down, RNA_Alphabet_Profile b, double over) const  {    TRACE(DBG_ALGEBRA,"rep","inside!!!");    if(a.p[ALPHA_PRO_BASEPAIR]>0 && b.p[ALPHA_PRO_BASEPAIR]>0)      {	// pair replacement	return a.p[ALPHA_PRO_BASEPAIR]*b.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_rep_score +	       down+over;      }    else      {	if(a.p[ALPHA_PRO_BASE]>0 && b.p[ALPHA_PRO_BASE]>0)	  {		double s=0;	    // base replacement  		for(int i=ALPHA_PRO_BASE_A;i<=ALPHA_PRO_BASE_U;i++)			for(int j=ALPHA_PRO_BASE_A;j<=ALPHA_PRO_BASE_U;j++)				s+= i==j ? a.p[i]*b.p[j]*m_s.m_b_match_score : a.p[i]*b.p[j]*m_s.m_b_rep_score;		if(s==0) // no sequence information			s=a.p[ALPHA_PRO_BASE]*b.p[ALPHA_PRO_BASE]*m_s.m_b_rep_score;		return s+down+over;	  }	else	  {	    // undefined operation (replace base by basepair ??)	    return DBL_POS/4;	  }	        }	       };  double del(RNA_Alphabet_Profile a,double down, double over) const  {    if(a.p[ALPHA_PRO_BASEPAIR]>0)      return a.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_del_score+down+over;    else      return a.p[ALPHA_PRO_BASE]*m_s.m_b_del_score+down+over;  };  double insert(double down,RNA_Alphabet_Profile b,double over) const  {    if(b.p[ALPHA_PRO_BASEPAIR]>0)      return b.p[ALPHA_PRO_BASEPAIR]*m_s.m_bp_del_score+down+over;    else      return b.p[ALPHA_PRO_BASE]*m_s.m_b_del_score+down+over;  };  double choice(double a, double  b) const  {
	  return min(a,b);
  };  double worst_score() const    {      return DBL_POS;    };  DoubleDistProfileAlgebra(const Score &s)    : m_s(s) {};};
/* ****************************************** *//*             SZAlgebra Classes              *//* ****************************************** */class IntSimiSZAlgebra : public IntScoreSZAlgebraType{ private:  Score m_s; public:  int empty() const {return 0;};	  int replace(RNA_Alphabet a,int down, RNA_Alphabet b) const  {    if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR)      return m_s.m_bp_rep_score+down;    else      {	if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR)	  return INT_MIN/4;	else	  {	    if(a==b)	      return m_s.m_b_match_score+down;	    else	      return m_s.m_b_rep_score+down;	  }      }	       };  int del(RNA_Alphabet a,int down) const  {    if(a==ALPHA_BASEPAIR)      return m_s.m_bp_del_score+down;    else      return m_s.m_b_del_score+down;  };  int insert(int down,RNA_Alphabet b) const  {    if(b==ALPHA_BASEPAIR)      return m_s.m_bp_del_score+down;    else      return m_s.m_b_del_score+down;  };  int choice(int a, int  b) const  {
	  return max(a,b);
  };  int worst_score() const  {    return INT_MIN;  };  IntSimiSZAlgebra(const Score &s)    : m_s(s) {};};class IntDistSZAlgebra : public IntScoreSZAlgebraType
{
 private:
  Score m_s;

 public:
  int empty() const {return 0;};
  int replace(RNA_Alphabet a,int down, RNA_Alphabet b) const
  {
    if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR)
      return m_s.m_bp_rep_score+down;
    else
      {
	if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR)
	  return INT_MAX/4;
	else
	  {
	    if(a==b)
	      return m_s.m_b_match_score+down;
	    else
	      return m_s.m_b_rep_score+down;
	  }
      }	     
  };

  int del(RNA_Alphabet a,int down) const
  {
    if(a==ALPHA_BASEPAIR)
      return m_s.m_bp_del_score+down;
    else
      return m_s.m_b_del_score+down;
  };

  int insert(int down,RNA_Alphabet b) const
  {
    if(b==ALPHA_BASEPAIR)
      return m_s.m_bp_del_score+down;
    else
      return m_s.m_b_del_score+down;
  };

  int choice(int a, int  b) const
  {
	  return min(a,b);
  };

  int worst_score() const
  {
    return INT_MAX;
  };

  IntDistSZAlgebra(const Score &s)
    : m_s(s) {};
};/* ****************************************** *//*           General Algebra Classe           *//* ****************************************** *//** Distance algebra for forests */class IntDist_Algebra : public IntScore_AlgebraType{ private:  Score m_s; public:  int empty() const {return 0;};  int replace(RNA_Alphabet a,int down, RNA_Alphabet b, int over) const  {    if(a==ALPHA_BASEPAIR && b == ALPHA_BASEPAIR)      return m_s.m_bp_rep_score+down+over;    else      {	if(a==ALPHA_BASEPAIR || b==ALPHA_BASEPAIR)	  return INT_MAX/4;	else	  {	    if(a==b)	      return m_s.m_b_match_score+down+over;	    else	      return m_s.m_b_rep_score+down+over;	  }      }	       };  int del(RNA_Alphabet a,int down,int over) const  {    if(a==ALPHA_BASEPAIR)      return m_s.m_bp_del_score+down+over;    else      return m_s.m_b_del_score+down+over;  };  int insert(int down,RNA_Alphabet b,int over) const  {    if(b==ALPHA_BASEPAIR)      return m_s.m_bp_del_score+down+over;    else      return m_s.m_b_del_score+down+over;  };  int choice(int a, int  b) const  {
	  return min(a,b);
  };  int worst_score() const  {    return INT_MAX;  };  IntDist_Algebra(const Score &s)    : m_s(s) {};};#endif