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
|
// DNAml_rates.h
/* Compile time switches for various updates to program:
* 0 gives original version
* 1 gives new version
*/
#ifndef CXXFORWARD_H
#include <cxxforward.h>
#endif
#ifndef ARBDBT_H
#include <arbdbt.h>
#endif
#define Debug 1
// Program constants and parameters
#define maxsp 10000 // maximum number of species
#define maxsites 8000 // maximum number of sites
#define maxpatterns 8000 // max number of different site patterns
#define maxcategories 35 // maximum number of site types
#define nmlngth 10 // max. number of characters in species name
#define KI_MAX 256.0 // largest rate possible
#define RATE_STEP sqrt(sqrt(2.0)) // initial step size for rate search
#define MAX_ERROR 0.01 // max fractional error in rate calculation
#define MIN_INFO 4 // minimum number of informative sequences
#define UNDEF_CATEGORY 1 // category number to output for undefined rate
#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 unlikely -1.0E300 // low likelihood for initialization
#define decimal_point '.'
// the following macros are already defined in gmacros.h:
// #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)))
#define aint(x) ((double) ((int) (x)))
typedef double xtype;
struct node;
typedef node *nodeptr;
#if defined(Cxx11)
CONSTEXPR int MAXNODES = leafs_2_nodes(maxsp, ROOTED);
#else // !defined(Cxx11)
const int MAXNODES = 2*maxsp+1;
#endif
struct xarray {
xarray *prev;
xarray *next;
nodeptr owner;
xtype *a, *c, *g, *t;
};
struct node {
double z;
nodeptr next;
nodeptr back;
int number;
xarray *x;
int xcoord, ycoord, ymin, ymax;
char name[nmlngth+1]; // Space for null termination
char *tip; // Pointer to sequence data
};
struct tree {
double likelihood;
double log_f[maxpatterns];
nodeptr nodep[MAXNODES];
nodeptr start;
int mxtips;
int ntips;
int nextnode;
int opt_level;
bool smoothed;
bool rooted;
};
struct drawdata {
double tipmax;
int tipy;
};
|
