src/LocARNA/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