#ifndef _BLASR_SAM_REFERENCE_SEQUENCE_HPP_
#define _BLASR_SAM_REFERENCE_SEQUENCE_HPP_

#include <string>

#include <pbdata/sam/SAMKeywordValuePair.hpp>

class SAMReferenceSequence
{
public:
    std::string sequenceName;
    uint64_t length;
    std::string GetSequenceName() { return sequenceName; }
    //
    // By definining accessor functions here but no data, we can
    // economize on the amount of space used for each element.   This is
    // no big deal for references, but for pairwise alignments, it is
    // big.
    //
    std::string GetMD5() { return ""; }
    uint64_t GetLength() { return length; }
    std::string GetGenomeAssembly() { return ""; }
    std::string GetSpecies() { return ""; }
    std::string GetURI() { return ""; }

    enum SAMReferenceSequenceRequiredFields
    {
        SQ_SN,
        SQ_LN
    };

    static const char* SAMReferenceSequenceFieldNames[];

    void StoreValues(std::vector<SAMKeywordValuePair>& kvPairs, uint64_t lineNumber = 0);
};

class SAMFullReferenceSequence : public SAMReferenceSequence
{
public:
    std::string md5;
    std::string species;
    std::string uri;
    std::string genomeAssembly;
    std::string GetMD5() { return md5; }
    std::string GetSpecies() { return species; }
    std::string GetURI() { return uri; }
    std::string GetGenomeAssembly() { return genomeAssembly; }

    enum FullReferenceSequenceRequiredFields
    {
        SQ_AS,
        SQ_M5,
        SQ_SP,
        SQ_UR
    };

    static const char* SAMFullReferenceSequenceFieldNames[];

    void StoreValues(std::vector<SAMKeywordValuePair>& kvPairs, uint64_t lineNumber = 0);
};

#endif