added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / uchime_src / windex.h

diff --git a/uchime_src/windex.h b/uchime_src/windex.h
new file mode 100644 (file)
index 0000000..0b324ca
--- /dev/null
+++ b/uchime_src/windex.h
@@ -0,0 +1,71 @@
+#ifndef windex_h\r
+#define windex_h\r
+\r
+class SFasta;\r
+struct SeqDB;\r
+\r
+typedef uint32 word_t;\r
+typedef uint16 wordcount_t;\r
+typedef uint32 arrsize_t;\r
+typedef uint16 seqcountperword_t;\r
+typedef uint32 seqindex_t;\r
+typedef uint16 commonwordcount_t;\r
+\r
+const uint32 WindexFileHdr_Magic1 = 0x312DE41;\r
+const uint32 WindexFileHdr_Magic2 = 0x312DE42;\r
+const uint32 WindexFileHdr_Magic3 = 0x312DE43;\r
+const uint32 WindexFileHdr_Magic4 = 0x312DE44;\r
+\r
+struct WindexFileHdr\r
+       {\r
+       uint32 Magic1;\r
+       uint32 IsNucleo;\r
+       uint32 WordLength;\r
+       uint32 Magic2;\r
+       };\r
+\r
+class Windex\r
+       {\r
+public:\r
+       bool m_Nucleo;\r
+       bool m_RedAlpha;\r
+       unsigned m_WordLength;\r
+       unsigned m_AlphaSize;\r
+       unsigned m_WordCount;\r
+       unsigned m_Hi;\r
+       unsigned m_CapacityInc;\r
+       arrsize_t *m_Capacities;\r
+       arrsize_t *m_Sizes;\r
+       float *m_WordScores;\r
+       seqindex_t **m_SeedIndexes;\r
+       byte *m_UniqueCounts;\r
+       unsigned m_CharToLetter[256];\r
+\r
+public:\r
+       Windex();\r
+       void ToFile(const string &FileName) const;\r
+       void FromFile(const string &FileName);\r
+       void FromSFasta(SFasta &SF);\r
+       void FromSeqDB(const SeqDB &DB);\r
+       void Clear(bool ctor = false);\r
+       void AddWords(unsigned SeqIndex, const word_t *Words, unsigned N);\r
+       void Init(bool Nucleo, unsigned WordLength);\r
+       void Init2(bool Nucleo, unsigned TableSize);\r
+       void InitRed(unsigned WordLength);\r
+       void InitWordScores(const float *const *SubstMx);\r
+       void Reset();\r
+       void LogMe() const;\r
+       unsigned LogMemSize() const;\r
+       void LogWordStats(unsigned TopWords = 10) const;\r
+       const char *WordToStr(word_t Word) const;\r
+       word_t SeqToWord(const byte *Seq) const;\r
+       unsigned SeqToWords(const byte *Seq, unsigned L, word_t *Words) const;\r
+       unsigned SeqToWordsStep(unsigned Step, const byte *Seq, unsigned L, word_t *Words) const;\r
+       unsigned WordsToCounts(const word_t *Words, unsigned N,\r
+         word_t *UniqueWords, seqcountperword_t *Counts) const;\r
+       unsigned GetUniqueWords(const word_t *Words, unsigned N,\r
+         word_t *UniqueWords) const;\r
+       void LogSizeHisto() const;\r
+       };\r
+\r
+#endif // windex_h\r