removing chime source files from mother project.

[mothur.git] / orf.h

diff --git a/orf.h b/orf.h
deleted file mode 100644 (file)
index 90b29d1..0000000
--- a/orf.h
+++ /dev/null
@@ -1,37 +0,0 @@
-#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