X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=uchime_src%2Falpha.h;fp=uchime_src%2Falpha.h;h=e021b7fbc307ea1277a26d4a86275415cc167754;hb=7dab6ac3ae5a5f1ce37dca8cfacaa719881fd5b2;hp=0000000000000000000000000000000000000000;hpb=aa23898d895a8c04cc4582a8809343df0aef6622;p=mothur.git

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