Container.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_CONTAINER_HPP
#define EGGLIB_CONTAINER_HPP


namespace egglib {

    class Container {
    
        public:
      
            Container();
        
        
            Container(const Container& source);
        
        
            Container& operator= (const Container& source);


            Container(unsigned int number_of_sequences, char const* const* const cstring_array);


            virtual ~Container();

        
            virtual void clear();


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


            virtual void name(unsigned int pos, const char* name);


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


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


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


            virtual char get(unsigned int s, unsigned int p) const;


            virtual void group(unsigned int pos, unsigned int group);

        
            Container hslice(unsigned int a, unsigned int b) const;


            unsigned int ns() const;
        
        
            virtual unsigned int ls(unsigned int pos) const ;
        
        
            virtual const char* name(unsigned int pos) const;

        
            virtual const char* sequence(unsigned int pos) const;



            virtual unsigned int group(unsigned int pos) const;
        
        
            bool isEqual() const;


            unsigned int equalize(char ch='?');

        
            int find(const char* string, bool strict=true) const;


        protected:
            // The number of sequences
            unsigned int _ns;
        
            // The array of name lengths
            unsigned int* lnames;
    
            // The array of names
            char** names;
        
            // The array of sequences (as c-strings)
            char** sequences;
        
            // The array of groups
            unsigned int* groups;
        
            // Imports an array of c-strings
            virtual void setFromSource(unsigned int number_of_sequences, const char* const* const cstring_array);
        
            // Constructor helper
            virtual void copyObject(const Container&);
        
            // Constructor partial helper
            virtual void getNamesAndGroups(const Container&);
        
        private:
       
            // The array of sequence lengths
            unsigned int* lsequences;
        
            // Setup a valid empty object
            virtual void init();
    };
}
    
#endif