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

[mothur.git] / uchime_src / uc.h

diff --git a/uchime_src/uc.h b/uchime_src/uc.h
new file mode 100644 (file)
index 0000000..93ef892
--- /dev/null
+++ b/uchime_src/uc.h
@@ -0,0 +1,60 @@
+#ifndef uc_h\r
+#define uc_h\r
+\r
+#include "seqdb.h"\r
+#include "seq.h"\r
+#include "path.h"\r
+\r
+struct AlnData;\r
+\r
+class UCFile\r
+       {\r
+public:\r
+       FILE *m_File;\r
+       byte *m_Data;\r
+       vector<char> m_RecTypes;\r
+       vector<float> m_PctIds;\r
+       vector<const char *> m_Labels;\r
+       vector<const char *> m_SeedLabels;\r
+       vector<unsigned> m_SeedIndexes;\r
+       vector<const char *> m_CompressedPaths;\r
+       vector<unsigned> m_SeqLengths;\r
+       vector<unsigned> m_SortOrder;\r
+       vector<char> m_Strands;\r
+       vector<unsigned> m_Los;\r
+       vector<unsigned> m_SeedLos;\r
+\r
+public:\r
+       UCFile();\r
+       void Clear(bool ctor = false);\r
+       void Close();\r
+       void FromFile(const string &FileName);\r
+       void FromClstr(const string &FileName);\r
+       void ToFile(const string &FileName);\r
+       unsigned GetRecordCount() const;\r
+       void LogMe() const;\r
+       void ToClstr(const string &FileName);\r
+       void ToFasta(const string &FileName, const SeqDB &Input, bool Reformat);\r
+       void Create(const string &FileName);\r
+       void Sort();\r
+       void Flush() const;\r
+\r
+       void WriteNotMatched(unsigned L, const char *Label) const;\r
+       void WriteLibSeed(unsigned SeedIndex, unsigned L, const char *Label) const;\r
+       void WriteNewSeed(unsigned SeedIndex, unsigned L, const char *Label) const;\r
+       void WriteHit(const SeqData &SA, const SeqData &SB, double FractId,\r
+         const PathData &PD) const;\r
+       void WriteReject(const SeqData &SA, const SeqData &SB, double FractId,\r
+         const char *Path) const;\r
+       void WriteHit(unsigned SeedIndex, unsigned L, double PctId,\r
+         const char *CompressedPath, char Strand, unsigned Lo, unsigned SeedLo,\r
+         const char *Label, const char *SeedLabel) const;\r
+       void WriteHit(const AlnData &AD);\r
+       void WriteLibCluster(unsigned SeedIndex, unsigned Size, double AvgId,\r
+         const char *Label) const;\r
+       void WriteNewCluster(unsigned SeedIndex, unsigned Size, double AvgId,\r
+         const char *Label) const;\r
+       void WriteSeqX(FILE *f, const byte *Seq, unsigned L, const char *CompressedPath) const;\r
+       };\r
+\r
+#endif // uc_h\r