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| 2 | /* version 3.6. (c) Copyright 1993-2000 by the University of Washington. |
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| 3 | Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. |
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| 4 | Permission is granted to copy and use this program provided no fee is |
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| 5 | charged for it and provided that this copyright notice is not removed. */ |
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| 6 | |
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| 7 | /* |
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| 8 | seq.h: included in dnacomp, dnadist, dnainvar, dnaml, dnamlk, dnamove, |
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| 9 | dnapars, dnapenny, protdist, protpars, & restml |
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| 10 | */ |
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| 11 | |
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| 12 | #define maxcutter 8 /* maximum number of bases in a site in restml */ |
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| 13 | |
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| 14 | /* move */ |
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| 15 | /* All the below moved here in the Great TreeRead Migration of '96 */ |
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| 16 | |
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| 17 | #define ebcdic EBCDIC |
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| 18 | #define MAXNCH 20 |
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| 19 | |
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| 20 | /* All of this came over from cons.h -plc*/ |
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| 21 | #define OVER 7 |
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| 22 | #define ADJACENT_PAIRS 1 |
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| 23 | #define CORR_IN_1_AND_2 2 |
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| 24 | #define ALL_IN_1_AND_2 3 |
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| 25 | #define NO_PAIRING 4 |
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| 26 | #define ALL_IN_FIRST 5 |
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| 27 | #define TREE1 8 |
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| 28 | #define TREE2 9 |
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| 29 | |
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| 30 | #define FULL_MATRIX 11 |
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| 31 | #define VERBOSE 22 |
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| 32 | #define SPARSE 33 |
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| 33 | |
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| 34 | /* Used in proml, promlk, dnaml, dnamlk for undefined bestyet*/ |
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| 35 | #define UNDEFINED 1.0 |
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| 36 | |
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| 37 | |
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| 38 | /* Number of columns per block in a matrix output */ |
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| 39 | #define COLUMNS_PER_BLOCK 10 |
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| 40 | |
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| 41 | |
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| 42 | /*end move*/ |
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| 43 | |
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| 44 | |
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| 45 | typedef struct gbases { |
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| 46 | baseptr base; |
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| 47 | struct gbases *next; |
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| 48 | } gbases; |
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| 49 | |
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| 50 | typedef struct nuview_data { |
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| 51 | /* A big 'ol collection of pointers used in nuview */ |
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| 52 | double *yy, *wwzz, *vvzz, *vzsumr, *vzsumy, *sum, *sumr, *sumy; |
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| 53 | sitelike *xx; |
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| 54 | } nuview_data; |
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| 55 | |
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| 56 | struct LOC_hyptrav { |
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| 57 | boolean bottom; |
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| 58 | node *r; |
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| 59 | long *hypset; |
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| 60 | boolean maybe, nonzero; |
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| 61 | long tempset, anc; |
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| 62 | } ; |
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| 63 | |
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| 64 | |
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| 65 | extern long nonodes, endsite, outgrno, nextree, which; |
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| 66 | |
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| 67 | extern boolean interleaved, printdata, outgropt, treeprint, dotdiff, transvp; |
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| 68 | |
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| 69 | extern steptr weight, category, alias, location, ally; |
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| 70 | |
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| 71 | #ifndef OLDC |
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| 72 | /* function prototypes */ |
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| 73 | void free_all_x_in_array (long, pointarray); |
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| 74 | void free_all_x2_in_array (long, pointarray); |
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| 75 | void alloctemp(node **, long *, long); |
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| 76 | void freetemp(node **); |
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| 77 | void freetree2 (pointarray, long); |
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| 78 | void inputdata(long); |
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| 79 | void alloctree(pointarray *, long, boolean); |
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| 80 | void allocx(long, long, pointarray, boolean); |
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| 81 | |
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| 82 | void prot_allocx(long, long, pointarray, boolean); |
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| 83 | void allocx2(long, long, long, pointarray, boolean); |
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| 84 | void setuptree(pointarray, long, boolean); |
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| 85 | void setuptree2(tree); |
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| 86 | void alloctip(node *, long *); |
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| 87 | void alloctrans(transptr *, long, long); |
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| 88 | void getbasefreqs(double, double, double, double, double *, double *, |
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| 89 | double *, double *, double *, double *, double *, |
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| 90 | double *xi, double *, double *, boolean, boolean); |
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| 91 | void empiricalfreqs(double *,double *,double *,double *,steptr,pointarray); |
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| 92 | void sitesort(long, steptr); |
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| 93 | void sitecombine(long); |
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| 94 | |
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| 95 | void sitescrunch(long); |
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| 96 | void sitesort2(long, steptr); |
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| 97 | void sitecombine2(long, steptr); |
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| 98 | void sitescrunch2(long, long, long, steptr); |
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| 99 | void makevalues(pointarray, long *, boolean); |
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| 100 | void makevalues2(long, pointarray, long, long, sequence, steptr); |
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| 101 | void fillin(node *, node *, node *); |
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| 102 | long getlargest(long *); |
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| 103 | void multifillin(node *, node *, long); |
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| 104 | void sumnsteps(node *, node *, node *, long, long); |
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| 105 | |
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| 106 | void sumnsteps2(node *, node *, node *, long, long, long *); |
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| 107 | void multisumnsteps(node *, node *, long, long, long *); |
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| 108 | void multisumnsteps2(node *); |
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| 109 | boolean alltips(node *, node *); |
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| 110 | void gdispose(node *, node **, pointarray); |
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| 111 | void preorder(node *, node *, node *, node *, node *, node *, long); |
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| 112 | void updatenumdesc(node *, node *, long); |
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| 113 | void add(node *,node *,node *,node **,boolean,pointarray,node **,long *); |
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| 114 | void findbelow(node **below, node *item, node *fork); |
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| 115 | |
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| 116 | void re_move(node *item, node **fork, node **root, boolean recompute, |
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| 117 | pointarray, node **, long *); |
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| 118 | void postorder(node *p); |
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| 119 | void getnufork(node **, node **, pointarray, long *); |
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| 120 | void reroot(node *, node *); |
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| 121 | void reroot2(node *, node *); |
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| 122 | void reroot3(node *, node *, node *, node *, node **); |
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| 123 | void savetraverse(node *); |
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| 124 | void newindex(long, node *); |
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| 125 | void flipindexes(long, pointarray); |
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| 126 | boolean parentinmulti(node *); |
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| 127 | |
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| 128 | long sibsvisited(node *, long *); |
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| 129 | long smallest(node *, long *); |
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| 130 | void bintomulti(node **, node **, node **, long *); |
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| 131 | void backtobinary(node **, node *, node **); |
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| 132 | boolean outgrin(node *, node *); |
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| 133 | void flipnodes(node *, node *); |
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| 134 | void moveleft(node *, node *, node **); |
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| 135 | void savetree(node *, long *, pointarray, node **, long *); |
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| 136 | void addnsave(node *, node *, node *, node **, node **,boolean, |
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| 137 | pointarray, long *, long *); |
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| 138 | void addbestever(long *, long *, long, boolean, long *, bestelm *); |
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| 139 | |
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| 140 | void addtiedtree(long, long *, long, boolean,long *, bestelm *); |
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| 141 | void clearcollapse(pointarray); |
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| 142 | void clearbottom(pointarray); |
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| 143 | void collabranch(node *, node *, node *); |
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| 144 | boolean allcommonbases(node *, node *, boolean *); |
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| 145 | void findbottom(node *, node **); |
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| 146 | boolean moresteps(node *, node *); |
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| 147 | boolean passdown(node *, node *, node *, node *, node *, node *, |
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| 148 | node *, node *, node *, boolean); |
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| 149 | boolean trycollapdesc(node *, node *, node *, node *, node *, |
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| 150 | node *, node *, node *, node *, boolean , long *); |
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| 151 | void setbottom(node *); |
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| 152 | |
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| 153 | boolean zeroinsubtree(node *, node *, node *, node *, node *, |
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| 154 | node *, node *, node *, boolean, node *, long *); |
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| 155 | boolean collapsible(node *, node *, node *, node *, node *, |
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| 156 | node *, node *, node *, boolean, node *, long *, pointarray); |
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| 157 | void replaceback(node **, node *, node *, node **, long *); |
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| 158 | void putback(node *, node *, node *, node **); |
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| 159 | void savelocrearr(node *, node *, node *, node *, node *, node *, |
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| 160 | node *, node *, node *, node **, long, long *, boolean, |
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| 161 | boolean , boolean *, long *, bestelm *, pointarray , |
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| 162 | node **, long *); |
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| 163 | void clearvisited(pointarray); |
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| 164 | void hyprint(long, long, struct LOC_hyptrav *,pointarray, Char *); |
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| 165 | void gnubase(gbases **, gbases **, long); |
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| 166 | void chuckbase(gbases *, gbases **); |
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| 167 | void hyptrav(node *, long *, long, long, boolean,pointarray, |
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| 168 | gbases **, Char *); |
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| 169 | |
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| 170 | void hypstates(long , node *, pointarray, gbases **, Char *); |
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| 171 | void initbranchlen(node *p); |
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| 172 | void initmin(node *, long, boolean); |
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| 173 | void initbase(node *, long); |
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| 174 | void inittreetrav(node *, long); |
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| 175 | void compmin(node *, node *); |
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| 176 | void minpostorder(node *, pointarray); |
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| 177 | void branchlength(node *,node *,double *,pointarray); |
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| 178 | void printbranchlengths(node *); |
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| 179 | void branchlentrav(node *,node *,long,long,double *,pointarray); |
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| 180 | |
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| 181 | void treelength(node *, long, pointarray); |
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| 182 | void coordinates(node *, long *, double, long *); |
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| 183 | void drawline(long, double, node *); |
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| 184 | void printree(node *, double); |
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| 185 | void writesteps(long, boolean, steptr, node *); |
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| 186 | void treeout(node *, long, long *, node *); |
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| 187 | void treeout3(node *, long, long *, node *); |
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| 188 | void drawline2(long, double, tree); |
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| 189 | void drawline3(long, double, node *); |
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| 190 | void copynode(node *, node *, long); |
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| 191 | |
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| 192 | void prot_copynode(node *, node *, long); |
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| 193 | void copy_(tree *, tree *, long, long); |
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| 194 | void prot_copy_(tree *, tree *, long, long); |
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| 195 | void standev(long, long, long, double, double *, long **, longer); |
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| 196 | void standev2(long, long, long, long, double, double *, double **, |
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| 197 | steptr, longer); |
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| 198 | void freetip(node *); |
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| 199 | void freenontip(node *); |
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| 200 | void freenodes(long, pointarray); |
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| 201 | void freenode(node **); |
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| 202 | void freetree(long, pointarray); |
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| 203 | |
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| 204 | void freex(long, pointarray); |
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| 205 | void freex2(long, pointarray); |
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| 206 | void freegarbage(gbases **); |
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| 207 | void freegrbg(node **); |
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| 208 | /*function prototypes*/ |
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| 209 | #endif |
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| 210 | |
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