1 | /* |
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2 | * |
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3 | * ********************************************************************* |
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4 | * (C) COPYRIGHT 1995 UNIVERSITY OF CHICAGO |
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5 | * ********************************************************************* |
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6 | * |
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7 | * This software was authored by |
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8 | * |
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9 | * D. Levine |
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10 | * Mathematics and Computer Science Division Argonne National Laboratory |
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11 | * Argonne IL 60439 |
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12 | * levine@mcs.anl.gov |
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13 | * (708) 252-6735 |
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14 | * (708) 252-5986 (FAX) |
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15 | * |
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16 | * with programming assistance of participants in Argonne National |
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17 | * Laboratory's SERS program. |
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18 | * |
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19 | * This program contains material protectable under copyright laws of the |
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20 | * United States. Permission is hereby granted to use it, reproduce it, |
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21 | * to translate it into another language, and to redistribute it to |
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22 | * others at no charge except a fee for transferring a copy, provided |
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23 | * that you conspicuously and appropriately publish on each copy the |
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24 | * University of Chicago's copyright notice, and the disclaimer of |
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25 | * warranty and Government license included below. Further, permission |
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26 | * is hereby granted, subject to the same provisions, to modify a copy or |
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27 | * copies or any portion of it, and to distribute to others at no charge |
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28 | * materials containing or derived from the material. |
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29 | * |
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30 | * The developers of the software ask that you acknowledge its use in any |
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31 | * document referencing work based on the program, such as published |
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32 | * research. Also, they ask that you supply to Argonne National |
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33 | * Laboratory a copy of any published research referencing work based on |
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34 | * the software. |
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35 | * |
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36 | * Any entity desiring permission for further use must contact: |
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37 | * |
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38 | * J. Gleeson |
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39 | * Industrial Technology Development Center Argonne National Laboratory |
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40 | * Argonne IL 60439 |
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41 | * gleesonj@smtplink.eid.anl.gov |
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42 | * (708) 252-6055 |
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43 | * |
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44 | * ******************************************************************** |
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45 | * DISCLAIMER |
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46 | * |
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47 | * THIS PROGRAM WAS PREPARED AS AN ACCOUNT OF WORK SPONSORED BY AN AGENCY |
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48 | * OF THE UNITED STATES GOVERNMENT. NEITHER THE UNIVERSITY OF CHICAGO, |
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49 | * THE UNITED STATES GOVERNMENT NOR ANY OF THEIR EMPLOYEES MAKE ANY |
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50 | * WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR |
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51 | * RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY |
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52 | * INFORMATION OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT |
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53 | * INFRINGE PRIVATELY OWNED RIGHTS. |
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54 | * |
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55 | * ********************************************************************** |
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56 | * GOVERNMENT LICENSE |
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57 | * |
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58 | * The Government is granted for itself and others acting on its behalf a |
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59 | * paid-up, non-exclusive, irrevocable worldwide license in this computer |
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60 | * software to reproduce, prepare derivative works, and perform publicly |
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61 | * and display publicly. |
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62 | */ |
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63 | |
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64 | /***************************************************************************** |
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65 | * File: mutation.c: This file contains the data structure neutral mutation |
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66 | * routines |
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67 | * |
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68 | * Authors: David M. Levine, Philip L. Hallstrom, David M. Noelle, |
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69 | * Brian P. Walenz |
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70 | *****************************************************************************/ |
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71 | |
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72 | #include "pgapack.h" |
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73 | |
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74 | /*U**************************************************************************** |
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75 | PGAMutate - This routine performs mutation on a string. The type of mutation |
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76 | depends on the data type. Refer to the user guide for data-specific |
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77 | examples. |
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78 | |
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79 | Category: Operators |
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80 | |
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81 | Inputs: |
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82 | ctx - context variable |
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83 | p - index of string to mutate |
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84 | pop - symbolic constant of the population containing p |
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85 | |
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86 | Output: |
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87 | The number of mutations performed. Member p in population pop is |
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88 | mutated by side-effect. |
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89 | |
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90 | Example: |
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91 | Mutate the best string in the population, until 10 or more mutations |
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92 | have occured. |
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93 | |
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94 | PGAContext *ctx; |
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95 | int p, count = 0; |
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96 | : |
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97 | p = PGAGetBestIndex(ctx, PGA_NEWPOP); |
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98 | while (count < 10) { |
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99 | count += PGAMutate(ctx, p, PGA_NEWPOP); |
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100 | } |
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101 | |
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102 | ****************************************************************************U*/ |
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103 | int PGAMutate(PGAContext *ctx, int p, int pop) |
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104 | { |
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105 | double mr; |
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106 | int count; |
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107 | int fp; |
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108 | PGADebugEntered("PGAMutate"); |
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109 | |
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110 | mr = ctx->ga.MutationProb; |
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111 | if (ctx->fops.Mutation) { |
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112 | fp = ((p == PGA_TEMP1) || (p == PGA_TEMP2)) ? p : p+1; |
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113 | count = (*ctx->fops.Mutation)(&ctx, &fp, &pop, &mr); |
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114 | } else { |
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115 | count = (*ctx->cops.Mutation)( ctx, p, pop, mr ); |
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116 | } |
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117 | |
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118 | if ( count > 0 ) |
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119 | PGASetEvaluationUpToDateFlag(ctx, p, pop, PGA_FALSE); |
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120 | |
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121 | PGADebugExited("PGAMutate"); |
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122 | |
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123 | return(count); |
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124 | } |
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125 | |
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126 | /*U**************************************************************************** |
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127 | PGASetMutationType - set type of mutation to use. Only effects integer- |
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128 | and real-valued strings. Binary-valued strings are always complemented. |
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129 | In character-valued strings, one alphabetic character is replaced with |
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130 | another chosen uniformly randomly. The alphabetic characters will be lower, |
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131 | upper, or mixed case depending on how the strings were initialized. |
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132 | |
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133 | Valid choices are PGA_MUTATION_CONSTANT (Real/Integer), PGA_MUTATION_RANGE |
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134 | (Real/Integer), PGA_MUTATION_UNIFORM (Real), PGA_MUTATION_GAUSSIAN (Real), |
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135 | and PGA_MUTATION_PERMUTE (Integer). The default for integer-valued strings |
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136 | conforms to how the strings were initialized. The default for real-valued |
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137 | strings is PGA_MUTATION_GAUSSIAN. See the user guide for more details. |
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138 | |
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139 | Category: Operators |
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140 | |
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141 | Inputs: |
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142 | ctx - context variable |
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143 | mutation_type - symbolic constant to specify the mutation type |
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144 | |
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145 | Outputs: |
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146 | None |
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147 | |
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148 | Example: |
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149 | PGAContext *ctx; |
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150 | : |
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151 | PGASetMutationType(ctx, PGA_MUTATION_UNIFORM); |
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152 | |
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153 | ****************************************************************************U*/ |
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154 | void PGASetMutationType( PGAContext *ctx, int mutation_type) |
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155 | { |
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156 | PGADebugEntered("PGASetMutationType"); |
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157 | |
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158 | switch (mutation_type) |
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159 | { |
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160 | case PGA_MUTATION_CONSTANT: |
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161 | case PGA_MUTATION_RANGE: |
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162 | case PGA_MUTATION_UNIFORM: |
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163 | case PGA_MUTATION_GAUSSIAN: |
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164 | case PGA_MUTATION_PERMUTE: |
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165 | ctx->ga.MutationType = mutation_type; |
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166 | break; |
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167 | default: |
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168 | PGAError ( ctx, |
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169 | "PGASetMutationType: Invalid value of mutation_type:", |
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170 | PGA_FATAL, PGA_INT, (void *) &mutation_type); |
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171 | break; |
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172 | } |
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173 | |
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174 | PGADebugExited("PGASetMutationType"); |
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175 | } |
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176 | |
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177 | /*U*************************************************************************** |
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178 | PGAGetMutationType - Returns the type of mutation used |
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179 | |
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180 | Category: Operators |
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181 | |
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182 | Inputs: |
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183 | ctx - context variable |
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184 | |
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185 | Outputs: |
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186 | Returns the integer corresponding to the symbolic constant |
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187 | used to specify the type of mutation specified |
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188 | |
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189 | Example: |
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190 | PGAContext *ctx; |
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191 | int mutatetype; |
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192 | : |
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193 | mutatetype = PGAGetMutationType(ctx); |
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194 | switch (mutatetype) { |
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195 | case PGA_MUTATION_CONSTANT: |
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196 | printf("Mutation Type = PGA_MUTATION_CONSTANT\n"); |
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197 | break; |
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198 | case PGA_MUTATION_RANGE: |
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199 | printf("Mutation Type = PGA_MUTATION_RANGE\n"); |
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200 | break; |
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201 | case PGA_MUTATION_UNIFORM: |
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202 | printf("Mutation Type = PGA_MUTATION_UNIFORM\n"); |
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203 | break; |
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204 | case PGA_MUTATION_GAUSSIAN: |
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205 | printf("Mutation Type = PGA_MUTATION_GAUSSIAN\n"); |
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206 | break; |
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207 | case PGA_MUTATION_PERMUTE: |
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208 | printf("Mutation Type = PGA_MUTATION_PERMUTE\n"); |
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209 | break; |
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210 | } |
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211 | |
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212 | ***************************************************************************U*/ |
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213 | int PGAGetMutationType (PGAContext *ctx) |
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214 | { |
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215 | PGADebugEntered("PGAGetMutationType"); |
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216 | PGAFailIfNotSetUp("PGAGetMutationType"); |
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217 | PGADebugExited("PGAGetMutationType"); |
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218 | return(ctx->ga.MutationType); |
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219 | } |
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220 | |
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221 | /*U**************************************************************************** |
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222 | PGASetMutationRealValue - Set multiplier to mutate PGA_DATATYPE_REAL |
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223 | strings with. The use of this value depends on the type of mutation |
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224 | being used. The default value is 0.1. See the user guide for more details. |
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225 | |
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226 | Category: Operators |
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227 | |
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228 | Inputs: |
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229 | ctx - context variable |
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230 | val - the mutation value to use for Real mutation |
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231 | |
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232 | Outputs: |
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233 | None |
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234 | |
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235 | Example: |
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236 | PGAContext *ctx; |
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237 | : |
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238 | PGASetMutationRealValue(ctx,50.0); |
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239 | |
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240 | ****************************************************************************U*/ |
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241 | void PGASetMutationRealValue( PGAContext *ctx, double val) |
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242 | { |
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243 | PGADebugEntered("PGASetMutationRealValue"); |
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244 | |
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245 | if (val < 0.0) |
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246 | PGAError ( ctx, |
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247 | "PGASetMutationRealValue: Invalid value of val:", |
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248 | PGA_FATAL, PGA_DOUBLE, (void *) &val); |
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249 | else |
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250 | ctx->ga.MutateRealValue = val; |
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251 | |
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252 | PGADebugExited("PGASetMutationRealValue"); |
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253 | } |
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254 | |
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255 | /*U*************************************************************************** |
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256 | PGAGetMutationRealValue - Returns the value of the multiplier used to |
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257 | mutate PGA_DATATYPE_REAL strings with. |
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258 | |
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259 | Category: Operators |
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260 | |
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261 | Inputs: |
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262 | ctx - context variable |
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263 | |
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264 | Outputs: |
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265 | The value of the multiplier used to mutate PGA_DATATYPE_REAL strings with |
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266 | |
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267 | Example: |
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268 | PGAContext *ctx; |
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269 | double val; |
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270 | : |
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271 | val = PGAGetMutationRealValue(ctx); |
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272 | |
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273 | ***************************************************************************U*/ |
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274 | double PGAGetMutationRealValue (PGAContext *ctx) |
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275 | { |
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276 | PGADebugEntered("PGAGetMutationRealValue"); |
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277 | PGAFailIfNotSetUp("PGAGetMutationRealValue"); |
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278 | |
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279 | PGADebugExited("PGAGetMutationRealValue"); |
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280 | |
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281 | return(ctx->ga.MutateRealValue); |
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282 | } |
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283 | |
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284 | /*U**************************************************************************** |
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285 | PGASetMutationIntegerValue - Set multiplier to mutate PGA_DATATYPE_INTEGER |
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286 | strings with. The use of this value depends on the type of mutation |
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287 | being used. The default value is 1. See the user guide for more details. |
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288 | |
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289 | Category: Operators |
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290 | |
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291 | Inputs: |
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292 | ctx - context variable |
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293 | val - the mutation value to use for Integer mutation |
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294 | |
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295 | Outputs: |
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296 | None |
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297 | |
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298 | Example: |
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299 | PGAContext *ctx; |
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300 | : |
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301 | PGASetMutationIntegerValue(ctx, 5); |
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302 | |
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303 | ****************************************************************************U*/ |
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304 | void PGASetMutationIntegerValue( PGAContext *ctx, int val) |
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305 | { |
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306 | PGADebugEntered("PGASetMutationIntegerValue"); |
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307 | |
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308 | if (val < 0.0) |
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309 | PGAError ( ctx, |
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310 | "PGASetMutationIntegerValue: Invalid value of val:", |
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311 | PGA_FATAL, PGA_DOUBLE, (void *) &val); |
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312 | else |
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313 | ctx->ga.MutateIntegerValue = val; |
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314 | |
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315 | PGADebugExited("PGASetMutationIntegerValue"); |
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316 | } |
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317 | |
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318 | |
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319 | /*U*************************************************************************** |
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320 | PGAGetMutationIntegerValue - Returns the value of the multiplier |
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321 | used to mutate PGA_DATATYPE_INTEGER strings with. |
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322 | |
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323 | Category: Operators |
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324 | |
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325 | Inputs: |
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326 | ctx - context variable |
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327 | |
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328 | Outputs: |
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329 | The value of the multiplier used to mutate PGA_DATATYPE_INTEGER |
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330 | strings with |
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331 | |
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332 | Example: |
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333 | PGAContext *ctx; |
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334 | int ival; |
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335 | : |
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336 | ival = PGAGetMutationIntegerValue(ctx); |
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337 | |
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338 | ***************************************************************************U*/ |
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339 | int PGAGetMutationIntegerValue (PGAContext *ctx) |
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340 | { |
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341 | PGADebugEntered("PGAGetMutationIntegerValue"); |
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342 | PGAFailIfNotSetUp("PGAGetMutationIntegerValue"); |
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343 | |
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344 | PGADebugExited("PGAGetMutationIntegerValue"); |
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345 | |
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346 | return(ctx->ga.MutateIntegerValue); |
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347 | } |
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348 | |
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349 | /*U**************************************************************************** |
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350 | PGASetMutationBoundedFlag - If this flag is set to PGA_TRUE, then for |
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351 | Integer and Real strings whenever a gene is mutated, if it underflows |
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352 | (overflows) the lower (upper)bound it is reset to the lower (upper) bound. |
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353 | In this way all allele values remain within the range the integer strings |
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354 | were initialized on. If this flag is PGA_FALSE (the default), the alleles |
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355 | may take any values. |
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356 | |
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357 | Category: Operators |
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358 | |
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359 | Inputs: |
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360 | ctx - context variable |
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361 | flag - either PGA_TRUE or PGA_FALSE |
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362 | |
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363 | Outputs: |
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364 | None |
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365 | |
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366 | Example: |
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367 | PGAContext *ctx; |
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368 | : |
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369 | PGASetMutationBoundedFlag(ctx, PGA_TRUE); |
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370 | |
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371 | ****************************************************************************U*/ |
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372 | void PGASetMutationBoundedFlag(PGAContext *ctx, int val) |
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373 | { |
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374 | PGADebugEntered("PGASetMutationBoundedFlag"); |
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375 | |
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376 | switch (val) |
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377 | { |
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378 | case PGA_TRUE: |
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379 | case PGA_FALSE: |
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380 | ctx->ga.MutateBoundedFlag = val; |
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381 | break; |
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382 | default: |
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383 | PGAError(ctx, "PGASetMutationBoundedFlag: Invalid value:", |
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384 | PGA_FATAL, PGA_INT, (void *) &val); |
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385 | break; |
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386 | } |
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387 | |
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388 | PGADebugExited("PGASetMutationBoundedFlag"); |
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389 | } |
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390 | |
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391 | |
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392 | /*U**************************************************************************** |
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393 | PGAGetMutationBoundedFlag - returns PGA_TRUE or PGA_FALSE to indicate |
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394 | whether mutated integer strings remain in the range specified when |
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395 | initialized with PGASetIntegerInitRange. |
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396 | |
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397 | Category: Operators |
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398 | |
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399 | Inputs: |
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400 | ctx - context variable |
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401 | |
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402 | Outputs: |
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403 | PGA_TRUE if restricted to the given range, otherwise PGA_FALSE. |
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404 | |
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405 | Example: |
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406 | PGAContext *ctx; |
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407 | int val; |
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408 | : |
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409 | val = PGAGetMutationBoundedFlag(ctx); |
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410 | |
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411 | ****************************************************************************U*/ |
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412 | int PGAGetMutationBoundedFlag(PGAContext *ctx) |
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413 | { |
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414 | PGADebugEntered ("PGAGetMutationBoundedFlag"); |
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415 | PGAFailIfNotSetUp("PGAGetMutationBoundedFlag"); |
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416 | PGADebugExited ("PGAGetMutationBoundedFlag"); |
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417 | return (ctx->ga.MutateBoundedFlag); |
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418 | } |
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419 | |
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420 | |
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421 | |
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422 | /*U**************************************************************************** |
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423 | PGASetMutationProb - Specifies the probability that a given allele will |
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424 | be mutated. If this is called without calling PGASetMutationType(), the |
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425 | default mutation type is PGA_MUTATION_FIXED. The default probability is |
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426 | the reciprocal of the string length. |
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427 | |
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428 | Category: Operators |
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429 | |
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430 | Inputs: |
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431 | ctx - context variable |
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432 | p - the mutation probability |
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433 | |
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434 | Outputs: |
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435 | None |
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436 | |
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437 | Example: |
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438 | PGAContext *ctx; |
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439 | : |
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440 | PGASetMutationProb(ctx,0.001); |
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441 | |
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442 | ****************************************************************************U*/ |
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443 | void PGASetMutationProb(PGAContext *ctx, double mutation_prob) |
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444 | { |
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445 | PGADebugEntered("PGASetMutationProb"); |
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446 | |
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447 | if ((mutation_prob < 0.0) || (mutation_prob > 1.0)) |
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448 | PGAError ( ctx, |
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449 | "PGASetMutationProb: Invalid value of mutation_prob:", |
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450 | PGA_FATAL, PGA_DOUBLE, (void *) &mutation_prob); |
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451 | else |
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452 | ctx->ga.MutationProb = mutation_prob; |
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453 | |
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454 | PGADebugExited("PGASetMutationProb"); |
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455 | } |
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456 | |
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457 | /*U*************************************************************************** |
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458 | PGAGetMutationProb - Returns the probability of mutation. |
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459 | |
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460 | Category: Operators |
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461 | |
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462 | Inputs: |
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463 | ctx - context variable |
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464 | |
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465 | Outputs: |
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466 | The mutation probability |
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467 | |
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468 | Example: |
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469 | PGAContext *ctx; |
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470 | double pm; |
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471 | : |
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472 | pm = PGAGetMutateProb(ctx); |
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473 | |
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474 | ***************************************************************************U*/ |
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475 | double PGAGetMutationProb (PGAContext *ctx) |
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476 | { |
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477 | PGADebugEntered("PGAGetMutationProb"); |
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478 | PGAFailIfNotSetUp("PGAGetMutationProb"); |
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479 | PGADebugExited("PGAGetMutationProb"); |
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480 | return(ctx->ga.MutationProb); |
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481 | } |
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