simcfg.c File Reference

#include "readcfg.h"
#include "rns.h"
#include <math.h>
#include <stdlib.h>
#include <string.h>

Include dependency graph for simcfg.c:

Go to the source code of this file.

Functions
static int	decodeFrand (str setting, void *frandPtr)
static int	decodeInt (str setting, void *intPtr)
static int	decodeProb (str setting, void *doublePtr)
void	readSimCfg (cstr fname)

Variables
static struct S_cfgLine	cfg_lines []

Function Documentation

static int decodeFrand ( str  setting, void *  frandPtr  )

static

Definition at line 10 of file simcfg.c.

References initFrand(), and setCfgError().

static int decodeInt ( str  setting, void *  intPtr  )

static

Definition at line 44 of file simcfg.c.

static int decodeProb ( str  setting, void *  doublePtr  )

static

Definition at line 48 of file simcfg.c.

References setCfgError().

void readSimCfg

(

cstr

fname

)

Definition at line 60 of file simcfg.c.

References cfg_lines, errorf(), helixAtRate, helixGcDruck, helixGcRate, l2hrpb_Init, loopAtRate, loopGcDruck, loopGcRate, mrpb_Init, mutationRate, orgLen, pairPart, readCfg(), splitRate, S_Frand::teiler, and timeSteps.

Referenced by ARB_main().

Variable Documentation

static struct S_cfgLine cfg_lines

static

Initial value:

= {

    
    

    { "OriginLen",          "3000",             decodeInt,          &orgLen,            "Number of base positions in origin species" },
    { "OriginHelixPart",    "0.5",              decodeProb,         &orgHelixPart,      "size of helical part in origin species (0.5 means 50% helix and 50% loop regions)" },
    { "MutRatePerBase",     "0.5 0.01 0.4",     decodeFrand,        &mrpb_Init,         "mutation rate per base position (used for origin only)" },
    { "Loop2HelixRate",     "0.2 0.01 0.1",     decodeFrand,        &l2hrpb_Init,       "loop<->helix conversion rate per base position (used for origin only)" },
    { "TimeSteps",          "50",               decodeInt,          &timeSteps,         "number of time steps" },
    { "TransitionRate",     "0.5",              decodeProb,         &transitionRate,    "transition rate" },
    { "TransversionRate",   "0.5",              decodeProb,         &transversionRate,  "transversion rate" },

    
    

    { "PairPart",           "0.85 0.1 0.01",    decodeFrand,        &pairPart,          "part of pairing helix positions (mean value, low frequent part, high frequent part)" },
    { "MutationRate",       "0.01 0.005 0.001", decodeFrand,        &mutationRate,      "mutation rate" },
    { "SplitProb",          "0.2 0.1 0.01",     decodeFrand,        &splitRate,         "split rate (split into two species)" },
    { "Helix-GC-Pressure",  "0.72 0.11 0.01",   decodeFrand,        &helixGcDruck,      "part of G-C bonds in helical regions" },
    { "Helix-GC-Rate",      "0.5 0.001 0.001",  decodeFrand,        &helixGcRate,       "G:C rate in helical regions" },
    { "Helix-AT-Rate",      "0.5 0.001 0.001",  decodeFrand,        &helixAtRate,       "A:T rate in helical regions" },
    { "Loop-GC-Pressure",   "0.62 0.05 0.01",   decodeFrand,        &loopGcDruck,       "part of G-C bonds in loop regions" },
    { "Loop-GC-Rate",       "0.5 0.001 0.001",  decodeFrand,        &loopGcRate,        "G:C rate in loop regions" },
    { "Loop-AT-Rate",       "0.5 0.001 0.001",  decodeFrand,        &loopAtRate,        "A:T rate in loop regions" },

    { NULL, 0, 0, 0, 0 }
}

Definition at line 8 of file simcfg.c.

Referenced by readSimCfg().