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src/biu/Alphabet.hh

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#ifndef ALPHABET_HH_
#define ALPHABET_HH_


#include <vector>
#include <string>
#include <map>

namespace biu
{

    class Alphabet
    {
    public:
        typedef size_t  AlphElem;
        typedef unsigned char   CAlphElem;
        
        typedef std::vector<AlphElem> Sequence;
        
        typedef std::vector<CAlphElem> CSequence;
        
    private:
    
        typedef std::map<std::string, AlphElem> STR2ALPH_TYPE;
        
        STR2ALPH_TYPE string2alph;  
        
        std::vector<std::string> alph2string;   
        
        size_t elementLength;       
        
    public:
    
        Alphabet(   const std::string& alphabetString, 
                    const size_t elementLength_);
        
        Alphabet(const std::vector<std::string> & alphabetStrings);
        
        virtual ~Alphabet();

        bool operator== (const Alphabet& alph2) const;
        bool operator!= (const Alphabet& alph2) const;

        size_t getAlphabetSize() const {
            return alph2string.size();
        }
        
        size_t getElementLength() const { 
            return elementLength;
        }
    
        // string to sequence to string
    
        Sequence getSequence(const std::string& seqString) const;
        
        AlphElem getElement(const std::string& alphElemStr) const;
        
        std::string getString(const Alphabet::Sequence& sequence) const;
        
        std::string getString(const Alphabet::AlphElem& elem) const;
        
        CSequence compress(const Alphabet::Sequence& sequence) const;
        
        Sequence decompress(const CSequence& sequence, const size_t seqLength) const;
        
    
        // miscellaneous
    
        bool isAlphabetString(const std::string& str) const;
        
        bool isAlphabetSequence(const Sequence& seq) const;
        
        size_t getIndex(const AlphElem& elem) const;
        
        size_t getIndex(const std::string& elemStr) const;
        
        AlphElem getElement(const size_t index) const;
        
    };

} // namespace biu

#endif /*ALPHABET_HH_*/