| 1 | /* |
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| 2 | * protst.h Adachi, J. 1996.03.12 |
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| 3 | * Copyright (C) 1993-1996 J. Adachi & M. Hasegawa, All rights reserved. |
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| 4 | */ |
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| 5 | |
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| 6 | #include "molphy.h" |
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| 7 | #include "matrixut.h" |
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| 8 | |
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| 9 | #define NUMAMI 20 |
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| 10 | #define NUMNUC 4 |
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| 11 | |
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| 12 | #ifndef NUC |
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| 13 | #define TPMRADIX NUMAMI |
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| 14 | #define INFOMOL "Amino" |
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| 15 | #define LOGFILE "Protst.log" |
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| 16 | #else /* NUC*/ |
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| 17 | #define TPMRADIX NUMNUC |
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| 18 | #define INFOMOL "Nucleic" |
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| 19 | #define LOGFILE "Nucst.log" |
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| 20 | #endif /* NUC*/ |
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| 21 | |
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| 22 | #define MAXCOLUMN 80 |
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| 23 | #define LINESITES 60 |
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| 24 | #define MAXELEMENT 17 |
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| 25 | #define BUFLINE 512 |
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| 26 | #define MAXWORD 32 |
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| 27 | #define MAXOVER 50 |
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| 28 | #define MAXLENG 30 |
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| 29 | #define NMLNGTH 10 /* max. num. of characters in species name with S or I */ |
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| 30 | #define SWITCHES "ac:hHiILSvwzZ" |
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| 31 | #define VERSION "1.2.1" |
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| 32 | #define DATE "Mar 12 1996" |
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| 33 | |
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| 34 | typedef int ivectpmty[TPMRADIX]; |
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| 35 | typedef double dvectpmty[TPMRADIX]; |
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| 36 | typedef dvectpmty dmattpmty[TPMRADIX]; |
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| 37 | |
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| 38 | extern char *Cacid1[]; |
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| 39 | extern char *Cacid3[]; |
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| 40 | |
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| 41 | |
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| 42 | #ifdef MAIN_MODULE |
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| 43 | |
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| 44 | #define EXTERN |
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| 45 | int Tpmradix = TPMRADIX; |
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| 46 | char *Infomol = INFOMOL; |
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| 47 | |
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| 48 | #else |
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| 49 | |
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| 50 | #define EXTERN extern |
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| 51 | EXTERN int Tpmradix; |
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| 52 | EXTERN char *Infomol; |
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| 53 | |
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| 54 | #endif |
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| 55 | |
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| 56 | EXTERN FILE *Logfp; |
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| 57 | EXTERN time_t Ct0; |
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| 58 | |
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| 59 | EXTERN boolean Align_optn; /* a option Alignment viewer */ |
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| 60 | EXTERN boolean Colmn_optn; /* c option Column */ |
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| 61 | EXTERN boolean Ctacit_optn; /* C option taCiturnity */ |
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| 62 | EXTERN boolean Inlvd_optn; /* I option interleaved input format */ |
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| 63 | EXTERN boolean Info_optn; /* i option */ |
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| 64 | EXTERN boolean Logfl_optn; /* L option */ |
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| 65 | EXTERN boolean Multi_optn; /* m option multiple data sets */ |
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| 66 | EXTERN boolean Seque_optn; /* S option PHYLIP Sequential input format */ |
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| 67 | EXTERN boolean Tstv_optn; /* t option with decimal number */ |
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| 68 | EXTERN boolean Toptim_optn; /* t option without decimal number */ |
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| 69 | EXTERN boolean Verbs_optn; /* v option Verbose to stderr */ |
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| 70 | EXTERN boolean Write_optn; /* w option output sequence infomation */ |
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| 71 | EXTERN boolean Debug_optn; /* z option */ |
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| 72 | EXTERN boolean Debug; /* Z option */ |
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| 73 | |
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| 74 | EXTERN char *Prog_name; |
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| 75 | EXTERN int Maxspc; |
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| 76 | EXTERN int Numspc; |
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| 77 | EXTERN int Maxpair; |
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| 78 | EXTERN int Numpair; |
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| 79 | EXTERN int Maxsite; |
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| 80 | EXTERN int Numsite; |
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| 81 | EXTERN int Numptrn; |
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| 82 | EXTERN int Linesites; |
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| 83 | EXTERN int Maxcolumn; |
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| 84 | EXTERN int Maxelement; |
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| 85 | |
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| 86 | EXTERN char **Identif; |
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| 87 | EXTERN char **Sciname; |
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| 88 | EXTERN char **Engname; |
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| 89 | EXTERN cmatrix Seqchar; |
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| 90 | EXTERN imatrix Seqconint; |
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| 91 | EXTERN ivector Weight; |
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| 92 | EXTERN dvectpmty Freqemp; |
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| 93 | |
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| 94 | |
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| 95 | EXTERN int Numnoindel; /* ST */ |
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| 96 | EXTERN ivector Insdel; /* ST */ |
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