// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
//
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//    notice, this list of conditions and the following disclaimer.
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//    disclaimer in the documentation and/or other materials provided
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// SUCH DAMAGE.

// Author: David Alexander

#include <string>

//
// For testing purposes, N and M are defined as two phony DNA bases
// that are complementary
//

static char ComplementArray[] = {
    3,     2,   1,   0, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, '-', 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 'T', 127, 'G', 127, 127, 127, 'C',
    127, 127, 127, 127, 127, 'N', 'M', 127,
    127, 127, 127, 127, 'A', 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 't', 127, 'g', 127, 127, 127, 'c',
    127, 127, 127, 127, 127, 'n', 'm', 127,
    127, 127, 127, 127, 'a', 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127,
    127, 127, 127, 127, 127, 127, 127, 127
};

namespace ConsensusCore {

    char ComplementaryBase(char base)
    {
       return ComplementArray[(int)base];
    }

    std::string Complement(const std::string& input)
    {
        std::string output(input.length(), 127);
        for (unsigned int i = 0; i < input.length(); i++)
        {
            output[i] = ComplementArray[(int)input[i]];
        }
        return output;
    }

    std::string Reverse(const std::string& input)
    {
        return std::string(input.rbegin(), input.rend());
    }

    std::string ReverseComplement(const std::string& input)
    {
        return Reverse(Complement(input));
    }
}
