1 | // =============================================================== // |
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2 | // // |
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3 | // File : arb_dnarates.cxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Institute of Microbiology (Technical University Munich) // |
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7 | // http://www.arb-home.de/ // |
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8 | // // |
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9 | // =============================================================== // |
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10 | |
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11 | /* Maximum likelihood site rate calculation, Gary Olsen, 1991, 1992. |
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12 | * |
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13 | * Portions based on the program dnaml version 3.3 by Joseph Felsenstein |
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14 | * |
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15 | * Copyright notice from dnaml: |
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16 | * |
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17 | * version 3.3. (c) Copyright 1986, 1990 by the University of Washington |
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18 | * and Joseph Felsenstein. Written by Joseph Felsenstein. Permission is |
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19 | * granted to copy and use this program provided no fee is charged for it |
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20 | * and provided that this copyright notice is not removed. |
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21 | */ |
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22 | |
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23 | // Conversion to C by Gary Olsen, 1991 |
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24 | |
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25 | #define programName "DNAml_rates" |
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26 | #define programVersion "1.0.0" |
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27 | #define programDate "April 11, 1992" |
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28 | |
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29 | #include "DNAml_rates_1_0.h" |
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30 | |
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31 | #include <aw_awar_defs.hxx> |
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32 | |
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33 | #include <unistd.h> |
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34 | #include <cmath> |
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35 | |
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36 | #define assert(bed) arb_assert(bed) |
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37 | |
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38 | // Global variables |
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39 | |
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40 | static xarray |
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41 | *usedxtip, *freextip; |
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42 | |
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43 | static double |
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44 | dLidki[maxpatterns], // change in pattern i likelihood with rate |
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45 | bestki[maxpatterns], // best rate for pattern i |
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46 | bestLi[maxpatterns], // best likelihood found for pattern i |
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47 | patrate[maxpatterns]; // current rate for pattern i |
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48 | |
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49 | static double |
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50 | xi, xv, ttratio, // transition/transversion info |
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51 | freqa, freqc, freqg, freqt, // base frequencies |
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52 | freqr, freqy, invfreqr, invfreqy, |
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53 | freqar, freqcy, freqgr, freqty, |
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54 | fracchange; // random matching frequency (in a sense) |
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55 | |
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56 | static int |
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57 | info[maxsites+1], // number of informative nucleotides |
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58 | patsite[maxsites+1], // site corresponding to pattern |
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59 | pattern[maxsites+1], // pattern number corresponding to site |
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60 | patweight[maxsites+1], // weight of given pattern |
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61 | weight[maxsites+1]; // weight of sequence site |
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62 | |
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63 | static int |
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64 | categs, // number of rate categories |
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65 | endsite, // number of unique sequence patterns |
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66 | mininfo, // minimum number of informative sequences for rate est |
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67 | numsp, // number of species |
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68 | sites, // number of input sequence positions |
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69 | weightsum; // sum of weights of positions in analysis |
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70 | |
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71 | static bool |
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72 | anerror, // error flag |
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73 | freqsfrom, // use empirical base frequencies |
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74 | interleaved, // input data are in interleaved format |
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75 | printdata, // echo data to output stream |
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76 | writefile, // put weight and rate data in file |
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77 | userweights; // use user-supplied position weight mask |
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78 | |
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79 | static char |
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80 | *y[maxsp+1]; // sequence data array |
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81 | |
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82 | |
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83 | // ======================================================================= |
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84 | // PROGRAM |
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85 | // ======================================================================= |
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86 | |
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87 | static void getnums(FILE *INFILE) { |
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88 | // input number of species, number of sites |
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89 | printf("\n%s, version %s, %s\n\n", |
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90 | programName, |
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91 | programVersion, |
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92 | programDate); |
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93 | printf("Portions based on Joseph Felsenstein's Nucleic acid sequence\n"); |
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94 | printf("Maximum Likelihood method, version 3.3\n\n"); |
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95 | |
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96 | if (fscanf(INFILE, "%d %d", &numsp, &sites) != 2) { |
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97 | printf("ERROR: Problem reading number of species and sites\n"); |
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98 | anerror = true; |
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99 | return; |
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100 | } |
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101 | printf("%d Species, %d Sites\n\n", numsp, sites); |
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102 | |
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103 | if (numsp > maxsp) { |
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104 | printf("ERROR: Too many species; adjust program constants\n"); |
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105 | anerror = true; |
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106 | } |
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107 | else if (numsp < 4) { |
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108 | printf("ERROR: Too few species (need at least 4)\n"); |
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109 | anerror = true; |
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110 | } |
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111 | |
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112 | if (sites > maxsites) { |
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113 | printf("ERROR: Too many sites; adjust program constants\n"); |
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114 | anerror = true; |
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115 | } |
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116 | else if (sites < 1) { |
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117 | printf("ERROR: Too few sites\n"); |
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118 | anerror = true; |
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119 | } |
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120 | } |
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121 | |
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122 | inline int min(int i, int j) { return i<j ? i : j; } |
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123 | inline bool digit(int ch) { return (ch >= '0' && ch <= '9'); } |
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124 | inline bool white(int ch) { return (ch == ' ' || ch == '\n' || ch == '\t'); } |
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125 | |
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126 | static void uppercase(int *chptr) { |
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127 | // convert character to upper case -- either ASCII or EBCDIC |
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128 | int ch = *chptr; |
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129 | if ((ch >= 'a' && ch <= 'i') || |
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130 | (ch >= 'j' && ch <= 'r') || |
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131 | (ch >= 's' && ch <= 'z')) |
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132 | { |
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133 | *chptr = ch + 'A' - 'a'; |
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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 | static int base36(int ch) { |
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139 | if (ch >= '0' && ch <= '9') return (ch - '0'); |
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140 | else if (ch >= 'A' && ch <= 'I') return (ch - 'A' + 10); |
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141 | else if (ch >= 'J' && ch <= 'R') return (ch - 'J' + 19); |
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142 | else if (ch >= 'S' && ch <= 'Z') return (ch - 'S' + 28); |
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143 | else if (ch >= 'a' && ch <= 'i') return (ch - 'a' + 10); |
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144 | else if (ch >= 'j' && ch <= 'r') return (ch - 'j' + 19); |
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145 | else if (ch >= 's' && ch <= 'z') return (ch - 's' + 28); |
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146 | else return -1; |
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147 | } |
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148 | |
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149 | |
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150 | static int itobase36(int i) { |
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151 | if (i < 0) return '?'; |
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152 | if (i < 10) return (i + '0'); |
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153 | if (i < 19) return (i - 10 + 'A'); |
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154 | if (i < 28) return (i - 19 + 'J'); |
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155 | if (i < 36) return (i - 28 + 'S'); |
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156 | return '?'; |
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157 | } |
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158 | |
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159 | |
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160 | static int findch(int c, FILE *INFILE) { |
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161 | int ch; |
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162 | while ((ch = getc(INFILE)) != EOF && ch != c) ; |
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163 | return ch; |
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164 | } |
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165 | |
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166 | |
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167 | static void inputweights(FILE *INFILE) { |
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168 | // input the character weights 0, 1, 2 ... 9, A, B, ... Y, Z |
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169 | |
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170 | for (int i = 2; i <= nmlngth; i++) (void) getc(INFILE); |
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171 | |
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172 | weightsum = 0; |
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173 | int i = 1; |
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174 | while (i <= sites) { |
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175 | int ch = getc(INFILE); |
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176 | int wi = base36(ch); |
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177 | if (wi >= 0) { |
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178 | weightsum += weight[i++] = wi; |
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179 | } |
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180 | else if (! white(ch)) { |
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181 | printf("ERROR: Bad weight character: '%c'", ch); |
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182 | printf(" Weights must be a digit or a letter.\n"); |
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183 | anerror = true; |
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184 | return; |
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185 | } |
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186 | } |
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187 | |
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188 | if (findch('\n', INFILE) == EOF) { // skip to end of line |
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189 | printf("ERROR: Missing newline at end of weight data\n"); |
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190 | anerror = true; |
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191 | } |
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192 | } |
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193 | |
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194 | |
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195 | static void getoptions(FILE *INFILE) { |
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196 | categs = 0; // Number of rate categories |
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197 | freqsfrom = false; // Use empirical base frequencies |
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198 | interleaved = true; // By default, data format is interleaved |
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199 | mininfo = MIN_INFO; // Default minimum number of informative seqs |
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200 | printdata = false; // Don't echo data to output stream |
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201 | ttratio = 2.0; // Transition/transversion rate ratio |
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202 | userweights = false; // User-defined position weights |
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203 | writefile = false; // Do not write to file |
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204 | |
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205 | int extranum = 0; |
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206 | int ch; |
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207 | while ((ch = getc(INFILE)) != '\n' && ch != EOF) { |
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208 | uppercase (& ch); |
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209 | switch (ch) { |
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210 | case '1': printdata = ! printdata; break; |
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211 | case 'C': categs = -1; extranum++; break; |
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212 | case 'F': freqsfrom = true; break; |
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213 | case 'I': interleaved = ! interleaved; break; |
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214 | case 'L': break; |
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215 | case 'M': mininfo = 0; extranum++; break; |
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216 | case 'T': ttratio = -1.0; extranum++; break; |
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217 | case 'U': break; |
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218 | case 'W': userweights = true; weightsum = 0; extranum++; break; |
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219 | case 'Y': writefile = ! writefile; break; |
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220 | case ' ': break; |
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221 | case '\t': break; |
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222 | default: |
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223 | printf("ERROR: Bad option character: '%c'\n", ch); |
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224 | anerror = true; |
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225 | return; |
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226 | } |
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227 | } |
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228 | |
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229 | if (ch == EOF) { |
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230 | printf("ERROR: End-of-file in options list\n"); |
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231 | anerror = true; |
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232 | return; |
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233 | } |
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234 | |
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235 | // process lines with auxiliary data |
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236 | |
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237 | while (extranum-- && ! anerror) { |
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238 | ch = getc(INFILE); |
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239 | uppercase (& ch); |
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240 | switch (ch) { |
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241 | |
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242 | case 'C': |
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243 | if (categs >= 0) { |
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244 | printf("ERROR: Unexpected Categories data\n"); |
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245 | anerror = true; |
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246 | } |
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247 | else if (fscanf(INFILE, "%d", &categs) != 1 || findch('\n', INFILE)==EOF) { |
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248 | printf("ERROR: Problem reading number of rate categories\n"); |
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249 | anerror = true; |
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250 | } |
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251 | else if (categs < 1 || categs > maxcategories) { |
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252 | printf("ERROR: Bad number of rate categories: %d\n", categs); |
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253 | anerror = true; |
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254 | } |
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255 | break; |
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256 | |
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257 | case 'M': // Minimum informative sequences |
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258 | if (mininfo > 0) { |
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259 | printf("ERROR: Unexpected Min informative residues data\n"); |
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260 | anerror = true; |
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261 | } |
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262 | else if (fscanf(INFILE, "%d", &mininfo)!=1 || findch('\n', INFILE)==EOF) { |
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263 | printf("ERROR: Problem reading min informative residues\n"); |
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264 | anerror = true; |
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265 | } |
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266 | else if (mininfo < 2 || mininfo > numsp) { |
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267 | printf("ERROR: Bad number for informative residues: %d\n", |
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268 | mininfo); |
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269 | anerror = true; |
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270 | } |
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271 | break; |
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272 | |
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273 | case 'T': // Transition/transversion ratio |
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274 | if (ttratio >= 0.0) { |
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275 | printf("ERROR: Unexpected Transition/transversion data\n"); |
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276 | anerror = true; |
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277 | } |
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278 | else if (fscanf(INFILE, "%lf", &ttratio)!=1 || findch('\n', INFILE)==EOF) { |
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279 | printf("ERROR: Problem reading transition/transversion data\n"); |
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280 | anerror = true; |
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281 | } |
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282 | break; |
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283 | |
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284 | case 'W': // Weights |
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285 | if (! userweights || weightsum > 0) { |
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286 | printf("ERROR: Unexpected Weights data\n"); |
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287 | anerror = true; |
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288 | } |
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289 | else { |
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290 | inputweights(INFILE); |
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291 | } |
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292 | break; |
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293 | |
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294 | default: |
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295 | printf("ERROR: Auxiliary data line starts with '%c'\n", ch); |
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296 | anerror = true; |
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297 | break; |
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298 | } |
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299 | } |
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300 | |
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301 | if (anerror) return; |
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302 | |
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303 | if (categs < 0) { |
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304 | printf("ERROR: Category data missing from input\n"); |
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305 | anerror = true; |
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306 | return; |
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307 | } |
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308 | |
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309 | if (mininfo <= 0) { |
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310 | printf("ERROR: Minimum informative residues missing from input\n"); |
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311 | anerror = true; |
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312 | return; |
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313 | } |
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314 | else { |
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315 | printf("There must be at least %d informative residues per column\n\n", mininfo); |
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316 | } |
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317 | |
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318 | if (ttratio < 0.0) { |
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319 | printf("ERROR: Transition/transversion data missing from input\n"); |
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320 | anerror = true; |
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321 | return; |
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322 | } |
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323 | |
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324 | if (! userweights) { |
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325 | for (int i = 1; i <= sites; i++) weight[i] = 1; |
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326 | weightsum = sites; |
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327 | } |
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328 | else if (weightsum < 1) { |
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329 | printf("ERROR: Weight data invalid or missing from input\n"); |
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330 | anerror = true; |
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331 | return; |
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332 | } |
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333 | |
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334 | } |
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335 | |
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336 | |
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337 | static void getbasefreqs(FILE *INFILE) { |
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338 | if (freqsfrom) printf("Empirical "); |
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339 | printf("Base Frequencies:\n\n"); |
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340 | |
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341 | if (! freqsfrom) { |
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342 | if (fscanf(INFILE, "%lf%lf%lf%lf", &freqa, &freqc, &freqg, &freqt) != 4 |
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343 | || findch('\n', INFILE) == EOF) { |
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344 | printf("ERROR: Problem reading user base frequencies\n"); |
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345 | anerror = true; |
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346 | } |
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347 | } |
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348 | |
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349 | printf(" A %10.5f\n", freqa); |
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350 | printf(" C %10.5f\n", freqc); |
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351 | printf(" G %10.5f\n", freqg); |
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352 | printf(" T(U) %10.5f\n\n", freqt); |
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353 | freqr = freqa + freqg; |
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354 | invfreqr = 1.0/freqr; |
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355 | freqar = freqa * invfreqr; |
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356 | freqgr = freqg * invfreqr; |
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357 | freqy = freqc + freqt; |
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358 | invfreqy = 1.0/freqy; |
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359 | freqcy = freqc * invfreqy; |
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360 | freqty = freqt * invfreqy; |
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361 | printf("Transition/transversion ratio = %10.6f\n\n", ttratio); |
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362 | double suma = ttratio*freqr*freqy - (freqa*freqg + freqc*freqt); |
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363 | double sumb = freqa*freqgr + freqc*freqty; |
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364 | xi = suma/(suma+sumb); |
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365 | xv = 1.0 - xi; |
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366 | ttratio = xi / xv; |
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367 | if (xi <= 0.0) { |
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368 | printf("WARNING: This transition/transversion ratio is\n"); |
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369 | printf(" impossible with these base frequencies!\n"); |
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370 | xi = 3/5; |
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371 | xv = 2/5; |
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372 | printf("Transition/transversion parameter reset\n\n"); |
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373 | } |
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374 | printf("(Transition/transversion parameter = %10.6f)\n\n", xi/xv); |
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375 | fracchange = xi*(2*freqa*freqgr + 2*freqc*freqty) |
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376 | + xv*(1.0 - freqa*freqa - freqc*freqc |
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377 | - freqg*freqg - freqt*freqt); |
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378 | } |
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379 | |
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380 | |
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381 | static void getyspace() { |
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382 | long size = 4 * (sites/4 + 1); |
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383 | char *y0 = (char*)malloc((unsigned) (sizeof(char) * size * (numsp+1))); |
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384 | |
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385 | if (!y0) { |
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386 | printf("ERROR: Unable to obtain space for data array\n"); |
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387 | anerror = true; |
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388 | } |
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389 | else { |
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390 | for (int i = 0; i <= numsp; i++) { |
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391 | y[i] = y0; |
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392 | y0 += size; |
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393 | } |
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394 | } |
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395 | } |
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396 | |
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397 | |
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398 | static void setuptree(tree *tr, const int numSp) { |
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399 | nodeptr p = NULL; |
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400 | |
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401 | for (int i = 1; i <= numSp; i++) { // Set-up tips |
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402 | p = (nodeptr)malloc(sizeof(node)); |
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403 | if (!p) { anerror = true; break; } |
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404 | |
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405 | p->x = NULL; |
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406 | p->tip = NULL; |
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407 | p->number = i; |
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408 | p->next = NULL; |
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409 | p->back = NULL; |
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410 | tr->nodep[i] = p; |
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411 | } |
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412 | |
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413 | const int nodes = leafs_2_nodes(numSp, ROOTED); |
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414 | for (int i = numSp+1; i <= nodes && !anerror; i++) { // internal nodes |
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415 | nodeptr q = NULL; |
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416 | for (int j = 1; j <= 3; j++) { |
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417 | p = (nodeptr)malloc(sizeof(node)); |
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418 | if (!p) { anerror = true; break; } |
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419 | |
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420 | p->x = NULL; |
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421 | p->tip = NULL; |
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422 | p->number = i; |
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423 | p->next = q; |
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424 | p->back = NULL; |
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425 | q = p; |
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426 | } |
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427 | if (!anerror) { |
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428 | p->next->next->next = p; |
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429 | tr->nodep[i] = p; |
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430 | } |
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431 | } |
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432 | |
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433 | tr->likelihood = unlikely; |
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434 | tr->start = tr->nodep[1]; |
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435 | tr->mxtips = numSp; |
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436 | tr->ntips = 0; |
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437 | tr->nextnode = 0; |
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438 | tr->opt_level = 0; |
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439 | tr->smoothed = false; |
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440 | |
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441 | if (anerror) printf("ERROR: Unable to obtain sufficient memory"); |
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442 | } |
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443 | |
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444 | |
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445 | static void freeTreeNode(nodeptr p) { |
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446 | // Free a tree node (sector) |
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447 | if (p) { |
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448 | if (p->x) { |
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449 | free(p->x->a); |
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450 | free(p->x); |
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451 | } |
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452 | free(p); |
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453 | } |
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454 | } |
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455 | |
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456 | static void freeTree(tree *tr) { |
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457 | for (int i = 1; i <= tr->mxtips; i++) freeTreeNode(tr->nodep[i]); |
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458 | |
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459 | for (int i = tr->mxtips+1; i <= 2*(tr->mxtips)-2; i++) { |
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460 | nodeptr p = tr->nodep[i]; |
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461 | if (p) { |
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462 | nodeptr q = p->next; |
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463 | if (q) { |
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464 | freeTreeNode(q->next); |
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465 | freeTreeNode(q); |
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466 | } |
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467 | freeTreeNode(p); |
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468 | } |
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469 | } |
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470 | } |
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471 | |
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472 | |
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473 | static void getdata(tree *tr, FILE *INFILE) { |
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474 | // read sequences |
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475 | |
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476 | int meaning[256]; // meaning of input characters |
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477 | { |
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478 | for (int i = 0; i <= 255; i++) meaning[i] = 0; |
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479 | |
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480 | meaning['A'] = 1; |
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481 | meaning['B'] = 14; |
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482 | meaning['C'] = 2; |
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483 | meaning['D'] = 13; |
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484 | meaning['G'] = 4; |
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485 | meaning['H'] = 11; |
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486 | meaning['K'] = 12; |
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487 | meaning['M'] = 3; |
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488 | meaning['N'] = 15; |
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489 | meaning['O'] = 15; |
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490 | meaning['R'] = 5; |
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491 | meaning['S'] = 6; |
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492 | meaning['T'] = 8; |
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493 | meaning['U'] = 8; |
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494 | meaning['V'] = 7; |
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495 | meaning['W'] = 9; |
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496 | meaning['X'] = 15; |
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497 | meaning['Y'] = 10; |
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498 | meaning['?'] = 15; |
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499 | meaning['-'] = 15; |
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500 | } |
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501 | |
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502 | int basesread = 0; |
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503 | int basesnew = 0; |
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504 | |
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505 | bool allread = false; |
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506 | bool firstpass = true; |
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507 | |
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508 | int ch = ' '; |
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509 | |
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510 | while (! allread) { |
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511 | for (int i = 1; i <= numsp; i++) { // Read data line |
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512 | if (firstpass) { // Read species names |
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513 | int j = 1; |
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514 | while (white(ch = getc(INFILE))) { // Skip blank lines |
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515 | if (ch == '\n') j = 1; else j++; |
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516 | } |
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517 | |
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518 | if (j > nmlngth) { |
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519 | printf("ERROR: Blank name for species %d; ", i); |
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520 | printf("check number of species,\n"); |
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521 | printf(" number of sites, and interleave option.\n"); |
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522 | anerror = true; |
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523 | return; |
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524 | } |
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525 | |
---|
526 | char *nameptr = tr->nodep[i]->name; |
---|
527 | for (int k = 1; k < j; k++) *nameptr++ = ' '; |
---|
528 | |
---|
529 | while (ch != '\n' && ch != EOF) { |
---|
530 | if (ch == '_' || white(ch)) ch = ' '; |
---|
531 | *nameptr++ = ch; |
---|
532 | if (++j > nmlngth) break; |
---|
533 | ch = getc(INFILE); |
---|
534 | } |
---|
535 | |
---|
536 | while (j++ <= nmlngth) *nameptr++ = ' '; |
---|
537 | *nameptr = '\0'; // add null termination |
---|
538 | |
---|
539 | if (ch == EOF) { |
---|
540 | printf("ERROR: End-of-file in name of species %d\n", i); |
---|
541 | anerror = true; |
---|
542 | return; |
---|
543 | } |
---|
544 | } |
---|
545 | |
---|
546 | int j = basesread; |
---|
547 | while ((j < sites) && ((ch = getc(INFILE)) != EOF) |
---|
548 | && ((! interleaved) || (ch != '\n'))) { |
---|
549 | uppercase (& ch); |
---|
550 | if (meaning[ch] || ch == '.') { |
---|
551 | j++; |
---|
552 | if (ch == '.') { |
---|
553 | if (i != 1) ch = y[1][j]; |
---|
554 | else { |
---|
555 | printf("ERROR: Dot (.) found at site %d of sequence 1\n", j); |
---|
556 | anerror = true; |
---|
557 | return; |
---|
558 | } |
---|
559 | } |
---|
560 | y[i][j] = ch; |
---|
561 | } |
---|
562 | else if (white(ch) || digit(ch)) ; |
---|
563 | else { |
---|
564 | printf("ERROR: Bad base (%c) at site %d of sequence %d\n", |
---|
565 | ch, j, i); |
---|
566 | anerror = true; |
---|
567 | return; |
---|
568 | } |
---|
569 | } |
---|
570 | |
---|
571 | if (ch == EOF) { |
---|
572 | printf("ERROR: End-of-file at site %d of sequence %d\n", j, i); |
---|
573 | anerror = true; |
---|
574 | return; |
---|
575 | } |
---|
576 | |
---|
577 | if (! firstpass && (j == basesread)) i--; // no data on line |
---|
578 | else if (i == 1) basesnew = j; |
---|
579 | else if (j != basesnew) { |
---|
580 | printf("ERROR: Sequences out of alignment\n"); |
---|
581 | printf(" %d (instead of %d) residues read in sequence %d\n", |
---|
582 | j - basesread, basesnew - basesread, i); |
---|
583 | anerror = true; |
---|
584 | return; |
---|
585 | } |
---|
586 | |
---|
587 | while (ch != '\n' && ch != EOF) ch = getc(INFILE); // flush line |
---|
588 | } |
---|
589 | firstpass = false; |
---|
590 | basesread = basesnew; |
---|
591 | allread = (basesread >= sites); |
---|
592 | } |
---|
593 | |
---|
594 | // Print listing of sequence alignment |
---|
595 | |
---|
596 | if (printdata) { |
---|
597 | int j = nmlngth - 5 + ((sites + ((sites-1)/10))/2); |
---|
598 | if (j < nmlngth - 1) j = nmlngth - 1; |
---|
599 | if (j > 37) j = 37; |
---|
600 | printf("Name"); for (int i=1; i<=j; i++) putchar(' '); printf("Sequences\n"); |
---|
601 | printf("----"); for (int i=1; i<=j; i++) putchar(' '); printf("---------\n"); |
---|
602 | putchar('\n'); |
---|
603 | |
---|
604 | for (int i = 1; i <= sites; i += 60) { |
---|
605 | int l = i + 59; |
---|
606 | if (l > sites) l = sites; |
---|
607 | |
---|
608 | if (userweights) { |
---|
609 | printf("Weights "); |
---|
610 | for (j = 11; j <= nmlngth+3; j++) putchar(' '); |
---|
611 | for (int k = i; k <= l; k++) { |
---|
612 | putchar(itobase36(weight[k])); |
---|
613 | if (((k % 10) == 0) && ((k % 60) != 0)) putchar(' '); |
---|
614 | } |
---|
615 | putchar('\n'); |
---|
616 | } |
---|
617 | |
---|
618 | for (j = 1; j <= numsp; j++) { |
---|
619 | printf("%s ", tr->nodep[j]->name); |
---|
620 | for (int k = i; k <= l; k++) { |
---|
621 | ch = y[j][k]; |
---|
622 | if ((j > 1) && (ch == y[1][k])) ch = '.'; |
---|
623 | putchar(ch); |
---|
624 | if (((k % 10) == 0) && ((k % 60) != 0)) putchar(' '); |
---|
625 | } |
---|
626 | putchar('\n'); |
---|
627 | } |
---|
628 | putchar('\n'); |
---|
629 | } |
---|
630 | } |
---|
631 | |
---|
632 | // Convert characters to meanings |
---|
633 | |
---|
634 | for (int i = 1; i <= sites; i++) info[i] = 0; |
---|
635 | |
---|
636 | for (int j = 1; j <= numsp; j++) { |
---|
637 | for (int i = 1; i <= sites; i++) { |
---|
638 | if ((y[j][i] = meaning[(int)y[j][i]]) != 15) info[i]++; |
---|
639 | } |
---|
640 | } |
---|
641 | |
---|
642 | for (int i = 1; i <= sites; i++) if (info[i] < MIN_INFO) weight[i] = 0; |
---|
643 | |
---|
644 | } |
---|
645 | |
---|
646 | |
---|
647 | static void sitesort() { |
---|
648 | // Shell sort keeping sites, weights in same order |
---|
649 | for (int gap = sites/2; gap > 0; gap /= 2) { |
---|
650 | for (int i = gap + 1; i <= sites; i++) { |
---|
651 | int j = i - gap; |
---|
652 | bool flip; |
---|
653 | do { |
---|
654 | flip = false; |
---|
655 | |
---|
656 | int jj = patsite[j]; |
---|
657 | int jg = patsite[j+gap]; |
---|
658 | |
---|
659 | bool tied = true; |
---|
660 | |
---|
661 | for (int k = 1; tied && (k <= numsp); k++) { |
---|
662 | flip = (y[k][jj] > y[k][jg]); |
---|
663 | tied = (y[k][jj] == y[k][jg]); |
---|
664 | } |
---|
665 | if (flip) { |
---|
666 | patsite[j] = jg; |
---|
667 | patsite[j+gap] = jj; |
---|
668 | j -= gap; |
---|
669 | } |
---|
670 | } |
---|
671 | while (flip && (j > 0)); |
---|
672 | } |
---|
673 | } |
---|
674 | } |
---|
675 | |
---|
676 | |
---|
677 | static void sitecombcrunch() { |
---|
678 | // combine sites that have identical patterns (and nonzero weight) |
---|
679 | int i = 0; |
---|
680 | patsite[0] = patsite[1]; |
---|
681 | patweight[0] = 0; |
---|
682 | |
---|
683 | for (int j = 1; j <= sites; j++) { |
---|
684 | bool tied = true; |
---|
685 | int sitei = patsite[i]; |
---|
686 | int sitej = patsite[j]; |
---|
687 | |
---|
688 | for (int k = 1; tied && (k <= numsp); k++) { |
---|
689 | tied = (y[k][sitei] == y[k][sitej]); |
---|
690 | } |
---|
691 | |
---|
692 | if (tied) { |
---|
693 | patweight[i] += weight[sitej]; |
---|
694 | } |
---|
695 | else { |
---|
696 | if (patweight[i] > 0) i++; |
---|
697 | patweight[i] = weight[sitej]; |
---|
698 | patsite[i] = sitej; |
---|
699 | } |
---|
700 | |
---|
701 | pattern[sitej] = i; |
---|
702 | } |
---|
703 | |
---|
704 | endsite = i; |
---|
705 | if (patweight[i] > 0) endsite++; |
---|
706 | } |
---|
707 | |
---|
708 | |
---|
709 | static void makeweights() { |
---|
710 | // make up weights vector to avoid duplicate computations |
---|
711 | for (int i = 1; i <= sites; i++) patsite[i] = i; |
---|
712 | sitesort(); |
---|
713 | sitecombcrunch(); |
---|
714 | if (endsite > maxpatterns) { |
---|
715 | printf("ERROR: Too many patterns in data\n"); |
---|
716 | printf(" Increase maxpatterns to at least %d\n", endsite); |
---|
717 | anerror = true; |
---|
718 | } |
---|
719 | else { |
---|
720 | printf("Analyzing %d distinct data patterns (columns)\n\n", endsite); |
---|
721 | } |
---|
722 | } |
---|
723 | |
---|
724 | |
---|
725 | static void makevalues(tree *tr) { |
---|
726 | // set up fractional likelihoods at tips |
---|
727 | for (int i = 1; i <= numsp; i++) { // Pack and move tip data |
---|
728 | for (int j = 0; j < endsite; j++) { |
---|
729 | y[i-1][j] = y[i][patsite[j]]; |
---|
730 | } |
---|
731 | nodeptr p = tr->nodep[i]; |
---|
732 | p->tip = &(y[i-1][0]); |
---|
733 | } |
---|
734 | } |
---|
735 | |
---|
736 | |
---|
737 | static void empiricalfreqs(tree *tr) { |
---|
738 | // Get empirical base frequencies from the data |
---|
739 | |
---|
740 | freqa = 0.25; |
---|
741 | freqc = 0.25; |
---|
742 | freqg = 0.25; |
---|
743 | freqt = 0.25; |
---|
744 | |
---|
745 | for (int k = 1; k <= 8; k++) { |
---|
746 | double suma = 0.0; |
---|
747 | double sumc = 0.0; |
---|
748 | double sumg = 0.0; |
---|
749 | double sumt = 0.0; |
---|
750 | |
---|
751 | |
---|
752 | for (int i = 1; i <= numsp; i++) { |
---|
753 | char *yptr = tr->nodep[i]->tip; |
---|
754 | for (int j = 0; j < endsite; j++) { |
---|
755 | int code = *yptr++; |
---|
756 | |
---|
757 | double fa = freqa * (code & 1); |
---|
758 | double fc = freqc * ((code >> 1) & 1); |
---|
759 | double fg = freqg * ((code >> 2) & 1); |
---|
760 | double ft = freqt * ((code >> 3) & 1); |
---|
761 | |
---|
762 | double wj = patweight[j] / (fa + fc + fg + ft); |
---|
763 | |
---|
764 | suma += wj * fa; |
---|
765 | sumc += wj * fc; |
---|
766 | sumg += wj * fg; |
---|
767 | sumt += wj * ft; |
---|
768 | } |
---|
769 | } |
---|
770 | |
---|
771 | double sum = suma + sumc + sumg + sumt; |
---|
772 | |
---|
773 | freqa = suma / sum; |
---|
774 | freqc = sumc / sum; |
---|
775 | freqg = sumg / sum; |
---|
776 | freqt = sumt / sum; |
---|
777 | } |
---|
778 | } |
---|
779 | |
---|
780 | |
---|
781 | static void getinput(tree *tr, FILE *INFILE) { |
---|
782 | getnums(INFILE); if (anerror) return; |
---|
783 | getoptions(INFILE); if (anerror) return; |
---|
784 | if (!freqsfrom) getbasefreqs(INFILE); if (anerror) return; |
---|
785 | getyspace(); if (anerror) return; |
---|
786 | setuptree(tr, numsp); if (anerror) return; |
---|
787 | getdata(tr, INFILE); if (anerror) return; |
---|
788 | makeweights(); if (anerror) return; |
---|
789 | makevalues (tr); if (anerror) return; |
---|
790 | if (freqsfrom) { |
---|
791 | empiricalfreqs (tr); if (anerror) return; |
---|
792 | getbasefreqs(INFILE); |
---|
793 | } |
---|
794 | } |
---|
795 | |
---|
796 | |
---|
797 | static xarray *setupxarray() { |
---|
798 | xarray *x = (xarray *) malloc((unsigned) sizeof(xarray)); |
---|
799 | if (x) { |
---|
800 | xtype *data = (xtype *) malloc((unsigned) (4 * endsite * sizeof(xtype))); |
---|
801 | if (data) { |
---|
802 | x->a = data; |
---|
803 | x->c = data += endsite; |
---|
804 | x->g = data += endsite; |
---|
805 | x->t = data + endsite; |
---|
806 | x->prev = x->next = x; |
---|
807 | x->owner = (nodeptr) NULL; |
---|
808 | } |
---|
809 | else { |
---|
810 | free(x); |
---|
811 | return (xarray *) NULL; |
---|
812 | } |
---|
813 | } |
---|
814 | return x; |
---|
815 | } |
---|
816 | |
---|
817 | |
---|
818 | static void linkxarray(int req, int min, xarray **freexptr, xarray **usedxptr) { |
---|
819 | // Link a set of xarrays |
---|
820 | |
---|
821 | xarray *first = NULL; |
---|
822 | xarray *prev = NULL; |
---|
823 | |
---|
824 | { |
---|
825 | int i = 0; |
---|
826 | xarray *x; |
---|
827 | do { |
---|
828 | x = setupxarray(); |
---|
829 | if (x) { |
---|
830 | if (! first) first = x; |
---|
831 | else { |
---|
832 | prev->next = x; |
---|
833 | x->prev = prev; |
---|
834 | } |
---|
835 | prev = x; |
---|
836 | i++; |
---|
837 | } |
---|
838 | else { |
---|
839 | printf("ERROR: Failure to get xarray memory.\n"); |
---|
840 | if (i < min) anerror = true; |
---|
841 | } |
---|
842 | } while ((i < req) && x); |
---|
843 | } |
---|
844 | |
---|
845 | if (first) { |
---|
846 | first->prev = prev; |
---|
847 | prev->next = first; |
---|
848 | } |
---|
849 | |
---|
850 | *freexptr = first; |
---|
851 | *usedxptr = NULL; |
---|
852 | } |
---|
853 | |
---|
854 | |
---|
855 | static void setupnodex(tree *tr) { |
---|
856 | for (int i = tr->mxtips + 1; (i <= 2*(tr->mxtips) - 2) && ! anerror; i++) { |
---|
857 | nodeptr p = tr->nodep[i]; |
---|
858 | p->x = setupxarray(); |
---|
859 | if (!p->x) { anerror = true; break; } |
---|
860 | } |
---|
861 | } |
---|
862 | |
---|
863 | static xarray *getxtip(nodeptr p) { |
---|
864 | xarray *new_xarray = NULL; |
---|
865 | if (p) { |
---|
866 | bool splice = false; |
---|
867 | |
---|
868 | if (p->x) { |
---|
869 | new_xarray = p->x; |
---|
870 | if (new_xarray == new_xarray->prev) ; // linked to self; leave it |
---|
871 | else if (new_xarray == usedxtip) usedxtip = usedxtip->next; // at head |
---|
872 | else if (new_xarray == usedxtip->prev) ; // already at tail |
---|
873 | else { // move to tail of list |
---|
874 | new_xarray->prev->next = new_xarray->next; |
---|
875 | new_xarray->next->prev = new_xarray->prev; |
---|
876 | splice = true; |
---|
877 | } |
---|
878 | } |
---|
879 | |
---|
880 | else if (freextip) { |
---|
881 | new_xarray = freextip; |
---|
882 | p->x = freextip; |
---|
883 | |
---|
884 | new_xarray->owner = p; |
---|
885 | if (new_xarray->prev != new_xarray) { // not only member of freelist |
---|
886 | new_xarray->prev->next = new_xarray->next; |
---|
887 | new_xarray->next->prev = new_xarray->prev; |
---|
888 | freextip = new_xarray->next; |
---|
889 | } |
---|
890 | else { |
---|
891 | freextip = NULL; |
---|
892 | } |
---|
893 | |
---|
894 | splice = true; |
---|
895 | } |
---|
896 | |
---|
897 | else if (usedxtip) { |
---|
898 | usedxtip->owner->x = NULL; |
---|
899 | new_xarray = usedxtip; |
---|
900 | p->x = usedxtip; |
---|
901 | new_xarray->owner = p; |
---|
902 | usedxtip = usedxtip->next; |
---|
903 | } |
---|
904 | |
---|
905 | else { |
---|
906 | printf ("ERROR: Unable to locate memory for a tip.\n"); |
---|
907 | anerror = true; |
---|
908 | exit(0); |
---|
909 | } |
---|
910 | |
---|
911 | if (splice) { |
---|
912 | if (usedxtip) { // list is not empty |
---|
913 | usedxtip->prev->next = new_xarray; |
---|
914 | new_xarray->prev = usedxtip->prev; |
---|
915 | usedxtip->prev = new_xarray; |
---|
916 | new_xarray->next = usedxtip; |
---|
917 | } |
---|
918 | else { |
---|
919 | usedxtip = new_xarray->prev = new_xarray->next = new_xarray; |
---|
920 | } |
---|
921 | } |
---|
922 | } |
---|
923 | return new_xarray; |
---|
924 | } |
---|
925 | |
---|
926 | |
---|
927 | static xarray *getxnode(nodeptr p) { |
---|
928 | // Ensure that internal node p has memory |
---|
929 | if (! (p->x)) { // Move likelihood array on this node to sector p |
---|
930 | nodeptr s; |
---|
931 | if ((s = p->next)->x || (s = s->next)->x) { |
---|
932 | p->x = s->x; |
---|
933 | s->x = NULL; |
---|
934 | } |
---|
935 | else { |
---|
936 | printf("ERROR in getxnode: Unable to locate memory at internal node."); |
---|
937 | exit(0); |
---|
938 | } |
---|
939 | } |
---|
940 | return p->x; |
---|
941 | } |
---|
942 | |
---|
943 | |
---|
944 | static void newview(nodeptr p) { |
---|
945 | // Update likelihoods at node |
---|
946 | |
---|
947 | if (p->tip) { // Make sure that data are at tip |
---|
948 | if (!p->x) { // they are not already there |
---|
949 | (void) getxtip(p); // they are not, so get memory |
---|
950 | |
---|
951 | xtype *x3a = &(p->x->a[0]); // Move tip data to xarray |
---|
952 | xtype *x3c = &(p->x->c[0]); |
---|
953 | xtype *x3g = &(p->x->g[0]); |
---|
954 | xtype *x3t = &(p->x->t[0]); |
---|
955 | |
---|
956 | char *yptr = p->tip; |
---|
957 | for (int i = 0; i < endsite; i++) { |
---|
958 | int code = *yptr++; |
---|
959 | *x3a++ = code & 1; |
---|
960 | *x3c++ = (code >> 1) & 1; |
---|
961 | *x3g++ = (code >> 2) & 1; |
---|
962 | *x3t++ = (code >> 3) & 1; |
---|
963 | } |
---|
964 | } |
---|
965 | } |
---|
966 | else { |
---|
967 | // Internal node needs update |
---|
968 | |
---|
969 | nodeptr q = p->next->back; |
---|
970 | nodeptr r = p->next->next->back; |
---|
971 | |
---|
972 | while ((! p->x) || (! q->x) || (! r->x)) { |
---|
973 | if (! q->x) newview(q); |
---|
974 | if (! r->x) newview(r); |
---|
975 | if (! p->x) (void) getxnode(p); |
---|
976 | } |
---|
977 | |
---|
978 | xtype *x1a = &(q->x->a[0]); |
---|
979 | xtype *x1c = &(q->x->c[0]); |
---|
980 | xtype *x1g = &(q->x->g[0]); |
---|
981 | xtype *x1t = &(q->x->t[0]); |
---|
982 | |
---|
983 | double z1 = q->z; |
---|
984 | double lz1 = (z1 > zmin) ? log(z1) : log(zmin); |
---|
985 | double xvlz1 = xv * lz1; |
---|
986 | |
---|
987 | xtype *x2a = &(r->x->a[0]); |
---|
988 | xtype *x2c = &(r->x->c[0]); |
---|
989 | xtype *x2g = &(r->x->g[0]); |
---|
990 | xtype *x2t = &(r->x->t[0]); |
---|
991 | |
---|
992 | double z2 = r->z; |
---|
993 | double lz2 = (z2 > zmin) ? log(z2) : log(zmin); |
---|
994 | double xvlz2 = xv * lz2; |
---|
995 | |
---|
996 | xtype *x3a = &(p->x->a[0]); |
---|
997 | xtype *x3c = &(p->x->c[0]); |
---|
998 | xtype *x3g = &(p->x->g[0]); |
---|
999 | xtype *x3t = &(p->x->t[0]); |
---|
1000 | |
---|
1001 | { |
---|
1002 | double *rptr = &(patrate[0]); |
---|
1003 | for (int i = 0; i < endsite; i++) { |
---|
1004 | double ki = *rptr++; |
---|
1005 | |
---|
1006 | double zz1 = exp(ki * lz1); |
---|
1007 | double zv1 = exp(ki * xvlz1); |
---|
1008 | |
---|
1009 | double fx1r = freqa * *x1a + freqg * *x1g; |
---|
1010 | double fx1y = freqc * *x1c + freqt * *x1t; |
---|
1011 | double fx1n = fx1r + fx1y; |
---|
1012 | |
---|
1013 | double tempi = fx1r * invfreqr; |
---|
1014 | double tempj = zv1 * (tempi-fx1n) + fx1n; |
---|
1015 | |
---|
1016 | double suma1 = zz1 * (*x1a++ - tempi) + tempj; |
---|
1017 | double sumg1 = zz1 * (*x1g++ - tempi) + tempj; |
---|
1018 | |
---|
1019 | tempi = fx1y * invfreqy; |
---|
1020 | tempj = zv1 * (tempi-fx1n) + fx1n; |
---|
1021 | |
---|
1022 | double sumc1 = zz1 * (*x1c++ - tempi) + tempj; |
---|
1023 | double sumt1 = zz1 * (*x1t++ - tempi) + tempj; |
---|
1024 | |
---|
1025 | double zz2 = exp(ki * lz2); |
---|
1026 | double zv2 = exp(ki * xvlz2); |
---|
1027 | |
---|
1028 | double fx2r = freqa * *x2a + freqg * *x2g; |
---|
1029 | double fx2y = freqc * *x2c + freqt * *x2t; |
---|
1030 | double fx2n = fx2r + fx2y; |
---|
1031 | |
---|
1032 | tempi = fx2r * invfreqr; |
---|
1033 | tempj = zv2 * (tempi-fx2n) + fx2n; |
---|
1034 | |
---|
1035 | *x3a++ = suma1 * (zz2 * (*x2a++ - tempi) + tempj); |
---|
1036 | *x3g++ = sumg1 * (zz2 * (*x2g++ - tempi) + tempj); |
---|
1037 | |
---|
1038 | tempi = fx2y * invfreqy; |
---|
1039 | tempj = zv2 * (tempi-fx2n) + fx2n; |
---|
1040 | |
---|
1041 | *x3c++ = sumc1 * (zz2 * (*x2c++ - tempi) + tempj); |
---|
1042 | *x3t++ = sumt1 * (zz2 * (*x2t++ - tempi) + tempj); |
---|
1043 | } |
---|
1044 | } |
---|
1045 | } |
---|
1046 | } |
---|
1047 | |
---|
1048 | |
---|
1049 | static void hookup(nodeptr p, nodeptr q, double z) { |
---|
1050 | p->back = q; |
---|
1051 | q->back = p; |
---|
1052 | p->z = q->z = z; |
---|
1053 | } |
---|
1054 | |
---|
1055 | |
---|
1056 | static void initrav(nodeptr p) { |
---|
1057 | if (! p->tip) { |
---|
1058 | initrav(p->next->back); |
---|
1059 | initrav(p->next->next->back); |
---|
1060 | newview(p); |
---|
1061 | } |
---|
1062 | } |
---|
1063 | |
---|
1064 | // ======================================================================= |
---|
1065 | // Read a tree from a file |
---|
1066 | // ======================================================================= |
---|
1067 | |
---|
1068 | static int treeFinishCom(FILE *INFILE) { |
---|
1069 | bool inquote = false; |
---|
1070 | int ch; |
---|
1071 | while ((ch = getc(INFILE)) != EOF && (inquote || ch != ']')) { |
---|
1072 | if (ch == '[' && ! inquote) { // comment; find its end |
---|
1073 | if ((ch = treeFinishCom(INFILE)) == EOF) break; |
---|
1074 | } |
---|
1075 | else if (ch == '\'') inquote = ! inquote; // start or end of quote |
---|
1076 | } |
---|
1077 | |
---|
1078 | return ch; |
---|
1079 | } |
---|
1080 | |
---|
1081 | |
---|
1082 | static int treeGetCh(FILE *INFILE) { |
---|
1083 | // get next nonblank, noncomment character |
---|
1084 | int ch; |
---|
1085 | |
---|
1086 | while ((ch = getc(INFILE)) != EOF) { |
---|
1087 | if (white(ch)) ; |
---|
1088 | else if (ch == '[') { // comment; find its end |
---|
1089 | if ((ch = treeFinishCom(INFILE)) == EOF) break; |
---|
1090 | } |
---|
1091 | else break; |
---|
1092 | } |
---|
1093 | |
---|
1094 | return ch; |
---|
1095 | } |
---|
1096 | |
---|
1097 | static void treeFlushLabel(FILE *INFILE) { |
---|
1098 | int ch = treeGetCh(INFILE); |
---|
1099 | if (ch == EOF) return; |
---|
1100 | |
---|
1101 | bool done = (ch == ':' || ch == ',' || ch == ')' || ch == '[' || ch == ';'); |
---|
1102 | if (!done) { |
---|
1103 | bool quoted = (ch == '\''); |
---|
1104 | if (quoted) ch = getc(INFILE); |
---|
1105 | |
---|
1106 | while (! done) { |
---|
1107 | if (quoted) { |
---|
1108 | if ((ch = findch('\'', INFILE)) == EOF) return; // find close quote |
---|
1109 | ch = getc(INFILE); // check next char |
---|
1110 | if (ch != '\'') done = true; // not doubled quote |
---|
1111 | } |
---|
1112 | else if (ch == ':' || ch == ',' || ch == ')' || ch == '[' |
---|
1113 | || ch == ';' || ch == '\n' || ch == EOF) { |
---|
1114 | done = true; |
---|
1115 | } |
---|
1116 | if (! done) done = ((ch = getc(INFILE)) == EOF); |
---|
1117 | } |
---|
1118 | } |
---|
1119 | |
---|
1120 | if (ch != EOF) (void) ungetc(ch, INFILE); |
---|
1121 | } |
---|
1122 | |
---|
1123 | |
---|
1124 | static int findTipName(tree *tr, int ch, FILE *INFILE) { |
---|
1125 | bool quoted = (ch == '\''); |
---|
1126 | if (quoted) ch = getc(INFILE); |
---|
1127 | |
---|
1128 | bool done = false; |
---|
1129 | int i = 0; |
---|
1130 | |
---|
1131 | char str[nmlngth+1]; |
---|
1132 | do { |
---|
1133 | if (quoted) { |
---|
1134 | if (ch == '\'') { |
---|
1135 | ch = getc(INFILE); |
---|
1136 | if (ch != '\'') done = true; |
---|
1137 | } |
---|
1138 | else if (ch == EOF) { |
---|
1139 | done = true; |
---|
1140 | } |
---|
1141 | else if (ch == '\n' || ch == '\t') { |
---|
1142 | ch = ' '; |
---|
1143 | } |
---|
1144 | } |
---|
1145 | else if (ch == ':' || ch == ',' || ch == ')' || ch == '[' || ch == '\n' || ch == EOF) { |
---|
1146 | done = true; |
---|
1147 | } |
---|
1148 | else if (ch == '_' || ch == '\t') { |
---|
1149 | ch = ' '; |
---|
1150 | } |
---|
1151 | |
---|
1152 | if (! done) { |
---|
1153 | if (i < nmlngth) str[i++] = ch; |
---|
1154 | ch = getc(INFILE); |
---|
1155 | } |
---|
1156 | } while (! done); |
---|
1157 | |
---|
1158 | if (ch == EOF) { |
---|
1159 | printf("ERROR: End-of-file in tree species name\n"); |
---|
1160 | return 0; |
---|
1161 | } |
---|
1162 | |
---|
1163 | (void) ungetc(ch, INFILE); |
---|
1164 | while (i < nmlngth) str[i++] = ' '; // Pad name |
---|
1165 | |
---|
1166 | int n = 1; |
---|
1167 | bool found; |
---|
1168 | do { |
---|
1169 | nodeptr q = tr->nodep[n]; |
---|
1170 | if (! (q->back)) { // Only consider unused tips |
---|
1171 | i = 0; |
---|
1172 | char *nameptr = q->name; |
---|
1173 | do { found = str[i] == *nameptr++; } while (found && (++i < nmlngth)); |
---|
1174 | } |
---|
1175 | else { |
---|
1176 | found = false; |
---|
1177 | } |
---|
1178 | } while ((! found) && (++n <= tr->mxtips)); |
---|
1179 | |
---|
1180 | if (! found) { |
---|
1181 | i = nmlngth; |
---|
1182 | do { str[i] = '\0'; } while (i-- && (str[i] <= ' ')); |
---|
1183 | printf("ERROR: Cannot find data for tree species: %s\n", str); |
---|
1184 | } |
---|
1185 | |
---|
1186 | return (found ? n : 0); |
---|
1187 | } |
---|
1188 | |
---|
1189 | |
---|
1190 | static double processLength(FILE *INFILE) { |
---|
1191 | int ch = treeGetCh(INFILE); // Skip comments |
---|
1192 | if (ch != EOF) (void) ungetc(ch, INFILE); |
---|
1193 | |
---|
1194 | double branch; |
---|
1195 | if (fscanf(INFILE, "%lf", &branch) != 1) { |
---|
1196 | printf("ERROR: Problem reading branch length in processLength:\n"); |
---|
1197 | |
---|
1198 | char str[41]; |
---|
1199 | if (fscanf(INFILE, "%40s", str) == 1) printf("%s\n", str); |
---|
1200 | |
---|
1201 | anerror = true; |
---|
1202 | branch = 0.0; |
---|
1203 | } |
---|
1204 | |
---|
1205 | return branch; |
---|
1206 | } |
---|
1207 | |
---|
1208 | |
---|
1209 | static void treeFlushLen(FILE *INFILE) { |
---|
1210 | int ch = treeGetCh(INFILE); |
---|
1211 | |
---|
1212 | if (ch == ':') (void) processLength(INFILE); |
---|
1213 | else if (ch != EOF) (void) ungetc(ch, INFILE); |
---|
1214 | } |
---|
1215 | |
---|
1216 | |
---|
1217 | static void treeNeedCh(int c1, const char *where, FILE *INFILE) { |
---|
1218 | int c2 = treeGetCh(INFILE); |
---|
1219 | if (c2 != c1) { |
---|
1220 | printf("ERROR: Missing '%c' %s tree; ", c1, where); |
---|
1221 | if (c2 == EOF) { |
---|
1222 | printf("End-of-File"); |
---|
1223 | } |
---|
1224 | else { |
---|
1225 | putchar('\''); |
---|
1226 | for (int i = 24; i-- && (c2 != EOF); c2 = getc(INFILE)) putchar(c2); |
---|
1227 | putchar('\''); |
---|
1228 | } |
---|
1229 | printf(" found instead\n"); |
---|
1230 | anerror = true; |
---|
1231 | } |
---|
1232 | } |
---|
1233 | |
---|
1234 | static void addElementLen(tree *tr, nodeptr p, FILE *INFILE) { |
---|
1235 | nodeptr q; |
---|
1236 | int ch = treeGetCh(INFILE); |
---|
1237 | if (ch == '(') { // A new internal node |
---|
1238 | int n = (tr->nextnode)++; |
---|
1239 | if (n > 2*(tr->mxtips) - 2) { |
---|
1240 | if (tr->rooted || n > 2*(tr->mxtips) - 1) { |
---|
1241 | printf("ERROR: Too many internal nodes. Is tree rooted?\n"); |
---|
1242 | printf(" Deepest splitting should be a trifurcation.\n"); |
---|
1243 | anerror = true; |
---|
1244 | return; |
---|
1245 | } |
---|
1246 | else { |
---|
1247 | tr->rooted = true; |
---|
1248 | } |
---|
1249 | } |
---|
1250 | q = tr->nodep[n]; |
---|
1251 | assert(q); |
---|
1252 | addElementLen(tr, q->next, INFILE); if (anerror) return; |
---|
1253 | treeNeedCh(',', "in", INFILE); if (anerror) return; |
---|
1254 | assert(q->next); |
---|
1255 | addElementLen(tr, q->next->next, INFILE); if (anerror) return; |
---|
1256 | treeNeedCh(')', "in", INFILE); if (anerror) return; |
---|
1257 | treeFlushLabel(INFILE); if (anerror) return; |
---|
1258 | } |
---|
1259 | |
---|
1260 | else { // A new tip |
---|
1261 | int n = findTipName(tr, ch, INFILE); |
---|
1262 | if (n <= 0) { anerror = true; return; } |
---|
1263 | q = tr->nodep[n]; |
---|
1264 | if (tr->start->number > n) tr->start = q; |
---|
1265 | (tr->ntips)++; |
---|
1266 | } |
---|
1267 | |
---|
1268 | treeNeedCh(':', "in", INFILE); if (anerror) return; |
---|
1269 | double branch = processLength(INFILE); if (anerror) return; |
---|
1270 | double z = exp(-branch / fracchange); |
---|
1271 | if (z > zmax) z = zmax; |
---|
1272 | hookup(p, q, z); |
---|
1273 | } |
---|
1274 | |
---|
1275 | |
---|
1276 | static void uprootTree(tree *tr, nodeptr p) { |
---|
1277 | if (p->tip || p->back) { |
---|
1278 | printf("ERROR: Unable to uproot tree.\n"); |
---|
1279 | printf(" Inappropriate node marked for removal.\n"); |
---|
1280 | anerror = true; |
---|
1281 | } |
---|
1282 | else { |
---|
1283 | int n = --(tr->nextnode); // last internal node added |
---|
1284 | if (n != tr->mxtips + tr->ntips - 1) { |
---|
1285 | printf("ERROR: Unable to uproot tree. Inconsistent\n"); |
---|
1286 | printf(" number of tips and nodes for rooted tree.\n"); |
---|
1287 | anerror = true; |
---|
1288 | } |
---|
1289 | else { |
---|
1290 | nodeptr q = p->next->back; // remove p from tree |
---|
1291 | nodeptr r = p->next->next->back; |
---|
1292 | |
---|
1293 | hookup(q, r, q->z * r->z); |
---|
1294 | |
---|
1295 | q = tr->nodep[n]; |
---|
1296 | r = q->next; |
---|
1297 | nodeptr s = q->next->next; |
---|
1298 | |
---|
1299 | if (tr->ntips > 2 && p != q && p != r && p != s) { |
---|
1300 | hookup(p, q->back, q->z); // move connections to p |
---|
1301 | hookup(p->next, r->back, r->z); |
---|
1302 | hookup(p->next->next, s->back, s->z); |
---|
1303 | } |
---|
1304 | |
---|
1305 | q->back = r->back = s->back = (nodeptr) NULL; |
---|
1306 | tr->rooted = false; |
---|
1307 | } |
---|
1308 | } |
---|
1309 | } |
---|
1310 | |
---|
1311 | |
---|
1312 | static void treeReadLen(tree *tr, FILE *INFILE) { |
---|
1313 | for (int i = 1; i <= tr->mxtips; i++) tr->nodep[i]->back = (nodeptr) NULL; |
---|
1314 | |
---|
1315 | tr->start = tr->nodep[tr->mxtips]; |
---|
1316 | tr->ntips = 0; |
---|
1317 | tr->nextnode = tr->mxtips + 1; |
---|
1318 | tr->opt_level = 0; |
---|
1319 | tr->smoothed = false; |
---|
1320 | tr->rooted = false; |
---|
1321 | |
---|
1322 | nodeptr p = tr->nodep[(tr->nextnode)++]; |
---|
1323 | |
---|
1324 | treeNeedCh('(', "at start of", INFILE); if (anerror) return; |
---|
1325 | addElementLen(tr, p, INFILE); if (anerror) return; |
---|
1326 | treeNeedCh(',', "in", INFILE); if (anerror) return; |
---|
1327 | addElementLen(tr, p->next, INFILE); if (anerror) return; |
---|
1328 | |
---|
1329 | if (!tr->rooted) { |
---|
1330 | int ch = treeGetCh(INFILE); |
---|
1331 | if (ch == ',') { // An unrooted format |
---|
1332 | addElementLen(tr, p->next->next, INFILE); if (anerror) return; |
---|
1333 | } |
---|
1334 | else { // A rooted format |
---|
1335 | p->next->next->back = (nodeptr) NULL; |
---|
1336 | tr->rooted = true; |
---|
1337 | if (ch != EOF) (void) ungetc(ch, INFILE); |
---|
1338 | } |
---|
1339 | } |
---|
1340 | treeNeedCh(')', "in", INFILE); |
---|
1341 | if (anerror) { |
---|
1342 | printf("(This error also happens if the last species in the tree is unmarked)\n"); |
---|
1343 | return; |
---|
1344 | } |
---|
1345 | |
---|
1346 | |
---|
1347 | treeFlushLabel(INFILE); if (anerror) return; |
---|
1348 | treeFlushLen(INFILE); if (anerror) return; |
---|
1349 | treeNeedCh(';', "at end of", INFILE); if (anerror) return; |
---|
1350 | |
---|
1351 | if (tr->rooted) uprootTree(tr, p->next->next); if (anerror) return; |
---|
1352 | tr->start = p->next->next->back; // This is start used by treeString |
---|
1353 | |
---|
1354 | initrav(tr->start); |
---|
1355 | initrav(tr->start->back); |
---|
1356 | } |
---|
1357 | |
---|
1358 | // ======================================================================= |
---|
1359 | // End of Tree Reading |
---|
1360 | // ======================================================================= |
---|
1361 | |
---|
1362 | |
---|
1363 | static double evaluate(tree *tr, nodeptr p) { |
---|
1364 | nodeptr q = p->back; |
---|
1365 | while ((! p->x) || (! q->x)) { |
---|
1366 | if (! (p->x)) newview(p); |
---|
1367 | if (! (q->x)) newview(q); |
---|
1368 | } |
---|
1369 | |
---|
1370 | xtype *x1a = &(p->x->a[0]); |
---|
1371 | xtype *x1c = &(p->x->c[0]); |
---|
1372 | xtype *x1g = &(p->x->g[0]); |
---|
1373 | xtype *x1t = &(p->x->t[0]); |
---|
1374 | |
---|
1375 | xtype *x2a = &(q->x->a[0]); |
---|
1376 | xtype *x2c = &(q->x->c[0]); |
---|
1377 | xtype *x2g = &(q->x->g[0]); |
---|
1378 | xtype *x2t = &(q->x->t[0]); |
---|
1379 | |
---|
1380 | double z = p->z; |
---|
1381 | if (z < zmin) z = zmin; |
---|
1382 | |
---|
1383 | double lz = log(z); |
---|
1384 | double xvlz = xv * lz; |
---|
1385 | |
---|
1386 | int *wptr = &(patweight[0]); |
---|
1387 | double *rptr = &(patrate[0]); |
---|
1388 | double *log_f = tr->log_f; |
---|
1389 | |
---|
1390 | double sum = 0.0; |
---|
1391 | |
---|
1392 | for (int i = 0; i < endsite; i++) { |
---|
1393 | double fx1a = freqa * *x1a++; |
---|
1394 | double fx1g = freqg * *x1g++; |
---|
1395 | double fx1c = freqc * *x1c++; |
---|
1396 | double fx1t = freqt * *x1t++; |
---|
1397 | |
---|
1398 | double suma = fx1a * *x2a + fx1c * *x2c + fx1g * *x2g + fx1t * *x2t; |
---|
1399 | |
---|
1400 | double fx2r = freqa * *x2a++ + freqg * *x2g++; |
---|
1401 | double fx2y = freqc * *x2c++ + freqt * *x2t++; |
---|
1402 | double fx1r = fx1a + fx1g; |
---|
1403 | double fx1y = fx1c + fx1t; |
---|
1404 | |
---|
1405 | double sumc = (fx1r + fx1y) * (fx2r + fx2y); |
---|
1406 | double sumb = fx1r * fx2r * invfreqr + fx1y * fx2y * invfreqy; |
---|
1407 | |
---|
1408 | suma -= sumb; |
---|
1409 | sumb -= sumc; |
---|
1410 | |
---|
1411 | double ki = *rptr++; |
---|
1412 | double zz = exp(ki * lz); |
---|
1413 | double zv = exp(ki * xvlz); |
---|
1414 | |
---|
1415 | double term = log(zz * suma + zv * sumb + sumc); |
---|
1416 | sum += *wptr++ * term; |
---|
1417 | *log_f++ = term; |
---|
1418 | } |
---|
1419 | |
---|
1420 | tr->likelihood = sum; |
---|
1421 | return sum; |
---|
1422 | } |
---|
1423 | |
---|
1424 | |
---|
1425 | static void dli_dki(nodeptr p) { |
---|
1426 | // d(Li)/d(ki) |
---|
1427 | |
---|
1428 | nodeptr q = p->back; |
---|
1429 | while ((! p->x) || (! q->x)) { |
---|
1430 | if (! p->x) newview(p); |
---|
1431 | if (! q->x) newview(q); |
---|
1432 | } |
---|
1433 | |
---|
1434 | xtype *x1a = &(p->x->a[0]); |
---|
1435 | xtype *x1c = &(p->x->c[0]); |
---|
1436 | xtype *x1g = &(p->x->g[0]); |
---|
1437 | xtype *x1t = &(p->x->t[0]); |
---|
1438 | |
---|
1439 | xtype *x2a = &(q->x->a[0]); |
---|
1440 | xtype *x2c = &(q->x->c[0]); |
---|
1441 | xtype *x2g = &(q->x->g[0]); |
---|
1442 | xtype *x2t = &(q->x->t[0]); |
---|
1443 | |
---|
1444 | double z = p->z; |
---|
1445 | if (z < zmin) z = zmin; |
---|
1446 | |
---|
1447 | double lz = log(z); |
---|
1448 | double xvlz = xv * lz; |
---|
1449 | |
---|
1450 | double *rptr = &(patrate[0]); |
---|
1451 | int *wptr = &(patweight[0]); |
---|
1452 | |
---|
1453 | for (int i = 0; i < endsite; i++) { |
---|
1454 | double fx1a = freqa * *x1a++; |
---|
1455 | double fx1g = freqg * *x1g++; |
---|
1456 | double fx1c = freqc * *x1c++; |
---|
1457 | double fx1t = freqt * *x1t++; |
---|
1458 | |
---|
1459 | double suma = fx1a * *x2a + fx1c * *x2c + fx1g * *x2g + fx1t * *x2t; |
---|
1460 | |
---|
1461 | double fx2r = freqa * *x2a++ + freqg * *x2g++; |
---|
1462 | double fx2y = freqc * *x2c++ + freqt * *x2t++; |
---|
1463 | double fx1r = fx1a + fx1g; |
---|
1464 | double fx1y = fx1c + fx1t; |
---|
1465 | |
---|
1466 | double sumc = (fx1r + fx1y) * (fx2r + fx2y); |
---|
1467 | double sumb = fx1r * fx2r * invfreqr + fx1y * fx2y * invfreqy; |
---|
1468 | |
---|
1469 | suma -= sumb; |
---|
1470 | sumb -= sumc; |
---|
1471 | |
---|
1472 | double ki = *rptr++; |
---|
1473 | |
---|
1474 | suma *= exp(ki * lz); |
---|
1475 | sumb *= exp(ki * xvlz); |
---|
1476 | |
---|
1477 | dLidki[i] += *wptr++ * lz * (suma + sumb*xv); |
---|
1478 | } |
---|
1479 | } |
---|
1480 | |
---|
1481 | static void spanSubtree(nodeptr p) { |
---|
1482 | dli_dki (p); |
---|
1483 | |
---|
1484 | if (! p->tip) { |
---|
1485 | spanSubtree(p->next->back); |
---|
1486 | spanSubtree(p->next->next->back); |
---|
1487 | } |
---|
1488 | } |
---|
1489 | |
---|
1490 | |
---|
1491 | static void findSiteRates(tree *tr, double ki_min, double ki_max, double d_ki, double max_error) { |
---|
1492 | if (ki_min <= 0.0 || ki_max <= ki_min) { |
---|
1493 | printf("ERROR: Bad rate value limits to findSiteRates\n"); |
---|
1494 | anerror = true; |
---|
1495 | return; |
---|
1496 | } |
---|
1497 | else if (d_ki <= 1.0) { |
---|
1498 | printf("ERROR: Bad rate step to findSiteRates\n"); |
---|
1499 | anerror = true; |
---|
1500 | return; |
---|
1501 | } |
---|
1502 | |
---|
1503 | for (int i = 0; i < endsite; i++) { |
---|
1504 | bestki[i] = 1.0; // dummy initial rates |
---|
1505 | bestLi[i] = unlikely; |
---|
1506 | } |
---|
1507 | |
---|
1508 | for (double ki = ki_min; ki <= ki_max; ki *= d_ki) { |
---|
1509 | for (int i = 0; i < endsite; i++) patrate[i] = ki; |
---|
1510 | initrav(tr->start); |
---|
1511 | initrav(tr->start->back); |
---|
1512 | (void) evaluate(tr, tr->start->back); |
---|
1513 | for (int i = 0; i < endsite; i++) { |
---|
1514 | if (tr->log_f[i] > bestLi[i]) { |
---|
1515 | bestki[i] = ki; |
---|
1516 | bestLi[i] = tr->log_f[i]; |
---|
1517 | } |
---|
1518 | } |
---|
1519 | } |
---|
1520 | |
---|
1521 | for (int i = 0; i < endsite; i++) patrate[i] = bestki[i]; |
---|
1522 | initrav(tr->start); |
---|
1523 | initrav(tr->start->back); |
---|
1524 | |
---|
1525 | while (d_ki > 1.0 + max_error) { |
---|
1526 | for (int i = 0; i < endsite; i++) dLidki[i] = 0.0; |
---|
1527 | spanSubtree(tr->start->back); |
---|
1528 | if (! tr->start->tip) { |
---|
1529 | spanSubtree(tr->start->next->back); |
---|
1530 | spanSubtree(tr->start->next->next->back); |
---|
1531 | } |
---|
1532 | |
---|
1533 | d_ki = sqrt(d_ki); |
---|
1534 | double inv_d_ki = 1.0/d_ki; |
---|
1535 | for (int i = 0; i < endsite; i++) { |
---|
1536 | if (dLidki[i] > 0.0) { |
---|
1537 | patrate[i] *= d_ki; |
---|
1538 | if (patrate[i] > ki_max) patrate[i] = ki_max; |
---|
1539 | } |
---|
1540 | else { |
---|
1541 | patrate[i] *= inv_d_ki; |
---|
1542 | if (patrate[i] < ki_min) patrate[i] = ki_min; |
---|
1543 | } |
---|
1544 | } |
---|
1545 | |
---|
1546 | initrav(tr->start); |
---|
1547 | initrav(tr->start->back); |
---|
1548 | } |
---|
1549 | } |
---|
1550 | |
---|
1551 | |
---|
1552 | static double subtreeLength(nodeptr p) { |
---|
1553 | double sum = -fracchange * log(p->z); |
---|
1554 | if (! p->tip) { |
---|
1555 | sum += subtreeLength(p->next->back); |
---|
1556 | sum += subtreeLength(p->next->next->back); |
---|
1557 | } |
---|
1558 | |
---|
1559 | return sum; |
---|
1560 | } |
---|
1561 | |
---|
1562 | |
---|
1563 | static double treeLength(tree *tr) { |
---|
1564 | double sum = subtreeLength(tr->start->back); |
---|
1565 | if (! tr->start->tip) { |
---|
1566 | sum += subtreeLength(tr->start->next->back); |
---|
1567 | sum += subtreeLength(tr->start->next->next->back); |
---|
1568 | } |
---|
1569 | |
---|
1570 | return sum; |
---|
1571 | } |
---|
1572 | |
---|
1573 | |
---|
1574 | static void categorize(int Sites, |
---|
1575 | int Categs, |
---|
1576 | int Weight[], // one based |
---|
1577 | int Pattern[], // one based |
---|
1578 | double Patrate[], // zero based |
---|
1579 | double categrate[], // zero based |
---|
1580 | int sitecateg[]) // one based |
---|
1581 | { |
---|
1582 | double min_1 = 1.0E37; |
---|
1583 | double min_2 = 1.0E37; |
---|
1584 | double max_1 = 0.0; |
---|
1585 | double max_2 = 0.0; |
---|
1586 | |
---|
1587 | for (int i = 1; i <= Sites; i++) { |
---|
1588 | if (Weight[i] > 0) { |
---|
1589 | double ki = Patrate[Pattern[i]]; |
---|
1590 | if (ki < min_2) { |
---|
1591 | if (ki < min_1) { |
---|
1592 | if (ki < 0.995 * min_1) min_2 = min_1; |
---|
1593 | min_1 = ki; |
---|
1594 | } |
---|
1595 | else if (ki > 1.005 * min_1) { |
---|
1596 | min_2 = ki; |
---|
1597 | } |
---|
1598 | } |
---|
1599 | else if (ki > max_2) { |
---|
1600 | if (ki > max_1) { |
---|
1601 | if (ki > 1.005 * max_1) max_2 = max_1; |
---|
1602 | max_1 = ki; |
---|
1603 | } |
---|
1604 | else if (ki < 0.995 * max_1) { |
---|
1605 | max_2 = ki; |
---|
1606 | } |
---|
1607 | } |
---|
1608 | } |
---|
1609 | } |
---|
1610 | |
---|
1611 | double a = (Categs - 3.0)/log(max_2/min_2); |
---|
1612 | double b = - a * log(min_2) + 2.0; |
---|
1613 | |
---|
1614 | categrate[0] = min_1; |
---|
1615 | for (int k = 1; k <= Categs-2; k++) categrate[k] = min_2 * exp((k-1)/a); |
---|
1616 | if (Categs>0) categrate[Categs-1] = max_1; |
---|
1617 | |
---|
1618 | for (int i = 1; i <= Sites; i++) { |
---|
1619 | if (Weight[i] > 0) { |
---|
1620 | double ki = Patrate[Pattern[i]]; |
---|
1621 | if (ki < 0.99 * min_2) sitecateg[i] = 1; |
---|
1622 | else if (ki > 1.00 * max_2) sitecateg[i] = Categs; |
---|
1623 | else sitecateg[i] = nint(a * log(Patrate[Pattern[i]]) + b); |
---|
1624 | } |
---|
1625 | else { |
---|
1626 | sitecateg[i] = Categs; |
---|
1627 | } |
---|
1628 | } |
---|
1629 | } |
---|
1630 | |
---|
1631 | |
---|
1632 | static char *arb_filter; |
---|
1633 | static char *alignment_name; |
---|
1634 | static GBDATA *gb_main; |
---|
1635 | |
---|
1636 | static void getArbFilter() { |
---|
1637 | //! Get the calling filter, needed to expand weights afterwards |
---|
1638 | GB_begin_transaction(gb_main); |
---|
1639 | arb_filter = GBT_read_string(gb_main, AWAR_GDE_EXPORT_FILTER); |
---|
1640 | alignment_name = GBT_get_default_alignment(gb_main); |
---|
1641 | GB_commit_transaction(gb_main); |
---|
1642 | } |
---|
1643 | |
---|
1644 | static int get_next_SAI_count() { |
---|
1645 | GBDATA *gb_sai_count = GB_search(gb_main, "arb_dnarates/sai_count", GB_FIND); |
---|
1646 | if (!gb_sai_count) { |
---|
1647 | gb_sai_count = GB_search(gb_main, "arb_dnarates/sai_count", GB_INT); |
---|
1648 | } |
---|
1649 | int count = GB_read_int(gb_sai_count); |
---|
1650 | count++; |
---|
1651 | GB_write_int(gb_sai_count, count); |
---|
1652 | return count; |
---|
1653 | } |
---|
1654 | |
---|
1655 | static GBDATA *create_next_SAI() { |
---|
1656 | GBDATA *gb_sai = NULL; |
---|
1657 | char sai_name[100]; |
---|
1658 | |
---|
1659 | while (1) { |
---|
1660 | sprintf(sai_name, "POS_VAR_BY_ML_%i", get_next_SAI_count()); |
---|
1661 | gb_sai = GBT_find_SAI(gb_main, sai_name); |
---|
1662 | if (!gb_sai) { // sai_name is not used yet |
---|
1663 | gb_sai = GBT_find_or_create_SAI(gb_main, sai_name); |
---|
1664 | printf("Writing '%s'\n", sai_name); |
---|
1665 | break; |
---|
1666 | } |
---|
1667 | } |
---|
1668 | return gb_sai; |
---|
1669 | } |
---|
1670 | |
---|
1671 | static bool writeToArb() { |
---|
1672 | GB_ERROR error = NULL; |
---|
1673 | GB_begin_transaction(gb_main); |
---|
1674 | |
---|
1675 | long ali_len = GBT_get_alignment_len(gb_main, alignment_name); |
---|
1676 | char *cats = (char *)GB_calloc(ali_len+1, sizeof(char)); // categories |
---|
1677 | float *rates = (float *)GB_calloc(ali_len, sizeof(float)); // rates to export |
---|
1678 | char category_string[1024]; |
---|
1679 | |
---|
1680 | // check filter has correct length |
---|
1681 | { |
---|
1682 | long filter_len = strlen(arb_filter); |
---|
1683 | if (filter_len != ali_len) { |
---|
1684 | error = GBS_global_string("Filter length (%li) does not match alignment length (%li)", |
---|
1685 | filter_len, ali_len); |
---|
1686 | } |
---|
1687 | } |
---|
1688 | |
---|
1689 | // fill in rates and categories |
---|
1690 | if (!error) { |
---|
1691 | double categrate[maxcategories]; // rate of a given category |
---|
1692 | int sitecateg[maxsites+1]; // category of a given site |
---|
1693 | |
---|
1694 | categorize(sites, categs, weight, pattern, patrate, categrate, sitecateg); |
---|
1695 | |
---|
1696 | int i = 1; // thanks to pascal |
---|
1697 | for (int ali_pos = 0; ali_pos < ali_len; ali_pos++) { |
---|
1698 | if (arb_filter[ali_pos] == '0') { |
---|
1699 | cats[ali_pos] = '.'; |
---|
1700 | rates[ali_pos] = KI_MAX; |
---|
1701 | continue; // filter says not written |
---|
1702 | } |
---|
1703 | if (weight[i] > 0) { |
---|
1704 | rates[ali_pos] = patrate[pattern[i]]; |
---|
1705 | cats[ali_pos] = itobase36(categs - sitecateg[i]); |
---|
1706 | } |
---|
1707 | else { |
---|
1708 | rates[i] = KI_MAX; // infinite rate |
---|
1709 | cats[ali_pos] = '.'; |
---|
1710 | } |
---|
1711 | i++; |
---|
1712 | } |
---|
1713 | |
---|
1714 | int unfiltered_sites = i-1; |
---|
1715 | if (unfiltered_sites != sites) { |
---|
1716 | error = GBS_global_string("Filter positions (%i) do not match input sequence positions (%i)", |
---|
1717 | unfiltered_sites, sites); |
---|
1718 | } |
---|
1719 | |
---|
1720 | // write categories |
---|
1721 | if (!error) { |
---|
1722 | char *p = category_string; |
---|
1723 | p[0] = 0; // if no categs |
---|
1724 | |
---|
1725 | for (int k = 1; k <= categs; k ++) { |
---|
1726 | sprintf(p, " %G", categrate[categs-k]); |
---|
1727 | p += strlen(p); |
---|
1728 | } |
---|
1729 | } |
---|
1730 | } |
---|
1731 | |
---|
1732 | |
---|
1733 | if (!error) { |
---|
1734 | GBDATA *gb_sai = create_next_SAI(); |
---|
1735 | if (!gb_sai) { |
---|
1736 | error = GB_await_error(); |
---|
1737 | } |
---|
1738 | else { |
---|
1739 | GBDATA *gb_data = GBT_add_data(gb_sai, alignment_name, "rates", GB_FLOATS); // @@@ AFAIK not used anywhere |
---|
1740 | GB_write_floats(gb_data, rates, ali_len); |
---|
1741 | |
---|
1742 | gb_data = GBT_add_data(gb_sai, alignment_name, "data", GB_STRING); |
---|
1743 | GB_write_string(gb_data, cats); |
---|
1744 | |
---|
1745 | gb_data = GBT_add_data(gb_sai, alignment_name, "_CATEGORIES", GB_STRING); |
---|
1746 | GB_write_string(gb_data, category_string); |
---|
1747 | |
---|
1748 | gb_data = GBT_add_data(gb_sai, alignment_name, "_TYPE", GB_STRING); |
---|
1749 | GB_write_string(gb_data, "PVML: Positional Variability by ML (Olsen)"); |
---|
1750 | } |
---|
1751 | } |
---|
1752 | |
---|
1753 | error = GB_end_transaction(gb_main, error); |
---|
1754 | if (error) { |
---|
1755 | fprintf(stderr, "Error in arb_dnarates: %s\n", error); |
---|
1756 | } |
---|
1757 | return !error; |
---|
1758 | } |
---|
1759 | |
---|
1760 | static void openArb(const char *dbname) { |
---|
1761 | gb_main = GB_open(dbname, "rw"); |
---|
1762 | if (!gb_main) { |
---|
1763 | if (strcmp(dbname, ":") == 0) { |
---|
1764 | GB_warning("Cannot find ARB server"); |
---|
1765 | } |
---|
1766 | else { |
---|
1767 | GB_warningf("Cannot open DB '%s'", dbname); |
---|
1768 | } |
---|
1769 | exit(EXIT_FAILURE); |
---|
1770 | } |
---|
1771 | } |
---|
1772 | |
---|
1773 | static void saveArb(const char *saveAs) { |
---|
1774 | GB_ERROR error = GB_save(gb_main, saveAs, "a"); |
---|
1775 | if (error) { |
---|
1776 | GB_warningf("Error saving '%s': %s", saveAs, error); |
---|
1777 | exit(EXIT_FAILURE); |
---|
1778 | } |
---|
1779 | } |
---|
1780 | |
---|
1781 | static void closeArb() { |
---|
1782 | GB_close(gb_main); |
---|
1783 | } |
---|
1784 | |
---|
1785 | static void wrfile(FILE *outfile, |
---|
1786 | int Sites, |
---|
1787 | int Categs, |
---|
1788 | int Weight[], // one based |
---|
1789 | double categrate[], // zero based |
---|
1790 | int sitecateg[]) // one based |
---|
1791 | { |
---|
1792 | for (int k = 1; k <= Sites; k += 60) { |
---|
1793 | int j = min(k + 59, Sites); |
---|
1794 | |
---|
1795 | fprintf(outfile, "%s ", k == 1 ? "Weights " : " "); |
---|
1796 | |
---|
1797 | for (int i = k; i <= j; i++) { |
---|
1798 | putc(itobase36(Weight[i]), outfile); |
---|
1799 | if (((i % 10) == 0) && ((i % 60) != 0)) putc(' ', outfile); |
---|
1800 | } |
---|
1801 | |
---|
1802 | putc('\n', outfile); |
---|
1803 | } |
---|
1804 | for (int k = 1; k <= Categs; k += 7) { |
---|
1805 | int j = min(k + 6, Categs); |
---|
1806 | |
---|
1807 | if (k == 1) fprintf(outfile, "C %2d", Categs); |
---|
1808 | else fprintf(outfile, " "); |
---|
1809 | |
---|
1810 | for (int i = k-1; i < j; i++) fprintf(outfile, " %9.5f", categrate[i]); |
---|
1811 | |
---|
1812 | putc('\n', outfile); |
---|
1813 | } |
---|
1814 | |
---|
1815 | for (int k = 1; k <= Sites; k += 60) { |
---|
1816 | int j = min(k + 59, Sites); |
---|
1817 | |
---|
1818 | fprintf(outfile, "%s ", k == 1 ? "Categories" : " "); |
---|
1819 | |
---|
1820 | for (int i = k; i <= j; i++) { |
---|
1821 | putc(itobase36(sitecateg[i]), outfile); |
---|
1822 | if (((i % 10) == 0) && ((i % 60) != 0)) putc(' ', outfile); |
---|
1823 | } |
---|
1824 | |
---|
1825 | putc('\n', outfile); |
---|
1826 | } |
---|
1827 | |
---|
1828 | } |
---|
1829 | |
---|
1830 | |
---|
1831 | static void summarize(int treenum) { |
---|
1832 | printf(" Site Rate\n"); |
---|
1833 | printf(" ---- ---------\n"); |
---|
1834 | |
---|
1835 | for (int i = 1; i <= sites; i++) { |
---|
1836 | if (weight[i] > 0) { |
---|
1837 | printf("%6d %11.4f\n", i, patrate[pattern[i]]); |
---|
1838 | } |
---|
1839 | else { |
---|
1840 | printf("%6d Undefined\n", i); |
---|
1841 | } |
---|
1842 | } |
---|
1843 | |
---|
1844 | putchar('\n'); |
---|
1845 | |
---|
1846 | if (categs > 1) { |
---|
1847 | double categrate[maxcategories]; // rate of a given category |
---|
1848 | int sitecateg[maxsites+1]; // category of a given site |
---|
1849 | |
---|
1850 | categorize(sites, categs, weight, pattern, patrate, categrate, sitecateg); |
---|
1851 | |
---|
1852 | wrfile(stdout, sites, categs, weight, categrate, sitecateg); |
---|
1853 | putchar('\n'); |
---|
1854 | |
---|
1855 | if (writefile) { |
---|
1856 | char filename[512]; |
---|
1857 | if (treenum <= 0) { |
---|
1858 | (void) sprintf(filename, "%s.%d", "weight_rate", getpid()); |
---|
1859 | } |
---|
1860 | else { |
---|
1861 | (void) sprintf(filename, "%s_%2d.%d", "weight_rate", treenum, getpid()); |
---|
1862 | } |
---|
1863 | |
---|
1864 | FILE *outfile = fopen(filename, "w"); |
---|
1865 | if (outfile) { |
---|
1866 | wrfile(outfile, sites, categs, weight, categrate, sitecateg); |
---|
1867 | (void) fclose(outfile); |
---|
1868 | printf("Weights and categories also written to %s\n\n", filename); |
---|
1869 | } |
---|
1870 | } |
---|
1871 | } |
---|
1872 | } |
---|
1873 | |
---|
1874 | |
---|
1875 | static void makeUserRates(tree *tr, FILE *INFILE) { |
---|
1876 | int numtrees; |
---|
1877 | if (fscanf(INFILE, "%d", &numtrees) != 1 || findch('\n', INFILE) == EOF) { |
---|
1878 | printf("ERROR: Problem reading number of user trees\n"); |
---|
1879 | anerror = true; |
---|
1880 | return; |
---|
1881 | } |
---|
1882 | |
---|
1883 | printf("User-defined %s:\n\n", (numtrees == 1) ? "tree" : "trees"); |
---|
1884 | |
---|
1885 | for (int which = 1; which <= numtrees; which++) { |
---|
1886 | for (int i = 0; i < endsite; i++) patrate[i] = 1.0; |
---|
1887 | |
---|
1888 | treeReadLen(tr, INFILE); |
---|
1889 | if (anerror) break; |
---|
1890 | |
---|
1891 | double tree_length = treeLength(tr); |
---|
1892 | |
---|
1893 | printf("%d taxon user-supplied tree read\n\n", tr->ntips); |
---|
1894 | printf("Total length of tree branches = %8.6f\n\n", tree_length); |
---|
1895 | |
---|
1896 | findSiteRates(tr, 0.5/tree_length, KI_MAX, RATE_STEP, MAX_ERROR); |
---|
1897 | if (anerror) break; |
---|
1898 | |
---|
1899 | summarize(numtrees == 1 ? 0 : which); if (anerror) break; |
---|
1900 | } |
---|
1901 | |
---|
1902 | } |
---|
1903 | |
---|
1904 | inline bool is_char(const char *name, char c) { return name[0] == c && !name[1]; } |
---|
1905 | inline bool wantSTDIN(const char *iname) { return is_char(iname, '-'); } |
---|
1906 | |
---|
1907 | int ARB_main(int argc, char *argv[]) { |
---|
1908 | // Maximum Likelihood Site Rate |
---|
1909 | const char *dbname = ":"; |
---|
1910 | const char *dbsavename = NULL; |
---|
1911 | bool help = false; |
---|
1912 | const char *error = NULL; |
---|
1913 | const char *inputname = NULL; |
---|
1914 | FILE *infile = NULL; |
---|
1915 | |
---|
1916 | switch (argc) { |
---|
1917 | case 3: error = "'dbname' may only be used together with 'dbsavename'"; break; |
---|
1918 | |
---|
1919 | case 4: |
---|
1920 | dbname = argv[2]; |
---|
1921 | dbsavename = argv[3]; |
---|
1922 | // fall-through |
---|
1923 | case 2: |
---|
1924 | inputname = argv[1]; |
---|
1925 | infile = wantSTDIN(inputname) ? stdin : fopen(inputname, "rt"); |
---|
1926 | if (!infile) error = GB_IO_error("reading", inputname); |
---|
1927 | break; |
---|
1928 | |
---|
1929 | case 0: |
---|
1930 | case 1: error = "missing arguments"; break; |
---|
1931 | |
---|
1932 | default : error = "too many arguments"; break; |
---|
1933 | } |
---|
1934 | |
---|
1935 | if (error) { |
---|
1936 | fprintf(stderr, "arb_dnarates: Error: %s\n", error); |
---|
1937 | help = true; |
---|
1938 | } |
---|
1939 | |
---|
1940 | if (help) { |
---|
1941 | fputs("Usage: arb_dnarates input [dbname dbsavename]\n" |
---|
1942 | " Expects phylip sequence data as 'input'.\n" |
---|
1943 | " Reads from STDIN if 'input' is '-'.\n" |
---|
1944 | " (e.g. cat data.phyl | arb_dnarates - ...\n" |
---|
1945 | " or arb_dnarates data.phyl ...)\n" |
---|
1946 | " Expects a 'dbname' or a running ARB DB server.\n" |
---|
1947 | " - Reads " AWAR_GDE_EXPORT_FILTER " from server.\n" |
---|
1948 | " - Saves calculated SAI to server (POS_VAR_BY_ML_...)\n" |
---|
1949 | " Using 'dbname' does only make sense for unittests!\n" |
---|
1950 | , stderr); |
---|
1951 | exit(EXIT_FAILURE); |
---|
1952 | } |
---|
1953 | |
---|
1954 | // using arb_dnarates only makes sense with a running db server |
---|
1955 | // (because result is written there) |
---|
1956 | GB_shell shell; |
---|
1957 | openArb(dbname); |
---|
1958 | getArbFilter(); // Note: expects AWAR_GDE_EXPORT_FILTER in running db server |
---|
1959 | |
---|
1960 | { |
---|
1961 | tree curtree; |
---|
1962 | for (int i = 0; i<MAXNODES; ++i) { |
---|
1963 | curtree.nodep[i] = 0; |
---|
1964 | } |
---|
1965 | |
---|
1966 | tree *tr = &curtree; |
---|
1967 | getinput(tr, infile); |
---|
1968 | if (!anerror) linkxarray(3, 3, & freextip, & usedxtip); |
---|
1969 | if (!anerror) setupnodex(tr); |
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1970 | if (!anerror) makeUserRates(tr, infile); |
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1971 | if (!anerror) { |
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1972 | anerror = !writeToArb(); |
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1973 | if (!anerror && dbsavename) saveArb(dbsavename); |
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1974 | } |
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1975 | closeArb(); |
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1976 | if (!anerror) freeTree(tr); |
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1977 | } |
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1978 | |
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1979 | if (wantSTDIN(inputname)) fclose(infile); |
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1980 | |
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1981 | return anerror ? EXIT_FAILURE : EXIT_SUCCESS; |
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1982 | } |
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