1 | #include "simcfg.h" |
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2 | #include "readcfg.h" |
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3 | #include <math.h> |
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4 | #include <stdlib.h> |
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5 | #include <string.h> |
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6 | #include "rns.h" |
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7 | |
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8 | static struct S_cfgLine cfg_lines[]; |
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9 | |
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10 | /* -------------------------------------------------------------------------- */ |
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11 | /* static int decodeFrand(str setting, void *frandPtr) */ |
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12 | /* ------------------------------------------------------ 20.05.95 18.19 ---- */ |
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13 | static int decodeFrand(str setting, void *frandPtr) |
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14 | { |
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15 | str medium = strtok(setting, " "), |
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16 | low = strtok(NULL, " "), |
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17 | high = strtok(NULL, " "); |
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18 | |
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19 | if (medium && low && high) |
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20 | { |
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21 | double med_val = atof(medium), |
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22 | low_val = atof(low), |
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23 | high_val = atof(high); |
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24 | |
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25 | if (med_val<=0.0 || med_val>=1.0) |
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26 | { |
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27 | setCfgError("The average value has to be BETWEEN 0.0 and 1.0"); |
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28 | return 0; |
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29 | } |
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30 | else |
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31 | { |
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32 | double change = fabs(low_val)+fabs(high_val); |
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33 | |
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34 | if (change>=med_val || change>=(1.0-med_val)) |
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35 | { |
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36 | setCfgError("The sum of low and high frequent part is too big and " |
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37 | "reaches one of the borders of the allowed range ]0.0, 1.1["); |
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38 | |
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39 | return 0; |
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40 | } |
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41 | } |
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42 | |
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43 | *((Frand*)frandPtr) = initFrand(med_val, low_val, high_val); |
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44 | |
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45 | return 1; |
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46 | } |
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47 | |
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48 | setCfgError("Syntax is: <meanvalue> <lowfreqpart> <highfreqpart>"); |
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49 | |
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50 | return 0; |
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51 | } |
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52 | /* -------------------------------------------------------------------------- */ |
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53 | /* static int decodeInt(str setting, void *intPtr) */ |
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54 | /* ------------------------------------------------------ 20.05.95 12.33 ---- */ |
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55 | static int decodeInt(str setting, void *intPtr) |
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56 | { |
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57 | *((int*)intPtr) = atoi(setting); |
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58 | return 1; |
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59 | } |
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60 | /* -------------------------------------------------------------------------- */ |
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61 | /* static int decodeProb(str setting, void *doublePtr) */ |
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62 | /* ------------------------------------------------------ 17.05.95 21.55 ---- */ |
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63 | static int decodeProb(str setting, void *doublePtr) |
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64 | { |
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65 | double *dptr = (double*)doublePtr; |
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66 | |
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67 | *dptr = atof(setting); |
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68 | |
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69 | if (*dptr<0.0 || *dptr>1.0) |
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70 | { |
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71 | setCfgError("Probability has to be between 0.0 and 1.0"); |
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72 | return 0; |
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73 | } |
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74 | |
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75 | return 1; |
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76 | } |
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77 | /* -------------------------------------------------------------------------- */ |
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78 | /* void readSimCfg(cstr fname) */ |
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79 | /* ------------------------------------------------------ 17.05.95 22:10 ---- */ |
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80 | void readSimCfg(cstr fname) |
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81 | { |
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82 | int lenTeiler, |
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83 | stepTeiler; |
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84 | |
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85 | if (!readCfg(fname, cfg_lines)) errorf("Error reading config '%s'", fname); |
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86 | |
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87 | lenTeiler = (int)sqrt(orgLen); |
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88 | stepTeiler = (int)sqrt(timeSteps); |
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89 | |
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90 | mrpb_Init->teiler = lenTeiler; |
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91 | l2hrpb_Init->teiler = lenTeiler; |
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92 | pairPart->teiler = stepTeiler; |
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93 | mutationRate->teiler = stepTeiler; |
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94 | splitRate->teiler = stepTeiler; |
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95 | helixGcDruck->teiler = stepTeiler; |
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96 | helixGcRate->teiler = stepTeiler; |
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97 | helixAtRate->teiler = stepTeiler; |
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98 | loopGcDruck->teiler = stepTeiler; |
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99 | loopGcRate->teiler = stepTeiler; |
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100 | loopAtRate->teiler = stepTeiler; |
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101 | } |
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102 | |
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103 | static struct S_cfgLine cfg_lines[] = |
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104 | { |
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105 | |
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106 | /* /---------------------------------------\ */ |
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107 | /* | Nur zur Initialisierung notwendig : | */ |
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108 | /* \---------------------------------------/ */ |
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109 | |
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110 | { "OriginLen", "3000", decodeInt, &orgLen, "Number of base positions in origin species" }, |
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111 | { "OriginHelixPart", "0.5", decodeProb, &orgHelixPart, "size of helical part in origin species (0.5 means 50% helix and 50% loop regions)" }, |
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112 | { "MutRatePerBase", "0.5 0.01 0.4", decodeFrand, &mrpb_Init, "mutation rate per base position (used for origin only)" }, |
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113 | { "Loop2HelixRate", "0.2 0.01 0.1", decodeFrand, &l2hrpb_Init, "loop<->helix conversion rate per base position (used for origin only)" }, |
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114 | { "TimeSteps", "50", decodeInt, &timeSteps, "number of time steps" }, |
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115 | { "TransitionRate", "0.5", decodeProb, &transitionRate, "transition rate" }, |
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116 | { "TransversionRate", "0.5", decodeProb, &transversionRate, "transversion rate" }, |
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117 | |
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118 | /* /-----------------------------------------------------------------\ */ |
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119 | /* | Parameter, welche sich whrend des Baumdurchlaufs verndern : | */ |
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120 | /* \-----------------------------------------------------------------/ */ |
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121 | |
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122 | { "PairPart", "0.85 0.1 0.01", decodeFrand, &pairPart, "part of pairing helix positions (mean value, low frequent part, high frequent part)" }, |
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123 | { "MutationRate", "0.01 0.005 0.001", decodeFrand, &mutationRate, "mutation rate" }, |
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124 | { "SplitProb", "0.2 0.1 0.01", decodeFrand, &splitRate, "split rate (split into two species)" }, |
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125 | { "Helix-GC-Pressure", "0.72 0.11 0.01", decodeFrand, &helixGcDruck, "part of G-C bonds in helical regions" }, |
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126 | { "Helix-GC-Rate", "0.5 0.001 0.001", decodeFrand, &helixGcRate, "G:C rate in helical regions" }, |
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127 | { "Helix-AT-Rate", "0.5 0.001 0.001", decodeFrand, &helixAtRate, "A:T rate in helical regions" }, |
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128 | { "Loop-GC-Pressure", "0.62 0.05 0.01", decodeFrand, &loopGcDruck, "part of G-C bonds in loop regions" }, |
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129 | { "Loop-GC-Rate", "0.5 0.001 0.001", decodeFrand, &loopGcRate, "G:C rate in loop regions" }, |
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130 | { "Loop-AT-Rate", "0.5 0.001 0.001", decodeFrand, &loopAtRate, "A:T rate in loop regions" }, |
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131 | |
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132 | /* { "", "", decode, &, "" }, */ |
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133 | |
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134 | { NULL, 0, 0, 0, 0 } |
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135 | }; |
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136 | |
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