1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
|
/* fastDNAml.h */
#define headerName "fastDNAml.h"
#define headerVersion "1.2.1"
#define headerDate "March 9, 1998"
#ifndef dnaml_h
#include <stdlib.h>
/* Compile time switches for various updates to program:
* 0 gives original version
* 1 gives new version
*/
#define ReturnSmoothedView 1 /* Propagate changes back after smooth */
#define BestInsertAverage 1 /* Build three taxon tree analytically */
#define DeleteCheckpointFile 0 /* Remove checkpoint file when done */
#define Debug 0
/* Program constants and parameters */
#define maxlogf 1024 /* maximum number of user trees */
#define maxcategories 35 /* maximum number of site types */
#define smoothings 32 /* maximum smoothing passes through tree */
#define iterations 10 /* maximum iterations of makenewz per insert */
#define newzpercycle 1 /* iterations of makenewz per tree traversal */
#define nmlngth 10 /* number of characters in species name */
#define deltaz 0.00001 /* test of net branch length change in update */
#define zmin 1.0E-15 /* max branch prop. to -log(zmin) (= 34) */
#define zmax (1.0 - 1.0E-6) /* min branch prop. to 1.0-zmax (= 1.0E-6) */
#define defaultz 0.9 /* value of z assigned as starting point */
#define unlikely -1.0E300 /* low likelihood for initialization */
/* These values are used to rescale the lilelihoods at a given site so that
* there is no floating point underflow.
*/
#define twotothe256 \
115792089237316195423570985008687907853269984665640564039457584007913129639936.0
/* 2**256 (exactly) */
#define minlikelihood (1.0/twotothe256) /* 2**(-256) */
#define log_minlikelihood (-177.445678223345993274) /* log(1.0/twotothe256) */
/* The next two values are used for scaling the tree that is sketched in the
* output file.
*/
#define down 2
#define over 60
#define checkpointname "checkpoint"
#define badEval 1.0
#define badZ 0.0
#define badRear -1
#define badSigma -1.0
#define TRUE 1
#define FALSE 0
#define treeNone 0
#define treeNewick 1
#define treeProlog 2
#define treePHYLIP 3
#define treeMaxType 3
#define treeDefType treePHYLIP
#define ABS(x) (((x)<0) ? (-(x)) : (x))
#define MIN(x,y) (((x)<(y)) ? (x) : (y))
#define MAX(x,y) (((x)>(y)) ? (x) : (y))
#define LOG(x) (((x)>0) ? log(x) : hang("log domain error"))
#define NINT(x) ((int) ((x)>0 ? ((x)+0.5) : ((x)-0.5)))
#if ! Vectorize
typedef char yType;
#else
typedef int yType;
#endif
typedef int boolean;
typedef double xtype;
typedef struct likelihood_vector {
xtype a, c, g, t;
long exp;
} likelivector;
typedef struct xmantyp {
struct xmantyp *prev;
struct xmantyp *next;
struct noderec *owner;
likelivector *lv;
} xarray;
typedef struct noderec {
double z, z0;
struct noderec *next;
struct noderec *back;
int number;
xarray *x;
int xcoord, ycoord, ymin, ymax;
char name[nmlngth+1]; /* Space for null termination */
yType *tip; /* Pointer to sequence data */
} node, *nodeptr;
typedef struct {
int numsp; /* number of species (also tr->mxtips) */
int sites; /* number of input sequence positions */
yType **y; /* sequence data array */
boolean freqread; /* user base frequencies have been read */
/* To do: DNA specific values should get packaged into structure */
double freqa, freqc, freqg, freqt, /* base frequencies */
freqr, freqy, invfreqr, invfreqy,
freqar, freqcy, freqgr, freqty;
double ttratio, xi, xv, fracchange; /* transition/transversion */
/* End of DNA specific values */
int *wgt; /* weight per sequence pos */
int *wgt2; /* weight per pos (booted) */
int categs; /* number of rate categories */
double catrat[maxcategories+1]; /* rates per categories */
int *sitecat; /* category per sequence pos */
} rawdata;
typedef struct {
int *alias; /* site representing a pattern */
int *aliaswgt; /* weight by pattern */
int endsite; /* # of sequence patterns */
int wgtsum; /* sum of weights of positions */
int *patcat; /* category per pattern */
double *patrat; /* rates per pattern */
double *wr; /* weighted rate per pattern */
double *wr2; /* weight*rate**2 per pattern */
} cruncheddata;
typedef struct {
double likelihood;
double *log_f; /* info for signif. of trees */
node **nodep;
node *start;
node *outgrnode;
int mxtips;
int ntips;
int nextnode;
int opt_level;
int log_f_valid; /* log_f value sites */
int global; /* branches to cross in full tree */
int partswap; /* branches to cross in partial tree */
int outgr; /* sequence number to use in rooting tree */
boolean prelabeled; /* the possible tip names are known */
boolean smoothed;
boolean rooted;
boolean userlen; /* use user-supplied branch lengths */
rawdata *rdta; /* raw data structure */
cruncheddata *cdta; /* crunched data structure */
} tree;
typedef struct conntyp {
double z; /* branch length */
node *p, *q; /* parent and child sectors */
void *valptr; /* pointer to value of subtree */
int descend; /* pointer to first connect of child */
int sibling; /* next connect from same parent */
} connect, *connptr;
typedef struct {
double likelihood;
double *log_f; /* info for signif. of trees */
connect *links; /* pointer to first connect (start) */
node *start;
int nextlink; /* index of next available connect */
/* tr->start = tpl->links->p */
int ntips;
int nextnode;
int opt_level; /* degree of branch swapping explored */
int scrNum; /* position in sorted list of scores */
int tplNum; /* position in sorted list of trees */
int log_f_valid; /* log_f value sites */
boolean prelabeled; /* the possible tip names are known */
boolean smoothed; /* branch optimization converged? */
} topol;
typedef struct {
double best; /* highest score saved */
double worst; /* lowest score saved */
topol *start; /* starting tree for optimization */
topol **byScore;
topol **byTopol;
int nkeep; /* maximum topologies to save */
int nvalid; /* number of topologies saved */
int ninit; /* number of topologies initialized */
int numtrees; /* number of alternatives tested */
boolean improved;
} bestlist;
typedef struct {
long boot; /* bootstrap random number seed */
int extra; /* extra output information switch */
boolean empf; /* use empirical base frequencies */
boolean interleaved; /* input data are in interleaved format */
long jumble; /* jumble random number seed */
int nkeep; /* number of best trees to keep */
int numutrees; /* number of user trees to read */
boolean prdata; /* echo data to output stream */
boolean qadd; /* test addition without full smoothing */
boolean restart; /* resume addition to partial tree */
boolean root; /* use user-supplied outgroup */
boolean trprint; /* print tree to output stream */
int trout; /* write tree to "treefile" */
boolean usertree; /* use user-supplied trees */
boolean userwgt; /* use user-supplied position weight mask */
} analdef;
typedef struct {
double tipmax;
int tipy;
} drawdata;
void exit(int);
#if ANSI || MALLOC_VOID
void *malloc();
#elif !defined(__STDC__)
char *malloc();
#endif
#define Malloc(x) malloc((unsigned) (x)) /* BSD */
/* #define Malloc(x) malloc((size_t) (x)) */ /* System V */
#define Free(x) (void) free((char *) (x)) /* BSD */
/* #define Free(x) free((void *) (x)) */ /* System V */
char *likelihood_key = "likelihood";
char *ntaxa_key = "ntaxa";
char *opt_level_key = "opt_level";
char *smoothed_key = "smoothed";
#define dnaml_h
#endif /* #if undef dnaml_h */
|
