source: tags/arb-6.0/TOOLS/DNAml_rates_1_0.h

Last change on this file was 12313, checked in by westram, 8 years ago
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File size: 2.4 KB
Line 
1//  DNAml_rates.h
2
3/*  Compile time switches for various updates to program:
4 *    0 gives original version
5 *    1 gives new version
6 */
7
8#ifndef CXXFORWARD_H
9#include <cxxforward.h>
10#endif
11#ifndef ARBDBT_H
12#include <arbdbt.h>
13#endif
14
15#define Debug 1
16
17//  Program constants and parameters
18
19#define maxsp         10000  // maximum number of species
20#define maxsites      8000  // maximum number of sites
21#define maxpatterns   8000  // max number of different site patterns
22#define maxcategories   35  // maximum number of site types
23#define nmlngth         10  // max. number of characters in species name
24#define KI_MAX       256.0  // largest rate possible
25#define RATE_STEP sqrt(sqrt(2.0)) // initial step size for rate search
26#define MAX_ERROR     0.01  // max fractional error in rate calculation
27#define MIN_INFO         4  // minimum number of informative sequences
28#define UNDEF_CATEGORY   1  // category number to output for undefined rate
29#define zmin       1.0E-15  // max branch prop. to -log(zmin) (= 34)
30#define zmax (1.0 - 1.0E-6) // min branch prop. to 1.0-zmax (= 1.0E-6)
31#define unlikely  -1.0E300  // low likelihood for initialization
32#define decimal_point   '.'
33
34// the following macros are already defined in gmacros.h:
35// #define ABS(x)    (((x)< 0)  ? -(x) : (x))
36// #define MIN(x, y) (((x)<(y)) ?  (x) : (y))
37// #define MAX(x, y) (((x)>(y)) ?  (x) : (y))
38#define LOG(x)    (((x)> 0) ? log(x) : hang("log domain error"))
39#define nint(x)   ((int) ((x)>0 ? ((x)+0.5) : ((x)-0.5)))
40#define aint(x)   ((double) ((int) (x)))
41
42
43typedef double  xtype;
44struct          node;
45typedef node   *nodeptr;
46
47#if defined(Cxx11)
48CONSTEXPR int MAXNODES = leafs_2_nodes(maxsp, ROOTED);
49#else // !defined(Cxx11)
50const int MAXNODES = 2*maxsp+1;
51#endif
52
53struct xarray {
54    xarray  *prev;
55    xarray  *next;
56    nodeptr  owner;
57    xtype   *a, *c, *g, *t;
58};
59
60struct node {
61    double   z;
62    nodeptr  next;
63    nodeptr  back;
64    int      number;
65    xarray  *x;
66    int      xcoord, ycoord, ymin, ymax;
67    char     name[nmlngth+1];             //  Space for null termination
68    char    *tip;                         //  Pointer to sequence data
69};
70
71
72struct tree {
73    double  likelihood;
74    double  log_f[maxpatterns];
75    nodeptr nodep[MAXNODES];
76    nodeptr start;
77    int     mxtips;
78    int     ntips;
79    int     nextnode;
80    int     opt_level;
81    bool    smoothed;
82    bool    rooted;
83};
84
85struct drawdata {
86    double tipmax;
87    int    tipy;
88};
89
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