Mercurial > repos > rliterman > csp2
view CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/src/tigr/translate.hh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
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//-- Values and function for DNA -> Amino Acid translation #ifndef __TRANSLATE_HH #define __TRANSLATE_HH #include <cstdio> #include <cstring> long int Translate_DNA (char * A, char * tA, int Frame); // function to translate dna sequence to aminoacid sequence // uses esttrans' headers and algo // A as read in from gene.h Read_String // tA should be an empty string, malloced to atleast (len A / 3) // frame is 1,2,3,4,5,6 // returns new (strlen(A+1)) or -1 on error // See end of file for source. #define BAD_PEP_CHAR -1 #define SKIP_PEP_CHAR -2 #define NUM_DNA_SYMBOLS 16 #define DNA_A 0 #define DNA_C 1 #define DNA_G 2 #define DNA_TU 3 #define DNA_M 4 #define DNA_R 5 #define DNA_W 6 #define DNA_S 7 #define DNA_Y 8 #define DNA_K 9 #define DNA_V 10 #define DNA_H 11 #define DNA_D 12 #define DNA_B 13 #define DNA_XN 14 #define DNA_dot 15 #define AA_LEN 8192 #define DNA_LEN 32768 #define AA_LINE_LEN 60 const int compdna[NUM_DNA_SYMBOLS] = { DNA_TU, DNA_G, DNA_C, DNA_A, DNA_K, DNA_Y, DNA_W, DNA_S, DNA_R, DNA_M, DNA_B, DNA_D, DNA_H, DNA_V, DNA_XN, DNA_dot }; const int transdna[256] = { BAD_PEP_CHAR, /* 0 NUL*/ BAD_PEP_CHAR, /* 1 SOH*/ BAD_PEP_CHAR, /* 2 STX*/ BAD_PEP_CHAR, /* 3 ETX*/ BAD_PEP_CHAR, /* 4 EOT*/ BAD_PEP_CHAR, /* 5 ENQ*/ BAD_PEP_CHAR, /* 6 ACK*/ BAD_PEP_CHAR, /* 7 BEL*/ BAD_PEP_CHAR, /* 8 BS */ SKIP_PEP_CHAR, /* 9 HT */ SKIP_PEP_CHAR, /* 10 NL */ SKIP_PEP_CHAR, /* 11 VT */ SKIP_PEP_CHAR, /* 12 NP */ SKIP_PEP_CHAR, /* 13 CR */ BAD_PEP_CHAR, /* 14 SO */ BAD_PEP_CHAR, /* 15 SI */ BAD_PEP_CHAR, /* 16 DLE*/ BAD_PEP_CHAR, /* 17 DC1*/ BAD_PEP_CHAR, /* 18 DC2*/ BAD_PEP_CHAR, /* 19 DC3*/ BAD_PEP_CHAR, /* 20 DC4*/ BAD_PEP_CHAR, /* 21 NAK*/ BAD_PEP_CHAR, /* 22 SYN*/ BAD_PEP_CHAR, /* 23 ETB*/ BAD_PEP_CHAR, /* 24 CAN*/ BAD_PEP_CHAR, /* 25 EM */ BAD_PEP_CHAR, /* 26 SUB*/ BAD_PEP_CHAR, /* 27 ESC*/ BAD_PEP_CHAR, /* 28 FS */ BAD_PEP_CHAR, /* 29 GS */ BAD_PEP_CHAR, /* 30 RS */ BAD_PEP_CHAR, /* 31 US */ SKIP_PEP_CHAR, /* 32 SP */ BAD_PEP_CHAR, /* 33 ! */ BAD_PEP_CHAR, /* 34 " */ BAD_PEP_CHAR, /* 35 # */ BAD_PEP_CHAR, /* 36 $ */ BAD_PEP_CHAR, /* 37 % */ BAD_PEP_CHAR, /* 38 & */ BAD_PEP_CHAR, /* 39 ' */ BAD_PEP_CHAR, /* 40 ( */ BAD_PEP_CHAR, /* 41 ) */ BAD_PEP_CHAR, /* 42 * */ BAD_PEP_CHAR, /* 43 + */ BAD_PEP_CHAR, /* 44 , */ BAD_PEP_CHAR, /* 45 - */ DNA_dot, /* 46 . */ BAD_PEP_CHAR, /* 47 / */ BAD_PEP_CHAR, /* 48 0 */ BAD_PEP_CHAR, /* 49 1 */ BAD_PEP_CHAR, /* 50 2 */ BAD_PEP_CHAR, /* 51 3 */ BAD_PEP_CHAR, /* 52 4 */ BAD_PEP_CHAR, /* 53 5 */ BAD_PEP_CHAR, /* 54 6 */ BAD_PEP_CHAR, /* 55 7 */ BAD_PEP_CHAR, /* 56 8 */ BAD_PEP_CHAR, /* 57 9 */ BAD_PEP_CHAR, /* 58 : */ BAD_PEP_CHAR, /* 59 ; */ BAD_PEP_CHAR, /* 60 < */ BAD_PEP_CHAR, /* 61 = */ BAD_PEP_CHAR, /* 62 > */ BAD_PEP_CHAR, /* 63 ? */ BAD_PEP_CHAR, /* 64 @ */ DNA_A, /* 65 A */ DNA_B, /* 66 B */ DNA_C, /* 67 C */ DNA_D, /* 68 D */ BAD_PEP_CHAR, /* 69 E */ BAD_PEP_CHAR, /* 70 F */ DNA_G, /* 71 G */ DNA_H, /* 72 H */ BAD_PEP_CHAR, /* 73 I */ BAD_PEP_CHAR, /* 74 J */ DNA_K, /* 75 K */ BAD_PEP_CHAR, /* 76 L */ DNA_M, /* 77 M */ DNA_XN, /* 78 N */ BAD_PEP_CHAR, /* 79 O */ BAD_PEP_CHAR, /* 80 P */ BAD_PEP_CHAR, /* 81 Q */ DNA_R, /* 82 R */ DNA_S, /* 83 S */ DNA_TU, /* 84 T */ DNA_TU, /* 85 U */ DNA_V, /* 86 V */ DNA_W, /* 87 W */ DNA_XN, /* 88 X */ DNA_Y, /* 89 Y */ BAD_PEP_CHAR, /* 90 Z */ BAD_PEP_CHAR, /* 91 [ */ BAD_PEP_CHAR, /* 92 \ */ BAD_PEP_CHAR, /* 93 ] */ BAD_PEP_CHAR, /* 94 ^ */ BAD_PEP_CHAR, /* 95 _ */ BAD_PEP_CHAR, /* 96 ` */ DNA_A, /* 97 a */ DNA_B, /* 98 b */ DNA_C, /* 99 c */ DNA_D, /*100 d */ BAD_PEP_CHAR, /*101 e */ BAD_PEP_CHAR, /*102 f */ DNA_G, /*103 g */ DNA_H, /*104 h */ BAD_PEP_CHAR, /*105 i */ BAD_PEP_CHAR, /*106 j */ DNA_K, /*107 k */ BAD_PEP_CHAR, /*108 l */ DNA_M, /*109 m */ DNA_XN, /*110 n */ BAD_PEP_CHAR, /*111 o */ BAD_PEP_CHAR, /*112 p */ BAD_PEP_CHAR, /*113 q */ DNA_R, /*114 r */ DNA_S, /*115 s */ DNA_TU, /*116 t */ DNA_TU, /*117 u */ DNA_V, /*118 v */ DNA_W, /*119 w */ DNA_XN, /*120 x */ DNA_Y, /*121 y */ BAD_PEP_CHAR, /*122 z */ BAD_PEP_CHAR, /*123 { */ BAD_PEP_CHAR, /*124 | */ BAD_PEP_CHAR, /*125 } */ BAD_PEP_CHAR, /*126 ~ */ BAD_PEP_CHAR, /*127 DEL*/ BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR, BAD_PEP_CHAR }; const char universal[NUM_DNA_SYMBOLS * NUM_DNA_SYMBOLS * NUM_DNA_SYMBOLS] = { 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