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

[mothur.git] / uchime_src / alpha.h

diff --git a/uchime_src/alpha.h b/uchime_src/alpha.h
new file mode 100644 (file)
index 0000000..e021b7f
--- /dev/null
+++ b/uchime_src/alpha.h
@@ -0,0 +1,50 @@
+#ifndef alpha_h\r
+#define alpha_h\r
+\r
+#include <limits.h>\r
+#include <string>\r
+\r
+using namespace std;\r
+\r
+const unsigned INVALID_LETTER = 0;\r
+const unsigned char INVALID_CHAR = '?';\r
+\r
+extern unsigned g_CharToLetterAmino[];\r
+extern unsigned g_CharToLetterAminoStop[];\r
+extern unsigned char g_LetterToCharAmino[];\r
+extern unsigned g_CharToLetterNucleo[];\r
+extern unsigned char g_LetterToCharNucleo[];\r
+extern unsigned g_CodonWordToAminoLetter[];\r
+extern char g_CodonWordToAminoChar[];\r
+extern unsigned char g_CharToCompChar[];\r
+extern unsigned g_CharToCompLetter[];\r
+extern bool g_IsAminoChar[];\r
+extern bool g_IsNucleoChar[];\r
+extern bool g_IsACGTU[];\r
+extern float g_AminoFreqs[];\r
+\r
+extern unsigned g_CharToLetterRed[];\r
+extern unsigned char g_LetterToCharRed[];\r
+extern unsigned g_RedAlphaSize;\r
+\r
+void LogRedAlphaRed();\r
+void ReadRedAlphaFromFile(const string &FileName);\r
+unsigned char GetAminoCharFrom3NucChars(unsigned char c1, unsigned char c2,\r
+  unsigned char c3);\r
+\r
+static inline bool AminoLetterIsStartCodon(unsigned char Letter)\r
+       {\r
+       return Letter == 10;\r
+       }\r
+\r
+static inline bool AminoLetterIsStopCodon(unsigned char Letter)\r
+       {\r
+       return Letter == 20;\r
+       }\r
+\r
+const char *WordToStr(unsigned Word, unsigned WordLength, bool Nucleo);\r
+const char *WordToStrNucleo(unsigned Word, unsigned WordLength);\r
+const char *WordToStrAmino(unsigned Word, unsigned WordLength);\r
+const char *WordToStrAmino2(unsigned Word, unsigned WordLength, char *Str);\r
+\r
+#endif // alpha_h\r