1 | /* RAxML-VI-HPC (version 2.2) a program for sequential and parallel estimation of phylogenetic trees |
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2 | * Copyright August 2006 by Alexandros Stamatakis |
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3 | * |
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4 | * Partially derived from |
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5 | * fastDNAml, a program for estimation of phylogenetic trees from sequences by Gary J. Olsen |
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6 | * |
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7 | * and |
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8 | * |
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9 | * Programs of the PHYLIP package by Joe Felsenstein. |
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10 | * |
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11 | * This program is free software; you may redistribute it and/or modify its |
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12 | * under the terms of the GNU General Public License as published by the Free |
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13 | * Software Foundation; either version 2 of the License, or (at your option) |
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14 | * any later version. |
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15 | * |
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16 | * This program is distributed in the hope that it will be useful, but |
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17 | * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY |
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18 | * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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19 | * for more details. |
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20 | * |
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21 | * |
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22 | * For any other enquiries send an Email to Alexandros Stamatakis |
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23 | * Alexandros.Stamatakis@epfl.ch |
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24 | * |
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25 | * When publishing work that is based on the results from RAxML-VI-HPC please cite: |
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26 | * |
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27 | * Alexandros Stamatakis:"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models". |
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28 | * Bioinformatics 2006; doi: 10.1093/bioinformatics/btl446 |
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29 | */ |
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30 | |
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31 | #ifndef WIN32 |
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32 | #include <sys/times.h> |
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33 | #include <sys/types.h> |
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34 | #include <sys/time.h> |
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35 | #include <unistd.h> |
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36 | #endif |
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37 | |
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38 | #include <math.h> |
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39 | #include <time.h> |
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40 | #include <stdlib.h> |
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41 | #include <stdio.h> |
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42 | #include <ctype.h> |
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43 | #include <string.h> |
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44 | |
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45 | #include "axml.h" |
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46 | |
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47 | extern int Thorough; |
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48 | extern infoList iList; |
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49 | extern char seq_file[1024]; |
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50 | |
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51 | |
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52 | |
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53 | |
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54 | |
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55 | |
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56 | |
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57 | |
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58 | |
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59 | |
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60 | |
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61 | void computeBOOTRAPID (tree *tr, analdef *adef, long *radiusSeed) |
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62 | { |
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63 | int i, bestTrav, impr; |
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64 | double lh, previousLh, difference, epsilon; |
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65 | bestlist *bestT, *bt; |
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66 | int countIT; |
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67 | |
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68 | bestT = (bestlist *) rax_malloc(sizeof(bestlist)); |
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69 | bestT->ninit = 0; |
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70 | initBestTree(bestT, 1, tr->mxtips); |
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71 | saveBestTree(bestT, tr); |
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72 | |
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73 | bt = (bestlist *) rax_malloc(sizeof(bestlist)); |
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74 | bt->ninit = 0; |
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75 | initBestTree(bt, 5, tr->mxtips); |
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76 | |
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77 | initInfoList(10); |
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78 | |
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79 | difference = 10.0; |
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80 | epsilon = 0.01; |
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81 | |
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82 | bestTrav = adef->bestTrav = 5 + 11 * randum(radiusSeed); |
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83 | |
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84 | Thorough = 1; |
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85 | |
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86 | impr = 1; |
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87 | |
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88 | if(tr->doCutoff) |
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89 | tr->itCount = 0; |
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90 | |
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91 | tr->bigCutoff = TRUE; |
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92 | |
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93 | for(countIT = 0; countIT < 2 && impr; countIT++) |
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94 | { |
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95 | recallBestTree(bestT, 1, tr); |
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96 | treeEvaluate(tr, 1); |
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97 | saveBestTree(bestT, tr); |
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98 | |
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99 | lh = previousLh = tr->likelihood; |
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100 | |
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101 | treeOptimizeRapid(tr, 1, bestTrav, adef, bt); |
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102 | |
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103 | impr = 0; |
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104 | |
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105 | for(i = 1; i <= bt->nvalid; i++) |
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106 | { |
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107 | recallBestTree(bt, i, tr); |
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108 | |
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109 | |
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110 | treeEvaluate(tr, 0.25); |
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111 | |
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112 | difference = ((tr->likelihood > previousLh)? |
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113 | tr->likelihood - previousLh: |
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114 | previousLh - tr->likelihood); |
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115 | if(tr->likelihood > lh && difference > epsilon) |
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116 | { |
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117 | impr = 1; |
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118 | lh = tr->likelihood; |
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119 | saveBestTree(bestT, tr); |
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120 | } |
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121 | } |
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122 | |
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123 | } |
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124 | |
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125 | tr->bigCutoff = FALSE; |
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126 | |
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127 | recallBestTree(bestT, 1, tr); |
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128 | freeBestTree(bestT); |
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129 | rax_free(bestT); |
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130 | freeBestTree(bt); |
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131 | rax_free(bt); |
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132 | freeInfoList(); |
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133 | } |
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134 | |
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135 | |
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136 | |
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137 | |
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138 | |
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139 | |
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140 | |
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141 | void optimizeRAPID(tree *tr, analdef *adef) |
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142 | { |
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143 | int i, impr, bestTrav; |
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144 | |
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145 | double lh, previousLh, difference, epsilon; |
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146 | bestlist *bestT, *bt; |
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147 | |
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148 | bestT = (bestlist *) rax_malloc(sizeof(bestlist)); |
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149 | bestT->ninit = 0; |
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150 | initBestTree(bestT, 1, tr->mxtips); |
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151 | |
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152 | bt = (bestlist *) rax_malloc(sizeof(bestlist)); |
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153 | bt->ninit = 0; |
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154 | initBestTree(bt, 20, tr->mxtips); |
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155 | |
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156 | initInfoList(50); |
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157 | |
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158 | difference = 10.0; |
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159 | epsilon = 0.01; |
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160 | |
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161 | Thorough = 0; |
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162 | |
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163 | |
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164 | |
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165 | saveBestTree(bestT, tr); |
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166 | bestTrav = adef->bestTrav = determineRearrangementSetting(tr, adef, bestT, bt); |
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167 | saveBestTree(bestT, tr); |
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168 | |
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169 | impr = 1; |
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170 | if(tr->doCutoff) |
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171 | tr->itCount = 0; |
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172 | |
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173 | while(impr) |
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174 | { |
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175 | recallBestTree(bestT, 1, tr); |
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176 | treeEvaluate(tr, 1); |
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177 | |
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178 | |
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179 | saveBestTree(bestT, tr); |
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180 | |
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181 | lh = previousLh = tr->likelihood; |
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182 | |
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183 | treeOptimizeRapid(tr, 1, bestTrav, adef, bt); |
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184 | |
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185 | impr = 0; |
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186 | |
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187 | for(i = 1; i <= bt->nvalid; i++) |
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188 | { |
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189 | recallBestTree(bt, i, tr); |
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190 | treeEvaluate(tr, 0.25); |
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191 | |
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192 | difference = ((tr->likelihood > previousLh)? |
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193 | tr->likelihood - previousLh: |
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194 | previousLh - tr->likelihood); |
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195 | if(tr->likelihood > lh && difference > epsilon) |
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196 | { |
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197 | impr = 1; |
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198 | lh = tr->likelihood; |
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199 | saveBestTree(bestT, tr); |
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200 | } |
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201 | } |
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202 | } |
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203 | |
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204 | recallBestTree(bestT, 1, tr); |
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205 | freeBestTree(bestT); |
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206 | rax_free(bestT); |
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207 | freeBestTree(bt); |
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208 | rax_free(bt); |
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209 | freeInfoList(); |
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210 | } |
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211 | |
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212 | |
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213 | |
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214 | void thoroughOptimization(tree *tr, analdef *adef, topolRELL_LIST *rl, int index) |
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215 | { |
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216 | int i, impr; |
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217 | int rearrangementsMin = 1, rearrangementsMax = adef->stepwidth; |
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218 | double lh, previousLh, difference, epsilon; |
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219 | bestlist *bestT, *bt; |
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220 | |
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221 | bestT = (bestlist *) rax_malloc(sizeof(bestlist)); |
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222 | bestT->ninit = 0; |
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223 | initBestTree(bestT, 1, tr->mxtips); |
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224 | |
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225 | bt = (bestlist *) rax_malloc(sizeof(bestlist)); |
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226 | bt->ninit = 0; |
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227 | initBestTree(bt, 20, tr->mxtips); |
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228 | |
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229 | initInfoList(50); |
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230 | |
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231 | difference = 10.0; |
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232 | epsilon = 0.01; |
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233 | |
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234 | |
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235 | saveBestTree(bestT, tr); |
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236 | |
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237 | impr = 1; |
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238 | if(tr->doCutoff) |
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239 | tr->itCount = 0; |
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240 | |
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241 | Thorough = 1; |
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242 | impr = 1; |
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243 | |
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244 | while(1) |
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245 | { |
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246 | recallBestTree(bestT, 1, tr); |
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247 | if(impr) |
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248 | { |
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249 | rearrangementsMin = 1; |
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250 | rearrangementsMax = adef->stepwidth; |
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251 | } |
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252 | else |
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253 | { |
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254 | rearrangementsMax += adef->stepwidth; |
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255 | rearrangementsMin += adef->stepwidth; |
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256 | if(rearrangementsMax > adef->max_rearrange) |
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257 | goto cleanup; |
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258 | } |
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259 | |
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260 | treeEvaluate(tr, 1.0); |
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261 | previousLh = lh = tr->likelihood; |
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262 | saveBestTree(bestT, tr); |
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263 | |
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264 | treeOptimizeRapid(tr, rearrangementsMin, rearrangementsMax, adef, bt); |
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265 | |
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266 | impr = 0; |
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267 | |
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268 | for(i = 1; i <= bt->nvalid; i++) |
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269 | { |
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270 | recallBestTree(bt, i, tr); |
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271 | |
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272 | treeEvaluate(tr, 0.25); |
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273 | |
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274 | difference = ((tr->likelihood > previousLh)? |
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275 | tr->likelihood - previousLh: |
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276 | previousLh - tr->likelihood); |
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277 | if(tr->likelihood > lh && difference > epsilon) |
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278 | { |
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279 | impr = 1; |
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280 | lh = tr->likelihood; |
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281 | saveBestTree(bestT, tr); |
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282 | } |
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283 | } |
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284 | |
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285 | |
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286 | } |
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287 | |
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288 | cleanup: |
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289 | saveTL(rl, tr, index); |
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290 | freeBestTree(bestT); |
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291 | rax_free(bestT); |
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292 | freeBestTree(bt); |
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293 | rax_free(bt); |
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294 | freeInfoList(); |
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295 | } |
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296 | |
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297 | |
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298 | |
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299 | |
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300 | /*********************************************************************************************************************/ |
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301 | |
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302 | |
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303 | |
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304 | |
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305 | |
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306 | |
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307 | |
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308 | |
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309 | |
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310 | |
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311 | static boolean qupdate (tree *tr, nodeptr p) |
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312 | { |
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313 | nodeptr q; |
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314 | double z0[NUM_BRANCHES], z[NUM_BRANCHES]; |
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315 | int i; |
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316 | |
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317 | q = p->back; |
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318 | for(i = 0; i < tr->numBranches; i++) |
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319 | z0[i] = q->z[i]; |
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320 | |
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321 | makenewzGeneric(tr, p, q, z0, 1, z, FALSE); |
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322 | |
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323 | for(i = 0; i < tr->numBranches; i++) |
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324 | p->z[i] = q->z[i] = z[i]; |
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325 | |
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326 | return TRUE; |
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327 | } |
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328 | |
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329 | |
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330 | |
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331 | |
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332 | |
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333 | static boolean qsmoothLocal(tree *tr, nodeptr p, int n) |
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334 | { |
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335 | nodeptr q; |
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336 | |
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337 | if(n == 0) |
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338 | return TRUE; |
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339 | else |
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340 | { |
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341 | if (! qupdate(tr, p)) return FALSE; /* Adjust branch */ |
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342 | if (!isTip(p->number, tr->rdta->numsp)) |
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343 | { /* Adjust descendants */ |
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344 | q = p->next; |
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345 | while (q != p) |
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346 | { |
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347 | if (! qsmoothLocal(tr, q->back, n - 1)) return FALSE; |
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348 | q = q->next; |
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349 | } |
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350 | |
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351 | newviewGeneric(tr, p); |
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352 | } |
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353 | |
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354 | return TRUE; |
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355 | } |
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356 | } |
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357 | |
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358 | static void quickSmoothLocal(tree *tr, int n) |
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359 | { |
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360 | nodeptr p = tr->insertNode; |
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361 | nodeptr q; |
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362 | |
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363 | if(n == 0) |
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364 | { |
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365 | evaluateGeneric(tr, p); |
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366 | } |
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367 | else |
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368 | { |
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369 | qsmoothLocal(tr, p->back, n - 1); |
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370 | if(!isTip(p->number, tr->rdta->numsp)) |
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371 | { |
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372 | q = p->next; |
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373 | while(q != p) |
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374 | { |
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375 | qsmoothLocal(tr, q->back, n - 1); |
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376 | q = q->next; |
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377 | } |
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378 | } |
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379 | evaluateGeneric(tr, p); |
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380 | } |
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381 | } |
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382 | |
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383 | |
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384 | |
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385 | |
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386 | int treeOptimizeThorough(tree *tr, int mintrav, int maxtrav) |
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387 | { |
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388 | int i; |
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389 | bestlist *bestT; |
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390 | |
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391 | nodeRectifier(tr); |
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392 | |
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393 | bestT = (bestlist *) rax_malloc(sizeof(bestlist)); |
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394 | bestT->ninit = 0; |
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395 | initBestTree(bestT, 1, tr->mxtips); |
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396 | |
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397 | if (maxtrav > tr->ntips - 3) |
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398 | maxtrav = tr->ntips - 3; |
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399 | |
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400 | tr->startLH = tr->endLH = tr->likelihood; |
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401 | |
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402 | for(i = 1; i <= tr->mxtips + tr->mxtips - 2; i++) |
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403 | { |
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404 | |
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405 | |
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406 | tr->bestOfNode = unlikely; |
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407 | if(rearrangeBIG(tr, tr->nodep[i], mintrav, maxtrav)) |
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408 | { |
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409 | |
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410 | if((tr->endLH > tr->startLH) && (tr->bestOfNode != unlikely)) |
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411 | { |
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412 | restoreTreeFast(tr); |
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413 | quickSmoothLocal(tr, 3); |
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414 | tr->startLH = tr->endLH = tr->likelihood; |
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415 | } |
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416 | else |
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417 | { |
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418 | if(tr->bestOfNode != unlikely) |
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419 | { |
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420 | resetBestTree(bestT); |
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421 | saveBestTree(bestT, tr); |
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422 | restoreTreeFast(tr); |
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423 | quickSmoothLocal(tr, 3); |
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424 | if(tr->likelihood < tr->startLH) |
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425 | { |
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426 | int res; |
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427 | res = recallBestTree(bestT, 1, tr); |
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428 | assert(res > 0); |
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429 | } |
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430 | else |
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431 | tr->startLH = tr->endLH = tr->likelihood; |
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432 | } |
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433 | } |
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434 | } |
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435 | |
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436 | |
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437 | } |
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438 | |
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439 | freeBestTree(bestT); |
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440 | rax_free(bestT); |
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441 | |
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442 | return 1; |
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443 | } |
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