sequence.hh

#ifndef LOCARNA_SEQUENCE_HH
#define LOCARNA_SEQUENCE_HH

#ifdef HAVE_CONFIG_H
#  include <config.h>
#endif

#include <vector>
#include "multiple_alignment.hh"


namespace LocARNA {
    
    class Sequence:
        public MultipleAlignment {
        
        // BEWARE: don't define attributes in sequence! In
        // MultipleAlignment.as_sequence(), we rely on a simple upcast
        // to convert MultipleAlignment objects to Sequence objects
        
    public:
        
        Sequence(): MultipleAlignment() {}
        
        Sequence(const std::string &name,
                 const std::string &sequence)
            : MultipleAlignment(name,sequence) {
        }
        
        AliColumn
        operator [](size_type col_index) const {
            return column(col_index);
        }
        
        std::vector<std::string> 
        names() const;
        
    };
    
} // end namespace LocARNA

#endif