1 /* These constants can be changed if necessary */
2 #define NMLNGTH    10        /* required # of characters in sequence name */
3 #define iters      50        /* how hard to try to estimate theta */
4 #define menu       true      /* are we using the menu? */
5 #define epsilon    0.0000001 /* a small number */
6 #define thetaout   false     /* create "thetafile" with running tally
7                                   of theta estimates? */
8 #define onebestree true      /* "true" = only single bestree in file "bestree"
9                                 "false" = running tally of bestrees in file
10                                 "bestree" */
11 #define MINTHETA   0.00001     /* low end of table */
12 #define MAXTHETA   10.0      /* high end of table */
13 #define THETALID   1000.0     /* maximum allowable theta */
14 #define GLID       100000.0   /* maximum allowable g */
15 #define EXPMIN    -40.0      /* minimum value of "x" in "exp(x)" */
16 #define EXPMAX     200.0     /* maximum value of "x" in "exp(x)" */
17 #define EPSILON    10e-50    /* a really small number */
18 #define REPEAT_TOLERANCE 50   /* how many times (sequentially) should the
19                                 exact same prior-likelihood value be
20                                 encountered in point estimation before
21                                 giving up.
22                                 ALSO
23                                 how many times do we reset huge growth */
24 
25 /* these constants are used only in dealing with the changing population
26    size */
27 #define LHOP_TOLERANCE 10e-5 /* when to start using an approximation in
28                                 calculating likelihoods; the +tolerance
29                                 is the upper bound and -tolerance the lower */
30 
31 /* The following program constants should not be changed */
32 #define point        "."
33 #define rootlength   10000       /* length of root branch must be much
34                                     larger than the total height of the
35                                     tree */
36 #define LINESIZE     128         /* this is actually (maximum linesize)+1
37                                     because of trailing '\0' */
38 #define NUMBOOL       10         /* number of boolean tokens in parameter
39                                     file */
40 #define NUMNUMBER      8         /* number of numeric (double) tokens in
41                                     parameter file */
42 #define POSMAX       DBL_MAX     /* largest positive number */
43 #define NEGMAX  -(DBL_MAX - 1.0) /* smallest negative number */
44 #define NUM_TYPE_CHAINS 2        /* number of different kinds of chains */
45 #define NUMPARAMETERS   2        /* number of parameters of interest */
46 #define baseA          0
47 #define baseC          1
48 #define baseG          2
49 #define baseT          3
50