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#ifndef _BLASR_FASTA_SEQUENCE_HPP_
#define _BLASR_FASTA_SEQUENCE_HPP_
#include <cstdint>
#include <cstring>
#include <iostream>
#include <ostream>
#include <string>
#include <string>
#include <pbdata/Enumerations.h>
#include <pbdata/Types.h>
#include <pbdata/DNASequence.hpp>
#include <pbdata/NucConversion.hpp>
#include <pbdata/reads/ZMWGroupEntry.hpp>
//
// NO proteins for now.
class FASTASequence : public DNASequence
{
private:
// Whether or not to delete title in Free()
// regardless of deleteOnExit (to prevent memory leak
// when ReferenceSubstring and CopyTitle are called together).
bool deleteTitleOnExit;
public:
char *title;
int titleLength;
FASTASequence();
inline ~FASTASequence();
void PrintSeq(std::ostream &out, int lineLength = 50, char delim = '>') const;
int GetStorageSize() const;
std::string GetName() const;
void ShallowCopy(const FASTASequence &rhs);
std::string GetTitle() const;
void DeleteTitle();
void CopyTitle(const char *str, int strlen);
void CopyTitle(std::string str);
void GetFASTATitle(std::string &fastaTitle) const;
void CopySubsequence(FASTASequence &rhs, int readStart, int readEnd = -1);
void AppendToTitle(std::string str);
void Assign(FASTASequence &rhs);
void MakeRC(FASTASequence &rhs, DNALength rhsPos = 0, DNALength rhsLength = 0);
// Reverse complement sequence, and leave title as is.
FASTASequence &ReverseComplementSelf(void);
void operator=(const FASTASequence &rhs);
void Copy(const FASTASequence &rhs);
void Copy(const std::string &rhsTitle, const std::string &rhsSeq);
void Copy(const std::string &rhsSeq);
#ifdef USE_PBBAM
/// Copies a BamRecord as a FASTASequence.
void Copy(const PacBio::BAM::BamRecord &record);
#endif
void Free();
};
inline FASTASequence::~FASTASequence() { FASTASequence::Free(); }
#endif
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