Mercurial > repos > rliterman > csp2
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/src/tigr/translate.hh Tue Mar 18 17:55:14 2025 -0400 @@ -0,0 +1,581 @@ +//-- 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] = { + 'K','N','K','N','X','K','X','X','N','X','X','X','X','X','X','X', + 'T','T','T','T','T','T','T','T','T','T','T','T','T','T','T','X', + 'R','S','R','S','X','R','X','X','S','X','X','X','X','X','X','X', + 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