1 #ifndef _RNA_ALPHABET_ 2 #define _RNA_ALPHABET_ 3 4 #include <string> 5 6 7 8 typedef char RNA_Alphabet; 9 10 /** pair alphabet of RNA_Alphabet */ 11 typedef struct { 12 RNA_Alphabet a; 13 RNA_Alphabet b; 14 } RNA_AlphaPair; 15 16 const int ALPHA_BASE_A='a'; 17 const int ALPHA_BASE_C='c'; 18 const int ALPHA_BASE_G='g'; 19 const int ALPHA_BASE_U='u'; 20 const int ALPHA_BASEPAIR='P'; 21 const int ALPHA_GAP='-'; 22 const int ALPHA_BASE='B'; 23 24 25 const int RNA_ALPHABET_SIZE=8; 26 27 const int ALPHA_PRO_BASE_A=0; 28 const int ALPHA_PRO_BASE_C=1; 29 const int ALPHA_PRO_BASE_G=2; 30 const int ALPHA_PRO_BASE_U=3; 31 const int ALPHA_PRO_BASEPAIR=4; 32 const int ALPHA_PRO_GAP=5; 33 const int ALPHA_PRO_BASE=6; 34 const int ALPHA_PRO_ANCHOR=7; 35 36 struct RNA_Alphabet_Profile { RNA_Alphabet_ProfileRNA_Alphabet_Profile37 RNA_Alphabet_Profile() {}; 38 39 double p[RNA_ALPHABET_SIZE]; 40 std::string columnStr; 41 }; 42 43 int alpha2RNA_Alpha(char c); 44 45 #endif 46