Align.hpp

/*
    Copyright 2008-2009 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_ALIGN_HPP
#define EGGLIB_ALIGN_HPP

#include "Container.hpp"
#include "CharMatrix.hpp"
#include <vector>

namespace egglib {


    class Align : public Container, public CharMatrix {
        public:
        
            Align();


            Align(unsigned int number_of_sequences, unsigned int alignment_length, char const * const * const cstring_array);


            Align(unsigned int number_of_sequences, unsigned int alignment_length);


            Align(const Align& align);


            Align(const Container& container);


            Align& operator=(const Align& align);


            Align& operator=(const Container& container);


            virtual ~Align();


            virtual unsigned int append(const char* name, const char* sequence, unsigned int group=0);


            virtual unsigned int removePosition(unsigned int pos);


            virtual unsigned int remove(unsigned int pos);


            virtual void sequence(unsigned int seq, const char* sequence);


            virtual inline const char* sequence(unsigned int pos) const { return Container::sequence(pos); }
            
            
            virtual  unsigned int ls() const;


            virtual unsigned int ls(unsigned int pos) const;


            inline char character(unsigned int s, unsigned int p) const { return sequences[s][p]; }


            virtual char get(unsigned int sequence, unsigned int position) const;


            virtual void set(unsigned int sequence, unsigned position, char ch);


            void binSwitch(unsigned int pos);


            Align vslice(std::vector<unsigned int> list_of_sites);


            Align vslice(unsigned int a, unsigned int b);


            virtual void clear();


            inline unsigned int numberOfSequences() const {
                return _ns;
            }


            inline unsigned int numberOfSites() const {
                return _ls;
            }


            inline unsigned int populationLabel(unsigned int sequenceIndex) const {
                return groups[sequenceIndex];
            }
            
            
            inline double sitePosition(unsigned int position) const {
                return (double) position;
            }


        protected:
        
            virtual void appendSequence(unsigned int pos, const char* sequence) {}

            // Initializer (creates a valid empty alignment)
            virtual void init();
        
            // Makes a deep copy of the specified data matrix - if cstring_array is NULL, then ignores it and pads with ?'s
            virtual void setFromSource(unsigned int number_of_sequences, unsigned int alignment_length, const char* const * const cstring_array);

            // Copies from a Container
            virtual void copyObject(const Container&);
            
            // Copies from an Align
            virtual void copyObject(const Align&);
            
            // Alignment length
            unsigned int _ls;
    };
}

#endif