1 | /* |
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2 | |
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3 | PHYML : a program that computes maximum likelihood phylogenies from |
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4 | DNA or AA homologous sequences |
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5 | |
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6 | Copyright (C) Stephane Guindon. Oct 2003 onward |
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7 | |
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8 | All parts of the source except where indicated are distributed under |
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9 | the GNU public licence. See http://www.opensource.org for details. |
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10 | |
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11 | */ |
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12 | |
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13 | #include "utilities.h" |
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14 | #include "options.h" |
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15 | #include "models.h" |
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16 | #include "free.h" |
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17 | |
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18 | /* int T_MAX_FILE; */ |
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19 | /* double MDBL_MIN; */ |
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20 | /* double UNLIKELY; */ |
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21 | |
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22 | #define BOLD "\033[00;01m" |
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23 | #define FLAT "\033[00;00m" |
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24 | #define LINE "\033[00;04m" |
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25 | |
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26 | /*********************************************************/ |
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27 | |
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28 | void Usage() |
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29 | { |
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30 | printf(BOLD"NAME\n" |
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31 | FLAT"\tphyml\n" |
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32 | FLAT"\tA simple, fast, and accurate algorithm to estimate\n" |
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33 | FLAT"\tlarge phylogenies by maximum likelihood.\n\n" |
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34 | FLAT"\tStephane Guindon and Olivier Gascuel,\n" |
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35 | FLAT"\tSystematic Biology 52(5):696-704, 2003.\n" |
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36 | FLAT"\tPlease cite this paper if you use this software in your publications.\n"); |
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37 | |
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38 | printf(BOLD"\nCOMMAND-LINE USE\n" |
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39 | BOLD"\tphyml "FLAT"[ " |
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40 | LINE"sequences"FLAT" " |
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41 | LINE"data_type"FLAT" " |
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42 | LINE"format"FLAT" " |
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43 | LINE"data_sets"FLAT" " |
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44 | LINE"bootstrap_sets"FLAT" " |
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45 | LINE"model"FLAT" " |
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46 | LINE"\n\t\t[kappa]"FLAT" " |
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47 | LINE"invar"FLAT" " |
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48 | LINE"nb_categ"FLAT" " |
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49 | LINE"alpha"FLAT" " |
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50 | LINE"tree"FLAT" " |
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51 | LINE"opt_topology"FLAT" " |
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52 | LINE"opt_lengths"FLAT" " |
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53 | "]\n"); |
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54 | |
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55 | printf(FLAT"\n\tYou can use phyml with no arguments, in this case change the value of\n" |
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56 | FLAT"\ta parameter by typing its corresponding character as shown on screen.\n\n" |
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57 | FLAT"\tYou can alternatively use phyml with the following arguments :\n"); |
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58 | |
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59 | printf(LINE"\n\tsequence_file" |
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60 | FLAT"\tDNA or Amino-Acids sequence filename (PHYLIP format)\n" |
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61 | |
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62 | LINE"\n\tdata type" |
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63 | FLAT"\t"BOLD"0"FLAT" = DNA | "BOLD"1"FLAT" = Amino-Acids\n" |
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64 | |
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65 | LINE"\n\tformat" |
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66 | FLAT"\t\t"BOLD"i"FLAT" = interleaved sequence format | " |
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67 | BOLD"s"FLAT" = sequential\n" |
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68 | |
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69 | LINE"\n\tdata_sets" |
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70 | FLAT"\tnumber of data sets to analyse (ex:3)\n" |
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71 | |
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72 | LINE"\n\tbootstrap_sets" |
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73 | FLAT"\tnumber of bootstrap data sets to generate (ex:2)\n" |
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74 | FLAT"\t\t\tonly works with one data set to analyse\n" |
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75 | |
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76 | LINE"\n\tmodel" |
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77 | FLAT"\t\tsubstitution model name\n" |
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78 | BOLD"\t\t\tJC69 | K2P | F81 | HKY | F84 | TN93 | GTR "FLAT"(DNA)\n" |
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79 | BOLD"\t\t\tJTT | MtREV | Dayhoff | WAG "FLAT"(Amino-Acids)\n" |
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80 | |
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81 | LINE"\n\tkappa" |
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82 | FLAT"\t\ttransition/transversion ratio, only for DNA sequences,\n" |
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83 | FLAT"\t\t\ta fixed value (ex:4.0) | "BOLD"e"FLAT" to get the maximum likelihood estimate\n" |
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84 | |
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85 | LINE"\n\tinvar" |
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86 | FLAT"\t\tproportion of invariable sites,\n" |
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87 | FLAT"\t\t\ta fixed value (ex:0.0) | "BOLD"e"FLAT" to get the maximum likelihood estimate\n" |
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88 | |
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89 | LINE"\n\tnb_categ" |
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90 | FLAT"\tnumber of relative substitution rate categories (ex:4)\n" |
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91 | |
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92 | LINE"\n\talpha" |
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93 | FLAT"\t\tgamma distribution parameter,\n" |
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94 | FLAT"\t\t\ta fixed value (ex:1.0) | "BOLD"e"FLAT" to get the maximum likelihood estimate\n" |
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95 | |
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96 | LINE"\n\ttree" |
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97 | FLAT"\t\tstarting tree filename (Newick format),\n" |
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98 | FLAT"\t\t\tyour tree filename | "BOLD"BIONJ"FLAT" for a distance-based tree\n" |
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99 | |
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100 | LINE"\n\topt_topology" |
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101 | FLAT"\toptimise tree topology ? "BOLD"y | n\n" |
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102 | |
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103 | LINE"\n\topt_lengths" |
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104 | FLAT"\toptimise branch lengths and rate parameters ? "BOLD"y | n\n"); |
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105 | |
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106 | printf( FLAT"\n\tExamples\n" |
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107 | FLAT"\tDNA sequences : "BOLD" ./phyml seqs1 0 i 2 0 HKY 4.0 e 1 1.0 BIONJ y n \n" |
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108 | FLAT"\n\tAA sequences : "BOLD" ./phyml seqs2 1 i 1 5 JTT 0.0 4 1.0 BIONJ n n \n"FLAT); |
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109 | Exit(""); |
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110 | } |
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111 | |
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112 | /*********************************************************/ |
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113 | |
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114 | #define N_SEQUENCEFILE 1 |
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115 | #define N_DATATYPE 2 |
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116 | #define N_FORMAT 3 |
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117 | #define N_DATASETS 4 |
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118 | #define N_BOOTSTRAPSETS 5 |
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119 | #define N_MODELNAME 6 |
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120 | #define N_KAPPA 7 |
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121 | #define N_PROPORTIONINVAR 7 /*same as kappa*/ |
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122 | #define N_NBCATG 8 |
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123 | #define N_ALPHA 9 |
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124 | #define N_STARTINGTREE 10 |
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125 | #define N_OPT_TOPO 11 |
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126 | #define N_OPT_LENGTHSRATES 12 |
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127 | |
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128 | #define N_NB_PARAMS_DNA 13 |
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129 | #define N_NB_PARAMS_AA 12 |
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130 | |
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131 | option *Get_Input(int argc, char **argv) |
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132 | { |
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133 | |
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134 | option* input = (option *)mCalloc(1,sizeof(option)); |
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135 | putchar('\n'); |
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136 | |
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137 | input->fp_seq = NULL; |
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138 | input->fp_input_tree = NULL; |
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139 | input->mod = Make_Model_Basic(); |
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140 | input->seqfile = (char *)mCalloc(T_MAX_FILE,sizeof(char)); |
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141 | input->modelname = (char *)mCalloc(50,sizeof(char)); |
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142 | input->nt_or_cd = (char *)mCalloc(50,sizeof(char)); |
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143 | input->inputtreefile = (char *)mCalloc(T_MAX_FILE,sizeof(char)); |
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144 | input->phyml_tree_file = (char *)mCalloc(T_MAX_FILE,sizeof(char)); |
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145 | input->phyml_stat_file = (char *)mCalloc(T_MAX_FILE,sizeof(char)); |
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146 | input->phyml_lk_file = (char *)mCalloc(T_MAX_FILE,sizeof(char)); |
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147 | |
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148 | |
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149 | Set_Defaults_Input(input); |
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150 | Set_Defaults_Model(input->mod); |
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151 | Set_Defaults_Optimiz(input->mod->s_opt); |
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152 | |
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153 | Translate_Custom_Mod_String(input->mod); |
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154 | Init_Optimiz(input->mod->s_opt); |
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155 | |
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156 | switch (argc) |
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157 | { |
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158 | case 1: |
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159 | Get_Input_Interactive(input); |
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160 | break; |
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161 | case 2: |
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162 | Usage(); |
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163 | break; |
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164 | default: |
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165 | if (isdigit((int)argv[N_DATATYPE][0])) |
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166 | { |
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167 | if (atoi(argv[N_DATATYPE])==0 && argc-1==N_NB_PARAMS_DNA) |
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168 | Get_Input_CommandLine_DNA(input, argc, argv); |
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169 | else if (atoi(argv[N_DATATYPE])==1 && argc-1==N_NB_PARAMS_AA) |
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170 | Get_Input_CommandLine_AA(input, argc, argv); |
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171 | else |
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172 | Usage(); |
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173 | } |
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174 | else |
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175 | Usage(); |
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176 | } |
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177 | |
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178 | /*print the parameter values*/ |
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179 | printf("\n\n\n"); |
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180 | |
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181 | printf("Sequence filename : \t\t\t\t %s\n", input->seqfile); |
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182 | |
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183 | printf("Data type : \t\t\t %s\n", (input->mod->datatype ? "aa" : "dna")); |
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184 | |
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185 | printf("Sequence format : \t\t\t\t %s\n", input->interleaved ? "interleaved" : "sequential"); |
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186 | |
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187 | printf("Number of data sets : \t\t\t\t %d\n", input->n_data_sets); |
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188 | |
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189 | printf("Nb of bootstrapped data sets : \t\t\t %d\n", input->mod->bootstrap); |
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190 | |
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191 | printf("Model name : \t\t\t\t\t %s\n", input->modelname); |
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192 | |
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193 | if (input->mod->datatype == NT) { |
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194 | if (input->mod->s_opt->opt_kappa) |
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195 | printf("ts/tv ratio : \t\t\t\t\t estimated\n"); |
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196 | else |
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197 | { |
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198 | if ((input->mod->whichmodel == 2)|| |
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199 | (input->mod->whichmodel == 4)|| |
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200 | (input->mod->whichmodel == 5)|| |
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201 | (input->mod->whichmodel == 6)) |
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202 | printf("ts/tv ratio : \t\t\t\t\t %f\n", input->mod->kappa); |
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203 | } |
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204 | } |
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205 | |
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206 | if (input->mod->s_opt->opt_pinvar) |
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207 | printf("Proportion of invariable sites :\t\t estimated\n"); |
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208 | else |
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209 | printf("Proportion of invariable sites :\t\t %f\n", input->mod->pinvar); |
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210 | |
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211 | printf("Number of subst. rate categs : \t\t\t %d\n", input->mod->n_catg); |
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212 | |
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213 | if (input->mod->s_opt->opt_alpha) |
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214 | printf("Gamma distribution parameter : \t\t\t estimated\n"); |
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215 | else |
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216 | printf("Gamma distribution parameter : \t\t\t %f\n", input->mod->alpha); |
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217 | |
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218 | printf("Starting tree : \t\t\t\t %s\n", (!input->inputtree) ? "BIONJ" : input->inputtreefile); |
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219 | |
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220 | printf("Optimise tree topology : \t\t\t %s\n", (input->mod->s_opt->opt_topo) ? "yes" : "no"); |
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221 | |
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222 | printf("Optimise branch lengths and rate parameters : \t %s\n", (input->mod->s_opt->opt_free_param) ? "yes" : "no"); |
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223 | |
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224 | |
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225 | return input; |
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226 | } |
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227 | |
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228 | |
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229 | |
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230 | void Get_Input_CommandLine_Common(option *input, int argc, char **argv) |
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231 | { |
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232 | (void)argc; // suppress warning |
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233 | char* p; |
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234 | |
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235 | |
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236 | |
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237 | p = argv[N_SEQUENCEFILE]; |
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238 | |
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239 | |
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240 | #ifdef PHYML |
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241 | |
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242 | strcpy(input->seqfile, p); |
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243 | input->fp_seq = Openfile(input->seqfile,0); |
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244 | |
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245 | #endif |
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246 | |
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247 | |
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248 | input->phyml_stat_file_open_mode = 1; /* stands for the "R" (Replacement) interactive option */ |
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249 | |
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250 | input->phyml_tree_file_open_mode = 1; /* stands for the "R" (Replacement) interactive option */ |
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251 | |
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252 | |
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253 | #ifdef PHYML |
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254 | strcpy(input->phyml_stat_file,input->seqfile); |
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255 | strcat(input->phyml_stat_file,"_phyml_stat.txt"); |
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256 | |
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257 | strcpy(input->phyml_tree_file,input->seqfile); |
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258 | strcat(input->phyml_tree_file,"_phyml_tree.txt"); |
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259 | |
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260 | strcpy(input->phyml_lk_file,input->seqfile); |
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261 | strcat(input->phyml_lk_file,"_phyml_lk.txt"); |
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262 | #endif |
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263 | |
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264 | |
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265 | |
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266 | p = argv[N_FORMAT]; |
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267 | input->interleaved = (!strcmp(p,"i")) ? 1 : 0; |
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268 | |
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269 | |
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270 | p = argv[N_DATASETS]; |
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271 | if (!atoi(p) || (input->n_data_sets = atoi(p)) < 0) |
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272 | Exit("\nThe number of data sets should be a positive integer\n"); |
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273 | |
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274 | |
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275 | p = argv[N_BOOTSTRAPSETS]; |
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276 | if ((input->mod->bootstrap = atoi(p)) < 0) |
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277 | Exit("\nThe number of bootstrapped data sets should be a positive or null integer\n"); |
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278 | |
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279 | if(!input->mod->bootstrap) |
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280 | { |
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281 | input->print_boot_trees = 0; |
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282 | input->fp_boot_tree = NULL; |
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283 | input->fp_boot_stats = NULL; |
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284 | |
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285 | } |
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286 | else |
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287 | { |
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288 | char *r; |
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289 | r = (char *)mCalloc(T_MAX_LINE, sizeof(char)); |
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290 | strcpy(r,input->seqfile); |
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291 | input->print_boot_trees = 1; |
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292 | input->fp_boot_tree = Openfile(strcat(r,"_phyml_boot_trees.txt"),1); |
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293 | strcpy(r,input->seqfile); |
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294 | input->fp_boot_stats = Openfile(strcat(r,"_phyml_boot_stats.txt"),1); |
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295 | Free(r); |
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296 | } |
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297 | |
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298 | |
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299 | p = argv[N_PROPORTIONINVAR]; |
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300 | if (!strcmp(p,"e")) |
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301 | { |
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302 | input->mod->s_opt->opt_pinvar = 1; |
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303 | input->mod->pinvar = 0.2; |
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304 | input->mod->invar = 1; |
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305 | } |
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306 | else |
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307 | { |
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308 | if((atof(p) < 0.0) || (atof(p) > 1.0)) |
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309 | { |
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310 | Exit("\nErr : the proportion of invariable sites must be a positive number between 0.0 and 1.0\n"); |
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311 | } |
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312 | else |
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313 | { |
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314 | input->mod->s_opt->opt_pinvar = 0; |
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315 | input->mod->pinvar = (double)atof(p); |
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316 | input->mod->invar = (input->mod->pinvar > 0.0+MDBL_MIN) ? 1 : 0; |
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317 | } |
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318 | } |
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319 | |
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320 | |
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321 | p = argv[N_NBCATG]; |
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322 | if (!atoi(p) || (input->mod->n_catg = atoi(p)) < 0) |
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323 | Exit("\nThe number of categories should be a positive integer\n"); |
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324 | |
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325 | |
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326 | p = argv[N_ALPHA]; |
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327 | if (!strcmp(p,"e")) |
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328 | { |
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329 | input->mod->s_opt->opt_alpha = 1; |
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330 | } |
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331 | else |
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332 | { |
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333 | input->mod->s_opt->opt_alpha = 0; |
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334 | input->mod->alpha = 1.0; |
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335 | |
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336 | if(!atof(p) || (input->mod->alpha = (double)atof(p)) < .0) |
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337 | Exit("\nAlpha must be a positive number\n"); |
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338 | } |
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339 | |
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340 | |
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341 | p = argv[N_STARTINGTREE]; |
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342 | if (!strcmp(p,"BIONJ")) |
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343 | { |
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344 | input->inputtree = 0; |
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345 | } |
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346 | else |
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347 | { |
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348 | input->inputtree = 1; |
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349 | strcpy(input->inputtreefile, p); |
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350 | input->fp_input_tree = Openfile(input->inputtreefile,0); |
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351 | } |
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352 | |
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353 | |
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354 | p = argv[N_OPT_TOPO]; |
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355 | input->mod->s_opt->opt_topo = (!strcmp(p,"y")) ? 1 : 0; |
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356 | |
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357 | |
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358 | p = argv[N_OPT_LENGTHSRATES]; |
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359 | input->mod->s_opt->opt_free_param = (!strcmp(p,"y")) ? 1 : 0; |
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360 | |
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361 | } |
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362 | |
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363 | /*Attention phyml compilé avec les symboles de compilation EVOLVE et OPTIMIZ n'est utilisable qu'en mode interactif */ |
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364 | void Get_Input_CommandLine_DNA(option *input, int argc, char **argv) |
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365 | { |
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366 | char* p; |
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367 | |
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368 | /*convert into AA syntax to have a common code with the AA case*/ |
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369 | char** argvbis; |
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370 | int i; |
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371 | char kappa[30]; |
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372 | model *mod; |
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373 | |
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374 | |
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375 | mod = input->mod; |
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376 | |
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377 | |
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378 | argvbis = (char**)calloc(argc-1, sizeof(char*)); |
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379 | for (i=0; i<N_KAPPA; i++) |
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380 | { |
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381 | argvbis[i] = (char*)malloc(T_MAX_FILE); |
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382 | strcpy(argvbis[i], argv[i]); |
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383 | } |
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384 | strcpy(kappa, argv[N_KAPPA]); |
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385 | for (i=N_KAPPA; i<argc-1; i++) |
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386 | { |
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387 | argvbis[i] = (char*)malloc(T_MAX_FILE); |
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388 | strcpy(argvbis[i], argv[i+1]); |
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389 | } |
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390 | |
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391 | Get_Input_CommandLine_Common(input, argc-1, argvbis); /*argv must not change*/ |
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392 | |
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393 | |
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394 | input->mod->datatype = 0; |
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395 | |
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396 | |
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397 | p = argvbis[N_MODELNAME]; |
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398 | strcpy(input->modelname, p); |
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399 | if (!strcmp(p,"JC69")) mod->whichmodel = 1; |
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400 | else if (!strcmp(p,"K2P")) mod->whichmodel = 2; |
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401 | else if (!strcmp(p,"F81")) mod->whichmodel = 3; |
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402 | else if (!strcmp(p,"HKY")) mod->whichmodel = 4; |
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403 | else if (!strcmp(p,"F84")) mod->whichmodel = 5; |
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404 | else if (!strcmp(p,"TN93")) mod->whichmodel = 6; |
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405 | else if (!strcmp(p,"GTR")) mod->whichmodel = 7; |
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406 | |
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407 | else Exit("\nUnknown model \n"); |
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408 | |
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409 | mod->ns = 4; |
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410 | |
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411 | p = kappa; |
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412 | if (!strcmp(p,"e")) |
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413 | { |
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414 | mod->s_opt->opt_kappa = 1; |
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415 | mod->kappa = 4.0; |
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416 | |
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417 | if(mod->whichmodel == 6) |
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418 | mod->s_opt->opt_lambda = 1; |
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419 | if((mod->whichmodel == 1) || |
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420 | (mod->whichmodel == 3) || |
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421 | (mod->whichmodel == 7) || |
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422 | (mod->whichmodel == 8)) |
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423 | mod->s_opt->opt_kappa = 0; |
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424 | } |
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425 | else |
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426 | { |
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427 | mod->s_opt->opt_kappa = 0; |
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428 | mod->s_opt->opt_lambda = 0; |
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429 | |
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430 | if(!atof(p) || (mod->kappa = (double)atof(p)) < .0) |
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431 | Exit("\nThe ts/tv ratio should be a positive number\n"); |
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432 | } |
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433 | |
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434 | |
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435 | if( |
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436 | (mod->whichmodel == 1) || |
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437 | (mod->whichmodel == 3) || |
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438 | (mod->whichmodel == 7) || |
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439 | (mod->whichmodel == 8)) |
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440 | { |
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441 | mod->s_opt->opt_kappa = 0; |
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442 | mod->s_opt->opt_lambda = 0; |
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443 | } |
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444 | |
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445 | if(mod->whichmodel != 6) mod->s_opt->opt_lambda = 0; |
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446 | |
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447 | |
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448 | for (i=0; i<argc-1; i++) |
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449 | free(argvbis[i]); |
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450 | free(argvbis); |
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451 | } |
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452 | |
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453 | |
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454 | /*Attention phyml compilé avec les symboles de compilation EVOLVE et OPTIMIZ n'est utilisable qu'en mode interactif */ |
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455 | void Get_Input_CommandLine_AA(option *input, int argc, char **argv) |
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456 | { |
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457 | char* p; |
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458 | |
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459 | Get_Input_CommandLine_Common(input, argc, argv); |
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460 | |
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461 | input->mod->datatype = 1; |
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462 | |
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463 | |
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464 | p = argv[N_MODELNAME]; |
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465 | strcpy(input->modelname, p); |
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466 | if (!strcmp(p,"Dayhoff")) input->mod->whichmodel = 11; |
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467 | else if (!strcmp(p,"JTT")) input->mod->whichmodel = 12; |
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468 | else if (!strcmp(p,"MtREV")) input->mod->whichmodel = 13; |
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469 | else if (!strcmp(p,"WAG")) input->mod->whichmodel = 14; |
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470 | else if (!strcmp(p,"DCMut")) input->mod->whichmodel = 15; |
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471 | else if (!strcmp(p,"RtREV")) input->mod->whichmodel = 16; |
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472 | else if (!strcmp(p,"CpREV")) input->mod->whichmodel = 17; |
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473 | else if (!strcmp(p,"VT")) input->mod->whichmodel = 18; |
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474 | else if (!strcmp(p,"Blosum62"))input->mod->whichmodel = 19; |
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475 | else if (!strcmp(p,"MtMam")) input->mod->whichmodel = 20; |
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476 | else Exit("\nUnknown model name\n"); |
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477 | |
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478 | input->mod->ns = 20; |
---|
479 | |
---|
480 | if(input->mod->whichmodel != 6) input->mod->s_opt->opt_lambda = 0; |
---|
481 | } |
---|
482 | |
---|
483 | void Get_Input_Interactive(option *input) |
---|
484 | { |
---|
485 | char choix; |
---|
486 | char *s = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
487 | char *buff = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
488 | int n_trial; |
---|
489 | |
---|
490 | #ifdef EVOLVE |
---|
491 | |
---|
492 | char *n_data_sets; |
---|
493 | |
---|
494 | printf("Enter the tree file name > "); fflush(NULL); |
---|
495 | Getstring_Stdin(input->inputtreefile); |
---|
496 | input->fp_input_tree = Openfile(input->inputtreefile,0); |
---|
497 | printf("\n"); |
---|
498 | |
---|
499 | printf("Enter the reference sequence file name > "); fflush(NULL); |
---|
500 | Getstring_Stdin(input->seqfile); |
---|
501 | input->fp_seq = Openfile(input->seqfile,0); |
---|
502 | printf("\n"); |
---|
503 | |
---|
504 | printf("Number of data sets > "); |
---|
505 | n_data_sets = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
506 | Getstring_Stdin(n_data_sets); |
---|
507 | n_trial = 0; |
---|
508 | while((!atoi(n_data_sets)) || (atoi(n_data_sets) < 0)) |
---|
509 | { |
---|
510 | if(++n_trial > 10) Exit("\nErr : the number of sets must be a positive integer\n"); |
---|
511 | printf("\nThe number of sets must be a positive integer\n"); |
---|
512 | printf("Enter a new value > "); |
---|
513 | Getstring_Stdin(n_data_sets); |
---|
514 | } |
---|
515 | input->n_data_set_asked = atoi(n_data_sets); |
---|
516 | Free(n_data_sets); |
---|
517 | |
---|
518 | #elif OPTIMIZ |
---|
519 | |
---|
520 | printf("Enter the tree file name > "); fflush(NULL); |
---|
521 | Getstring_Stdin(input->inputtreefile); |
---|
522 | input->fp_input_tree = Openfile(input->inputtreefile,0); |
---|
523 | printf("\n"); |
---|
524 | |
---|
525 | printf("Enter the reference sequence file name > "); fflush(NULL); |
---|
526 | Getstring_Stdin(input->seqfile); |
---|
527 | input->fp_seq = Openfile(input->seqfile,0); |
---|
528 | printf("\n"); |
---|
529 | |
---|
530 | #elif PHYML |
---|
531 | |
---|
532 | printf("Enter the sequence file name > "); fflush(NULL); |
---|
533 | Getstring_Stdin(input->seqfile); |
---|
534 | input->fp_seq = Openfile(input->seqfile,0); |
---|
535 | |
---|
536 | #endif |
---|
537 | |
---|
538 | |
---|
539 | #ifdef PHYML |
---|
540 | strcpy(input->phyml_stat_file,input->seqfile); |
---|
541 | strcat(input->phyml_stat_file,"_phyml_stat.txt"); |
---|
542 | |
---|
543 | strcpy(input->phyml_tree_file,input->seqfile); |
---|
544 | strcat(input->phyml_tree_file,"_phyml_tree.txt"); |
---|
545 | |
---|
546 | strcpy(input->phyml_lk_file,input->seqfile); |
---|
547 | strcat(input->phyml_lk_file,"_phyml_lk.txt"); |
---|
548 | #endif |
---|
549 | |
---|
550 | |
---|
551 | #ifdef WIN32 |
---|
552 | #ifdef EVOLVE |
---|
553 | if(Filexists("evolve_out.txt")); |
---|
554 | #elif OPTIMIZ |
---|
555 | if(Filexists("optimiz_out.txt")) |
---|
556 | #elif PHYML |
---|
557 | if(Filexists(input->phyml_stat_file)) |
---|
558 | #endif |
---|
559 | #elif UNIX |
---|
560 | #ifdef EVOLVE |
---|
561 | if(Filexists("evolve_out")); |
---|
562 | #elif OPTIMIZ |
---|
563 | if(Filexists("optimiz_out")) |
---|
564 | #elif PHYML |
---|
565 | if(Filexists(input->phyml_stat_file)) |
---|
566 | #endif |
---|
567 | #endif |
---|
568 | { |
---|
569 | printf("\n"); |
---|
570 | #ifdef EVOLVE |
---|
571 | printf("A file 'evolve_out' already exists\n"); |
---|
572 | #elif OPTIMIZ |
---|
573 | printf("A file 'optimiz_out' already exists\n"); |
---|
574 | #elif PHYML |
---|
575 | printf("A file '%s' already exists\n",input->phyml_stat_file); |
---|
576 | #endif |
---|
577 | printf("Do you want to Replace it or Append to it ?\n"); |
---|
578 | n_trial = 0; |
---|
579 | do |
---|
580 | { |
---|
581 | printf("Please type R or A > "); |
---|
582 | scanf("%c",&choix); |
---|
583 | if(choix == '\n') choix = 'r'; |
---|
584 | else getchar(); |
---|
585 | if(++n_trial>10) Exit("\n"); |
---|
586 | Uppercase(&choix); |
---|
587 | } |
---|
588 | while((choix != 'R') && (choix != 'A')); |
---|
589 | if(choix == 'R') input->phyml_stat_file_open_mode = 1; |
---|
590 | else input->phyml_stat_file_open_mode = 2; |
---|
591 | } |
---|
592 | |
---|
593 | #ifdef WIN32 |
---|
594 | #ifdef EVOLVE |
---|
595 | if(Filexists("evolve_seq.txt")) |
---|
596 | #elif OPTIMIZ |
---|
597 | if(Filexists("optimiz_tree.txt")) |
---|
598 | #elif PHYML |
---|
599 | if(Filexists(input->phyml_tree_file)) |
---|
600 | #endif |
---|
601 | #elif UNIX |
---|
602 | #ifdef EVOLVE |
---|
603 | if(Filexists("evolve_seq")) |
---|
604 | #elif OPTIMIZ |
---|
605 | if(Filexists("optimiz_tree")) |
---|
606 | #elif PHYML |
---|
607 | if(Filexists(input->phyml_tree_file)) |
---|
608 | #endif |
---|
609 | #endif |
---|
610 | { |
---|
611 | printf("\n"); |
---|
612 | #ifdef EVOLVE |
---|
613 | printf("A file 'evolve_seq' already exists\n"); |
---|
614 | #elif OPTIMIZ |
---|
615 | printf("A file 'optimiz_tree' already exists\n"); |
---|
616 | #elif PHYML |
---|
617 | printf("A file '%s' already exists\n",input->phyml_tree_file); |
---|
618 | #endif |
---|
619 | printf("Do you want to Replace it or Append to it ?\n"); |
---|
620 | n_trial = 0; |
---|
621 | do |
---|
622 | { |
---|
623 | printf("Please type R or A > "); |
---|
624 | scanf("%c",&choix); |
---|
625 | if(choix == '\n') choix = 'X'; |
---|
626 | else getchar(); |
---|
627 | Uppercase(&choix); |
---|
628 | if(++n_trial>10) Exit("\n"); |
---|
629 | } |
---|
630 | while((choix != 'R') && (choix != 'A')); |
---|
631 | if(choix == 'R') input->phyml_tree_file_open_mode = 1; |
---|
632 | else input->phyml_tree_file_open_mode = 2; |
---|
633 | } |
---|
634 | |
---|
635 | choix = 0; |
---|
636 | |
---|
637 | |
---|
638 | do |
---|
639 | { |
---|
640 | #ifdef WIN32 |
---|
641 | system("cls"); |
---|
642 | #elif UNIX |
---|
643 | printf("\033[2J\033[H"); |
---|
644 | #endif |
---|
645 | |
---|
646 | |
---|
647 | #ifdef EVOLVE |
---|
648 | printf("\n - EVOLVE - \n\n\n"); |
---|
649 | #elif OPTIMIZ |
---|
650 | printf("\n - OPTIMIZ - \n\n\n"); |
---|
651 | #elif PHYML |
---|
652 | printf("\n - PHYML %s - \n\n\n",VERSION); |
---|
653 | #endif |
---|
654 | |
---|
655 | printf("Settings for this run:\n\n"); |
---|
656 | |
---|
657 | |
---|
658 | printf(" D " |
---|
659 | " Data type (DNA/AA) " |
---|
660 | " %-15s \n", |
---|
661 | (input->mod->datatype)?("AA"):("DNA")); |
---|
662 | |
---|
663 | |
---|
664 | printf(" I " |
---|
665 | " Input sequences interleaved (or sequential) " |
---|
666 | " %-15s \n", |
---|
667 | (input->interleaved)?("interleaved"):("sequential")); |
---|
668 | |
---|
669 | |
---|
670 | strcpy(s,""); |
---|
671 | sprintf(s," (%d sets)",input->n_data_sets); |
---|
672 | strcpy(buff,(input->n_data_sets > 1)?("yes"):("no")); |
---|
673 | buff=strcat(buff,(input->n_data_sets > 1)?(s):("\0")); |
---|
674 | printf(" S " |
---|
675 | " Analyze multiple data sets " |
---|
676 | " %-15s \n",buff); |
---|
677 | |
---|
678 | strcpy(buff,(input->mod->bootstrap > 0)?("yes"):("no")); |
---|
679 | if(input->mod->bootstrap > 0) sprintf(buff+strlen(buff)," (%d replicate%s)", |
---|
680 | input->mod->bootstrap, |
---|
681 | (input->mod->bootstrap>1)?("s"):("")); |
---|
682 | |
---|
683 | printf(" B " |
---|
684 | " Non parametric bootstrap analysis " |
---|
685 | " %-15s \n",buff); |
---|
686 | |
---|
687 | if (input->mod->datatype == NT) |
---|
688 | { |
---|
689 | if(!strcmp(input->nt_or_cd,"nucleotides")) |
---|
690 | { |
---|
691 | printf(" M " |
---|
692 | " Model of nucleotide substitution " |
---|
693 | " %-15s \n", input->modelname); |
---|
694 | |
---|
695 | if((input->mod->whichmodel < 8) && (input->mod->whichmodel > 2)) |
---|
696 | printf(" E " |
---|
697 | " Base frequency estimates (empirical/ML) " |
---|
698 | " %-15s \n", |
---|
699 | (input->mod->s_opt->opt_bfreq)?("ML"):("empirical")); |
---|
700 | |
---|
701 | else if(input->mod->whichmodel == 8) |
---|
702 | { |
---|
703 | |
---|
704 | printf(" E " |
---|
705 | " Optimise equilibrium frequencies " |
---|
706 | " %-15s \n", |
---|
707 | (input->mod->s_opt->opt_bfreq)?("yes"):("no")); |
---|
708 | |
---|
709 | } |
---|
710 | |
---|
711 | |
---|
712 | if(input->mod->whichmodel == 8) |
---|
713 | { |
---|
714 | printf(" F " |
---|
715 | " Equilibrium frequencies " |
---|
716 | " %-15s \n", |
---|
717 | (input->mod->user_b_freq[0]<.0)?("empirical"):("user defined")); |
---|
718 | |
---|
719 | printf(" K " |
---|
720 | " Current custom model " |
---|
721 | " %-15s \n", input->mod->custom_mod_string); |
---|
722 | |
---|
723 | printf(" W " |
---|
724 | " Optimise relative rate parameters " |
---|
725 | " %-15s \n",(input->mod->s_opt->opt_rr_param)?("yes"):("no")); |
---|
726 | |
---|
727 | } |
---|
728 | |
---|
729 | |
---|
730 | } |
---|
731 | else |
---|
732 | printf(" M " |
---|
733 | " Model of codon substitution " |
---|
734 | " %-15s \n", input->modelname); |
---|
735 | } |
---|
736 | else |
---|
737 | { |
---|
738 | printf(" M " |
---|
739 | " Model of amino-acids substitution " |
---|
740 | " %-15s \n", input->modelname); |
---|
741 | } |
---|
742 | |
---|
743 | |
---|
744 | if ((input->mod->datatype == NT) && |
---|
745 | ((input->mod->whichmodel == 2)|| |
---|
746 | (input->mod->whichmodel == 4)|| |
---|
747 | (input->mod->whichmodel == 5)|| |
---|
748 | (input->mod->whichmodel == 6))) |
---|
749 | { |
---|
750 | if (input->mod->s_opt->opt_kappa) { |
---|
751 | strcpy(s,"estimated"); |
---|
752 | } |
---|
753 | else { |
---|
754 | sprintf(s,"fixed (ts/tv = %3.2f)",input->mod->kappa); |
---|
755 | } |
---|
756 | |
---|
757 | printf(" T " |
---|
758 | " Ts/tv ratio (fixed/estimated) " |
---|
759 | " %-15s \n",s); |
---|
760 | } |
---|
761 | |
---|
762 | if (input->mod->s_opt->opt_pinvar) { |
---|
763 | strcpy(s,"estimated"); |
---|
764 | } |
---|
765 | else { |
---|
766 | sprintf(s,"fixed (p-invar = ""%3.2f)",input->mod->pinvar); |
---|
767 | } |
---|
768 | |
---|
769 | printf(" V " |
---|
770 | " Proportion of invariable sites (fixed/estimated)" |
---|
771 | " %-15s \n",s); |
---|
772 | |
---|
773 | |
---|
774 | printf(" R " |
---|
775 | " One category of substitution rate (yes/no) " |
---|
776 | " %-15s \n", |
---|
777 | (input->mod->n_catg > 1)?("no"):("yes")); |
---|
778 | |
---|
779 | if(input->mod->n_catg > 1) |
---|
780 | { |
---|
781 | printf(" C " |
---|
782 | " Number of substitution rate categories " |
---|
783 | " %-15d \n", |
---|
784 | input->mod->n_catg); |
---|
785 | } |
---|
786 | |
---|
787 | |
---|
788 | if(input->mod->n_catg > 1) |
---|
789 | { |
---|
790 | if (input->mod->s_opt->opt_alpha) { |
---|
791 | strcpy(s,"estimated"); |
---|
792 | } |
---|
793 | else { |
---|
794 | sprintf(s,"fixed (alpha = %3.2f)",input->mod->alpha); |
---|
795 | } |
---|
796 | |
---|
797 | printf(" A " |
---|
798 | " Gamma distribution parameter (fixed/estimated) " |
---|
799 | " %-15s \n",s); |
---|
800 | } |
---|
801 | |
---|
802 | |
---|
803 | #ifdef PHYML |
---|
804 | printf(" U " |
---|
805 | " Input tree (BIONJ/user tree) " |
---|
806 | " %-15s \n", |
---|
807 | (!input->inputtree)?("BIONJ"):("user tree")); |
---|
808 | |
---|
809 | printf(" O " |
---|
810 | " Optimise tree topology " |
---|
811 | " %-15s \n", |
---|
812 | (input->mod->s_opt->opt_topo)?("yes"):("no")); |
---|
813 | |
---|
814 | |
---|
815 | #endif |
---|
816 | |
---|
817 | #ifdef EVOLVE |
---|
818 | strcpy(s,""); |
---|
819 | (input->seq_len==-1)?((int)strcpy(s,"Reference data set length")):((int)sprintf(s,"l = %d",input->seq_len)); |
---|
820 | |
---|
821 | printf(" L " |
---|
822 | " Sequence length " |
---|
823 | " %-15s \n",s); |
---|
824 | #elif PHYML |
---|
825 | if(!input->mod->s_opt->opt_topo) |
---|
826 | { |
---|
827 | printf(" L " |
---|
828 | " Optimise branch lengths & rate parameters " |
---|
829 | " %-15s \n", |
---|
830 | (input->mod->s_opt->opt_free_param)?("yes"):("no")); |
---|
831 | } |
---|
832 | else |
---|
833 | { |
---|
834 | printf(" L " |
---|
835 | " Last optimisation step on numerical parameters " |
---|
836 | " %-15s \n", |
---|
837 | (input->mod->s_opt->last_opt)?("yes"):("no")); |
---|
838 | } |
---|
839 | |
---|
840 | #endif |
---|
841 | |
---|
842 | |
---|
843 | |
---|
844 | printf("\n"); |
---|
845 | |
---|
846 | printf("\nAre these settings correct? " |
---|
847 | "(type Y or letter for one to change) "); |
---|
848 | |
---|
849 | scanf("%c",&choix); |
---|
850 | if(choix == '\n') choix = 'X'; |
---|
851 | else getchar(); /* \n */ |
---|
852 | |
---|
853 | Uppercase(&choix); |
---|
854 | |
---|
855 | if ((choix == 'Y') || (choix == 'y')) |
---|
856 | break; |
---|
857 | |
---|
858 | switch(choix) |
---|
859 | { |
---|
860 | |
---|
861 | #ifdef PHYML |
---|
862 | case 'B' : |
---|
863 | { |
---|
864 | if(input->mod->bootstrap > 0) input->mod->bootstrap = 0; |
---|
865 | else |
---|
866 | { |
---|
867 | char *r; |
---|
868 | char answer; |
---|
869 | |
---|
870 | |
---|
871 | if(input->n_data_sets > 1) |
---|
872 | Exit("\n. Bootstrap option is not allowed with multiple data sets\n"); |
---|
873 | |
---|
874 | printf("Number of replicates > "); |
---|
875 | r = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
876 | Getstring_Stdin(r); |
---|
877 | n_trial = 0; |
---|
878 | while((!atoi(r)) || (atoi(r) < 0)) |
---|
879 | { |
---|
880 | if(++n_trial > 10) Exit("\nErr : the number of replicates must be a positive integer\n"); |
---|
881 | printf("\nThe number of replicates must be a positive integer\n"); |
---|
882 | printf("Enter a new value > "); |
---|
883 | Getstring_Stdin(r); |
---|
884 | } |
---|
885 | input->mod->bootstrap = atoi(r); |
---|
886 | |
---|
887 | printf("Print bootstrap trees (and statistics) ? (%s) > ", |
---|
888 | (input->print_boot_trees)?("Y/n"):("y/N")); |
---|
889 | |
---|
890 | scanf("%c",&answer); |
---|
891 | if(answer == '\n') answer = (input->print_boot_trees)?('Y'):('N'); |
---|
892 | else getchar(); |
---|
893 | |
---|
894 | switch(answer) |
---|
895 | { |
---|
896 | case 'Y' : case 'y' : |
---|
897 | { |
---|
898 | input->print_boot_trees = 1; |
---|
899 | strcpy(r,input->seqfile); |
---|
900 | input->fp_boot_tree = Openfile(strcat(r,"_phyml_boot_trees.txt"),1); |
---|
901 | strcpy(r,input->seqfile); |
---|
902 | input->fp_boot_stats = Openfile(strcat(r,"_phyml_boot_stats.txt"),1); |
---|
903 | break; |
---|
904 | } |
---|
905 | case 'N' : case 'n' : |
---|
906 | { |
---|
907 | input->print_boot_trees = 0; |
---|
908 | input->fp_boot_tree = NULL; |
---|
909 | input->fp_boot_stats = NULL; |
---|
910 | break; |
---|
911 | } |
---|
912 | } |
---|
913 | Free(r); |
---|
914 | } |
---|
915 | break; |
---|
916 | } |
---|
917 | |
---|
918 | |
---|
919 | case 'U' : |
---|
920 | { |
---|
921 | if(!input->inputtree) |
---|
922 | { |
---|
923 | input->inputtree = 1; |
---|
924 | printf("Enter the name of the tree file > "); |
---|
925 | Getstring_Stdin(input->inputtreefile); |
---|
926 | input->fp_input_tree = Openfile(input->inputtreefile,0); |
---|
927 | } |
---|
928 | else input->inputtree = 0; |
---|
929 | break; |
---|
930 | } |
---|
931 | #endif |
---|
932 | case 'O' : |
---|
933 | { |
---|
934 | input->mod->s_opt->opt_topo = |
---|
935 | (input->mod->s_opt->opt_topo)?(0):(1); |
---|
936 | break; // unintentional fallthrough fixed --ralf |
---|
937 | } |
---|
938 | |
---|
939 | case 'W' : |
---|
940 | { |
---|
941 | input->mod->s_opt->opt_rr_param = |
---|
942 | (input->mod->s_opt->opt_rr_param)?(0):(1); |
---|
943 | break; |
---|
944 | } |
---|
945 | |
---|
946 | case 'K' : |
---|
947 | { |
---|
948 | int i,j; |
---|
949 | char **rr_param,*rr; |
---|
950 | model *mod; |
---|
951 | int curr_param; |
---|
952 | |
---|
953 | if(input->mod->whichmodel == 8) |
---|
954 | { |
---|
955 | rr_param = (char **)mCalloc(5,sizeof(char *)); |
---|
956 | For(i,5) rr_param[i] = (char *)mCalloc(10,sizeof(char)); |
---|
957 | rr = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
958 | |
---|
959 | mod = input->mod; |
---|
960 | |
---|
961 | n_trial = 0; |
---|
962 | do |
---|
963 | { |
---|
964 | printf("Enter a new custom model > "); |
---|
965 | Getstring_Stdin(input->mod->custom_mod_string); |
---|
966 | if(strlen(input->mod->custom_mod_string) == 6) |
---|
967 | { |
---|
968 | For(i,6) |
---|
969 | { |
---|
970 | while(!isdigit((int)input->mod->custom_mod_string[i])) |
---|
971 | { |
---|
972 | if(++n_trial > 10) Exit("\nErr : this string is not valid !\n"); |
---|
973 | printf("\nThis string is not valid\n"); |
---|
974 | printf("Enter a new model > "); |
---|
975 | Getstring_Stdin(input->mod->custom_mod_string); |
---|
976 | } |
---|
977 | } |
---|
978 | if(i == 6) break; |
---|
979 | } |
---|
980 | else |
---|
981 | { |
---|
982 | printf("\nThe string should be of length 6\n"); |
---|
983 | n_trial++; |
---|
984 | } |
---|
985 | }while(n_trial < 10); |
---|
986 | if(n_trial == 10) Exit(""); |
---|
987 | |
---|
988 | Translate_Custom_Mod_String(input->mod); |
---|
989 | |
---|
990 | strcpy(rr_param[0],"A<->C"); |
---|
991 | strcpy(rr_param[1],"A<->G"); |
---|
992 | strcpy(rr_param[2],"A<->T"); |
---|
993 | strcpy(rr_param[3],"C<->G"); |
---|
994 | strcpy(rr_param[4],"C<->T"); |
---|
995 | |
---|
996 | printf("\nSet the relative rate values (G<->T is fixed to 1.0) \n"); |
---|
997 | curr_param = 0; |
---|
998 | For(i,mod->n_diff_rr_param) |
---|
999 | { |
---|
1000 | For(j,mod->n_rr_param_per_cat[i]) |
---|
1001 | if(mod->rr_param_num[i][j] == 5) break; |
---|
1002 | |
---|
1003 | if(j == mod->n_rr_param_per_cat[i]) |
---|
1004 | { |
---|
1005 | printf("["); |
---|
1006 | For(j,mod->n_rr_param_per_cat[i]) |
---|
1007 | { |
---|
1008 | printf("%s",rr_param[mod->rr_param_num[i][j]]); |
---|
1009 | if(j<mod->n_rr_param_per_cat[i]-1) printf(" = "); |
---|
1010 | } |
---|
1011 | printf("]"); |
---|
1012 | |
---|
1013 | printf(" (current=%.2f) > ",mod->rr_param_values[i]); |
---|
1014 | |
---|
1015 | Getstring_Stdin(rr); |
---|
1016 | |
---|
1017 | if(rr[0] != '\0') |
---|
1018 | { |
---|
1019 | n_trial = 0; |
---|
1020 | while((atof(rr) < .0)) |
---|
1021 | { |
---|
1022 | if(++n_trial > 10) |
---|
1023 | Exit("\nErr : the value of this parameter must be a positive number\n"); |
---|
1024 | printf("The value of this parameter must be a positive number\n"); |
---|
1025 | printf("Enter a new value > "); |
---|
1026 | Getstring_Stdin(rr); |
---|
1027 | } |
---|
1028 | input->mod->rr_param_values[curr_param] = (double)atof(rr); |
---|
1029 | } |
---|
1030 | For(j,mod->n_rr_param_per_cat[i]) |
---|
1031 | mod->rr_param[mod->rr_param_num[i][j]] = |
---|
1032 | mod->rr_param_values+curr_param; |
---|
1033 | curr_param++; |
---|
1034 | } |
---|
1035 | else |
---|
1036 | { |
---|
1037 | For(j,mod->n_rr_param_per_cat[i]) |
---|
1038 | mod->rr_param_values[mod->rr_param_num[i][j]] = 1.0; |
---|
1039 | For(j,mod->n_rr_param_per_cat[i]) |
---|
1040 | mod->rr_param[mod->rr_param_num[i][j]] = |
---|
1041 | mod->rr_param_values+5; |
---|
1042 | } |
---|
1043 | } |
---|
1044 | |
---|
1045 | For(i,5) Free(rr_param[i]); |
---|
1046 | Free(rr_param); |
---|
1047 | Free(rr); |
---|
1048 | } |
---|
1049 | break; |
---|
1050 | } |
---|
1051 | |
---|
1052 | case 'F' : |
---|
1053 | { |
---|
1054 | int i; |
---|
1055 | |
---|
1056 | if(input->mod->whichmodel == 8) |
---|
1057 | { |
---|
1058 | if(input->mod->user_b_freq[0] >= .0) |
---|
1059 | For(i,4) input->mod->user_b_freq[i] = -1.; |
---|
1060 | else |
---|
1061 | { |
---|
1062 | char **bases; |
---|
1063 | char *bs; |
---|
1064 | double sum; |
---|
1065 | |
---|
1066 | bases = (char **)mCalloc(4,sizeof(char *)); |
---|
1067 | For(i,4) bases[i] = (char *)mCalloc(50,sizeof(char)); |
---|
1068 | bs = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
1069 | |
---|
1070 | strcpy(bases[0],"f(A) > "); |
---|
1071 | strcpy(bases[1],"f(C) > "); |
---|
1072 | strcpy(bases[2],"f(G) > "); |
---|
1073 | strcpy(bases[3],"f(T) > "); |
---|
1074 | |
---|
1075 | printf("Set nucleotide frequencies \n"); |
---|
1076 | sum = .0; |
---|
1077 | For(i,4) |
---|
1078 | { |
---|
1079 | printf("%s",bases[i]); |
---|
1080 | |
---|
1081 | Getstring_Stdin(bs); |
---|
1082 | |
---|
1083 | n_trial = 0; |
---|
1084 | |
---|
1085 | while((atof(bs) < .0001) || |
---|
1086 | (bs[0] == '\0')) |
---|
1087 | { |
---|
1088 | if(++n_trial > 10) |
---|
1089 | Exit("\nErr : the value of this parameter must be a positive number\n"); |
---|
1090 | printf("The value of this parameter must be a positive number\n"); |
---|
1091 | printf("Enter a new value > "); |
---|
1092 | Getstring_Stdin(bs); |
---|
1093 | } |
---|
1094 | input->mod->user_b_freq[i] = (double)atof(bs); |
---|
1095 | sum += input->mod->user_b_freq[i]; |
---|
1096 | } |
---|
1097 | |
---|
1098 | For(i,4) |
---|
1099 | { |
---|
1100 | input->mod->user_b_freq[i] /= sum; |
---|
1101 | } |
---|
1102 | |
---|
1103 | For(i,4) Free(bases[i]); |
---|
1104 | Free(bases); |
---|
1105 | Free(bs); |
---|
1106 | } |
---|
1107 | } |
---|
1108 | break; |
---|
1109 | } |
---|
1110 | |
---|
1111 | case 'E' : |
---|
1112 | { |
---|
1113 | if((input->mod->whichmodel > 10) || |
---|
1114 | (input->mod->whichmodel < 3)) Exit("\n. Invalid choice...\n"); |
---|
1115 | input->mod->s_opt->opt_bfreq = (input->mod->s_opt->opt_bfreq)?(0):(1); |
---|
1116 | break; |
---|
1117 | } |
---|
1118 | |
---|
1119 | case 'D' : |
---|
1120 | { |
---|
1121 | if(input->mod->datatype == NT) |
---|
1122 | { |
---|
1123 | input->mod->datatype = 1; |
---|
1124 | input->mod->stepsize = 1; |
---|
1125 | input->mod->ns = 20; |
---|
1126 | input->mod->whichmodel = 12; |
---|
1127 | strcpy(input->modelname,"JTT"); |
---|
1128 | } |
---|
1129 | else |
---|
1130 | { |
---|
1131 | input->mod->ns = 4; |
---|
1132 | input->mod->datatype = 0; |
---|
1133 | input->mod->stepsize = 1; |
---|
1134 | input->mod->whichmodel = 4; |
---|
1135 | strcpy(input->modelname,"HKY"); |
---|
1136 | strcpy(input->nt_or_cd,"nucleotides"); |
---|
1137 | } |
---|
1138 | break; |
---|
1139 | } |
---|
1140 | |
---|
1141 | case 'M' : |
---|
1142 | { |
---|
1143 | if(input->mod->datatype == NT) |
---|
1144 | { |
---|
1145 | if(!strcmp(input->nt_or_cd,"nucleotides")) |
---|
1146 | { |
---|
1147 | if(input->mod->whichmodel == 1) |
---|
1148 | { |
---|
1149 | input->mod->whichmodel = 2; |
---|
1150 | strcpy(input->modelname,"K2P"); |
---|
1151 | } |
---|
1152 | else if(input->mod->whichmodel == 2) |
---|
1153 | { |
---|
1154 | input->mod->whichmodel = 3; |
---|
1155 | strcpy(input->modelname,"F81"); |
---|
1156 | input->mod->s_opt->opt_kappa = 0; |
---|
1157 | } |
---|
1158 | else if(input->mod->whichmodel == 3) |
---|
1159 | { |
---|
1160 | input->mod->whichmodel = 4; |
---|
1161 | strcpy(input->modelname,"HKY"); |
---|
1162 | } |
---|
1163 | else if(input->mod->whichmodel == 4) |
---|
1164 | { |
---|
1165 | input->mod->whichmodel = 5; |
---|
1166 | strcpy(input->modelname,"F84"); |
---|
1167 | } |
---|
1168 | else if(input->mod->whichmodel == 5) |
---|
1169 | { |
---|
1170 | input->mod->whichmodel = 6; |
---|
1171 | strcpy(input->modelname,"TN93"); |
---|
1172 | if(input->mod->s_opt->opt_kappa) input->mod->s_opt->opt_lambda = 1; |
---|
1173 | } |
---|
1174 | else if(input->mod->whichmodel == 6) |
---|
1175 | { |
---|
1176 | input->mod->whichmodel = 7; |
---|
1177 | strcpy(input->modelname,"GTR"); |
---|
1178 | input->mod->s_opt->opt_kappa = 0; |
---|
1179 | } |
---|
1180 | else if(input->mod->whichmodel == 7) |
---|
1181 | { |
---|
1182 | input->mod->whichmodel = 8; |
---|
1183 | strcpy(input->modelname,"custom"); |
---|
1184 | input->mod->s_opt->opt_kappa = 0; |
---|
1185 | } |
---|
1186 | |
---|
1187 | else if(input->mod->whichmodel == 8) |
---|
1188 | { |
---|
1189 | input->mod->whichmodel = 1; |
---|
1190 | strcpy(input->modelname,"JC69"); |
---|
1191 | input->mod->s_opt->opt_kappa = 0; |
---|
1192 | } |
---|
1193 | } |
---|
1194 | } |
---|
1195 | else |
---|
1196 | { |
---|
1197 | if(input->mod->whichmodel == 11) |
---|
1198 | { |
---|
1199 | input->mod->whichmodel = 12; |
---|
1200 | strcpy(input->modelname,"JTT"); |
---|
1201 | } |
---|
1202 | else if(input->mod->whichmodel == 12) |
---|
1203 | { |
---|
1204 | input->mod->whichmodel = 13; |
---|
1205 | strcpy(input->modelname,"MtREV"); |
---|
1206 | } |
---|
1207 | else if(input->mod->whichmodel == 13) |
---|
1208 | { |
---|
1209 | input->mod->whichmodel = 14; |
---|
1210 | strcpy(input->modelname,"WAG"); |
---|
1211 | } |
---|
1212 | else if(input->mod->whichmodel == 14) |
---|
1213 | { |
---|
1214 | input->mod->whichmodel = 15; |
---|
1215 | strcpy(input->modelname,"DCMut"); |
---|
1216 | } |
---|
1217 | else if(input->mod->whichmodel == 15) |
---|
1218 | { |
---|
1219 | input->mod->whichmodel = 16; |
---|
1220 | strcpy(input->modelname,"RtREV"); |
---|
1221 | } |
---|
1222 | else if(input->mod->whichmodel == 16) |
---|
1223 | { |
---|
1224 | input->mod->whichmodel = 17; |
---|
1225 | strcpy(input->modelname,"CpREV"); |
---|
1226 | } |
---|
1227 | else if(input->mod->whichmodel == 17) |
---|
1228 | { |
---|
1229 | input->mod->whichmodel = 18; |
---|
1230 | strcpy(input->modelname,"VT"); |
---|
1231 | } |
---|
1232 | else if(input->mod->whichmodel == 18) |
---|
1233 | { |
---|
1234 | input->mod->whichmodel = 19; |
---|
1235 | strcpy(input->modelname,"Blosum62"); |
---|
1236 | } |
---|
1237 | else if(input->mod->whichmodel == 19) |
---|
1238 | { |
---|
1239 | input->mod->whichmodel = 20; |
---|
1240 | strcpy(input->modelname,"MtMam"); |
---|
1241 | } |
---|
1242 | else if(input->mod->whichmodel == 20) |
---|
1243 | { |
---|
1244 | input->mod->whichmodel = 11; |
---|
1245 | strcpy(input->modelname,"Dayhoff"); |
---|
1246 | } |
---|
1247 | } |
---|
1248 | break; |
---|
1249 | } |
---|
1250 | |
---|
1251 | case 'R' : |
---|
1252 | { |
---|
1253 | (input->mod->n_catg == 1)?(input->mod->n_catg = 4):(input->mod->n_catg = 1); |
---|
1254 | break; |
---|
1255 | } |
---|
1256 | |
---|
1257 | case 'C' : |
---|
1258 | { |
---|
1259 | char *c; |
---|
1260 | printf("Enter your number of categories > "); |
---|
1261 | c = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
1262 | Getstring_Stdin(c); |
---|
1263 | n_trial = 0; |
---|
1264 | while((!atoi(c)) || (atoi(c) < 0)) |
---|
1265 | { |
---|
1266 | if(++n_trial > 10) Exit("\nErr : the number of categories must be a positive integer\n"); |
---|
1267 | printf("\nThe number of categories must be a positive integer\n"); |
---|
1268 | printf("Enter a new value > "); |
---|
1269 | Getstring_Stdin(c); |
---|
1270 | } |
---|
1271 | input->mod->n_catg = atoi(c); |
---|
1272 | Free(c); |
---|
1273 | break; |
---|
1274 | } |
---|
1275 | |
---|
1276 | |
---|
1277 | case 'A' : |
---|
1278 | { |
---|
1279 | char answer; |
---|
1280 | |
---|
1281 | switch(input->mod->s_opt->opt_alpha) |
---|
1282 | { |
---|
1283 | case 0 : |
---|
1284 | { |
---|
1285 | printf("Optimise alpha ? [Y/n] "); |
---|
1286 | scanf("%c",&answer); |
---|
1287 | if(answer == '\n') answer = 'Y'; |
---|
1288 | else getchar(); |
---|
1289 | break; |
---|
1290 | } |
---|
1291 | case 1 : |
---|
1292 | { |
---|
1293 | printf("Optimise alpha ? [N/y] "); |
---|
1294 | scanf("%c",&answer); |
---|
1295 | if(answer == '\n') answer = 'N'; |
---|
1296 | else getchar(); |
---|
1297 | break; |
---|
1298 | } |
---|
1299 | default : Exit("\n"); |
---|
1300 | } |
---|
1301 | |
---|
1302 | n_trial = 0; |
---|
1303 | while((answer != 'Y') && (answer != 'y') && |
---|
1304 | (answer != 'N') && (answer != 'n')) |
---|
1305 | { |
---|
1306 | if(++n_trial > 10) Exit("\nErr : wrong answers !"); |
---|
1307 | printf("Optimise alpha ? [N/y] "); |
---|
1308 | scanf("%c",&answer); |
---|
1309 | if(answer == '\n') answer = 'N'; |
---|
1310 | else getchar(); |
---|
1311 | } |
---|
1312 | |
---|
1313 | switch(answer) |
---|
1314 | { |
---|
1315 | case 'Y' : case 'y' : |
---|
1316 | { |
---|
1317 | input->mod->s_opt->opt_alpha = 1; |
---|
1318 | input->mod->s_opt->opt_free_param = 1; |
---|
1319 | break; |
---|
1320 | } |
---|
1321 | case 'N' : case 'n' : |
---|
1322 | { |
---|
1323 | char *a; |
---|
1324 | a = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
1325 | input->mod->alpha = 10.0; |
---|
1326 | input->mod->s_opt->opt_alpha = 0; |
---|
1327 | printf("Enter your value of alpha > "); |
---|
1328 | Getstring_Stdin(a); |
---|
1329 | n_trial = 0; |
---|
1330 | while((!atof(a)) || (atof(a) < .0)) |
---|
1331 | { |
---|
1332 | if(++n_trial > 10) Exit("\nErr : alpha must be a positive number\n"); |
---|
1333 | printf("Alpha must be a positive number\n"); |
---|
1334 | printf("Enter a new value > "); |
---|
1335 | Getstring_Stdin(a); |
---|
1336 | } |
---|
1337 | input->mod->alpha = (double)atof(a); |
---|
1338 | Free(a); |
---|
1339 | input->mod->s_opt->opt_alpha = 0; |
---|
1340 | break; |
---|
1341 | } |
---|
1342 | } |
---|
1343 | break; |
---|
1344 | } |
---|
1345 | |
---|
1346 | case 'T' : |
---|
1347 | { |
---|
1348 | char answer; |
---|
1349 | |
---|
1350 | if((input->mod->datatype) || |
---|
1351 | (input->mod->whichmodel == 1) || |
---|
1352 | (input->mod->whichmodel == 3) || |
---|
1353 | (input->mod->whichmodel == 7)) |
---|
1354 | Exit("\n 'T' is not a valid choice for this model\n"); |
---|
1355 | |
---|
1356 | switch(input->mod->s_opt->opt_kappa) |
---|
1357 | { |
---|
1358 | case 0 : |
---|
1359 | { |
---|
1360 | printf("Optimise ts/tv ratio ? [Y/n] "); |
---|
1361 | scanf("%c", &answer); |
---|
1362 | if(answer == '\n') answer = 'Y'; |
---|
1363 | else getchar(); |
---|
1364 | break; |
---|
1365 | } |
---|
1366 | case 1 : |
---|
1367 | { |
---|
1368 | printf("Optimise ts/tv ratio ? [N/y] "); |
---|
1369 | scanf("%c", &answer); |
---|
1370 | if(answer == '\n') answer = 'N'; |
---|
1371 | else getchar(); |
---|
1372 | break; |
---|
1373 | } |
---|
1374 | default : Exit("\n"); |
---|
1375 | } |
---|
1376 | |
---|
1377 | n_trial = 0; |
---|
1378 | while((answer != 'Y') && (answer != 'y') && |
---|
1379 | (answer != 'N') && (answer != 'n')) |
---|
1380 | { |
---|
1381 | if(++n_trial > 10) Exit("\nErr : wrong answers !"); |
---|
1382 | printf("Optimise ts/tv ratio ? [N/y] "); |
---|
1383 | scanf("%c", &answer); |
---|
1384 | if(answer == '\n') answer = 'N'; |
---|
1385 | else getchar(); |
---|
1386 | } |
---|
1387 | |
---|
1388 | switch(answer) |
---|
1389 | { |
---|
1390 | case 'Y' : case 'y' : |
---|
1391 | { |
---|
1392 | input->mod->kappa = 4.0; |
---|
1393 | input->mod->s_opt->opt_free_param = 1; |
---|
1394 | input->mod->s_opt->opt_kappa = 1; |
---|
1395 | input->mod->s_opt->opt_kappa = 1; |
---|
1396 | if(input->mod->whichmodel == 6) |
---|
1397 | input->mod->s_opt->opt_lambda = 1; |
---|
1398 | break; |
---|
1399 | } |
---|
1400 | case 'N' : case 'n' : |
---|
1401 | { |
---|
1402 | char *t; |
---|
1403 | t = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
1404 | input->mod->s_opt->opt_kappa = 0; |
---|
1405 | printf("Enter your value of the ts/tv ratio > "); |
---|
1406 | Getstring_Stdin(t); |
---|
1407 | n_trial = 0; |
---|
1408 | while((!atof(t)) || (atof(t) < .0)) |
---|
1409 | { |
---|
1410 | if(++n_trial > 10) Exit("\nErr : the ts/tv ratio must be a positive number\n"); |
---|
1411 | printf("The ratio must be a positive number\n"); |
---|
1412 | printf("Enter a new value > "); |
---|
1413 | Getstring_Stdin(t); |
---|
1414 | } |
---|
1415 | input->mod->kappa = (double)atof(t); |
---|
1416 | input->mod->s_opt->opt_kappa = 0; |
---|
1417 | input->mod->s_opt->opt_lambda = 0; |
---|
1418 | Free(t); |
---|
1419 | break; |
---|
1420 | } |
---|
1421 | } |
---|
1422 | break; |
---|
1423 | } |
---|
1424 | |
---|
1425 | case 'I' : |
---|
1426 | { |
---|
1427 | if(input->interleaved) |
---|
1428 | input->interleaved = 0; |
---|
1429 | else input->interleaved = 1; |
---|
1430 | break; |
---|
1431 | } |
---|
1432 | |
---|
1433 | case 'S' : |
---|
1434 | { |
---|
1435 | char *c; |
---|
1436 | |
---|
1437 | printf("How many data sets > "); |
---|
1438 | c = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
1439 | Getstring_Stdin(c); |
---|
1440 | n_trial = 0; |
---|
1441 | while((!atoi(c)) || (atoi(c) < 0)) |
---|
1442 | { |
---|
1443 | if(++n_trial > 10) Exit("\nErr : The number of data sets must be a positive integer\n"); |
---|
1444 | printf("\nThe number of data sets must be a positive integer\n"); |
---|
1445 | printf("Enter a new value > "); |
---|
1446 | Getstring_Stdin(c); |
---|
1447 | } |
---|
1448 | input->n_data_sets = atoi(c); |
---|
1449 | |
---|
1450 | if((input->mod->bootstrap > 1) && (input->n_data_sets > 1)) |
---|
1451 | Exit("\n. Bootstrap option is not allowed with multiple data sets\n"); |
---|
1452 | |
---|
1453 | Free(c); |
---|
1454 | break; |
---|
1455 | } |
---|
1456 | |
---|
1457 | case 'V' : |
---|
1458 | { |
---|
1459 | char answer; |
---|
1460 | |
---|
1461 | switch(input->mod->s_opt->opt_pinvar) |
---|
1462 | { |
---|
1463 | case 0 : |
---|
1464 | { |
---|
1465 | printf("Optimise p-invar ? [Y/n] "); |
---|
1466 | scanf("%c", &answer); |
---|
1467 | if(answer == '\n') answer = 'Y'; |
---|
1468 | else getchar(); |
---|
1469 | break; |
---|
1470 | } |
---|
1471 | case 1 : |
---|
1472 | { |
---|
1473 | printf("Optimise p-invar ? [N/y] "); |
---|
1474 | scanf("%c", &answer); |
---|
1475 | if(answer == '\n') answer = 'N'; |
---|
1476 | else getchar(); |
---|
1477 | break; |
---|
1478 | } |
---|
1479 | default : Exit("\n"); |
---|
1480 | } |
---|
1481 | |
---|
1482 | n_trial = 0; |
---|
1483 | while((answer != 'Y') && (answer != 'y') && |
---|
1484 | (answer != 'N') && (answer != 'n')) |
---|
1485 | { |
---|
1486 | if(++n_trial > 10) Exit("\nErr : wrong answers !"); |
---|
1487 | printf("Optimise p-invar ? [N/y] "); |
---|
1488 | scanf("%c", &answer); |
---|
1489 | if(answer == '\n') answer = 'N'; |
---|
1490 | else getchar(); |
---|
1491 | } |
---|
1492 | |
---|
1493 | switch(answer) |
---|
1494 | { |
---|
1495 | case 'Y' : case 'y' : |
---|
1496 | { |
---|
1497 | input->mod->s_opt->opt_free_param = 1; |
---|
1498 | input->mod->s_opt->opt_pinvar = 1; |
---|
1499 | input->mod->pinvar = 0.2; |
---|
1500 | input->mod->invar = 1; |
---|
1501 | break; |
---|
1502 | } |
---|
1503 | case 'N' : case 'n' : |
---|
1504 | { |
---|
1505 | char *p; |
---|
1506 | p = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
1507 | printf("Enter your value of p-invar > "); |
---|
1508 | Getstring_Stdin(p); |
---|
1509 | n_trial = 0; |
---|
1510 | while((atof(p) < 0.0) || (atof(p) > 1.0)) |
---|
1511 | { |
---|
1512 | if(++n_trial > 10) |
---|
1513 | Exit("\nErr : the proportion of invariable sites must be a positive number between 0.0 and 1.0\n"); |
---|
1514 | printf("The proportion must be a positive number between 0.0 and 1.0\n"); |
---|
1515 | printf("Enter a new value > "); |
---|
1516 | Getstring_Stdin(p); |
---|
1517 | } |
---|
1518 | input->mod->pinvar = (double)atof(p); |
---|
1519 | |
---|
1520 | if(input->mod->pinvar > 0.0+MDBL_MIN) input->mod->invar = 1; |
---|
1521 | else input->mod->invar = 0; |
---|
1522 | |
---|
1523 | Free(p); |
---|
1524 | |
---|
1525 | input->mod->s_opt->opt_pinvar = 0; |
---|
1526 | break; |
---|
1527 | } |
---|
1528 | } |
---|
1529 | break; |
---|
1530 | } |
---|
1531 | |
---|
1532 | #ifdef EVOLVE |
---|
1533 | case 'L' : |
---|
1534 | { |
---|
1535 | char *len; |
---|
1536 | len = (char *)mCalloc(T_MAX_LINE,sizeof(char)); |
---|
1537 | printf("Enter the sequence length > "); |
---|
1538 | Getstring_Stdin(len); |
---|
1539 | n_trial = 0; |
---|
1540 | while((!atof(len)) || (atof(len) < 0.0-MDBL_MIN)) |
---|
1541 | { |
---|
1542 | if(++n_trial > 10) |
---|
1543 | Exit("\nErr : sequence length must be a positive integer \n"); |
---|
1544 | printf("Sequence length must be a positive integer \n"); |
---|
1545 | printf("Enter a new value > "); |
---|
1546 | Getstring_Stdin(len); |
---|
1547 | } |
---|
1548 | input->seq_len = (double)atoi(len); |
---|
1549 | Free(len); |
---|
1550 | break; |
---|
1551 | } |
---|
1552 | #elif PHYML |
---|
1553 | case 'L' : |
---|
1554 | { |
---|
1555 | if(!input->mod->s_opt->opt_topo) |
---|
1556 | { |
---|
1557 | input->mod->s_opt->opt_free_param = |
---|
1558 | (input->mod->s_opt->opt_free_param)?(0):(1); |
---|
1559 | |
---|
1560 | if(!input->mod->s_opt->opt_free_param) |
---|
1561 | { |
---|
1562 | input->mod->s_opt->opt_alpha = 0; |
---|
1563 | input->mod->s_opt->opt_kappa = 0; |
---|
1564 | input->mod->s_opt->opt_lambda = 0; |
---|
1565 | input->mod->s_opt->opt_bl = 0; |
---|
1566 | input->mod->s_opt->opt_pinvar = 0; |
---|
1567 | input->mod->s_opt->opt_rr_param = 0; |
---|
1568 | input->mod->s_opt->opt_topo = 0; |
---|
1569 | } |
---|
1570 | } |
---|
1571 | else |
---|
1572 | { |
---|
1573 | input->mod->s_opt->last_opt = |
---|
1574 | (input->mod->s_opt->last_opt)?(0):(1); |
---|
1575 | } |
---|
1576 | break; |
---|
1577 | } |
---|
1578 | |
---|
1579 | #endif |
---|
1580 | |
---|
1581 | default : |
---|
1582 | { |
---|
1583 | printf("Not a valid choice\n"); |
---|
1584 | break; |
---|
1585 | } |
---|
1586 | } |
---|
1587 | }while(1); |
---|
1588 | |
---|
1589 | if((input->mod->whichmodel == 1) || (input->mod->whichmodel == 3)) |
---|
1590 | { |
---|
1591 | input->mod->s_opt->opt_kappa = 0; |
---|
1592 | input->mod->s_opt->opt_lambda = 0; |
---|
1593 | } |
---|
1594 | |
---|
1595 | if(input->mod->whichmodel != 6) input->mod->s_opt->opt_lambda = 0; |
---|
1596 | |
---|
1597 | |
---|
1598 | Free(s); |
---|
1599 | Free(buff); |
---|
1600 | |
---|
1601 | } |
---|
1602 | |
---|
1603 | /*********************************************************/ |
---|