// GaussianAlphabet.h
// 18 Nov 2008

// This file contains the definition of the GaussianAlphabet class;
// This is derived from the alphabet class, but supports additional
// name/value pairs for describing Bystroff and deBrevern protein blocks.


#ifndef GAUSSIANALPHABET
#define GAUSSIANALPHABET

#include "Alphabet/Alphabet.h"

namespace Gauss {

const double GAUSSIAN_WILDCARD = 1e10;

   struct GaussianDefinition {
       string feature;     // the type of feature
       vector<double> val; // the measures for each feature
       int idx;            // the residue index relative to the current residue
   };

}

class GaussianAlphabet : public Alphabet {
    private:
	// required stuff for things derived from NamedClass
	static IdObject ID;

	static void init_is_a(IdObject *self)
	{
	    self->add_is_a(Alphabet::classID());
	}

	virtual int read_knowing_type(std::istream &in);
	virtual void write_knowing_type(std::ostream &out) const;

	// called to initialize the Gaussian command table used by
	// read_knowing_type
	void init_command_table(void);

	// command table for reading Gaussian alphabets
	static NameToPtr *CommandTable;


	int Dimensions;

	std::vector<Gauss::GaussianDefinition> Centers;

    protected:
	// read commands for each command

	static int ReadDimensions(std::istream &in,
				  Alphabet *change,
				  AlphabetInputCommand *self);

	static int ReadDefinition(std::istream &in,
				  Alphabet *change,
				  AlphabetInputCommand *self);
	static int ReadCenter(std::istream &in,
			      Alphabet *change,
			      AlphabetInputCommand *self);

	// print commands for each command
	void print_dimensions(std::ostream &out) const;
	void print_definition(std::ostream &out) const;
	void print_centers(std::ostream &out) const;

    public:
	// local data

	// required stuff for things derived from NamedClass
	static  IdObject *classID(void)
	{
	    return &GaussianAlphabet::ID;
	}

	virtual IdObject *type(void) const
	{
	    return &GaussianAlphabet::ID;
	}

	GaussianAlphabet() : Dimensions(2)

	{
	}

	Base first_all_match_wildcard(void) const;

	// accessors for all of the relavant members
	
	inline int dimensions(void) const
	{
	    return Dimensions;
	}

	inline const std::vector<Gauss::GaussianDefinition> &centers(void)
									  const
	{
	    return Centers;
	}
};

#endif // GAUSSIANALPHABET