| 1 | /* |
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| 2 | * tridist.h Adachi, J. 1995.09.22 |
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| 3 | * Copyright (C) 1993-1995 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 UPPERLIMIT 500.0 /* upper limit on branch length (subsutitutions) */ |
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| 10 | #define LOWERLIMIT 0.001 /* lower limit on branch length (subsutitutions) */ |
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| 11 | #define EPSILON 0.001 |
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| 12 | #define MAXCOLUMN 80 |
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| 13 | #define BUFLINE 512 |
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| 14 | #define MAXOVER 50 |
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| 15 | #define MAXLENG 30 |
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| 16 | #define NMLNGTH 10 /* max. num. of characters in species name with S or I */ |
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| 17 | #define SWITCHES "Hhilm:o:St:T:uvwzZ" |
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| 18 | #define VERSION "1.2.5" |
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| 19 | #define DATE "Oct 30 1995" |
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| 20 | |
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| 21 | #define TREEFEXT ".tre" |
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| 22 | #define EPSFILEEXT ".eps" |
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| 23 | #define TPLGYFEXT ".tpl" |
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| 24 | #ifdef NJ |
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| 25 | #define TPLGYFILE "njdist.tpl" |
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| 26 | #define EPSFILE "njdist.eps" |
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| 27 | #else /* NJ */ |
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| 28 | #define TPLGYFILE "tridist.tpl" |
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| 29 | #define EPSFILE "tridist.eps" |
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| 30 | #endif /* NJ */ |
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| 31 | |
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| 32 | typedef struct node { |
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| 33 | struct node *isop; |
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| 34 | struct node *kinp; |
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| 35 | int descen; /* descendants */ |
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| 36 | int num; |
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| 37 | double length; |
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| 38 | } Node; |
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| 39 | |
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| 40 | typedef struct tree { |
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| 41 | Node *rootp; |
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| 42 | Node *firstp; |
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| 43 | Node **brnchp; |
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| 44 | double ablength; |
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| 45 | double rssleast; |
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| 46 | int npara; |
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| 47 | imatrix paths; |
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| 48 | } Tree; |
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| 49 | |
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| 50 | #ifdef MAIN_MODULE |
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| 51 | #define EXTERN |
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| 52 | #else |
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| 53 | #define EXTERN extern |
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| 54 | #endif |
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| 55 | |
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| 56 | EXTERN FILE *Epsfp; |
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| 57 | EXTERN time_t Ct0; |
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| 58 | |
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| 59 | EXTERN boolean Upgma_optn; /* u option UPGMA */ |
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| 60 | EXTERN boolean Least_optn; /* l option least squares */ |
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| 61 | EXTERN boolean Outgr_optn; /* o option */ |
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| 62 | EXTERN boolean Tfile_optn; /* T option Tree file option */ |
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| 63 | EXTERN boolean Tplgy_optn; /* t option topology file option */ |
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| 64 | EXTERN boolean Seque_optn; /* S option PHYLIP Sequential input format */ |
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| 65 | EXTERN boolean Verbs_optn; /* v option Verbose to stderr */ |
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| 66 | EXTERN boolean Info_optn; /* i option get Information */ |
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| 67 | EXTERN boolean Multi_optn; /* m option multiple data sets */ |
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| 68 | EXTERN boolean Write_optn; /* w option output more infomation */ |
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| 69 | EXTERN boolean Relia_optn; /* R option Reliability of a branch */ |
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| 70 | EXTERN boolean Debug_optn; /* z option output debug data */ |
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| 71 | EXTERN boolean Debug; /* Z option output more debug data */ |
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| 72 | |
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| 73 | EXTERN char *Epsfile; |
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| 74 | EXTERN char *Prog_name; |
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| 75 | EXTERN char *Comment; |
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| 76 | EXTERN int Numspc; |
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| 77 | EXTERN int Numtree; |
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| 78 | EXTERN int Cnotree; |
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| 79 | EXTERN int Maxbrnch; |
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| 80 | EXTERN int Numbrnch; |
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| 81 | EXTERN int Numpair; |
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| 82 | EXTERN int Numexe; /* number of executes */ |
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| 83 | EXTERN int Cnoexe; /* curent numbering of executes */ |
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| 84 | EXTERN int Outgroup; |
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| 85 | EXTERN double Proportion; |
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| 86 | |
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| 87 | EXTERN Tree *Ctree; |
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| 88 | EXTERN char **Identif; |
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| 89 | EXTERN char **Sciname; |
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| 90 | EXTERN char **Engname; |
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| 91 | EXTERN dmatrix Distanmat; |
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| 92 | EXTERN dvector Distanvec; |
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| 93 | EXTERN dvector Lengths; |
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| 94 | EXTERN dmatrix Reliprob; |
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