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

[mothur.git] / uchime_src / orf.h

diff --git a/uchime_src/orf.h b/uchime_src/orf.h
new file mode 100644 (file)
index 0000000..90b29d1
--- /dev/null
+++ b/uchime_src/orf.h
@@ -0,0 +1,37 @@
+#ifndef orf_h\r
+#define orf_h\r
+\r
+#include "alpha.h"\r
+\r
+struct ORFData\r
+       {\r
+       const byte *NucSeq;\r
+       const byte *AminoSeq;\r
+       int Frame;\r
+       unsigned NucL;\r
+       unsigned AminoL;\r
+       unsigned NucLo;\r
+       unsigned NucHi;\r
+       ORFData *Next;\r
+\r
+       unsigned GetNucPosFirstBase() const;\r
+       unsigned GetAAPos(unsigned NucPos) const;\r
+       unsigned GetCodex(unsigned NucPos) const;\r
+       unsigned GetNucLo(unsigned AALo, unsigned AAHi) const;\r
+       unsigned GetNucHi(unsigned AALo, unsigned AAHi) const;\r
+       unsigned GetAALo(unsigned NucLo, unsigned NucHi) const;\r
+       unsigned GetAAHi(unsigned NucLo, unsigned NucHi) const;\r
+       unsigned GetNucPosFirstBaseInCodon(unsigned AAPos) const;\r
+       unsigned GetNucPosLastBaseInCodon(unsigned AAPos) const;\r
+       unsigned RoundToCodonLo(unsigned NucPos) const;\r
+       unsigned RoundToCodonHi(unsigned NucPos) const;\r
+       void LogMe() const;\r
+       void LogMe2() const;\r
+       };\r
+\r
+const byte ORFEND = '.';\r
+\r
+void GetORFs(const byte *NucSeq, unsigned NucL, vector<ORFData> &ORFs,\r
+  unsigned ORFStyle, int FindFrame, int Sign);\r
+\r
+#endif // orf_h\r