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#ifndef sfasta_h
#define sfasta_h
#include "myutils.h"
#include "seq.h"
typedef void (*ON_START_XSEQ)(const SeqData &SD);
typedef void (*ON_END_XSEQ)(const SeqData &SD);
// Sequential reader for FASTA file format.
// Serves sequences in file order to save memory.
// Caches biggish chunks to compromise memory vs. speed.
class SFasta
{
public:
string m_FileName;
FILE *m_File;
bool m_AllowGaps;
off_t m_FileSize;
// Position to start next read
off_t m_FilePos;
// Cached data.
byte *m_Buffer;
// Bytes allocated to m_Buffer
unsigned m_BufferSize;
// Current position in buffer, normally points to '>'
unsigned m_BufferOffset;
// File data in buffer <= m_BufferSize
unsigned m_BufferBytes;
// Current label
// Points into m_Buffer, not a separate buffer.
char *m_Label;
// Current sequence length
unsigned m_SeqLength;
// Current seq index
unsigned m_SeqIndex;
unsigned m_ShortestLength;
unsigned m_LongestLength;
unsigned m_TooShortCount;
unsigned m_TooLongCount;
unsigned m_TooPolyCount;
private:
bool m_IsNucleoSet;
bool m_IsNucleo;
public:
SFasta();
~SFasta();
void Clear();
void Open(const string &FileName);
void Rewind();
bool SetIsNucleo();
bool GetIsNucleo() const { asserta(m_IsNucleoSet); return m_IsNucleo; };
// Get next sequence.
// Returns zero on end-of-file
const byte *GetNextSeq();
// Get next sequence as SeqData object, return false on end-of-file.
bool GetNextSD(SeqData &SD);
// Length of most recent sequence returned by GetNextSeq().
unsigned GetSeqLength() const { return m_SeqLength; }
// Label of most recent sequence returned by GetNextSeq().
const char *GetLabel() const { return m_Label; }
// Index of most recent sequence returned by GetNextSeq().
unsigned GetSeqIndex() const { return m_SeqIndex; }
unsigned GetPctDoneX10() const;
double GetPctDone() const;
void LogMe() const;
private:
void FillCache();
const byte *GetNextSeqLo();
};
#endif // sfasta_h
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