1 | /* ----------------------------------------------------------------- |
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2 | * Project: ARB |
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3 | * |
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4 | * Module: consensus [abbrev.:CON] |
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5 | * |
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6 | * Exported Classes: x |
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7 | * |
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8 | * Global Functions: x |
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9 | * |
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10 | * Global Variables: AWARS: |
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11 | * AW_STRING, "tmp/con/alignment" : name of alignment |
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12 | * AW_STRING, "tmp/con/which_species" : only marked species ? |
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13 | * AW_STRING, "con/group" : allow Sgrouping ? |
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14 | * AW_STRING, "con/countgaps" |
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15 | * AW_DOUBLE, "con/fupper" |
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16 | * AW_INT, "con/lower" |
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17 | * AW_INT, "con/gapbound" : result is '-' if more than |
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18 | * 'gapbound' per cent gaps |
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19 | * AW_DOUBLE, "con/fconsidbound" : if frequency of character is |
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20 | * more than 'fconsidbound' per cent, this |
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21 | * character can contribute to groups |
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22 | * AW_STRING, "tmp/con/name" : save with this name |
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23 | * AW_STRING, "con/result" : result has one or more lines ? |
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24 | * |
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25 | * Global Structures: x |
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26 | * |
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27 | * Private Classes: . |
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28 | * |
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29 | * Private Functions: . |
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30 | * |
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31 | * Private Variables: . |
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32 | * |
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33 | * Dependencies: Needs consens.fig and CON_groups.fig |
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34 | * |
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35 | * Description: This module calculates the consensus of sequences of |
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36 | * bases or amino acids. The result can be one or more lines |
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37 | * of characters and it is written to the extended data of |
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38 | * the alignment. |
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39 | * |
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40 | * Integration Notes: To use this module the main function must have a |
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41 | * callback to the function |
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42 | * AW_window *AP_open_consensus_window( AW_root *aw_root) |
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43 | * and the function void AP_create_consensus_var |
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44 | * (AW_root *aw_root, AW_default aw_def) has to be called. |
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45 | * |
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46 | * ----------------------------------------------------------------- |
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47 | */ |
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48 | |
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49 | #include "NT_local.h" |
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50 | #include <awt_sel_boxes.hxx> |
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51 | #include <arb_progress.h> |
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52 | #include <aw_root.hxx> |
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53 | #include <aw_msg.hxx> |
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54 | #include <aw_awar.hxx> |
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55 | #include <arbdbt.h> |
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56 | #include <arb_strbuf.h> |
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57 | |
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58 | #define AWAR_MAX_FREQ "tmp/CON_MAX_FREQ/" |
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59 | |
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60 | #define AWAR_MAX_FREQ_NO_GAPS AWAR_MAX_FREQ "no_gaps" |
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61 | #define AWAR_MAX_FREQ_SAI_NAME AWAR_MAX_FREQ "sai_name" |
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62 | |
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63 | enum { |
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64 | BAS_GAP, |
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65 | BAS_A, BAS_C, BAS_G, BAS_T, BAS_N, |
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66 | |
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67 | MAX_BASES, |
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68 | MAX_AMINOS = 27, |
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69 | MAX_GROUPS = 40 |
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70 | }; |
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71 | |
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72 | /* ----------------------------------------------------------------- |
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73 | * Function: CON_evaluatestatistic |
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74 | * |
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75 | * Arguments: int **statistic,char **groupflags, |
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76 | * char *groupnames |
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77 | * Returns: char *result |
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78 | * |
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79 | * Description: This function creates one or more result strings out |
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80 | * of table statistic. Memory for result is allocated |
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81 | * and later freed in function CON_calculate_cb |
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82 | * |
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83 | * NOTE: Usage of groupflags and groupnames see function |
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84 | * CON_makegrouptable. |
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85 | * |
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86 | * Global Variables referenced: . |
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87 | * |
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88 | * Global Variables modified: x |
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89 | * |
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90 | * AWARs referenced: . |
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91 | * |
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92 | * AWARs modified: x |
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93 | * |
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94 | * Dependencies: Always check that behavior is identical to that |
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95 | * of ED4_char_table::build_consensus_string() |
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96 | * ----------------------------------------------------------------- |
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97 | */ |
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98 | static void CON_evaluatestatistic(char *&result, int **statistic, char **groupflags, |
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99 | char *groupnames, int alignlength, double fupper, int lower, |
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100 | double fconsidbound, int gapbound, int countgap, int numgroups) |
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101 | { |
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102 | int row=0; |
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103 | int j = 0; |
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104 | int groupfr[MAX_GROUPS]; // frequency of group |
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105 | int highestfr, highestgr; |
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106 | |
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107 | arb_progress progress("calculating result", alignlength); |
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108 | |
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109 | result=(char *)GB_calloc(alignlength+1, 1); |
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110 | |
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111 | for (int column=0; column<alignlength; column++) { |
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112 | long numentries = 0; |
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113 | for (row=0; statistic[row]; row++) numentries += statistic[row][column]; |
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114 | if (numentries==0) { |
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115 | result[column]='.'; |
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116 | } |
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117 | else { |
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118 | if (numentries-statistic[0][column]==0) { |
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119 | result[column]='='; // 100 per cent `-` -> `=` |
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120 | } |
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121 | else { |
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122 | if (!countgap) { |
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123 | numentries -= statistic[0][column]; |
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124 | statistic[0][column]=0; |
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125 | } |
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126 | |
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127 | if ((statistic[0][column]*100/numentries)>gapbound) { |
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128 | result[column]='-'; |
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129 | } |
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130 | else { |
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131 | for (j=0; j<numgroups; j++) { |
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132 | groupfr[j]=0; |
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133 | } |
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134 | |
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135 | row=0; |
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136 | while (statistic[row]) { |
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137 | if ((statistic[row][column]*100.0)>=fconsidbound*numentries) { |
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138 | for (j=numgroups-1; j>=0; j--) { |
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139 | if (groupflags[j][row]) { |
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140 | groupfr[j] += statistic[row][column]; |
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141 | } |
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142 | } |
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143 | } |
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144 | row++; |
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145 | } |
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146 | |
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147 | highestfr=0; |
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148 | highestgr=0; |
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149 | for (j=0; j<numgroups; j++) { |
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150 | if (groupfr[j] > highestfr) { |
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151 | highestfr=groupfr[j]; |
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152 | highestgr=j; |
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153 | } |
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154 | } |
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155 | |
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156 | if ((highestfr*100.0/numentries)>=fupper) { |
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157 | result[column]=groupnames[highestgr]; |
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158 | } |
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159 | else if ((highestfr*100/numentries)>=lower) { |
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160 | char c=groupnames[highestgr]; |
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161 | if (c>='A' && c<='Z') { |
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162 | c=c-'A'+'a'; |
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163 | } |
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164 | result[column]=c; |
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165 | } |
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166 | else { |
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167 | result[column]='.'; |
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168 | } |
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169 | } |
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170 | } |
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171 | } |
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172 | ++progress; |
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173 | } |
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174 | } |
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175 | |
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176 | |
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177 | |
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178 | /* ----------------------------------------------------------------- |
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179 | * Function: CON_makegrouptable |
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180 | * |
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181 | * Arguments: . |
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182 | * |
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183 | * Returns: char **gf [groupflags],char *groupnames |
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184 | * |
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185 | * Description: Creates table groupflags that is used in function |
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186 | * CON_evaluatestatistic. E.g. gf[10][3]=1 means, that |
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187 | * all characters c with convtable[c]==3 are members |
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188 | * of group 10. |
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189 | * Table groupnames is also created. |
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190 | * E.g. c=groupnames[5] gives abbrev of 5th group. |
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191 | * |
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192 | * NOTE: . |
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193 | * |
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194 | * Global Variables referenced: . |
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195 | * |
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196 | * Global Variables modified: x |
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197 | * |
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198 | * AWARs referenced: . |
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199 | * |
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200 | * AWARs modified: x |
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201 | * |
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202 | * Dependencies: . |
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203 | * ----------------------------------------------------------------- |
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204 | */ |
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205 | static int CON_makegrouptable(char **gf, char *groupnames, |
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206 | int isamino, int groupallowed) |
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207 | { |
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208 | for (int j=0; j<MAX_GROUPS; j++) { |
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209 | gf[j]=(char *)GB_calloc(MAX_GROUPS, 1); } |
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210 | |
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211 | if (!isamino) |
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212 | { |
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213 | strcpy(groupnames, "-ACGUMRWSYKVHDBN\0"); |
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214 | for (int i=1; i<MAX_BASES; i++) { |
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215 | gf[i][i]=1; } |
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216 | if (groupallowed) |
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217 | { |
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218 | gf[5][BAS_A]=1; gf[5][BAS_C]=1; |
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219 | gf[6][BAS_A]=1; gf[6][BAS_G]=1; |
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220 | gf[7][BAS_A]=1; gf[7][BAS_T]=1; |
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221 | gf[8][BAS_C]=1; gf[8][BAS_G]=1; |
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222 | gf[9][BAS_C]=1; gf[9][BAS_T]=1; |
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223 | gf[10][BAS_G]=1; gf[10][BAS_T]=1; |
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224 | gf[11][BAS_A]=1; gf[11][BAS_C]=1; gf[11][BAS_G]=1; |
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225 | gf[12][BAS_A]=1; gf[12][BAS_C]=1; gf[12][BAS_T]=1; |
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226 | gf[13][BAS_A]=1; gf[13][BAS_G]=1; gf[13][BAS_T]=1; |
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227 | gf[14][BAS_C]=1; gf[14][BAS_G]=1; gf[14][BAS_T]=1; |
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228 | gf[15][BAS_A]=1; gf[15][BAS_C]=1; |
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229 | gf[15][BAS_G]=1; gf[15][BAS_T]=1; |
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230 | return (16); |
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231 | } |
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232 | return (5); |
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233 | } |
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234 | else |
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235 | { |
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236 | strcpy(groupnames, "-ABCDEFGHI*KLMN.PQRST.VWXYZADHIF\0"); |
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237 | for (int i=1; i<MAX_AMINOS; i++) { |
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238 | gf[i][i]=1; } |
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239 | if (groupallowed) |
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240 | #define SC(x, P) gf[x][P-'A'+1] = 1 |
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241 | { |
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242 | SC(27, 'P'); SC(27, 'A'); SC(27, 'G'); SC(27, 'S'); SC(27, 'T'); |
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243 | // PAGST |
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244 | SC(28, 'Q'); SC(28, 'N'); SC(28, 'E'); SC(28, 'D'); SC(28, 'B'); |
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245 | SC(28, 'Z'); // QNEDBZ |
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246 | SC(29, 'H'); SC(29, 'K'); SC(29, 'R'); |
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247 | // HKR |
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248 | SC(30, 'L'); SC(30, 'I'); SC(30, 'V'); SC(30, 'M'); |
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249 | // LIVM |
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250 | SC(31, 'F'); SC(31, 'Y'); SC(31, 'W'); |
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251 | // FYW |
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252 | return (32); |
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253 | } |
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254 | #undef SC |
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255 | return (27); |
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256 | } |
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257 | } |
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258 | |
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259 | |
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260 | /* ----------------------------------------------------------------- |
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261 | * Function: CON_makestatistic |
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262 | * |
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263 | * Arguments: int *convtable |
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264 | * |
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265 | * Returns: int **statistic |
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266 | * |
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267 | * Description: This function fills the table statistic, that is used |
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268 | * later by function CON_evaluatestatistic. The filling |
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269 | * is done depending on table convtable, that is created |
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270 | * in function CON_maketables. Memory for statistic is |
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271 | * allocated also in function CON_maketables. |
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272 | * |
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273 | * |
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274 | * NOTE: . |
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275 | * |
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276 | * Global Variables referenced: . |
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277 | * |
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278 | * Global Variables modified: x |
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279 | * |
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280 | * AWARs referenced: . |
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281 | * |
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282 | * AWARs modified: x |
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283 | * |
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284 | * Dependencies: . |
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285 | * ----------------------------------------------------------------- |
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286 | */ |
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287 | |
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288 | |
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289 | static long CON_makestatistic(int **statistic, int *convtable, char *align, int onlymarked) { |
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290 | long maxalignlen = GBT_get_alignment_len(GLOBAL.gb_main, align); |
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291 | |
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292 | int nrofspecies; |
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293 | if (onlymarked) { |
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294 | nrofspecies = GBT_count_marked_species(GLOBAL.gb_main); |
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295 | } |
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296 | else { |
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297 | nrofspecies = GBT_get_species_count(GLOBAL.gb_main); |
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298 | } |
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299 | |
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300 | arb_progress progress(nrofspecies); |
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301 | progress.auto_subtitles("Examining sequence"); |
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302 | |
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303 | GBDATA *gb_species; |
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304 | if (onlymarked) { |
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305 | gb_species = GBT_first_marked_species(GLOBAL.gb_main); |
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306 | } |
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307 | else { |
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308 | gb_species = GBT_first_species(GLOBAL.gb_main); |
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309 | } |
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310 | |
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311 | while (gb_species) { |
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312 | GBDATA *alidata = GBT_read_sequence(gb_species, align); |
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313 | if (alidata) { |
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314 | unsigned char c; |
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315 | const unsigned char *data = (const unsigned char *)GB_read_char_pntr(alidata); |
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316 | |
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317 | int i = 0; |
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318 | while ((c=data[i])) { |
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319 | if ((c=='-') || ((c>='a')&&(c<='z')) || ((c>='A')&&(c<='Z')) |
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320 | || (c=='*')) { |
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321 | if (i > maxalignlen) break; |
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322 | statistic[convtable[c]][i] += 1; |
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323 | } |
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324 | i++; |
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325 | } |
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326 | } |
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327 | if (onlymarked) { |
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328 | gb_species = GBT_next_marked_species(gb_species); |
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329 | } |
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330 | else { |
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331 | gb_species = GBT_next_species(gb_species); |
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332 | } |
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333 | ++progress; |
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334 | } |
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335 | return nrofspecies; |
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336 | } |
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337 | |
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338 | |
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339 | /* ----------------------------------------------------------------- |
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340 | * Function: CON_maketables |
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341 | * |
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342 | * Arguments: long maxalignlen,int isamino |
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343 | * |
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344 | * Returns: return parameters: int *convtable,int **statistic |
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345 | * |
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346 | * Description: Creates tables convtable and statistic, that are |
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347 | * used by function CON_makestatistic. The memory |
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348 | * allocated for both tables is freed in the |
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349 | * function CON_calculate_cb. |
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350 | * E.g. convtable['c']=k means that the character c |
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351 | * is counted in table statistic in row k. |
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352 | * |
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353 | * NOTE: . |
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354 | * |
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355 | * Global Variables referenced: . |
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356 | * |
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357 | * Global Variables modified: x |
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358 | * |
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359 | * AWARs referenced: . |
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360 | * |
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361 | * AWARs modified: x |
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362 | * |
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363 | * Dependencies: . |
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364 | * ----------------------------------------------------------------- |
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365 | */ |
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366 | static void CON_maketables(int *convtable, int **statistic, long maxalignlen, int isamino) |
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367 | { |
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368 | int i; |
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369 | for (i=0; i<256; i++) { convtable[i]=0; } |
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370 | if (!isamino) { |
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371 | for (i='a'; i <= 'z'; i++) convtable[i] = BAS_N; |
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372 | for (i='A'; i <= 'Z'; i++) convtable[i] = BAS_N; |
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373 | |
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374 | convtable['a']=BAS_A; convtable['A']=BAS_A; |
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375 | convtable['c']=BAS_C; convtable['C']=BAS_C; |
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376 | convtable['g']=BAS_G; convtable['G']=BAS_G; |
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377 | convtable['t']=BAS_T; convtable['T']=BAS_T; |
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378 | convtable['u']=BAS_T; convtable['U']=BAS_T; |
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379 | |
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380 | |
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381 | for (i=0; i<MAX_BASES; i++) { |
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382 | statistic[i]=(int*)GB_calloc((unsigned int)maxalignlen, sizeof(int)); |
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383 | } |
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384 | statistic[MAX_BASES]=NULL; |
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385 | } |
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386 | else { |
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387 | for (i=0; i<MAX_AMINOS-1; i++) |
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388 | { |
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389 | convtable['a'+i]=i+1; |
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390 | convtable['A'+i]=i+1; |
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391 | } |
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392 | for (i=0; i<MAX_AMINOS; i++) { |
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393 | statistic[i]=(int*)GB_calloc((unsigned int)maxalignlen, sizeof(int)); |
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394 | } |
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395 | statistic[MAX_AMINOS]=NULL; |
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396 | convtable['*']=10; // 'J' |
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397 | } |
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398 | } |
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399 | |
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400 | // export results into database |
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401 | static GB_ERROR CON_export(char *savename, char *align, int **statistic, char *result, int *convtable, char *groupnames, int onlymarked, long nrofspecies, long maxalignlen, int countgaps, int gapbound, int groupallowed, double fconsidbound, double fupper, int lower, int resultiscomplex) { |
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402 | const char *off = "off"; |
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403 | const char *on = "on"; |
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404 | |
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405 | char *buffer = (char *)GB_calloc(2000, sizeof(char)); |
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406 | |
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407 | GBDATA *gb_extended = GBT_find_or_create_SAI(GLOBAL.gb_main, savename); |
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408 | GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING); |
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409 | GB_ERROR err = GB_write_string(gb_data, result); // @@@ result is ignored |
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410 | GBDATA *gb_options = GBT_add_data(gb_extended, align, "_TYPE", GB_STRING); |
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411 | |
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412 | const char *allvsmarked = onlymarked ? "marked" : "all"; |
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413 | const char *countgapsstring = countgaps ? on : off; |
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414 | const char *simplifystring = groupallowed ? on : off; |
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415 | |
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416 | sprintf(buffer, "CON: [species: %s] [number: %ld] [count gaps: %s] " |
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417 | "[threshold for gaps: %d] [simplify: %s] " |
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418 | "[threshold for character: %f] [upper: %f] [lower: %d]", |
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419 | allvsmarked, nrofspecies, countgapsstring, |
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420 | gapbound, simplifystring, |
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421 | fconsidbound, fupper, lower); |
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422 | |
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423 | err = GB_write_string(gb_options, buffer); |
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424 | |
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425 | GBDATA *gb_names = GB_search(GB_get_father(gb_options), "_SPECIES", GB_FIND); |
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426 | if (gb_names) GB_delete(gb_names); // delete old entry |
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427 | |
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428 | if (nrofspecies<20) { |
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429 | GBDATA *gb_species; |
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430 | GBS_strstruct *strstruct = GBS_stropen(1000); |
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431 | |
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432 | if (onlymarked) gb_species = GBT_first_marked_species(GLOBAL.gb_main); |
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433 | else gb_species = GBT_first_species(GLOBAL.gb_main); |
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434 | |
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435 | while (gb_species) { |
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436 | if (GBT_read_sequence(gb_species, align)) { |
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437 | GBDATA *gb_speciesname = GB_search(gb_species, "name", GB_FIND); |
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438 | const char *name = GB_read_char_pntr(gb_speciesname); |
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439 | |
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440 | GBS_strcat(strstruct, name); |
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441 | GBS_chrcat(strstruct, ' '); |
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442 | } |
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443 | if (onlymarked) gb_species = GBT_next_marked_species(gb_species); |
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444 | else gb_species = GBT_next_species(gb_species); |
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445 | } |
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446 | |
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447 | char *allnames = GBS_strclose(strstruct); |
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448 | err = GBT_write_string(GB_get_father(gb_options), "_SPECIES", allnames); |
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449 | free(allnames); |
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450 | } |
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451 | |
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452 | { |
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453 | char buffer2[256]; |
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454 | sprintf(buffer2, "%s/FREQUENCIES", align); |
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455 | GBDATA *gb_graph = GB_search(gb_extended, buffer2, GB_FIND); |
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456 | if (gb_graph) GB_delete(gb_graph); // delete old entry |
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457 | } |
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458 | // export additional information |
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459 | if (resultiscomplex) { |
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460 | GBDATA *gb_graph = GBT_add_data(gb_extended, align, "FREQUENCIES", GB_DB); |
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461 | char *charname = (char *)GB_calloc(5, sizeof(char)); |
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462 | |
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463 | // problem : aminos, especially '*' -> new order |
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464 | |
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465 | int *allreadycounted = (int*)GB_calloc((unsigned int)256, sizeof(char)); |
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466 | int *neworder = (int*)GB_calloc((unsigned int)256, sizeof(int)); |
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467 | int numdiffchars = 1; // first additional row (nr. 0) is max-row |
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468 | |
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469 | for (int c=0; c<256; c++) { |
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470 | int k = convtable[c]; |
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471 | if (k) { |
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472 | if (!(allreadycounted[k])) { |
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473 | allreadycounted[k] = 1; |
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474 | neworder[numdiffchars++] = k; |
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475 | } |
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476 | } |
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477 | } |
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478 | |
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479 | float **additional = (float**)GB_calloc((unsigned int)numdiffchars, sizeof(float*)); |
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480 | |
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481 | for (int group=0; group<numdiffchars; group++) { |
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482 | additional[group]=(float*)GB_calloc((unsigned int)maxalignlen, sizeof(float)); |
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483 | } |
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484 | |
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485 | int *absolutrow = (int*)GB_calloc((unsigned int)maxalignlen, sizeof(int)); |
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486 | |
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487 | for (long col=0; col<maxalignlen; col++) { |
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488 | int group2 = 1; |
---|
489 | int colsum = 0; |
---|
490 | while (neworder[group2]) { |
---|
491 | colsum += statistic[neworder[group2++]][col]; |
---|
492 | } |
---|
493 | if (countgaps) colsum += statistic[0][col]; |
---|
494 | absolutrow[col] = colsum; |
---|
495 | } |
---|
496 | |
---|
497 | for (long col=0; col<maxalignlen; col++) { |
---|
498 | if (absolutrow[col]) { |
---|
499 | int group2 = 1; |
---|
500 | float highest = 0; |
---|
501 | int diffchar; |
---|
502 | |
---|
503 | while ((diffchar=neworder[group2++])) { |
---|
504 | float relative = (float)statistic[diffchar][col] / (float)absolutrow[col]; |
---|
505 | if (relative>highest) highest = relative; |
---|
506 | additional[diffchar][col] = relative; |
---|
507 | } |
---|
508 | additional[0][col]=highest; |
---|
509 | } |
---|
510 | else { |
---|
511 | additional[0][col]=0.0; |
---|
512 | } |
---|
513 | } |
---|
514 | |
---|
515 | GBDATA *gb_relative = GB_search(gb_graph, "MAX", GB_FLOATS); |
---|
516 | err = GB_write_floats(gb_relative, additional[0], maxalignlen); |
---|
517 | |
---|
518 | for (int group=1; group<numdiffchars; group++) { |
---|
519 | char ch = groupnames[neworder[group]]; |
---|
520 | if (ch <'A' || ch>'Z') continue; |
---|
521 | |
---|
522 | sprintf(charname, "N%c", ch); |
---|
523 | gb_relative = GB_search(gb_graph, charname, GB_FLOATS); |
---|
524 | err = GB_write_floats(gb_relative, additional[group], maxalignlen); |
---|
525 | } |
---|
526 | |
---|
527 | free(charname); |
---|
528 | free(neworder); |
---|
529 | free(allreadycounted); |
---|
530 | |
---|
531 | for (int group=0; group<numdiffchars; group++) free(additional[group]); |
---|
532 | free(additional); |
---|
533 | } |
---|
534 | free(buffer); |
---|
535 | return err; |
---|
536 | } |
---|
537 | |
---|
538 | |
---|
539 | static void CON_cleartables(int **statistic, int isamino) { |
---|
540 | int i; |
---|
541 | int no_of_tables = isamino ? MAX_AMINOS : MAX_BASES; |
---|
542 | |
---|
543 | for (i = 0; i<no_of_tables; ++i) { |
---|
544 | free(statistic[i]); |
---|
545 | } |
---|
546 | } |
---|
547 | |
---|
548 | /* ----------------------------------------------------------------- |
---|
549 | * Function: void CON_calculate_cb(AW_window *aw ) |
---|
550 | * |
---|
551 | * Arguments: . |
---|
552 | * |
---|
553 | * Returns: . |
---|
554 | * |
---|
555 | * Description: main callback |
---|
556 | * This function calculates the consensus. |
---|
557 | * Function CON_makestatistic creates the |
---|
558 | * statistic and function CON_evaluatestatistic |
---|
559 | * evaluates the statistic. Then the result |
---|
560 | * string(s) are written to the extended data of |
---|
561 | * the alignment. |
---|
562 | * NOTE: . |
---|
563 | * |
---|
564 | * Global Variables referenced: . |
---|
565 | * |
---|
566 | * Global Variables modified: x |
---|
567 | * |
---|
568 | * AWARs referenced: |
---|
569 | * AW_STRING, "tmp/con/alignment" : name of alignment |
---|
570 | * AW_STRING, "tmp/con/which_species" : only marked species ? |
---|
571 | * AW_STRING, "con/group" : allow grouping ? |
---|
572 | * AW_STRING, "con/countgaps" |
---|
573 | * AW_DOUBLE, "con/fupper" |
---|
574 | * AW_INT, "con/lower" |
---|
575 | * AW_INT, "con/gapbound" : result is '-' if more than |
---|
576 | * 'gapbound' per cent gaps |
---|
577 | * AW_DOUBLE, "con/fconsidbound" : if frequency of character is |
---|
578 | * more than 'considbound' per cent, this |
---|
579 | * character can contribute to groups |
---|
580 | * AW_STRING, "tmp/intcon/name" : save with this name |
---|
581 | * AW_STRING, "con/result" : result has one or more lines ? |
---|
582 | * |
---|
583 | * AWARs modified: x |
---|
584 | * |
---|
585 | * Dependencies: CON_maketables |
---|
586 | * CON_makestatistic |
---|
587 | * CON_makegrouptable |
---|
588 | * CON_evaluatestatistic |
---|
589 | * ----------------------------------------------------------------- |
---|
590 | */ |
---|
591 | static void CON_calculate_cb(AW_window *aw) |
---|
592 | { |
---|
593 | AW_root *awr = aw->get_root(); |
---|
594 | char *align = awr->awar("tmp/con/alignment")->read_string(); |
---|
595 | GB_ERROR error = 0; |
---|
596 | |
---|
597 | GB_push_transaction(GLOBAL.gb_main); |
---|
598 | |
---|
599 | long maxalignlen = GBT_get_alignment_len(GLOBAL.gb_main, align); |
---|
600 | if (maxalignlen <= 0) error = GB_export_errorf("alignment '%s' doesn't exist", align); |
---|
601 | |
---|
602 | if (!error) { |
---|
603 | int isamino = GBT_is_alignment_protein(GLOBAL.gb_main, align); |
---|
604 | int onlymarked = 1; |
---|
605 | int resultiscomplex = 1; |
---|
606 | |
---|
607 | { |
---|
608 | char *marked = awr->awar("tmp/con/which_species")->read_string(); |
---|
609 | char *complexresult = awr->awar("con/result")->read_string(); |
---|
610 | |
---|
611 | if (strcmp("marked", marked) != 0) onlymarked = 0; |
---|
612 | if (strcmp("complex", complexresult) != 0) resultiscomplex = 0; |
---|
613 | |
---|
614 | free(complexresult); |
---|
615 | free(marked); |
---|
616 | } |
---|
617 | |
---|
618 | |
---|
619 | // creating the table for characters and allocating memory for 'statistic' |
---|
620 | int *statistic[MAX_AMINOS+1]; |
---|
621 | int convtable[256]; |
---|
622 | CON_maketables(convtable, statistic, maxalignlen, isamino); |
---|
623 | |
---|
624 | // filling the statistic table |
---|
625 | arb_progress progress("Calculating consensus"); |
---|
626 | |
---|
627 | long nrofspecies = CON_makestatistic(statistic, convtable, align, onlymarked); |
---|
628 | double fupper = awr->awar("con/fupper")->read_float(); |
---|
629 | int lower = (int)awr->awar("con/lower")->read_int(); |
---|
630 | |
---|
631 | if (fupper>100.0) fupper = 100; |
---|
632 | if (fupper<0) fupper = 0; |
---|
633 | if (lower<0) lower = 0; |
---|
634 | |
---|
635 | if (lower>fupper) { |
---|
636 | error = "fault: lower greater than upper"; |
---|
637 | } |
---|
638 | else { |
---|
639 | |
---|
640 | double fconsidbound = awr->awar("con/fconsidbound")->read_float(); |
---|
641 | if (fconsidbound>100) fconsidbound = 100; |
---|
642 | if (fconsidbound<0) fconsidbound = 0; |
---|
643 | |
---|
644 | int gapbound = (int)awr->awar("con/gapbound")->read_int(); |
---|
645 | if (gapbound<0) gapbound = 0; |
---|
646 | if (gapbound>100) gapbound = 100; |
---|
647 | |
---|
648 | int groupallowed, countgap; |
---|
649 | { |
---|
650 | char *group = awr->awar("con/group")->read_string(); |
---|
651 | char *countgaps = awr->awar("con/countgaps")->read_string(); |
---|
652 | |
---|
653 | groupallowed = strcmp("on", group) == 0; |
---|
654 | countgap = strcmp("on", countgaps) == 0; |
---|
655 | |
---|
656 | free(countgaps); |
---|
657 | free(group); |
---|
658 | } |
---|
659 | |
---|
660 | // creating the table for groups |
---|
661 | char *groupflags[40]; |
---|
662 | char groupnames[40]; |
---|
663 | int numgroups = CON_makegrouptable(groupflags, groupnames, isamino, groupallowed); |
---|
664 | |
---|
665 | // calculate and export the result strings |
---|
666 | char *result = 0; |
---|
667 | CON_evaluatestatistic(result, statistic, groupflags, groupnames, (int)maxalignlen, fupper, lower, fconsidbound, gapbound, countgap, numgroups); |
---|
668 | |
---|
669 | char *savename = awr->awar("tmp/con/name")->read_string(); |
---|
670 | |
---|
671 | error = CON_export(savename, align, statistic, result, convtable, groupnames, |
---|
672 | onlymarked, nrofspecies, maxalignlen, countgap, gapbound, groupallowed, |
---|
673 | fconsidbound, fupper, lower, resultiscomplex); |
---|
674 | |
---|
675 | // freeing allocated memory |
---|
676 | free(savename); |
---|
677 | free(result); |
---|
678 | for (int i=0; i<MAX_GROUPS; i++) free(groupflags[i]); |
---|
679 | } |
---|
680 | |
---|
681 | CON_cleartables(statistic, isamino); |
---|
682 | } |
---|
683 | |
---|
684 | free(align); |
---|
685 | GB_end_transaction_show_error(GLOBAL.gb_main, error, aw_message); |
---|
686 | } |
---|
687 | |
---|
688 | void AP_create_consensus_var(AW_root *aw_root, AW_default aw_def) |
---|
689 | { |
---|
690 | GB_transaction ta(GLOBAL.gb_main); |
---|
691 | { |
---|
692 | char *defali = GBT_get_default_alignment(GLOBAL.gb_main); |
---|
693 | aw_root->awar_string("tmp/con/alignment", defali, aw_def); |
---|
694 | free(defali); |
---|
695 | } |
---|
696 | aw_root->awar_string("tmp/con/which_species", "marked", aw_def); |
---|
697 | aw_root->awar_string("con/group", "off", aw_def); |
---|
698 | aw_root->awar_string("con/countgaps", "on", aw_def); |
---|
699 | aw_root->awar_float("con/fupper", 95, aw_def); |
---|
700 | aw_root->awar_int("con/lower", 70, aw_def); |
---|
701 | aw_root->awar_int("con/gapbound", 60, aw_def); |
---|
702 | aw_root->awar_float("con/fconsidbound", 30, aw_def); |
---|
703 | aw_root->awar_string("tmp/con/name", "CONSENSUS", aw_def); |
---|
704 | aw_root->awar_string("con/result", "single line", aw_def); |
---|
705 | |
---|
706 | aw_root->awar_string(AWAR_MAX_FREQ_SAI_NAME, "MAX_FREQUENCY", aw_def); |
---|
707 | aw_root->awar_int(AWAR_MAX_FREQ_NO_GAPS, 1, aw_def); |
---|
708 | |
---|
709 | } |
---|
710 | |
---|
711 | // Open window to show IUPAC tables |
---|
712 | static AW_window * CON_showgroupswin_cb(AW_root *aw_root) |
---|
713 | { |
---|
714 | AW_window_simple *aws = new AW_window_simple; |
---|
715 | aws->init(aw_root, "SHOW_IUPAC", "Show IUPAC"); |
---|
716 | aws->load_xfig("consensus/groups.fig"); |
---|
717 | aws->button_length(7); |
---|
718 | |
---|
719 | aws->at("ok"); aws->callback((AW_CB0)AW_POPDOWN); |
---|
720 | aws->create_button("CLOSE", "CLOSE", "O"); |
---|
721 | |
---|
722 | return (AW_window *)aws; |
---|
723 | } |
---|
724 | |
---|
725 | AW_window *AP_create_con_expert_window(AW_root *aw_root) { |
---|
726 | AW_window_simple *aws = new AW_window_simple; |
---|
727 | aws->init(aw_root, "BUILD_CONSENSUS", "CONSENSUS OF SEQUENCES"); |
---|
728 | aws->load_xfig("consensus/expert.fig"); |
---|
729 | aws->button_length(6); |
---|
730 | |
---|
731 | aws->at("cancel"); aws->callback((AW_CB0)AW_POPDOWN); |
---|
732 | aws->create_button("CLOSE", "CLOSE", "C"); |
---|
733 | |
---|
734 | aws->at("help"); aws->callback(makeHelpCallback("consensus.hlp")); |
---|
735 | aws->create_button("HELP", "HELP", "H"); |
---|
736 | |
---|
737 | aws->button_length(10); |
---|
738 | aws->at("showgroups"); aws->callback(AW_POPUP, (AW_CL)CON_showgroupswin_cb, 0); |
---|
739 | aws->create_button("SHOW_IUPAC", "show\nIUPAC...", "s"); |
---|
740 | aws->button_length(10); |
---|
741 | |
---|
742 | aws->at("which_species"); |
---|
743 | aws->create_toggle_field("tmp/con/which_species", NULL, ""); |
---|
744 | aws->insert_toggle("all", "1", "all"); |
---|
745 | aws->insert_default_toggle("marked", "1", "marked"); |
---|
746 | aws->update_toggle_field(); |
---|
747 | |
---|
748 | aws->at("which_alignment"); |
---|
749 | awt_create_selection_list_on_alignments(GLOBAL.gb_main, (AW_window *)aws, "tmp/con/alignment", "*="); |
---|
750 | |
---|
751 | aws->button_length(15); |
---|
752 | |
---|
753 | // activation of consensus calculation by button ... |
---|
754 | aws->at("calculate"); aws->callback((AW_CB0)CON_calculate_cb); |
---|
755 | aws->create_button("GO", "GO", "G"); |
---|
756 | |
---|
757 | aws->at("group"); |
---|
758 | aws->create_toggle_field("con/group", NULL, ""); |
---|
759 | aws->insert_toggle("on", "1", "on"); |
---|
760 | aws->insert_default_toggle("off", "1", "off"); |
---|
761 | aws->update_toggle_field(); |
---|
762 | |
---|
763 | aws->at("countgaps"); |
---|
764 | aws->create_toggle_field("con/countgaps", NULL, ""); |
---|
765 | aws->insert_toggle("on", "1", "on"); |
---|
766 | aws->insert_default_toggle("off", "1", "off"); |
---|
767 | aws->update_toggle_field(); |
---|
768 | |
---|
769 | aws->at("upper"); |
---|
770 | aws->create_input_field("con/fupper", 4); |
---|
771 | |
---|
772 | aws->at("lower"); |
---|
773 | aws->create_input_field("con/lower", 4); |
---|
774 | |
---|
775 | aws->at("considbound"); |
---|
776 | aws->create_input_field("con/fconsidbound", 4); |
---|
777 | |
---|
778 | aws->at("gapbound"); |
---|
779 | aws->create_input_field("con/gapbound", 4); |
---|
780 | |
---|
781 | aws->at("name"); |
---|
782 | aws->create_input_field("tmp/con/name", 10); |
---|
783 | |
---|
784 | aws->at("result"); |
---|
785 | aws->create_toggle_field("con/result", NULL, ""); |
---|
786 | aws->insert_toggle("single line", "1", "single line"); |
---|
787 | aws->insert_default_toggle("complex", "1", "complex"); |
---|
788 | aws->update_toggle_field(); |
---|
789 | |
---|
790 | aws->at("save_box"); |
---|
791 | awt_create_selection_list_on_sai(GLOBAL.gb_main, aws, "tmp/con/name", false); |
---|
792 | |
---|
793 | return aws; |
---|
794 | } |
---|
795 | |
---|
796 | /* ----------------------------------------------------------------- |
---|
797 | * Function: CON_calc_max_freq_cb( AW_window *aw) |
---|
798 | * |
---|
799 | * Description: Gets the maximum frequency for each columns. |
---|
800 | * |
---|
801 | * NOTE: |
---|
802 | * |
---|
803 | * ----------------------------------------------------------------- |
---|
804 | */ |
---|
805 | |
---|
806 | static void CON_calc_max_freq_cb(AW_window *aw) { |
---|
807 | arb_assert(!GB_have_error()); |
---|
808 | |
---|
809 | AW_root *awr = aw->get_root(); |
---|
810 | GB_ERROR error = NULL; |
---|
811 | |
---|
812 | GB_transaction ta(GLOBAL.gb_main); |
---|
813 | |
---|
814 | char *align = GBT_get_default_alignment(GLOBAL.gb_main); |
---|
815 | long maxalignlen = GBT_get_alignment_len(GLOBAL.gb_main, align); |
---|
816 | |
---|
817 | if (maxalignlen<=0) { |
---|
818 | GB_clear_error(); |
---|
819 | error = "alignment doesn't exist!"; |
---|
820 | } |
---|
821 | else { |
---|
822 | int isamino = GBT_is_alignment_protein(GLOBAL.gb_main, align); |
---|
823 | |
---|
824 | arb_progress progress("Calculating max. frequency"); |
---|
825 | |
---|
826 | int *statistic[MAX_AMINOS+1]; |
---|
827 | int convtable[256]; |
---|
828 | CON_maketables(convtable, statistic, maxalignlen, isamino); |
---|
829 | |
---|
830 | const int onlymarked = 1; |
---|
831 | long nrofspecies = CON_makestatistic(statistic, convtable, align, onlymarked); |
---|
832 | |
---|
833 | int end = isamino ? MAX_AMINOS : MAX_BASES; |
---|
834 | |
---|
835 | char *result1 = new char[maxalignlen+1]; |
---|
836 | char *result2 = new char[maxalignlen+1]; |
---|
837 | |
---|
838 | result1[maxalignlen] = 0; |
---|
839 | result2[maxalignlen] = 0; |
---|
840 | |
---|
841 | long no_gaps = awr->awar(AWAR_MAX_FREQ_NO_GAPS)->read_int(); |
---|
842 | |
---|
843 | for (int pos = 0; pos < maxalignlen; pos++) { |
---|
844 | int sum = 0; |
---|
845 | int max = 0; |
---|
846 | |
---|
847 | for (int i=0; i<end; i++) { |
---|
848 | if (no_gaps && (i == convtable[(unsigned char)'-'])) continue; |
---|
849 | sum += statistic[i][pos]; |
---|
850 | if (statistic[i][pos] > max) max = statistic[i][pos]; |
---|
851 | } |
---|
852 | if (sum == 0) { |
---|
853 | result1[pos] = '='; |
---|
854 | result2[pos] = '='; |
---|
855 | } |
---|
856 | else { |
---|
857 | result1[pos] = "01234567890"[(( 10*max)/sum)%11]; // @@@ why %11? |
---|
858 | result2[pos] = "01234567890"[((100*max)/sum)%10]; |
---|
859 | } |
---|
860 | } |
---|
861 | |
---|
862 | const char *savename = awr->awar(AWAR_MAX_FREQ_SAI_NAME)->read_char_pntr(); |
---|
863 | GBDATA *gb_extended = GBT_find_or_create_SAI(GLOBAL.gb_main, savename); |
---|
864 | if (!gb_extended) { |
---|
865 | error = GB_await_error(); |
---|
866 | } |
---|
867 | else { |
---|
868 | GBDATA *gb_data1 = GBT_add_data(gb_extended, align, "data", GB_STRING); |
---|
869 | GBDATA *gb_data2 = GBT_add_data(gb_extended, align, "dat2", GB_STRING); |
---|
870 | |
---|
871 | error = GB_write_string(gb_data1, result1); |
---|
872 | if (!error) error = GB_write_string(gb_data2, result2); |
---|
873 | |
---|
874 | GBDATA *gb_options = GBT_add_data(gb_extended, align, "_TYPE", GB_STRING); |
---|
875 | |
---|
876 | if (!error) { |
---|
877 | const char *type = GBS_global_string("MFQ: [species: %li] [exclude gaps: %li]", nrofspecies, no_gaps); |
---|
878 | error = GB_write_string(gb_options, type); |
---|
879 | } |
---|
880 | } |
---|
881 | |
---|
882 | delete [] result1; |
---|
883 | delete [] result2; |
---|
884 | CON_cleartables(statistic, isamino); |
---|
885 | } |
---|
886 | |
---|
887 | error = ta.close(error); |
---|
888 | if (error) aw_message(error); |
---|
889 | |
---|
890 | free(align); |
---|
891 | |
---|
892 | arb_assert(!GB_have_error()); |
---|
893 | } |
---|
894 | |
---|
895 | AW_window *AP_create_max_freq_window(AW_root *aw_root) { |
---|
896 | AW_window_simple *aws = new AW_window_simple; |
---|
897 | aws->init(aw_root, "MAX_FREQUENCY", "MAX FREQUENCY"); |
---|
898 | aws->load_xfig("consensus/max_freq.fig"); |
---|
899 | |
---|
900 | GB_push_transaction(GLOBAL.gb_main); |
---|
901 | |
---|
902 | aws->button_length(6); |
---|
903 | |
---|
904 | aws->at("cancel"); aws->callback((AW_CB0)AW_POPDOWN); |
---|
905 | aws->create_button("CLOSE", "CLOSE", "C"); |
---|
906 | |
---|
907 | aws->at("help"); aws->callback(makeHelpCallback("max_freq.hlp")); |
---|
908 | aws->create_button("HELP", "HELP", "H"); |
---|
909 | |
---|
910 | // activation of consensus calculation by button ... |
---|
911 | aws->at("go"); aws->callback((AW_CB0)CON_calc_max_freq_cb); |
---|
912 | aws->create_button("GO", "GO", "C"); |
---|
913 | |
---|
914 | aws->at("save"); |
---|
915 | aws->create_input_field(AWAR_MAX_FREQ_SAI_NAME, 1); |
---|
916 | |
---|
917 | aws->at("sai"); |
---|
918 | awt_create_selection_list_on_sai(GLOBAL.gb_main, aws, AWAR_MAX_FREQ_SAI_NAME, false); |
---|
919 | |
---|
920 | aws->at("gaps"); |
---|
921 | aws->create_toggle(AWAR_MAX_FREQ_NO_GAPS); |
---|
922 | |
---|
923 | GB_pop_transaction(GLOBAL.gb_main); |
---|
924 | |
---|
925 | return (AW_window *)aws; |
---|
926 | } |
---|
927 | |
---|