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#ifndef windex_h
#define windex_h
class SFasta;
struct SeqDB;
typedef uint32 word_t;
typedef uint16 wordcount_t;
typedef uint32 arrsize_t;
typedef uint16 seqcountperword_t;
typedef uint32 seqindex_t;
typedef uint16 commonwordcount_t;
const uint32 WindexFileHdr_Magic1 = 0x312DE41;
const uint32 WindexFileHdr_Magic2 = 0x312DE42;
const uint32 WindexFileHdr_Magic3 = 0x312DE43;
const uint32 WindexFileHdr_Magic4 = 0x312DE44;
struct WindexFileHdr
{
uint32 Magic1;
uint32 IsNucleo;
uint32 WordLength;
uint32 Magic2;
};
class Windex
{
public:
bool m_Nucleo;
bool m_RedAlpha;
unsigned m_WordLength;
unsigned m_AlphaSize;
unsigned m_WordCount;
unsigned m_Hi;
unsigned m_CapacityInc;
arrsize_t *m_Capacities;
arrsize_t *m_Sizes;
float *m_WordScores;
seqindex_t **m_SeedIndexes;
byte *m_UniqueCounts;
unsigned m_CharToLetter[256];
public:
Windex();
void ToFile(const string &FileName) const;
void FromFile(const string &FileName);
void FromSFasta(SFasta &SF);
void FromSeqDB(const SeqDB &DB);
void Clear(bool ctor = false);
void AddWords(unsigned SeqIndex, const word_t *Words, unsigned N);
void Init(bool Nucleo, unsigned WordLength);
void Init2(bool Nucleo, unsigned TableSize);
void InitRed(unsigned WordLength);
void InitWordScores(const float *const *SubstMx);
void Reset();
void LogMe() const;
unsigned LogMemSize() const;
void LogWordStats(unsigned TopWords = 10) const;
const char *WordToStr(word_t Word) const;
word_t SeqToWord(const byte *Seq) const;
unsigned SeqToWords(const byte *Seq, unsigned L, word_t *Words) const;
unsigned SeqToWordsStep(unsigned Step, const byte *Seq, unsigned L, word_t *Words) const;
unsigned WordsToCounts(const word_t *Words, unsigned N,
word_t *UniqueWords, seqcountperword_t *Counts) const;
unsigned GetUniqueWords(const word_t *Words, unsigned N,
word_t *UniqueWords) const;
void LogSizeHisto() const;
};
#endif // windex_h
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