1 | /* ----------------------------------------------------------------- |
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2 | * Project: ARB |
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3 | * |
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4 | * Module: conservation profile [abbrev.: CPRO] |
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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: |
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11 | * AWARS |
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12 | * AW_STRING, "cpro/alignment" : name of alignment |
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13 | * AW_STRING, "cpro/which_species" : all/marked |
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14 | * AW_STRING, "cpro/countgaps" : if off, drop gaps |
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15 | * AW_FLOAT, "cpro/rateofgroup" : how to rate, when two |
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16 | * characters belong to the same group [ 0.0 means don't rate ] |
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17 | * AW_INT, AWAR_CURSOR_POSITION: |
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18 | * column shown in func. CPRO_drawstatistic_cb |
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19 | * |
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20 | * Global Structures: CPRO |
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21 | * |
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22 | * Private Classes: . |
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23 | * |
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24 | * Private Functions: . |
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25 | * |
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26 | * Private Variables: . |
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27 | * |
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28 | * Dependencies: Needs cprofile.fig, CPROdraw.fig, CPROdens.fig |
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29 | * CPROxpert.fig CPROcalc.fig |
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30 | * |
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31 | * Description: x |
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32 | * |
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33 | * Integration Notes: The main function using this module must have a |
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34 | * callback to the function |
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35 | * AW_window *AP_open_cprofile_window( AW_root *aw_root) |
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36 | * and the function void create_consensus_var |
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37 | * (AW_root *aw_root, AW_default aw_def) has to be called. |
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38 | * |
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39 | * ----------------------------------------------------------------- |
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40 | */ |
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41 | #include <cstdlib> |
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42 | #include <cstdio> |
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43 | #include <cstring> |
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44 | #include <cmath> |
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45 | |
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46 | #include <memory.h> |
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47 | |
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48 | #include <iostream> |
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49 | |
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50 | #include <arbdb.h> |
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51 | #include <arbdbt.h> |
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52 | #include <aw_root.hxx> |
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53 | #include <aw_device.hxx> |
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54 | #include <aw_window.hxx> |
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55 | #include <aw_awars.hxx> |
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56 | #include <aw_global.hxx> |
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57 | #include <awt.hxx> |
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58 | #include <awt_sel_boxes.hxx> |
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59 | |
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60 | #define ap_assert(cond) arb_assert(cond) |
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61 | |
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62 | typedef GB_UINT4 STATTYPE; |
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63 | extern GBDATA *GLOBAL_gb_main; |
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64 | enum { |
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65 | GAP = 1, |
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66 | BAS_A = 2, |
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67 | BAS_C = 3, |
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68 | BAS_G = 4, |
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69 | BAS_T = 5 , |
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70 | MAX_BASES = 6, |
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71 | MAX_AMINOS =27+GAP |
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72 | }; |
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73 | #define GC_black 7 |
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74 | #define GC_blue 6 |
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75 | #define GC_green 5 |
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76 | #define GC_grid 4 |
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77 | |
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78 | |
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79 | struct CPRO_result_struct { |
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80 | STATTYPE **statistic; |
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81 | long maxalignlen; // length of longest sequence |
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82 | long resolution; // resolution of statistic table |
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83 | float ratio; // ratio between transitions and transversion |
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84 | long maxaccu; // highest number of compares per distance |
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85 | long memneeded; // memory required for this statistic |
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86 | char which_species[20]; // "marked vs all" , ... |
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87 | char drawmode; // smoothing |
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88 | char alignname[80]; // name of alignment |
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89 | char statisticexists; // was there yet a statistic calculated/loaded ? |
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90 | long leastcompares; // if less overlap between two sequences |
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91 | // comparison doesn't contribute to statistic |
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92 | long countgaps; // if 0, comparisons with gaps are not counted |
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93 | }; |
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94 | |
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95 | struct CPRO_struct { |
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96 | long numspecies; // number of species |
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97 | long maxresneeded; // not yet used (max distance of calculation) |
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98 | long partition; // size of partition in matrix of compares |
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99 | long leastaccu; // if less compares per distance don't show |
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100 | char *agonist; // list of species that contribute to statistic |
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101 | char *antagonist; // -^- |
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102 | char convtable[256]; // converts character to a token |
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103 | char grouptable[MAX_AMINOS]; // gives number of group, in which token is |
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104 | // member |
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105 | float grouprate; // ratio between transitions and transversions |
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106 | float distancecorrection; // results out of grouprate |
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107 | long column; // column of alignment that is shown |
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108 | float maxdistance; // statistic shows up to this point of distance |
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109 | long gridhorizontal; // grid over statistic |
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110 | long gridvertical; // -^- |
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111 | float Z_it_group; // last value , needed for smoothing |
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112 | float Z_it_equal; // -^- |
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113 | struct CPRO_result_struct result[2]; // info needed for each statistic |
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114 | } CPRO; |
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115 | |
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116 | |
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117 | /* ----------------------------------------------------------------- |
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118 | * Function: CPRO_readandallocate |
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119 | * |
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120 | * Arguments: char versus,char *align (name of alignment) |
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121 | * |
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122 | * Returns: modifies: |
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123 | * char **&speciesdata,GBDATA **&speciesdatabase |
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124 | * |
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125 | * Description: Memory for 'statistic', 'speciesdata', 'speciesdatabase', |
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126 | * 'agonist' and 'antagonist' is allocated. |
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127 | * Pointers to the sequences in the database are |
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128 | * read into array 'speciesdatabase'. |
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129 | * |
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130 | * |
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131 | * NOTE: . |
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132 | * |
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133 | * Global Variables referenced: . |
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134 | * |
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135 | * Global Variables modified: CPRO.agonist,CPRO.antagonist,CPRO.numspecies |
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136 | * |
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137 | * AWARs referenced: . |
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138 | * |
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139 | * AWARs modified: x |
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140 | * |
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141 | * Dependencies: . |
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142 | * ----------------------------------------------------------------- |
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143 | */ |
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144 | static void CPRO_readandallocate(char **&speciesdata,GBDATA **&speciesdatabase, |
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145 | char versus,char *align) |
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146 | { |
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147 | GBDATA *gb_species_data = GB_search(GLOBAL_gb_main,"species_data",GB_FIND); |
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148 | GBDATA *gb_species; |
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149 | |
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150 | aw_status("reading database"); |
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151 | |
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152 | long nrofspecies=0; |
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153 | gb_species = GBT_first_species_rel_species_data(gb_species_data); |
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154 | while(gb_species) |
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155 | { |
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156 | if(GBT_read_sequence(gb_species,align)){ |
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157 | nrofspecies++; } |
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158 | gb_species = GBT_next_species(gb_species); |
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159 | } |
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160 | CPRO.numspecies=nrofspecies; |
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161 | |
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162 | speciesdata=(char **)calloc((size_t)CPRO.numspecies,sizeof(char *)); |
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163 | CPRO.agonist=(char *)calloc((size_t)CPRO.numspecies,sizeof(char)); |
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164 | CPRO.antagonist=(char *)calloc((size_t)CPRO.numspecies,sizeof(char)); |
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165 | speciesdatabase=(GBDATA **)calloc((size_t)CPRO.numspecies+1,sizeof(GBDATA *)); // Null termintated |
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166 | GBDATA *alidata; |
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167 | |
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168 | long countspecies=0; |
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169 | gb_species = GBT_first_species_rel_species_data(gb_species_data); |
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170 | while(gb_species) |
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171 | { |
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172 | if( (alidata=GBT_read_sequence(gb_species,align)) ) |
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173 | { |
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174 | speciesdatabase[countspecies++]=alidata; |
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175 | } |
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176 | gb_species = GBT_next_species(gb_species); |
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177 | } |
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178 | |
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179 | for(long i=0;i<CPRO.numspecies;i++) |
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180 | { |
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181 | CPRO.agonist[i]=1; |
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182 | CPRO.antagonist[i]=1; |
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183 | } |
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184 | |
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185 | if(versus!=0) |
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186 | { |
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187 | for(long j=0;j<CPRO.numspecies;j++) |
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188 | { |
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189 | CPRO.antagonist[j]=0; |
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190 | if(GB_read_flag(GB_get_grandfather(speciesdatabase[j]))) |
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191 | CPRO.antagonist[j]=(char)1; |
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192 | } |
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193 | } |
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194 | if(versus==1) |
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195 | { |
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196 | long j; |
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197 | for(j=0;j<CPRO.numspecies;j++) CPRO.agonist[j]=CPRO.antagonist[j]; |
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198 | } |
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199 | } |
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200 | |
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201 | // frees memory allocated by function CPRO_readandallocate |
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202 | static void CPRO_deallocate(char **&speciesdata,GBDATA **&speciesdatabase) |
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203 | { |
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204 | for (long i=0;i<CPRO.numspecies;i++) freeset(speciesdata[i], 0); |
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205 | freeset(speciesdata, 0); |
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206 | |
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207 | free(speciesdatabase); |
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208 | free(CPRO.agonist); |
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209 | free(CPRO.antagonist); |
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210 | // 'CPRO.statistic' must not be freed, because it is needed in |
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211 | // function CPRO_drawstatistic |
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212 | } |
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213 | |
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214 | static void CPRO_allocstatistic(unsigned char which_statistic) |
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215 | { |
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216 | CPRO.result[which_statistic].statistic=(STATTYPE **)calloc((size_t)CPRO.result[which_statistic].resolution*3+3, sizeof(STATTYPE *)); |
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217 | for (long i=0;i<CPRO.result[which_statistic].resolution*3;i++) { |
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218 | CPRO.result[which_statistic].statistic[i]=(STATTYPE *)calloc((size_t)CPRO.result[which_statistic].maxalignlen, sizeof(STATTYPE)); |
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219 | } |
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220 | } |
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221 | |
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222 | static void CPRO_freestatistic(unsigned char which_statistic) |
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223 | { |
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224 | for(long j=0;j<CPRO.result[which_statistic].resolution*3;j++) { |
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225 | freeset(CPRO.result[which_statistic].statistic[j], 0); |
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226 | } |
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227 | freeset(CPRO.result[which_statistic].statistic, 0); |
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228 | } |
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229 | |
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230 | // memory not used is given back to system |
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231 | static void CPRO_workupstatistic(unsigned char which_statistic) |
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232 | { |
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233 | long base; |
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234 | long column,colmax,memneeded=0; |
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235 | long sum,hits,different,group; |
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236 | long hitsc,diffc,groupc; |
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237 | CPRO.maxresneeded=0; |
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238 | CPRO.result[which_statistic].maxaccu=0; |
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239 | for(long res=0;res<CPRO.result[which_statistic].resolution;res++) |
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240 | { |
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241 | base=res*3; |
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242 | hits=0;different=0;group=0; |
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243 | for(column=0;column<CPRO.result[which_statistic].maxalignlen;column++) |
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244 | { |
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245 | hitsc=(long)CPRO.result[which_statistic].statistic[base+0][column]; |
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246 | groupc=(long)CPRO.result[which_statistic].statistic[base+1][column]; |
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247 | diffc=(long)CPRO.result[which_statistic].statistic[base+2][column]; |
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248 | sum=hitsc+groupc+diffc; |
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249 | hits+=hitsc; group+=groupc; different+=diffc; |
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250 | |
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251 | if(sum) CPRO.maxresneeded=res+1; |
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252 | if(sum>CPRO.result[which_statistic].maxaccu) |
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253 | { |
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254 | CPRO.result[which_statistic].maxaccu=sum; |
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255 | colmax=column; |
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256 | } |
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257 | } |
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258 | if (hits) memneeded += CPRO.result[which_statistic].maxalignlen; |
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259 | else freeset(CPRO.result[which_statistic].statistic[base+0], 0); |
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260 | |
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261 | if (group) memneeded += CPRO.result[which_statistic].maxalignlen; |
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262 | else freeset(CPRO.result[which_statistic].statistic[base+1], 0); |
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263 | |
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264 | if (different) memneeded += CPRO.result[which_statistic].maxalignlen; |
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265 | else freeset(CPRO.result[which_statistic].statistic[base+2], 0); |
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266 | } |
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267 | if(!CPRO.result[which_statistic].maxaccu) CPRO.result[which_statistic].maxaccu=1; |
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268 | CPRO.result[which_statistic].memneeded=memneeded; |
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269 | } |
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270 | |
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271 | |
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272 | /* ----------------------------------------------------------------- |
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273 | * Function: CPRO_maketables |
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274 | * |
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275 | * Arguments: char isamino |
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276 | * |
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277 | * Returns: modifies: char *CPRO.convtable, |
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278 | * char *CPRO.grouptable |
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279 | * |
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280 | * Description: Fills tables CPRO.convtable and CPRO.grouptable, that are |
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281 | * used later, when making the statistic. Meaning of tables: |
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282 | * E.g. CPRO.convtable['a']=BAS_A means that char. 'a' is |
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283 | * converted into number BAS_A. Then CPRO.grouptable[BAS_A]=1 |
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284 | * and CPRO.grouptable[BAS_G]=1 means, that characters 'a' |
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285 | * and 'g' are both members of group 1. |
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286 | * |
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287 | * NOTE: . |
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288 | * |
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289 | * Global Variables referenced: . |
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290 | * |
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291 | * Global Variables modified: char *CPRO.convtable, char *CPRO.grouptable |
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292 | * |
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293 | * AWARs referenced: . |
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294 | * |
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295 | * AWARs modified: x |
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296 | * |
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297 | * Dependencies: . |
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298 | * ----------------------------------------------------------------- |
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299 | */ |
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300 | static void CPRO_maketables(char isamino,char countgaps) |
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301 | { |
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302 | long i; |
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303 | for(i=0;i<256;i++) { |
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304 | CPRO.convtable[i]=0; } |
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305 | if(!isamino) |
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306 | { |
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307 | if (countgaps) CPRO.convtable[(unsigned char)'-']=GAP; |
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308 | CPRO.convtable[(unsigned char)'a']=BAS_A; CPRO.convtable[(unsigned char)'A']=BAS_A; |
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309 | CPRO.convtable[(unsigned char)'c']=BAS_C; CPRO.convtable[(unsigned char)'C']=BAS_C; |
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310 | CPRO.convtable[(unsigned char)'g']=BAS_G; CPRO.convtable[(unsigned char)'G']=BAS_G; |
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311 | CPRO.convtable[(unsigned char)'t']=BAS_T; CPRO.convtable[(unsigned char)'T']=BAS_T; |
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312 | CPRO.convtable[(unsigned char)'u']=BAS_T; CPRO.convtable[(unsigned char)'U']=BAS_T; |
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313 | |
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314 | for (i=0;i<MAX_AMINOS;i++) { |
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315 | CPRO.grouptable[i]=0; |
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316 | } |
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317 | CPRO.grouptable[BAS_A]=1; CPRO.grouptable[BAS_G]=1; |
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318 | CPRO.grouptable[BAS_C]=2; CPRO.grouptable[BAS_T]=2; |
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319 | } |
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320 | else |
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321 | { |
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322 | if (countgaps) CPRO.convtable[(unsigned char)'-'] =GAP; |
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323 | for(i=0;i<MAX_AMINOS;i++) |
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324 | { |
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325 | CPRO.convtable[(unsigned char)'a'+i] = i+1+GAP; |
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326 | CPRO.convtable[(unsigned char)'A'+i] = i+1+GAP; |
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327 | } |
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328 | CPRO.convtable[(unsigned char)'*'] = 10+GAP ; /* 'J' */ |
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329 | |
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330 | for(i=0;i<MAX_AMINOS;i++) CPRO.grouptable[i] = 0; |
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331 | |
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332 | #define SC(x,P) CPRO.grouptable[(unsigned char)P-(unsigned char)'A'+1+GAP] = x |
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333 | SC(1,'P');SC(1,'A');SC(1,'G');SC(1,'S');SC(1,'T'); |
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334 | /* PAGST */ |
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335 | SC(2,'Q');SC(2,'N');SC(2,'E');SC(2,'D');SC(2,'B'); |
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336 | SC(2,'Z'); /* QNEDBZ */ |
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337 | SC(3,'H');SC(3,'K');SC(3,'R'); |
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338 | /* HKR */ |
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339 | SC(4,'L');SC(4,'I');SC(4,'V');SC(4,'M'); |
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340 | /* LIVM */ |
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341 | SC(5,'F');SC(5,'Y');SC(5,'W'); |
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342 | /* FYW */ |
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343 | #undef SC |
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344 | } |
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345 | } |
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346 | |
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347 | |
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348 | static void CPRO_entryinstatistic(char **speciesdata, long elemx,long elemy, unsigned char which_statistic) |
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349 | { |
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350 | unsigned char value1, value2 = 0; |
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351 | char *firstseq = speciesdata[elemx]; |
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352 | char *secondseq = speciesdata[elemy]; |
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353 | float rate = 0.0; |
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354 | long numofcolumns = 0; |
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355 | float distance = 0.0; |
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356 | |
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357 | |
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358 | if(elemx==elemy) return; |
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359 | if(!(CPRO.agonist[elemx])) return; |
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360 | if(!(CPRO.antagonist[elemy])) return; |
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361 | if((CPRO.agonist[elemy])&&(CPRO.antagonist[elemx])&&(elemy<elemx)) return; |
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362 | |
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363 | //add similarities (added 1.0 means equal, 0.0 means different) |
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364 | long counter; |
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365 | for(counter=0;counter<CPRO.result[which_statistic].maxalignlen;counter++) |
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366 | { |
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367 | if((value1=*firstseq)&&(value2=*secondseq)) |
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368 | { |
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369 | numofcolumns++; |
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370 | if(value1==value2) { |
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371 | rate=rate+1.0; } |
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372 | else if(CPRO.grouptable[value1]==CPRO.grouptable[value2]) { |
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373 | rate=rate+CPRO.grouprate; } // add transition weighted |
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374 | // between 1.0 and 0.0 |
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375 | } |
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376 | firstseq++; |
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377 | secondseq++; |
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378 | } |
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379 | |
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380 | if(numofcolumns<CPRO.result[which_statistic].leastcompares) return; |
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381 | distance=((float)numofcolumns-rate)/(float)numofcolumns; |
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382 | distance=distance*CPRO.distancecorrection; |
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383 | |
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384 | long column=(long)(distance*CPRO.result[which_statistic].resolution); |
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385 | |
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386 | if (column < 0 || column>= CPRO.result[which_statistic].resolution) return; |
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387 | |
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388 | STATTYPE *equalentry = CPRO.result[which_statistic].statistic[3*column]; |
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389 | STATTYPE *samegroupentry = CPRO.result[which_statistic].statistic[3*column+1]; |
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390 | STATTYPE *differententry = CPRO.result[which_statistic].statistic[3*column+2]; |
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391 | |
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392 | firstseq = speciesdata[elemx]; |
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393 | secondseq = speciesdata[elemy]; |
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394 | |
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395 | for(counter=0;counter<CPRO.result[which_statistic].maxalignlen;counter++) |
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396 | { |
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397 | if((value1=*firstseq)&&(value2=*secondseq)) |
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398 | // when gap or unaligned base goto next position |
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399 | { |
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400 | if(value1==value2) { (*equalentry)++; } |
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401 | else if(CPRO.grouptable[value1]==CPRO.grouptable[value2]) { |
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402 | (*samegroupentry)++; } |
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403 | else { (*differententry)++; } |
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404 | } |
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405 | firstseq++; |
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406 | secondseq++; |
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407 | equalentry++; |
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408 | samegroupentry++; |
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409 | differententry++; |
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410 | } |
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411 | |
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412 | |
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413 | |
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414 | } |
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415 | |
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416 | // is used by function CPRO_makestatistic |
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417 | // reads sequences of a segment into memory, converts them |
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418 | // and frees older sequences |
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419 | static void CPRO_readneededdata(char **speciesdata,GBDATA **speciesdatabase, |
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420 | long elemx1,long elemx2,long elemy1,long elemy2,unsigned char which_statistic) |
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421 | { |
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422 | long i=0,j=0; |
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423 | const char *tempdata; |
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424 | for(i=0;i<CPRO.numspecies;i++) { |
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425 | if ( (speciesdata[i]) && (i<elemy1) && (i>elemy2) && (i<elemx1) && (i>elemx2) ) { |
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426 | delete(speciesdata[i]); speciesdata[i]=0; |
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427 | } |
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428 | } |
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429 | |
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430 | if (elemx1<CPRO.numspecies) { |
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431 | for (i=elemx1;(i<=elemx2 && i<CPRO.numspecies);i++) { |
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432 | if ((CPRO.agonist[i])&&(!(speciesdata[i])) ) { |
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433 | tempdata=GB_read_char_pntr(speciesdatabase[i]); |
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434 | speciesdata[i]=(char*)calloc((unsigned int) CPRO.result[which_statistic].maxalignlen,1); |
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435 | for(j=0;j<CPRO.result[which_statistic].maxalignlen;j++) { |
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436 | speciesdata[i][j]=CPRO.convtable[(unsigned char)tempdata[j]]; |
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437 | } |
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438 | } |
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439 | } |
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440 | } |
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441 | if(elemy1<CPRO.numspecies) { |
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442 | for(i=elemy1;(i<=elemy2 && i<CPRO.numspecies);i++) { |
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443 | if( (CPRO.antagonist[i])&&(!(speciesdata[i])) ) { |
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444 | tempdata=GB_read_char_pntr(speciesdatabase[i]); |
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445 | speciesdata[i]=(char*)calloc((unsigned int) CPRO.result[which_statistic].maxalignlen,1); |
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446 | for(j=0;j<CPRO.result[which_statistic].maxalignlen;j++) { |
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447 | speciesdata[i][j]=CPRO.convtable[(unsigned char)tempdata[j]]; |
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448 | } |
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449 | } |
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450 | } |
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451 | } |
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452 | } |
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453 | |
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454 | |
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455 | /* ----------------------------------------------------------------- |
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456 | * Function: CPRO_makestatistic |
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457 | * |
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458 | * Arguments: char **speciesdata, |
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459 | * GBDATA **speciesdatabase |
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460 | * |
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461 | * Returns: 1 if successful, 0 if user abort |
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462 | * (without consequences) |
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463 | * |
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464 | * Description: This function compares every sequence with every sequence. |
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465 | * It devides the matrix into segments and goes through each |
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466 | * segment. Width of a segment depends on CPRO.partition. |
---|
467 | * MAX_MEMORY/2 is available. |
---|
468 | * When a new segment is entered, the corresponding |
---|
469 | * sequences are loaded into array 'speciesdata' by the function |
---|
470 | * CPRO_readneededdata. 'speciesdatabase' contains pointers of |
---|
471 | * sequences to the database. Comparison and evaluation of two |
---|
472 | * sequences is done by function CPRO_entryinstatistic. |
---|
473 | * |
---|
474 | * NOTE: . |
---|
475 | * |
---|
476 | * Global Variables referenced: |
---|
477 | * CPRO.numspecies,CPRO.result[which_statistic].maxalignlen |
---|
478 | * |
---|
479 | * Global Variables modified: x |
---|
480 | * |
---|
481 | * AWARs referenced: . |
---|
482 | * |
---|
483 | * AWARs modified: CPRO.result[which_statistic].statistic is modified |
---|
484 | * |
---|
485 | * Dependencies: CPRO_entryinstatistic , CPRO_readneededdata |
---|
486 | * ----------------------------------------------------------------- |
---|
487 | */ |
---|
488 | static char CPRO_makestatistic(char **speciesdata,GBDATA **speciesdatabase, unsigned char which_statistic) |
---|
489 | { |
---|
490 | long widthmatrix=CPRO.partition; |
---|
491 | long n=CPRO.numspecies; |
---|
492 | long comparesneeded=n*n; // (n*n-n)/2; |
---|
493 | long compares=0; |
---|
494 | long numofsegments=CPRO.numspecies/widthmatrix +1; |
---|
495 | long segmentx=0,segmenty=0,elemx=0,elemy=0; |
---|
496 | long elemx1=0,elemx2=0,elemy1=0,elemy2=0; |
---|
497 | |
---|
498 | if(CPRO.result[which_statistic].statisticexists) |
---|
499 | { |
---|
500 | CPRO_freestatistic(which_statistic); |
---|
501 | } |
---|
502 | else CPRO.result[which_statistic].statisticexists=1; |
---|
503 | |
---|
504 | CPRO_allocstatistic(which_statistic); |
---|
505 | |
---|
506 | aw_status("calculating"); |
---|
507 | |
---|
508 | for(segmentx=0;segmentx<numofsegments;segmentx++) |
---|
509 | { |
---|
510 | elemx1=widthmatrix*segmentx; |
---|
511 | elemx2=widthmatrix*(segmentx+1)-1; |
---|
512 | for(segmenty=0;segmenty<numofsegments;segmenty++) |
---|
513 | { |
---|
514 | elemy1=widthmatrix*segmenty; |
---|
515 | elemy2=widthmatrix*(segmenty+1)-1; |
---|
516 | //printf("Partition by %ld , %ld\n",elemx1,elemy1); |
---|
517 | CPRO_readneededdata(speciesdata,speciesdatabase, |
---|
518 | elemx1,elemx2,elemy1,elemy2,which_statistic); |
---|
519 | for(elemx=elemx1;elemx<=elemx2;elemx++) |
---|
520 | { |
---|
521 | for(elemy=elemy1;elemy<=elemy2;elemy++) |
---|
522 | { |
---|
523 | if((elemy<CPRO.numspecies)&&(elemx<CPRO.numspecies)) |
---|
524 | { |
---|
525 | CPRO_entryinstatistic(speciesdata, |
---|
526 | elemx,elemy,which_statistic); |
---|
527 | compares++; |
---|
528 | if(((compares/30)*30)==compares) |
---|
529 | { |
---|
530 | if(aw_status((double)compares |
---|
531 | /(double)comparesneeded)) return(0); |
---|
532 | } |
---|
533 | } |
---|
534 | } |
---|
535 | } |
---|
536 | } |
---|
537 | } |
---|
538 | return(1); |
---|
539 | } |
---|
540 | |
---|
541 | |
---|
542 | |
---|
543 | /* ----------------------------------------------------------------- |
---|
544 | * Function: CPRO_calculate_cb |
---|
545 | * |
---|
546 | * Arguments: . |
---|
547 | * |
---|
548 | * Returns: . |
---|
549 | * |
---|
550 | * Description: main callback |
---|
551 | * This function calculates the conservative profile. |
---|
552 | * Function CPRO_readandallocate allocates memory and |
---|
553 | * reads necessary data. Calculation of the statistic |
---|
554 | * is done in function CPRO_makestatistic. |
---|
555 | * Allocated memory is freed in function CPRO_deallocate. |
---|
556 | * |
---|
557 | * NOTE: . |
---|
558 | * |
---|
559 | * Global Variables referenced: . |
---|
560 | * |
---|
561 | * Global Variables modified: x |
---|
562 | * |
---|
563 | * AWARs referenced: cpro/alignment , cpro/which_species |
---|
564 | * cpro/countgaps , cpro/rateofgroups |
---|
565 | * |
---|
566 | * AWARs modified: x |
---|
567 | * |
---|
568 | * Dependencies: CPRO_readandallocate , CPRO_makestatistic , CPRO_deallocate |
---|
569 | * ----------------------------------------------------------------- |
---|
570 | */ |
---|
571 | |
---|
572 | static void CPRO_memrequirement_cb(AW_root *aw_root); // prototype |
---|
573 | |
---|
574 | static void CPRO_calculate_cb(AW_window *aw,AW_CL which_statistic) |
---|
575 | { |
---|
576 | AW_root *awr=aw->get_root(); |
---|
577 | char *align=awr->awar("cpro/alignment")->read_string(); |
---|
578 | char *marked=awr->awar("cpro/which_species")->read_string(); |
---|
579 | char versus=0; /* all vs all */ |
---|
580 | if(!(strcmp("marked",marked))) versus=1; /*marked vs marked*/ |
---|
581 | if(!(strcmp("markedall",marked))) versus=2; /* marked vs all*/ |
---|
582 | GB_ERROR faultmessage; |
---|
583 | free(marked); |
---|
584 | |
---|
585 | if(CPRO.result[which_statistic].statisticexists) |
---|
586 | { |
---|
587 | CPRO_freestatistic((char)which_statistic); |
---|
588 | CPRO.result[which_statistic].statisticexists=0; |
---|
589 | } |
---|
590 | |
---|
591 | strcpy(CPRO.result[which_statistic].alignname,align); |
---|
592 | CPRO.result[which_statistic].resolution=awr->awar("cpro/resolution")->read_int(); |
---|
593 | if (CPRO.result[which_statistic].resolution<=0) |
---|
594 | CPRO.result[which_statistic].resolution=1; |
---|
595 | CPRO.result[which_statistic].leastcompares= |
---|
596 | awr->awar("cpro/leastcompares")->read_int(); |
---|
597 | if (CPRO.result[which_statistic].leastcompares<=0) CPRO.result[which_statistic].leastcompares=1; |
---|
598 | |
---|
599 | if(versus==1) strcpy(CPRO.result[which_statistic].which_species,"m vs m"); |
---|
600 | else if(versus==2) strcpy(CPRO.result[which_statistic].which_species, "m vs all"); |
---|
601 | else strcpy(CPRO.result[which_statistic].which_species,"all vs all"); |
---|
602 | |
---|
603 | if( (faultmessage=GB_push_transaction(GLOBAL_gb_main)) ) |
---|
604 | { |
---|
605 | aw_question(faultmessage,"OK,EXIT"); |
---|
606 | delete align; |
---|
607 | return; |
---|
608 | } |
---|
609 | |
---|
610 | CPRO.result[which_statistic].maxalignlen = GBT_get_alignment_len(GLOBAL_gb_main,align); |
---|
611 | if(CPRO.result[which_statistic].maxalignlen<=0) { |
---|
612 | GB_pop_transaction(GLOBAL_gb_main); |
---|
613 | aw_message("Error: Select an alignment !"); |
---|
614 | delete align; |
---|
615 | return; |
---|
616 | } |
---|
617 | |
---|
618 | char isamino= GBT_is_alignment_protein(GLOBAL_gb_main,align); |
---|
619 | aw_openstatus("calculating");aw_status((double)0); |
---|
620 | |
---|
621 | GBDATA **speciesdatabase; // array of GBDATA-pointers to the species |
---|
622 | char **speciesdata;//array of pointers to strings that hold data of species |
---|
623 | |
---|
624 | // allocate memory for 'CPRO.statistic','speciesdata' and fill |
---|
625 | // 'speciesdatabase','agonist' and 'antagonist' |
---|
626 | CPRO_readandallocate(speciesdata,speciesdatabase,versus,align); |
---|
627 | |
---|
628 | char *countgapsstring=awr->awar("cpro/countgaps")->read_string(); |
---|
629 | char countgaps=1; |
---|
630 | if(strcmp("on",countgapsstring)) countgaps=0; |
---|
631 | free(countgapsstring); |
---|
632 | CPRO.result[which_statistic].countgaps=(long)countgaps; |
---|
633 | |
---|
634 | /* create convtable and grouptable */ |
---|
635 | CPRO_maketables(isamino,countgaps); |
---|
636 | CPRO.result[which_statistic].ratio=awr->awar("cpro/transratio")->read_float(); |
---|
637 | CPRO.grouprate=1-(0.5/CPRO.result[which_statistic].ratio); |
---|
638 | CPRO.distancecorrection=(CPRO.result[which_statistic].ratio+1)*2.0/3.0; |
---|
639 | |
---|
640 | /* fill the CPRO.statistic table */ |
---|
641 | char success=CPRO_makestatistic(speciesdata,speciesdatabase,(char)which_statistic); |
---|
642 | GBUSE(success); |
---|
643 | CPRO_workupstatistic((char)which_statistic); |
---|
644 | |
---|
645 | aw_closestatus(); |
---|
646 | |
---|
647 | CPRO_deallocate(speciesdata,speciesdatabase); |
---|
648 | free(align); |
---|
649 | if( (faultmessage=GB_pop_transaction(GLOBAL_gb_main)) ) |
---|
650 | { |
---|
651 | aw_question(faultmessage,"OK,EXIT"); |
---|
652 | return; |
---|
653 | } |
---|
654 | |
---|
655 | CPRO_memrequirement_cb(awr); |
---|
656 | |
---|
657 | } |
---|
658 | |
---|
659 | static void CPRO_memrequirement_cb(AW_root *aw_root) |
---|
660 | { |
---|
661 | char *align=aw_root->awar("cpro/alignment")->read_string(); |
---|
662 | char *marked=aw_root->awar("cpro/which_species")->read_string(); |
---|
663 | char versus=0; /* all vs all */ |
---|
664 | if(!(strcmp("marked",marked))) versus=1; |
---|
665 | if(!(strcmp("markedall",marked))) versus=2; |
---|
666 | free(marked); |
---|
667 | CPRO.partition=aw_root->awar("cpro/partition")->read_int(); |
---|
668 | if (CPRO.partition<=0) CPRO.partition=1; |
---|
669 | long resolution=aw_root->awar("cpro/resolution")->read_int(); |
---|
670 | if (resolution<=0) resolution=1; |
---|
671 | char buf[80]; |
---|
672 | GB_ERROR faultmessage; |
---|
673 | |
---|
674 | aw_root->awar("tmp/cpro/which1")->write_string(CPRO.result[0].which_species); |
---|
675 | aw_root->awar("tmp/cpro/which2")->write_string(CPRO.result[1].which_species); |
---|
676 | |
---|
677 | sprintf(buf,"%5ld",CPRO.result[0].resolution); aw_root->awar("tmp/cpro/nowres1")->write_string(buf); |
---|
678 | sprintf(buf,"%5ld",CPRO.result[1].resolution); aw_root->awar("tmp/cpro/nowres2")->write_string(buf); |
---|
679 | |
---|
680 | if(!(CPRO.result[0].statisticexists)) { |
---|
681 | aw_root->awar("tmp/cpro/memfor1")->write_string("0KB"); |
---|
682 | } |
---|
683 | else |
---|
684 | { |
---|
685 | sprintf(buf,"%ldKB",CPRO.result[0].memneeded/1024); |
---|
686 | aw_root->awar("tmp/cpro/memfor1")->write_string(buf); |
---|
687 | } |
---|
688 | |
---|
689 | if(!(CPRO.result[1].statisticexists)) { |
---|
690 | aw_root->awar("tmp/cpro/memfor2")->write_string("0KB"); |
---|
691 | } |
---|
692 | else |
---|
693 | { |
---|
694 | sprintf(buf,"%ldKB",CPRO.result[1].memneeded/1024); |
---|
695 | aw_root->awar("tmp/cpro/memfor2")->write_string(buf); |
---|
696 | } |
---|
697 | |
---|
698 | if( (faultmessage=GB_push_transaction(GLOBAL_gb_main)) ) { |
---|
699 | aw_question(faultmessage,"OK,EXIT"); |
---|
700 | free(align); |
---|
701 | return; |
---|
702 | } |
---|
703 | |
---|
704 | long len=GBT_get_alignment_len(GLOBAL_gb_main,align); |
---|
705 | |
---|
706 | if(len<=0) { |
---|
707 | GB_pop_transaction(GLOBAL_gb_main); |
---|
708 | aw_root->awar("tmp/cpro/mempartition")->write_string("???"); |
---|
709 | aw_root->awar("tmp/cpro/memstatistic")->write_string("???"); |
---|
710 | free(align); |
---|
711 | return; |
---|
712 | } |
---|
713 | |
---|
714 | |
---|
715 | /* GBDATA *gb_species; |
---|
716 | versus==1 -> marked vs marked |
---|
717 | if (versus==1) { |
---|
718 | gb_species = GBT_first_marked_species(gb_species_data); |
---|
719 | } else { |
---|
720 | gb_species = GBT_first_species(gb_species_data); |
---|
721 | } |
---|
722 | while(gb_species) |
---|
723 | { |
---|
724 | if(GBT_read_sequence(gb_species,align)){ |
---|
725 | nrofspecies++; |
---|
726 | } |
---|
727 | if (versus==1) { |
---|
728 | gb_species = GBT_next_marked_species(gb_species); |
---|
729 | }else{ |
---|
730 | gb_species = GBT_next_species(gb_species); |
---|
731 | } |
---|
732 | } |
---|
733 | CPRO.numspecies=nrofspecies; */ |
---|
734 | long mem; |
---|
735 | |
---|
736 | /*if(CPRO.numspecies<=2*CPRO.partition) mem=CPRO.numspecies*len; |
---|
737 | else mem=CPRO.partition*2*len; */ |
---|
738 | mem=CPRO.partition*len*2; // *2, because of row and column in matrix |
---|
739 | sprintf(buf,"%li KB",long(mem/1024)); |
---|
740 | aw_root->awar("tmp/cpro/mempartition")->write_string(buf); |
---|
741 | |
---|
742 | mem+=resolution*3*sizeof(STATTYPE)*len; |
---|
743 | sprintf(buf,"%li KB",long(mem/1024)); |
---|
744 | aw_root->awar("tmp/cpro/memstatistic")->write_string(buf); |
---|
745 | |
---|
746 | free(align); |
---|
747 | if( (faultmessage=GB_pop_transaction(GLOBAL_gb_main)) ) |
---|
748 | { |
---|
749 | aw_question(faultmessage,"OK,EXIT"); |
---|
750 | return; |
---|
751 | } |
---|
752 | } |
---|
753 | |
---|
754 | void create_cprofile_var(AW_root *aw_root, AW_default aw_def) |
---|
755 | { |
---|
756 | aw_root->awar_string( "cpro/alignment", "" ,aw_def); |
---|
757 | aw_root->awar_string( "cpro/which_species","marked",aw_def); |
---|
758 | aw_root->awar_string( "cpro/which_result","transversion",aw_def); |
---|
759 | aw_root->awar_string( "cpro/countgaps", "",aw_def); |
---|
760 | aw_root->awar_string( "cpro/condensename", "PVD",aw_def); |
---|
761 | aw_root->awar_float( "cpro/transratio",0.5,aw_def); |
---|
762 | aw_root->awar_int( AWAR_CURSOR_POSITION,1,GLOBAL_gb_main); |
---|
763 | aw_root->awar_int( "cpro/maxdistance",100,aw_def); |
---|
764 | aw_root->awar_int( "cpro/resolution",100,aw_def); |
---|
765 | aw_root->awar_int( "cpro/partition",100,aw_def); |
---|
766 | aw_root->awar_int( "cpro/drawmode0",0,aw_def); |
---|
767 | aw_root->awar_int( "cpro/drawmode1",0,aw_def); |
---|
768 | aw_root->awar_int( "cpro/leastaccu",3,aw_def); |
---|
769 | aw_root->awar_int( "cpro/leastmax",50,aw_def); |
---|
770 | aw_root->awar_int( "cpro/firsttoreach",50,aw_def); |
---|
771 | aw_root->awar_int( "cpro/firstreachedstep",4,aw_def); |
---|
772 | aw_root->awar_int( "cpro/leastcompares",300,aw_def); |
---|
773 | aw_root->awar_string("tmp/cpro/mempartition","",aw_def); |
---|
774 | aw_root->awar_int( "cpro/gridhorizontal",20,aw_def); |
---|
775 | aw_root->awar_int( "cpro/gridvertical",20,aw_def); |
---|
776 | aw_root->awar_string( "tmp/cpro/which1","",aw_def); |
---|
777 | aw_root->awar_string( "tmp/cpro/which2","",aw_def); |
---|
778 | aw_root->awar_string( "tmp/cpro/nowres1","",aw_def); |
---|
779 | aw_root->awar_string( "tmp/cpro/nowres2","",aw_def); |
---|
780 | aw_root->awar_string( "tmp/cpro/memstatistic","",aw_def); |
---|
781 | aw_root->awar_string( "tmp/cpro/memfor1","",aw_def); |
---|
782 | aw_root->awar_string( "tmp/cpro/memfor2","",aw_def); |
---|
783 | |
---|
784 | aw_create_selection_box_awars(aw_root, "cpro/save", ".", ".cpr", "", aw_def); |
---|
785 | aw_create_selection_box_awars(aw_root, "cpro/load", ".", ".cpr", "", aw_def); |
---|
786 | memset((char *)&CPRO,0,sizeof(struct CPRO_struct)); |
---|
787 | |
---|
788 | } |
---|
789 | |
---|
790 | static float CPRO_statisticaccumulation(long res,long column,unsigned char which_statistic) |
---|
791 | { |
---|
792 | STATTYPE hits=0, sum=0, group=0, different=0; |
---|
793 | long base=3*res; |
---|
794 | |
---|
795 | if(!(CPRO.result[which_statistic].statistic[base+0])) hits=0; |
---|
796 | else hits=CPRO.result[which_statistic].statistic[base+0][column]; |
---|
797 | |
---|
798 | if(!(CPRO.result[which_statistic].statistic[base+1])) group=0; |
---|
799 | else group=CPRO.result[which_statistic].statistic[base+1][column]; |
---|
800 | |
---|
801 | if(!(CPRO.result[which_statistic].statistic[base+2])) different=0; |
---|
802 | else different=CPRO.result[which_statistic].statistic[base+2][column]; |
---|
803 | |
---|
804 | sum=hits+group+different; |
---|
805 | |
---|
806 | return ((float)sum); |
---|
807 | } |
---|
808 | |
---|
809 | |
---|
810 | // reports how many equal,group and differ entries are at a certain distance |
---|
811 | // at a certain column; mode=1 means smoothing is on. |
---|
812 | void CPRO_getfromstatistic(float &equal,float &ingroup,long res,long column, unsigned char which_statistic,char mode) |
---|
813 | { |
---|
814 | STATTYPE hits=0, sum=0, group=0, different=0; |
---|
815 | long base=3*res; |
---|
816 | |
---|
817 | if(!(CPRO.result[which_statistic].statistic[base+0])) hits=0; |
---|
818 | else hits=CPRO.result[which_statistic].statistic[base+0][column]; |
---|
819 | |
---|
820 | if(!(CPRO.result[which_statistic].statistic[base+1])) group=0; |
---|
821 | else group=CPRO.result[which_statistic].statistic[base+1][column]; |
---|
822 | |
---|
823 | if(!(CPRO.result[which_statistic].statistic[base+2])) different=0; |
---|
824 | else different=CPRO.result[which_statistic].statistic[base+2][column]; |
---|
825 | |
---|
826 | sum=hits+group+different; |
---|
827 | |
---|
828 | if(!(mode)) |
---|
829 | { |
---|
830 | if(sum) |
---|
831 | { |
---|
832 | equal=(float)hits/(float)sum; |
---|
833 | ingroup=((float)hits+(float)group)/(float)sum; |
---|
834 | } |
---|
835 | else |
---|
836 | { |
---|
837 | equal=1.0; |
---|
838 | ingroup=1.0; |
---|
839 | } |
---|
840 | return; |
---|
841 | } |
---|
842 | else |
---|
843 | { |
---|
844 | float accu=pow(sum/(float)CPRO.result[which_statistic].maxaccu,0.0675); |
---|
845 | float distance=(float)CPRO.result[which_statistic].drawmode*.01* |
---|
846 | CPRO.result[which_statistic].resolution; |
---|
847 | float alpha=0.0; // alpha=0.0 no smoothing; alpha=0.99 high smoothing |
---|
848 | if(distance>0.0000001) |
---|
849 | { |
---|
850 | alpha=1.0-accu/distance; |
---|
851 | if(alpha<0) alpha=0; |
---|
852 | } |
---|
853 | |
---|
854 | if(res==0) |
---|
855 | { |
---|
856 | CPRO.Z_it_group=1.0; |
---|
857 | CPRO.Z_it_equal=1.0; |
---|
858 | } |
---|
859 | if(sum) |
---|
860 | { |
---|
861 | equal=(float)hits/(float)sum; |
---|
862 | ingroup=((float)hits+(float)group)/(float)sum; |
---|
863 | equal=(1-alpha)*equal+alpha*CPRO.Z_it_equal; |
---|
864 | ingroup=(1-alpha)*ingroup+alpha*CPRO.Z_it_group; |
---|
865 | } |
---|
866 | else |
---|
867 | { |
---|
868 | equal=CPRO.Z_it_equal; |
---|
869 | ingroup=CPRO.Z_it_group; |
---|
870 | } |
---|
871 | CPRO.Z_it_equal=equal; |
---|
872 | CPRO.Z_it_group=ingroup; |
---|
873 | } |
---|
874 | |
---|
875 | } |
---|
876 | |
---|
877 | void CPRO_box(AW_device *device,int gc,float l,float t,float width,float high) { |
---|
878 | device->box(gc, false, l, t, width, high, 1, (AW_CL)0, (AW_CL)0); |
---|
879 | } |
---|
880 | |
---|
881 | float CPRO_confidinterval(long res,long column,unsigned char which_statistic,char mode) |
---|
882 | { |
---|
883 | STATTYPE hits=0, sum=0, group=0, different=0; |
---|
884 | long base=3*res; |
---|
885 | |
---|
886 | if(!(CPRO.result[which_statistic].statistic[base+0])) hits=0; |
---|
887 | else hits=CPRO.result[which_statistic].statistic[base+0][column]; |
---|
888 | |
---|
889 | if(!(CPRO.result[which_statistic].statistic[base+1])) group=0; |
---|
890 | else group=CPRO.result[which_statistic].statistic[base+1][column]; |
---|
891 | |
---|
892 | if(!(CPRO.result[which_statistic].statistic[base+2])) different=0; |
---|
893 | else different=CPRO.result[which_statistic].statistic[base+2][column]; |
---|
894 | |
---|
895 | sum=hits+group+different; |
---|
896 | if(!(mode)) return(1/sqrt((float)sum)/2.0); |
---|
897 | else return(0.0); |
---|
898 | } |
---|
899 | |
---|
900 | void CPRO_drawstatistic (AW_device *device,unsigned char which_statistic) |
---|
901 | { |
---|
902 | float topdistance=70.0,leftdistance=40.0; |
---|
903 | float rightdistance=20.0,bottomdistance=10.0; |
---|
904 | float betweendistance=30.0; |
---|
905 | float firstavailable=.65; |
---|
906 | float secondavailable=.35; |
---|
907 | /* points are in the areas and without the frame */ |
---|
908 | float topfirst, leftfirst, widthfirst, highfirst; |
---|
909 | float topsecond, leftsecond, widthsecond, highsecond; |
---|
910 | float highboth; |
---|
911 | float equal,ingroup; |
---|
912 | char mode=CPRO.result[which_statistic].drawmode; |
---|
913 | |
---|
914 | AW_rectangle rect; |
---|
915 | device->get_area_size(&rect); |
---|
916 | device->reset(); |
---|
917 | device->clear(-1); |
---|
918 | |
---|
919 | topfirst=39.0; |
---|
920 | leftfirst=20.0; |
---|
921 | widthfirst=(rect.r-rect.l)-leftdistance-1-rightdistance; |
---|
922 | widthsecond=(rect.r-rect.l)-leftdistance-1-rightdistance; |
---|
923 | highboth=(rect.b-rect.t)-topdistance-bottomdistance-betweendistance-4; |
---|
924 | if((highboth<12.0)||(widthfirst<10.0)) return; |
---|
925 | |
---|
926 | highfirst=(float)(long)(highboth*firstavailable); |
---|
927 | highsecond=(float)(long)(highboth*secondavailable)+1; |
---|
928 | |
---|
929 | topfirst=topdistance+1; |
---|
930 | leftfirst=leftdistance; |
---|
931 | topsecond=rect.b-bottomdistance-highsecond; |
---|
932 | leftsecond=leftdistance+1; |
---|
933 | |
---|
934 | CPRO_box(device,GC_black,leftfirst-1,topfirst-1, |
---|
935 | widthfirst+2,highfirst+2); |
---|
936 | CPRO_box(device,GC_black,leftsecond-1,topsecond-1, |
---|
937 | widthsecond+2,highsecond+2); |
---|
938 | |
---|
939 | device->text(GC_black,"column",leftdistance+82,14,0,1,0,0); |
---|
940 | |
---|
941 | /* draw grid and inscribe axes*/ |
---|
942 | char buf[30]; |
---|
943 | long gridx,gridy; |
---|
944 | float xpos=leftdistance,ypos; |
---|
945 | sprintf(buf," character difference"); |
---|
946 | device->text(GC_black,buf,leftdistance-40,topdistance-7,0,1,0,0); |
---|
947 | device->text(GC_black," 0%", |
---|
948 | leftdistance-26,topdistance+4+highfirst,0,1,0,0); |
---|
949 | |
---|
950 | for(gridy=CPRO.gridhorizontal;gridy<100;gridy+=CPRO.gridhorizontal) |
---|
951 | { |
---|
952 | ypos=topdistance+1+(1.0-(float)gridy*0.01)*(highfirst-1); |
---|
953 | device->line(GC_grid,xpos,ypos,xpos+widthfirst,ypos,1,0,0); |
---|
954 | sprintf(buf,"%3ld%%",gridy); |
---|
955 | device->text(GC_black,buf,xpos-27,ypos+4,0,1,0,0); |
---|
956 | } |
---|
957 | device->text(GC_black,"100%",leftdistance-26,topdistance+5,0,1,0,0); |
---|
958 | |
---|
959 | device->text(GC_black,"sequence distance", |
---|
960 | leftdistance+widthfirst-95,topdistance+highfirst+25,0,1,0,0); |
---|
961 | device->text(GC_black," 0%", |
---|
962 | leftdistance-11,topdistance+14+highfirst,0,1,0,0); |
---|
963 | ypos=topdistance+1; |
---|
964 | |
---|
965 | for(gridx=CPRO.gridvertical;(float)gridx<=100.0*CPRO.maxdistance; |
---|
966 | gridx+=CPRO.gridvertical) |
---|
967 | { |
---|
968 | xpos=leftdistance+1+(float)gridx*0.01/CPRO.maxdistance*widthfirst; |
---|
969 | if((float)gridx*0.01<1.0*CPRO.maxdistance) |
---|
970 | device->line(GC_grid,xpos,ypos,xpos,ypos+highfirst,1,0,0); |
---|
971 | sprintf(buf,"%3ld%%",gridx); |
---|
972 | device->text(GC_black,buf,xpos-12,ypos+13+highfirst,0,1,0,0); |
---|
973 | } |
---|
974 | |
---|
975 | if(!CPRO.result[which_statistic].statisticexists) return; |
---|
976 | if((CPRO.column<1)||(CPRO.column>CPRO.result[which_statistic].maxalignlen)) |
---|
977 | return; |
---|
978 | |
---|
979 | /* fill first box */ |
---|
980 | float accu,confidinterval; |
---|
981 | float step=widthfirst/CPRO.result[which_statistic].resolution; |
---|
982 | float linelength=step/CPRO.maxdistance; |
---|
983 | float ytop,ybottom; |
---|
984 | |
---|
985 | long firstx; |
---|
986 | for(firstx=0; |
---|
987 | firstx<CPRO.result[which_statistic].resolution*CPRO.maxdistance; |
---|
988 | firstx++) |
---|
989 | { |
---|
990 | CPRO_getfromstatistic(equal,ingroup,(long)firstx,CPRO.column-1, |
---|
991 | which_statistic,mode); |
---|
992 | accu=CPRO_statisticaccumulation((long)firstx, |
---|
993 | CPRO.column-1,which_statistic); |
---|
994 | if(accu>=(float)CPRO.leastaccu) |
---|
995 | { |
---|
996 | xpos=(float)firstx*step/CPRO.maxdistance+leftfirst; |
---|
997 | ypos=topfirst+equal*highfirst; |
---|
998 | |
---|
999 | // do not draw outside canvas-box |
---|
1000 | if(xpos+linelength > leftfirst+widthfirst+1) continue; |
---|
1001 | |
---|
1002 | confidinterval=highfirst* |
---|
1003 | CPRO_confidinterval(firstx,CPRO.column-1,which_statistic,mode); |
---|
1004 | |
---|
1005 | ytop=ypos-confidinterval; |
---|
1006 | if(ytop>=topfirst) { |
---|
1007 | device->line(GC_blue,xpos,ytop,xpos+linelength,ytop,1,0,0); } |
---|
1008 | else { ytop=topfirst; } |
---|
1009 | device->line(GC_blue,xpos+linelength/2,ytop,xpos+linelength/2,ypos,1,0,0); |
---|
1010 | |
---|
1011 | ybottom=ypos+confidinterval; |
---|
1012 | if(ybottom<topfirst+highfirst) { |
---|
1013 | device->line(GC_blue,xpos,ybottom,xpos+linelength,ybottom,1,0,0);} |
---|
1014 | else { ybottom=topfirst+highfirst-1; } |
---|
1015 | device->line(GC_blue,xpos+linelength/2,ybottom,xpos+linelength/2,ypos,1,0,0); |
---|
1016 | |
---|
1017 | ypos=topfirst+ingroup*highfirst; |
---|
1018 | ytop=ypos-confidinterval; |
---|
1019 | if(ytop>=topfirst) { |
---|
1020 | device->line(GC_green,xpos,ytop,xpos+linelength,ytop,1,0,0); } |
---|
1021 | else { ytop=topfirst; } |
---|
1022 | device->line(GC_green,xpos+linelength/2,ytop,xpos+linelength/2,ypos,1,0,0); |
---|
1023 | |
---|
1024 | ybottom=ypos+confidinterval; |
---|
1025 | if(ybottom<topfirst+highfirst){ |
---|
1026 | device->line(GC_green,xpos,ybottom,xpos+linelength,ybottom,1,0,0);} |
---|
1027 | else { ybottom=topfirst+highfirst-1; } |
---|
1028 | device->line(GC_green,xpos+linelength/2,ybottom,xpos+linelength/2,ypos,1,0,0); |
---|
1029 | |
---|
1030 | } |
---|
1031 | } |
---|
1032 | |
---|
1033 | float resaccu; |
---|
1034 | float rate; |
---|
1035 | sprintf(buf," %5ld",CPRO.result[which_statistic].maxaccu); |
---|
1036 | device->text(GC_black," max",leftsecond-50,topsecond,0,1,0,0); |
---|
1037 | device->text(GC_black,buf,leftsecond-43,topsecond+10*1,0,1,0,0); |
---|
1038 | device->text(GC_black," pairs",leftsecond-50,topsecond+10*3,0,1,0,0); |
---|
1039 | |
---|
1040 | /*fill second box*/ |
---|
1041 | for(firstx=0;firstx<(long)widthsecond;firstx++) |
---|
1042 | { |
---|
1043 | resaccu=CPRO_statisticaccumulation( |
---|
1044 | (long)(firstx*CPRO.result[which_statistic].resolution |
---|
1045 | /widthsecond*CPRO.maxdistance),CPRO.column-1,which_statistic); |
---|
1046 | rate=1.0-(sqrt(resaccu)/sqrt(CPRO.result[which_statistic].maxaccu)); |
---|
1047 | device->line(GC_black,firstx+leftsecond,topsecond+rate*highsecond, |
---|
1048 | firstx+leftsecond,topsecond+highsecond,1,0,0); |
---|
1049 | } |
---|
1050 | } |
---|
1051 | |
---|
1052 | static void CPRO_resize_cb(AW_window *aws, AW_CL which_statistic, AW_CL) |
---|
1053 | { |
---|
1054 | AW_root *awr=aws->get_root(); |
---|
1055 | CPRO.column=awr->awar(AWAR_CURSOR_POSITION)->read_int(); |
---|
1056 | CPRO.gridvertical=(long)awr->awar("cpro/gridvertical")->read_int(); |
---|
1057 | CPRO.gridhorizontal=(long)awr->awar("cpro/gridhorizontal")->read_int(); |
---|
1058 | CPRO.leastaccu=awr->awar("cpro/leastaccu")->read_int(); |
---|
1059 | if (CPRO.leastaccu<=0) CPRO.leastaccu=1; |
---|
1060 | |
---|
1061 | AW_device *device=aws->get_device(AW_INFO_AREA); |
---|
1062 | device->reset(); |
---|
1063 | CPRO_drawstatistic(device,(char)which_statistic); |
---|
1064 | } |
---|
1065 | |
---|
1066 | static void CPRO_expose_cb( AW_window *aws,AW_CL which_statistic, AW_CL) |
---|
1067 | { |
---|
1068 | AW_root *awr=aws->get_root(); |
---|
1069 | CPRO.column=awr->awar(AWAR_CURSOR_POSITION)->read_int(); |
---|
1070 | char buf[80]; |
---|
1071 | sprintf(buf,"cpro/drawmode%d",(int)which_statistic); |
---|
1072 | CPRO.result[which_statistic].drawmode=(char)awr->awar(buf)->read_int(); |
---|
1073 | CPRO.gridvertical=(long)awr->awar("cpro/gridvertical")->read_int(); |
---|
1074 | CPRO.gridhorizontal=(long)awr->awar("cpro/gridhorizontal")->read_int(); |
---|
1075 | CPRO.leastaccu=awr->awar("cpro/leastaccu")->read_int(); |
---|
1076 | if (CPRO.leastaccu<=0) CPRO.leastaccu=1; |
---|
1077 | |
---|
1078 | long maxd=awr->awar("cpro/maxdistance")->read_int(); |
---|
1079 | if((maxd>0)&&(maxd<101))CPRO.maxdistance=(float)maxd/100.0; |
---|
1080 | |
---|
1081 | AW_device *device=aws->get_device (AW_INFO_AREA); |
---|
1082 | CPRO_drawstatistic(device,(char)which_statistic); |
---|
1083 | } |
---|
1084 | |
---|
1085 | static void CPRO_column_cb(AW_root *awr,AW_window *aws,AW_CL which_statistic) |
---|
1086 | { |
---|
1087 | char buf[80]; |
---|
1088 | sprintf(buf,"cpro/drawmode%d",(int)which_statistic); |
---|
1089 | CPRO.result[which_statistic].drawmode=(char)awr->awar(buf)->read_int(); |
---|
1090 | CPRO_expose_cb(aws,which_statistic,0); |
---|
1091 | } |
---|
1092 | |
---|
1093 | void CPRO_columnminus_cb(AW_window *aws) |
---|
1094 | { |
---|
1095 | AW_root *awr = aws->get_root(); |
---|
1096 | if (CPRO.column>1) awr->awar(AWAR_CURSOR_POSITION)->write_int(CPRO.column-1); |
---|
1097 | } |
---|
1098 | |
---|
1099 | void CPRO_columnplus_cb(AW_window *aws, AW_CL /*which_statistic*/, AW_CL) |
---|
1100 | { |
---|
1101 | AW_root *awr = aws->get_root(); |
---|
1102 | awr->awar(AWAR_CURSOR_POSITION)->write_int(CPRO.column+1); |
---|
1103 | /*if(CPRO.column<CPRO.result[which_statistic].maxalignlen) { awr->awar(AWAR_CURSOR_POSITION)->write_int(CPRO.column+1); }*/ |
---|
1104 | } |
---|
1105 | |
---|
1106 | void CPRO_savestatistic_cb(AW_window *aw,AW_CL which_statistic) |
---|
1107 | { |
---|
1108 | AW_root *awr = aw->get_root(); |
---|
1109 | char *filename = awr->awar("cpro/save/file_name")->read_string(); |
---|
1110 | GB_ERROR error = 0; |
---|
1111 | |
---|
1112 | if (!filename) { |
---|
1113 | error = "no filename"; |
---|
1114 | } |
---|
1115 | else { |
---|
1116 | const CPRO_result_struct& curr_stat = CPRO.result[which_statistic]; |
---|
1117 | if (!(curr_stat.statisticexists)) { |
---|
1118 | error = "calculate first!"; |
---|
1119 | } |
---|
1120 | else { |
---|
1121 | GBDATA *newbase = GB_open(filename,"wc"); |
---|
1122 | if (!newbase) error = GB_await_error(); |
---|
1123 | else { |
---|
1124 | error = GB_begin_transaction(newbase); |
---|
1125 | |
---|
1126 | if (!error) error = GBT_write_int (newbase, "cpro_resolution", curr_stat.resolution); |
---|
1127 | if (!error) error = GBT_write_int (newbase, "cpro_maxalignlen", curr_stat.maxalignlen); |
---|
1128 | if (!error) error = GBT_write_int (newbase, "cpro_maxaccu", curr_stat.maxaccu); |
---|
1129 | if (!error) error = GBT_write_int (newbase, "cpro_memneeded", curr_stat.memneeded); |
---|
1130 | if (!error) error = GBT_write_string(newbase, "cpro_alignname", curr_stat.alignname); |
---|
1131 | if (!error) error = GBT_write_string(newbase, "cpro_which_species", curr_stat.which_species); |
---|
1132 | if (!error) error = GBT_write_float (newbase, "cpro_ratio", curr_stat.ratio); |
---|
1133 | if (!error) error = GBT_write_int (newbase, "cpro_gaps", curr_stat.countgaps); |
---|
1134 | |
---|
1135 | if (!error) { |
---|
1136 | long maxalignlen = curr_stat.maxalignlen; |
---|
1137 | |
---|
1138 | for (long column = 0; column<curr_stat.resolution && !error; column++) { |
---|
1139 | GBDATA *gb_colrescontainer = GB_create_container(newbase,"column"); |
---|
1140 | GBDATA *gb_colentry; |
---|
1141 | GB_UINT4 *pointer; |
---|
1142 | |
---|
1143 | if (!error && (pointer = curr_stat.statistic[column*3+0])) { |
---|
1144 | gb_colentry = GB_create(gb_colrescontainer, "equal", GB_INTS); |
---|
1145 | error = GB_write_ints(gb_colentry, pointer, maxalignlen); |
---|
1146 | } |
---|
1147 | if (!error && (pointer = curr_stat.statistic[column*3+1])) { |
---|
1148 | gb_colentry = GB_create(gb_colrescontainer, "group", GB_INTS); |
---|
1149 | error = GB_write_ints(gb_colentry, pointer, maxalignlen); |
---|
1150 | } |
---|
1151 | if (!error && (pointer = curr_stat.statistic[column*3+2])) { |
---|
1152 | gb_colentry = GB_create(gb_colrescontainer, "different", GB_INTS); |
---|
1153 | error = GB_write_ints(gb_colentry, pointer, maxalignlen); |
---|
1154 | } |
---|
1155 | } |
---|
1156 | } |
---|
1157 | error = GB_end_transaction(newbase, error); |
---|
1158 | if (!error) error = GB_save(newbase,(char*)0,"b"); |
---|
1159 | } |
---|
1160 | |
---|
1161 | GB_close(newbase); |
---|
1162 | } |
---|
1163 | } |
---|
1164 | |
---|
1165 | free(filename); |
---|
1166 | aw->hide_or_notify(error); |
---|
1167 | } |
---|
1168 | |
---|
1169 | void CPRO_loadstatistic_cb(AW_window *aw,AW_CL which_statistic) |
---|
1170 | { |
---|
1171 | AW_root *awr = aw->get_root(); |
---|
1172 | char *filename = awr->awar("cpro/load/file_name")->read_string(); |
---|
1173 | GB_ERROR error = 0; |
---|
1174 | |
---|
1175 | if (!filename) { |
---|
1176 | error = "missing filename"; |
---|
1177 | } |
---|
1178 | else { |
---|
1179 | GBDATA *oldbase = GB_open(filename,"r"); |
---|
1180 | |
---|
1181 | if (!oldbase) { |
---|
1182 | error = GBS_global_string("can't read DB '%s'", filename); |
---|
1183 | } |
---|
1184 | else { |
---|
1185 | error = GB_begin_transaction(oldbase); |
---|
1186 | if (!error) { |
---|
1187 | if (CPRO.result[which_statistic].statisticexists) { |
---|
1188 | CPRO_freestatistic((char)which_statistic); |
---|
1189 | } |
---|
1190 | |
---|
1191 | GBDATA *gb_param = GB_search(oldbase,"cpro_resolution",GB_FIND); |
---|
1192 | if (!gb_param) error = "not a valid statistic"; |
---|
1193 | else { |
---|
1194 | CPRO.result[which_statistic].resolution = GB_read_int(gb_param); |
---|
1195 | |
---|
1196 | gb_param = GB_search(oldbase,"cpro_maxalignlen",GB_FIND); |
---|
1197 | CPRO.result[which_statistic].maxalignlen = GB_read_int(gb_param); |
---|
1198 | |
---|
1199 | gb_param=GB_search(oldbase,"cpro_maxaccu",GB_FIND); |
---|
1200 | CPRO.result[which_statistic].maxaccu=GB_read_int(gb_param); |
---|
1201 | |
---|
1202 | gb_param=GB_search(oldbase,"cpro_memneeded",GB_FIND); |
---|
1203 | CPRO.result[which_statistic].memneeded=GB_read_int(gb_param); |
---|
1204 | |
---|
1205 | gb_param=GB_search(oldbase,"cpro_alignname",GB_FIND); |
---|
1206 | strcpy(CPRO.result[which_statistic].alignname,GB_read_char_pntr(gb_param)); |
---|
1207 | |
---|
1208 | gb_param=GB_search(oldbase,"cpro_which_species",GB_FIND); |
---|
1209 | if(gb_param) strcpy(CPRO.result[which_statistic].which_species, GB_read_char_pntr(gb_param)); |
---|
1210 | |
---|
1211 | CPRO.result[which_statistic].statistic=(STATTYPE **)calloc((size_t)CPRO.result[which_statistic].resolution*3+3, sizeof(STATTYPE *)); |
---|
1212 | |
---|
1213 | GBDATA *gb_colrescontainer = GB_entry(oldbase, "column"); |
---|
1214 | for (long column=0; column<CPRO.result[which_statistic].resolution; column++) { |
---|
1215 | const char *field[] = { "equal", "group", "different" }; |
---|
1216 | for (int i = 0; i<3; i++) { |
---|
1217 | GBDATA *gb_colentry = GB_entry(gb_colrescontainer, field[i]); |
---|
1218 | if (gb_colentry) { |
---|
1219 | CPRO.result[which_statistic].statistic[column*3+i] = (STATTYPE*)GB_read_ints(gb_colentry); |
---|
1220 | } |
---|
1221 | } |
---|
1222 | gb_colrescontainer = GB_nextEntry(gb_colrescontainer); |
---|
1223 | } |
---|
1224 | |
---|
1225 | CPRO.result[which_statistic].statisticexists = 1; |
---|
1226 | CPRO_memrequirement_cb(awr); |
---|
1227 | } |
---|
1228 | } |
---|
1229 | error = GB_end_transaction(oldbase, error); |
---|
1230 | } |
---|
1231 | GB_close(oldbase); |
---|
1232 | } |
---|
1233 | |
---|
1234 | aw->hide_or_notify(error); |
---|
1235 | free(filename); |
---|
1236 | } |
---|
1237 | |
---|
1238 | static AW_window *CPRO_savestatisticwindow_cb(AW_root *aw_root,AW_CL cl_which_statistic) { |
---|
1239 | static AW_window *aw[2] = { 0, 0 }; // one window for each value of 'which_statistic' |
---|
1240 | |
---|
1241 | int which_statistic = int(cl_which_statistic); |
---|
1242 | ap_assert(which_statistic >= 0 && which_statistic <= 1); |
---|
1243 | |
---|
1244 | if (!aw[which_statistic]) { |
---|
1245 | AW_window_simple *aws = new AW_window_simple; |
---|
1246 | char *window_id = GBS_global_string_copy("SAVE_CPRO_STATISTIC_%i", which_statistic); |
---|
1247 | |
---|
1248 | aws->init( aw_root, window_id, "SAVE STATISTIC"); |
---|
1249 | aws->load_xfig("sel_box.fig"); |
---|
1250 | |
---|
1251 | aws->at("close");aws->callback((AW_CB0)AW_POPDOWN); |
---|
1252 | aws->create_button("CLOSE","CLOSE","C"); |
---|
1253 | |
---|
1254 | aws->at("save");aws->callback(CPRO_savestatistic_cb,which_statistic); |
---|
1255 | aws->create_button("SAVE","SAVE","S"); |
---|
1256 | |
---|
1257 | aws->callback( (AW_CB0)AW_POPDOWN); |
---|
1258 | aws->at("cancel"); |
---|
1259 | aws->create_button("CANCEL","CANCEL","C"); |
---|
1260 | |
---|
1261 | awt_create_selection_box(aws,"cpro/save"); |
---|
1262 | |
---|
1263 | free(window_id); |
---|
1264 | |
---|
1265 | aw[which_statistic] = aws; |
---|
1266 | } |
---|
1267 | return aw[which_statistic]; |
---|
1268 | } |
---|
1269 | |
---|
1270 | static AW_window *CPRO_loadstatisticwindow_cb(AW_root *aw_root, AW_CL cl_which_statistic) { |
---|
1271 | static AW_window *aw[2] = { 0, 0 }; // one window for each value of 'which_statistic' |
---|
1272 | |
---|
1273 | int which_statistic = int(cl_which_statistic); |
---|
1274 | ap_assert(which_statistic >= 0 && which_statistic <= 1); |
---|
1275 | |
---|
1276 | if (!aw[which_statistic]) { |
---|
1277 | AW_window_simple *aws = new AW_window_simple; |
---|
1278 | char *window_id = GBS_global_string_copy("LOAD_CPRO_STATISTIC_%i", which_statistic); |
---|
1279 | |
---|
1280 | aws->init(aw_root, window_id, "LOAD STATISTIC"); |
---|
1281 | aws->load_xfig("sel_box.fig"); |
---|
1282 | |
---|
1283 | aws->at("close");aws->callback((AW_CB0)AW_POPDOWN); |
---|
1284 | aws->create_button("CLOSE","CLOSE","C"); |
---|
1285 | |
---|
1286 | aws->at("save");aws->callback(CPRO_loadstatistic_cb,which_statistic); |
---|
1287 | aws->create_button("LOAD","LOAD","S"); |
---|
1288 | |
---|
1289 | awt_create_selection_box(aws,"cpro/load"); |
---|
1290 | |
---|
1291 | free(window_id); |
---|
1292 | |
---|
1293 | aw[which_statistic] = aws; |
---|
1294 | } |
---|
1295 | |
---|
1296 | return aw[which_statistic]; |
---|
1297 | } |
---|
1298 | |
---|
1299 | // search point of resolution when half maximum if reached (for condense) |
---|
1300 | float CPRO_gethalfmaximum(long column,float maximum,float firsttoreach, |
---|
1301 | char transversion,unsigned char which_statistic,char mode) |
---|
1302 | { |
---|
1303 | float equal,ingroup,interest; |
---|
1304 | float interval,sum; |
---|
1305 | float halfmax=0.0; |
---|
1306 | long res; |
---|
1307 | for(res=0;res<CPRO.result[which_statistic].resolution;res++) |
---|
1308 | { |
---|
1309 | sum=CPRO_statisticaccumulation(res,column,which_statistic); |
---|
1310 | if((long)sum>=CPRO.leastaccu) |
---|
1311 | { |
---|
1312 | CPRO_getfromstatistic(equal,ingroup,res,column, |
---|
1313 | which_statistic,mode); |
---|
1314 | if(transversion) interest=1.0-ingroup; |
---|
1315 | else interest=1.0-equal; |
---|
1316 | interval=CPRO_confidinterval(res,column,which_statistic,mode); |
---|
1317 | if(interest-interval>=maximum*firsttoreach) |
---|
1318 | { |
---|
1319 | res++; |
---|
1320 | break; |
---|
1321 | } |
---|
1322 | } |
---|
1323 | } |
---|
1324 | halfmax=(float)res/(float)CPRO.result[which_statistic].resolution; |
---|
1325 | return(halfmax-(float)CPRO.result[which_statistic].drawmode*0.01); |
---|
1326 | // delay depending on drawmode |
---|
1327 | } |
---|
1328 | |
---|
1329 | // search maximum distance in character (for condense) |
---|
1330 | float CPRO_getmaximum(long column,char transversion, |
---|
1331 | unsigned char which_statistic,char mode) |
---|
1332 | { |
---|
1333 | float maximum=-101.0,equal,ingroup,interest,sum,interval; |
---|
1334 | for(long res=0;res<CPRO.result[which_statistic].resolution;res++) |
---|
1335 | { |
---|
1336 | sum=CPRO_statisticaccumulation(res,column,which_statistic); |
---|
1337 | if((long)sum>=CPRO.leastaccu) |
---|
1338 | { |
---|
1339 | CPRO_getfromstatistic(equal,ingroup,res,column, |
---|
1340 | which_statistic,mode); |
---|
1341 | if(transversion) interest=1.0-ingroup; |
---|
1342 | else interest=1.0-equal; |
---|
1343 | interval=CPRO_confidinterval(res,column,which_statistic,mode); |
---|
1344 | if(interest-interval>maximum) maximum=interest-interval; |
---|
1345 | } |
---|
1346 | } |
---|
1347 | //printf("\n"); |
---|
1348 | return(maximum); |
---|
1349 | } |
---|
1350 | |
---|
1351 | void CPRO_condense_cb( AW_window *aw,AW_CL which_statistic ) |
---|
1352 | { |
---|
1353 | AW_root *aw_root = aw->get_root(); |
---|
1354 | char mode=CPRO.result[which_statistic].drawmode; |
---|
1355 | if(!(CPRO.result[which_statistic].statisticexists)) |
---|
1356 | { |
---|
1357 | aw_message("statistic doesn't exist !"); |
---|
1358 | return; |
---|
1359 | } |
---|
1360 | float leastmax=(float)(aw_root->awar("cpro/leastmax")->read_int())/100.0; |
---|
1361 | CPRO.leastaccu= aw_root->awar("cpro/leastaccu")->read_int(); |
---|
1362 | float firsttoreach=(float)(aw_root->awar("cpro/firsttoreach")->read_int())/100.0; |
---|
1363 | float firstreachedstep=(float) |
---|
1364 | (aw_root->awar("cpro/firstreachedstep")->read_int())/100.0; |
---|
1365 | char *transversionstring=aw_root->awar("cpro/which_result")->read_string(); |
---|
1366 | char transversion=1; |
---|
1367 | if(strcmp(transversionstring,"transversions")) transversion=0; |
---|
1368 | free(transversionstring); |
---|
1369 | long maxcol=CPRO.result[which_statistic].maxalignlen; |
---|
1370 | |
---|
1371 | char *savename=aw_root->awar("cpro/condensename")->read_string(); |
---|
1372 | if(savename[0]==0) |
---|
1373 | { |
---|
1374 | free(savename); |
---|
1375 | return; |
---|
1376 | } |
---|
1377 | |
---|
1378 | aw_openstatus("condense statistic");aw_status((double)0); |
---|
1379 | |
---|
1380 | char *result=(char *)calloc((unsigned int)maxcol+1,1); |
---|
1381 | |
---|
1382 | float maximum; |
---|
1383 | float reachedhalf; |
---|
1384 | char steps; |
---|
1385 | for(long column=0;column<maxcol;column++) |
---|
1386 | { |
---|
1387 | if(((column/100)*100)==column) aw_status((double)column/(double)maxcol); |
---|
1388 | maximum=CPRO_getmaximum(column,transversion,(char)which_statistic,mode); |
---|
1389 | if(maximum<-100.0) result[column]='.'; |
---|
1390 | else if(maximum<=0.0) result[column]='-'; |
---|
1391 | else |
---|
1392 | { |
---|
1393 | if(maximum>=leastmax) result[column]='A'; |
---|
1394 | else result[column]='a'; |
---|
1395 | reachedhalf=CPRO_gethalfmaximum(column,maximum,firsttoreach, |
---|
1396 | transversion,(char)which_statistic,mode); |
---|
1397 | for(steps=0;(reachedhalf>firstreachedstep)&&(steps<'Y'-'A');steps++) |
---|
1398 | reachedhalf-=firstreachedstep; |
---|
1399 | result[column]+=steps; |
---|
1400 | } |
---|
1401 | } |
---|
1402 | |
---|
1403 | GB_ERROR error = 0; |
---|
1404 | char *align=CPRO.result[which_statistic].alignname; |
---|
1405 | |
---|
1406 | aw_status("exporting result"); |
---|
1407 | |
---|
1408 | GB_begin_transaction(GLOBAL_gb_main); |
---|
1409 | |
---|
1410 | GBDATA *gb_extended = GBT_find_or_create_SAI(GLOBAL_gb_main,savename); |
---|
1411 | |
---|
1412 | GBDATA *gb_param; |
---|
1413 | const char *typestring = GBS_global_string("RATES BY DISTANCE: [%s] [UPPER_CASE%% %li]" |
---|
1414 | " [ INTERREST%% %li] [STEP/CHAR %li]", |
---|
1415 | (transversion)? "transversion":"all differences", |
---|
1416 | (long)(leastmax*100.0), |
---|
1417 | (long)(firsttoreach*100.0), |
---|
1418 | (long)(firstreachedstep*100.0) ); |
---|
1419 | |
---|
1420 | gb_param=GBT_add_data(gb_extended,align,"_TYPE",GB_STRING); |
---|
1421 | error=GB_write_string(gb_param,typestring); |
---|
1422 | |
---|
1423 | GBDATA *gb_data = GBT_add_data(gb_extended, align,"data", GB_STRING); |
---|
1424 | |
---|
1425 | error = GB_write_string(gb_data,result); |
---|
1426 | aw_closestatus(); |
---|
1427 | GB_end_transaction_show_error(GLOBAL_gb_main, error, aw_message); |
---|
1428 | |
---|
1429 | free(result); |
---|
1430 | free(savename); |
---|
1431 | } |
---|
1432 | |
---|
1433 | AW_window *CPRO_condensewindow_cb( AW_root *aw_root,AW_CL which_statistic ) |
---|
1434 | { |
---|
1435 | char buf[30]; |
---|
1436 | sprintf(buf,"CONDENSE STATISTIC %ld",(long)which_statistic+1); |
---|
1437 | |
---|
1438 | AW_window_simple *aws = new AW_window_simple; |
---|
1439 | aws->init( aw_root,buf, buf); |
---|
1440 | aws->load_xfig("cpro/condense.fig"); |
---|
1441 | aws->button_length( 8 ); |
---|
1442 | |
---|
1443 | aws->at("close");aws->callback((AW_CB0)AW_POPDOWN); |
---|
1444 | aws->create_button("CLOSE","CLOSE","C"); |
---|
1445 | |
---|
1446 | aws->at( "which_result" ); |
---|
1447 | aws->create_toggle_field( "cpro/which_result", NULL ,"" ); |
---|
1448 | aws->insert_default_toggle( " all\ndifferences", "1", "diffs" ); |
---|
1449 | aws->insert_toggle( " only\ntransversions", "1", "transversions" ); |
---|
1450 | aws->update_toggle_field(); |
---|
1451 | |
---|
1452 | aws->button_length(11); |
---|
1453 | aws->at("begin");aws->callback(CPRO_condense_cb,which_statistic); |
---|
1454 | aws->create_button("CONDENSE_AND_EXPORT", "CONDENSE\nAND EXPORT","E"); |
---|
1455 | |
---|
1456 | aws->at("name");aws->create_input_field("cpro/condensename",11); |
---|
1457 | |
---|
1458 | aws->at("save_box"); |
---|
1459 | awt_create_selection_list_on_extendeds(GLOBAL_gb_main,aws,"cpro/condensename"); |
---|
1460 | |
---|
1461 | return( AW_window *)aws; |
---|
1462 | } |
---|
1463 | |
---|
1464 | AW_window *CPRO_xpert_cb( AW_root *aw_root ) |
---|
1465 | { |
---|
1466 | static AW_window *expertwindow = 0; |
---|
1467 | if(expertwindow) return(expertwindow); |
---|
1468 | |
---|
1469 | AW_window_simple *aws = new AW_window_simple; |
---|
1470 | aws->init( aw_root, "CPRO_EXPERT_PROPS","EXPERT PROPERTIES"); |
---|
1471 | aws->load_xfig("cpro/expert.fig"); |
---|
1472 | aws->button_length( 8 ); |
---|
1473 | |
---|
1474 | aws->at("close");aws->callback((AW_CB0)AW_POPDOWN); |
---|
1475 | aws->create_button("CLOSE","CLOSE","C"); |
---|
1476 | |
---|
1477 | aws->at("partition"); |
---|
1478 | aws->create_input_field("cpro/partition",6); |
---|
1479 | |
---|
1480 | aws->at("leastaccu"); |
---|
1481 | aws->create_input_field("cpro/leastaccu",3); |
---|
1482 | |
---|
1483 | aws->at("leastcompares"); |
---|
1484 | aws->create_input_field("cpro/leastcompares",6); |
---|
1485 | |
---|
1486 | aws->at("gridvertical"); |
---|
1487 | aws->create_input_field("cpro/gridvertical",3); |
---|
1488 | |
---|
1489 | aws->at("gridhorizontal"); |
---|
1490 | aws->create_input_field("cpro/gridhorizontal",3); |
---|
1491 | |
---|
1492 | aws->at("leastmax"); |
---|
1493 | aws->create_input_field("cpro/leastmax",3); |
---|
1494 | |
---|
1495 | aws->at("firsttoreach"); |
---|
1496 | aws->create_input_field("cpro/firsttoreach",3); |
---|
1497 | |
---|
1498 | aws->at("firstreachedstep"); |
---|
1499 | aws->create_input_field("cpro/firstreachedstep",3); |
---|
1500 | |
---|
1501 | aws->label_length(8); |
---|
1502 | aws->button_length(8); |
---|
1503 | aws->at("mempartition");aws->create_button(0,"tmp/cpro/mempartition"); |
---|
1504 | |
---|
1505 | return expertwindow=(AW_window *)aws; |
---|
1506 | } |
---|
1507 | |
---|
1508 | AW_window *CPRO_showstatistic_cb( AW_root *aw_root, AW_CL which_statistic) |
---|
1509 | { |
---|
1510 | char buf[20]; |
---|
1511 | sprintf(buf,"SHOW STATISTIC %d\n",(int)which_statistic+1); |
---|
1512 | AW_window_simple *aws=new AW_window_simple; |
---|
1513 | aws->init( aw_root,buf,buf /*,400,(int)(10+which_statistic*300)*/); |
---|
1514 | aws->load_xfig("cpro/show.fig"); |
---|
1515 | aws->button_length(6); |
---|
1516 | |
---|
1517 | aws->at("close");aws->callback((AW_CB0)AW_POPDOWN); |
---|
1518 | aws->create_button("CLOSE","CLOSE","C"); |
---|
1519 | |
---|
1520 | //aws->at("xpert");aws->callback(AW_POPUP,(AW_CL)CPRO_xpert_cb,0); |
---|
1521 | |
---|
1522 | |
---|
1523 | aws->at("column"); |
---|
1524 | aws->create_input_field(AWAR_CURSOR_POSITION,4); |
---|
1525 | |
---|
1526 | aws->button_length(3); |
---|
1527 | aws->at("d");aws->callback((AW_CB0)CPRO_columnminus_cb); |
---|
1528 | aws->create_button(0,"-","1"); |
---|
1529 | aws->at("u");aws->callback((AW_CB2)CPRO_columnplus_cb,which_statistic,0); |
---|
1530 | aws->create_button(0,"+","2"); |
---|
1531 | |
---|
1532 | sprintf(buf,"cpro/drawmode%d",(int)which_statistic); |
---|
1533 | aws->at("drawmode");aws->create_option_menu(buf); |
---|
1534 | aws->insert_option( "no smoothing", "n",0); |
---|
1535 | aws->insert_option( "smoothing 1", "1",1); |
---|
1536 | aws->insert_option( "smoothing 2", "2",2); |
---|
1537 | aws->insert_option( "smoothing 3", "3",3); |
---|
1538 | aws->insert_option( "smoothing 5", "5",5); |
---|
1539 | aws->insert_option( "smoothing 10", "6",10); |
---|
1540 | aws->insert_option( "smoothing 15", "7",15); |
---|
1541 | aws->update_option_menu(); |
---|
1542 | |
---|
1543 | aw_root->awar(buf)->add_callback((AW_RCB)CPRO_column_cb,(AW_CL)aws,which_statistic); |
---|
1544 | aw_root->awar("cpro/gridhorizontal")->add_callback((AW_RCB)CPRO_column_cb,(AW_CL)aws,which_statistic); |
---|
1545 | aw_root->awar("cpro/gridvertical")->add_callback((AW_RCB)CPRO_column_cb,(AW_CL)aws,which_statistic); |
---|
1546 | |
---|
1547 | aws->at("maxdistance"); |
---|
1548 | //aws->label("max distance"); |
---|
1549 | aws->create_input_field("cpro/maxdistance",3); |
---|
1550 | |
---|
1551 | aws->set_resize_callback (AW_INFO_AREA, CPRO_resize_cb, which_statistic, 0); |
---|
1552 | aws->set_expose_callback (AW_INFO_AREA, CPRO_expose_cb, which_statistic, 0); |
---|
1553 | aw_root->awar(AWAR_CURSOR_POSITION)->add_callback((AW_RCB)CPRO_column_cb, (AW_CL)aws,which_statistic); |
---|
1554 | aw_root->awar("cpro/maxdistance")->add_callback((AW_RCB)CPRO_column_cb, (AW_CL)aws,which_statistic); |
---|
1555 | aw_root->awar("cpro/maxdistance")->add_callback((AW_RCB)CPRO_column_cb, (AW_CL)aws,which_statistic); |
---|
1556 | aws->button_length( 6); |
---|
1557 | |
---|
1558 | AW_device *device=aws->get_device (AW_INFO_AREA); |
---|
1559 | device->reset(); |
---|
1560 | |
---|
1561 | device->new_gc( GC_black ); |
---|
1562 | device->set_line_attributes(GC_black,0.3,AW_SOLID); |
---|
1563 | device->set_foreground_color(GC_black,AW_WINDOW_FG); |
---|
1564 | device->set_font(GC_black,0,10, 0); |
---|
1565 | device->new_gc( GC_blue ); |
---|
1566 | device->set_line_attributes(GC_blue,0.3,AW_SOLID); |
---|
1567 | device->set_foreground_color(GC_blue,AW_WINDOW_C1); |
---|
1568 | device->new_gc( GC_green ); |
---|
1569 | device->set_line_attributes(GC_green,0.3,AW_SOLID); |
---|
1570 | device->set_foreground_color(GC_green,AW_WINDOW_C2); |
---|
1571 | device->new_gc( GC_grid ); |
---|
1572 | device->set_line_attributes(GC_grid,0.3,AW_DOTTED); |
---|
1573 | device->set_foreground_color(GC_grid,AW_WINDOW_C3); |
---|
1574 | |
---|
1575 | return (AW_window *)aws; |
---|
1576 | } |
---|
1577 | |
---|
1578 | AW_window *CPRO_calculatewin_cb(AW_root *aw_root,AW_CL which_statistic) |
---|
1579 | { |
---|
1580 | char buf[30]; |
---|
1581 | sprintf(buf,"CALCULATE STATISTIC %ld",(long)which_statistic+1); |
---|
1582 | AW_window_simple *aws = new AW_window_simple; |
---|
1583 | aws->init( aw_root,buf,buf); |
---|
1584 | aws->load_xfig("cpro/calc.fig"); |
---|
1585 | aws->button_length( 10 ); |
---|
1586 | |
---|
1587 | aws->at("close");aws->callback((AW_CB0)AW_POPDOWN); |
---|
1588 | aws->create_button("CLOSE","CLOSE","C"); |
---|
1589 | |
---|
1590 | aws->at("resolution"); |
---|
1591 | aws->create_input_field("cpro/resolution",8); |
---|
1592 | |
---|
1593 | aws->at("transratio"); |
---|
1594 | aws->create_input_field("cpro/transratio",8); |
---|
1595 | |
---|
1596 | aws->at("which_alignment"); |
---|
1597 | awt_create_selection_list_on_ad(GLOBAL_gb_main, (AW_window *)aws,"cpro/alignment","*="); |
---|
1598 | |
---|
1599 | aws->button_length(10); |
---|
1600 | aws->at("xpert");aws->callback(AW_POPUP,(AW_CL)CPRO_xpert_cb,0); |
---|
1601 | aws->create_button("EXPERT_OPTIONS", "expert...","x"); |
---|
1602 | |
---|
1603 | aws->at("calculate"); |
---|
1604 | aws->callback(CPRO_calculate_cb,(AW_CL)which_statistic); |
---|
1605 | aws->create_button("CALCULATE","CALCULATE","A"); |
---|
1606 | |
---|
1607 | aws->at( "which_species" ); |
---|
1608 | aws->create_toggle_field( "cpro/which_species", NULL ,"" ); |
---|
1609 | aws->insert_toggle( "all vs all", "1", "all" ); |
---|
1610 | aws->insert_toggle( "marked vs marked", "1", "marked" ); |
---|
1611 | aws->insert_default_toggle( "marked vs all", "1", "markedall" ); |
---|
1612 | aws->update_toggle_field(); |
---|
1613 | |
---|
1614 | aws->at( "countgaps" ); |
---|
1615 | aws->create_toggle_field( "cpro/countgaps", NULL ,"" ); |
---|
1616 | aws->insert_toggle( "on", "1", "on" ); |
---|
1617 | aws->insert_default_toggle( "off", "1", "off" ); |
---|
1618 | aws->update_toggle_field(); |
---|
1619 | |
---|
1620 | aws->label_length(8); |
---|
1621 | aws->button_length(8); |
---|
1622 | aws->at("memstatistic"); |
---|
1623 | aws->create_button(0,"tmp/cpro/memstatistic"); |
---|
1624 | |
---|
1625 | return (AW_window *)aws; |
---|
1626 | |
---|
1627 | } |
---|
1628 | /* ----------------------------------------------------------------- |
---|
1629 | * Function: AP_open_cprofile_window |
---|
1630 | * |
---|
1631 | * Arguments: . |
---|
1632 | * |
---|
1633 | * Returns: . |
---|
1634 | * |
---|
1635 | * Description: Draws window, initializes callback for most important |
---|
1636 | * function, CPRO_begin_cb |
---|
1637 | * |
---|
1638 | * NOTE: . |
---|
1639 | * |
---|
1640 | * Global Variables referenced: . |
---|
1641 | * |
---|
1642 | * Global Variables modified: x |
---|
1643 | * |
---|
1644 | * AWARs referenced: . |
---|
1645 | * |
---|
1646 | * AWARs modified: x |
---|
1647 | * |
---|
1648 | * Dependencies: Needs xfig file cprofile.fig |
---|
1649 | * ----------------------------------------------------------------- |
---|
1650 | */ |
---|
1651 | AW_window * |
---|
1652 | AP_open_cprofile_window( AW_root *aw_root) |
---|
1653 | { |
---|
1654 | AW_window_simple *aws = new AW_window_simple; |
---|
1655 | aws->init( aw_root, "CPR_MAIN", "Conservation Profile: Distance Matrix"); |
---|
1656 | aws->load_xfig("cpro/main.fig"); |
---|
1657 | aws->button_length( 10 ); |
---|
1658 | |
---|
1659 | GB_push_transaction(GLOBAL_gb_main); |
---|
1660 | |
---|
1661 | aws->at("close");aws->callback((AW_CB0)AW_POPDOWN); |
---|
1662 | aws->create_button("CLOSE","CLOSE","C"); |
---|
1663 | |
---|
1664 | aws->at("help");aws->callback(AW_POPUP_HELP,(AW_CL)"pos_variability.ps"); |
---|
1665 | aws->create_button("HELP","HELP","H"); |
---|
1666 | |
---|
1667 | aws->button_length(10); |
---|
1668 | aws->at("xpert");aws->callback(AW_POPUP,(AW_CL)CPRO_xpert_cb,0); |
---|
1669 | aws->create_button("EXPERT_OPTIONS","expert...","x"); |
---|
1670 | |
---|
1671 | /* start action by button */ |
---|
1672 | aws->button_length(17); |
---|
1673 | aws->at("calculate1");aws->callback(AW_POPUP,(AW_CL)CPRO_calculatewin_cb,0); |
---|
1674 | aws->create_button("GO_STAT_1", "calculate as\nstatistic 1 ...","c"); |
---|
1675 | aws->at("calculate2");aws->callback(AW_POPUP,(AW_CL)CPRO_calculatewin_cb,1); |
---|
1676 | aws->create_button("GO_STAT_2", "calculate as\nstatistic 2 ...","a"); |
---|
1677 | |
---|
1678 | aws->button_length(17); |
---|
1679 | aws->at("save1");aws->callback(AW_POPUP,(AW_CL)CPRO_savestatisticwindow_cb,0); |
---|
1680 | aws->create_button("SAVE_STAT_1", "save\nstatistic 1 ...","s"); |
---|
1681 | aws->at("save2");aws->callback(AW_POPUP,(AW_CL)CPRO_savestatisticwindow_cb,1); |
---|
1682 | aws->create_button("SAVE_STAT_2", "save\nstatistic 2 ...","v"); |
---|
1683 | |
---|
1684 | aws->button_length( 17); |
---|
1685 | aws->at("show1");aws->callback(AW_POPUP,(AW_CL)CPRO_showstatistic_cb,0); |
---|
1686 | aws->create_button("SHOW_STAT_!", "show\ngraph 1 ...","h"); |
---|
1687 | aws->at("show2");aws->callback(AW_POPUP,(AW_CL)CPRO_showstatistic_cb,1); |
---|
1688 | aws->create_button("SHOW_STAT_2", "show\ngraph 2 ...","w"); |
---|
1689 | |
---|
1690 | aws->button_length( 17); |
---|
1691 | aws->at("load1");aws->callback(AW_POPUP,(AW_CL)CPRO_loadstatisticwindow_cb,0); |
---|
1692 | aws->create_button("LOAD_STAT_1", "load\nstatistic 1 ... ","l"); |
---|
1693 | aws->at("load2");aws->callback(AW_POPUP,(AW_CL)CPRO_loadstatisticwindow_cb,1); |
---|
1694 | aws->create_button("LOAD_STAT_2", "load\nstatistic 2 ...","d"); |
---|
1695 | |
---|
1696 | aws->at("condense1");aws->callback(AW_POPUP, (AW_CL)CPRO_condensewindow_cb,0); |
---|
1697 | aws->create_button("CONDENSE_STAT_1", "condense\nstatistic 1 ...","o"); |
---|
1698 | aws->at("condense2");aws->callback(AW_POPUP, (AW_CL)CPRO_condensewindow_cb,1); |
---|
1699 | aws->create_button("CONDENSE_STAT_2", "condense\nstatistic 2 ...","n"); |
---|
1700 | |
---|
1701 | aws->at("memfor1");aws->create_button(0,"tmp/cpro/memfor1"); |
---|
1702 | aws->at("memfor2");aws->create_button(0,"tmp/cpro/memfor2"); |
---|
1703 | aws->at("which1");aws->create_button(0,"tmp/cpro/which1"); |
---|
1704 | aws->at("which2");aws->create_button(0,"tmp/cpro/which2"); |
---|
1705 | aws->at("resolution1");aws->create_button(0,"tmp/cpro/nowres1"); |
---|
1706 | aws->at("resolution2");aws->create_button(0,"tmp/cpro/nowres2"); |
---|
1707 | |
---|
1708 | aw_root->awar("cpro/alignment")->add_callback(CPRO_memrequirement_cb); |
---|
1709 | aw_root->awar("cpro/partition")->add_callback(CPRO_memrequirement_cb); |
---|
1710 | aw_root->awar("cpro/resolution")->add_callback(CPRO_memrequirement_cb); |
---|
1711 | aw_root->awar("cpro/which_species")->add_callback(CPRO_memrequirement_cb); |
---|
1712 | |
---|
1713 | GB_pop_transaction(GLOBAL_gb_main); |
---|
1714 | |
---|
1715 | CPRO_memrequirement_cb(aw_root); |
---|
1716 | |
---|
1717 | return (AW_window *)aws; |
---|
1718 | } |
---|