DataMatrix.hpp

/*
    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol

    This file is part of the EggLib library.

    EggLib is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    EggLib is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
*/

#ifndef EGGLIB_DATAMATRIX_HPP
#define EGGLIB_DATAMATRIX_HPP


#include "CharMatrix.hpp"


namespace egglib {

    class DataMatrix : public CharMatrix {
    
    public:
    
        DataMatrix();


        DataMatrix(unsigned int numberOfSequences, unsigned int numberOfSites);


        DataMatrix(const DataMatrix&);


        DataMatrix(const CharMatrix&);

        
        virtual DataMatrix& operator=(const DataMatrix&);
        
        
        virtual DataMatrix& operator=(const CharMatrix&);


        virtual ~DataMatrix();
        
        
        unsigned int numberOfSites() const;


        unsigned int numberOfSequences() const;
        
        
        void set(unsigned int sequence, unsigned int site, int value);


        int get(unsigned int sequence, unsigned int site) const;
        
        
        inline int fget(unsigned int sequence, unsigned int site) const {
            return dataMatrix[sequence][site];
        }


        void sitePosition(unsigned int site, double value);


        double sitePosition(unsigned int site) const;


        void populationLabel(unsigned int sequence, unsigned int value);


        unsigned int populationLabel(unsigned int sequence) const;


        void clear();


        void resize(unsigned int newNumberOfSequences, unsigned int newNumberOfSites);


        void shift(int minimum);

        char character(unsigned int sequence, unsigned int site) const;
        


    private:
        
        // Initializes to default values (for empty object)
        void init();
        
        // Copies from a source object
        virtual void copy(const CharMatrix&);

        // Copies from a source object
        virtual void copy(const DataMatrix&);
        
        // Number of lines of the data matrix
        unsigned int _numberOfSequences;
        
        // Number of columns of the data matrix
        unsigned int _numberOfSites;
        
        // Data matrix
        int **dataMatrix;
        
        // Vector of site positions
        double *positions;
        
        // Vector of group indices
        unsigned int *groups;
    };
}

#endif