1 | #include <stdlib.h> |
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2 | #include "ali_prealigner.hxx" |
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3 | #include "ali_aligner.hxx" |
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4 | |
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5 | unsigned long random_stat[6] = {0, 0, 0, 0, 0, 0}; |
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6 | |
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7 | /***************************************************************************** |
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8 | * |
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9 | * structure ali_prealigner_mask |
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10 | * |
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11 | *****************************************************************************/ |
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12 | |
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13 | /* |
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14 | * Insert a new map |
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15 | */ |
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16 | void ali_prealigner_mask:: |
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17 | insert(ALI_MAP * in_map, float costs) |
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18 | { |
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19 | unsigned long i; |
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20 | |
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21 | calls++; |
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22 | if (map == 0) { |
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23 | map = in_map; |
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24 | cost_of_binding = costs; |
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25 | } else { |
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26 | if (costs > cost_of_binding) { |
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27 | delete in_map; |
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28 | return; |
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29 | } |
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30 | if (map->first_base() != in_map->first_base() || |
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31 | map->last_base() != in_map->last_base() || |
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32 | map->first_reference_base() != in_map->first_reference_base() || |
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33 | map->last_reference_base() != in_map->last_reference_base()) { |
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34 | ali_fatal_error("Incompatible maps", |
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35 | "ali_prealigner_mask::insert()"); |
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36 | } |
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37 | if (costs < cost_of_binding) { |
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38 | delete map; |
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39 | map = in_map; |
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40 | cost_of_binding = costs; |
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41 | last_new = calls; |
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42 | last_joins = 0; |
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43 | return; |
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44 | } |
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45 | joins++; |
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46 | last_joins++; |
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47 | for (i = map->first_base(); i <= map->last_base(); i++) |
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48 | if ((!map->is_undefined(i)) && map->position(i) != in_map->position(i)) |
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49 | map->undefine(i); |
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50 | delete in_map; |
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51 | } |
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52 | } |
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53 | |
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54 | /* |
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55 | * Delete expensive parts of solution |
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56 | */ |
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57 | void ali_prealigner_mask:: |
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58 | delete_expensive(ALI_PREALIGNER_CONTEXT * context, |
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59 | ALI_PROFILE * profile) |
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60 | { |
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61 | ALI_MAP *inverse_map; |
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62 | unsigned long start_hel, end_hel; |
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63 | unsigned long start_seq, end_seq; |
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64 | unsigned long start_mapped, end_mapped; |
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65 | unsigned long start_ok=0, end_ok=0; |
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66 | int start_ok_flag; |
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67 | unsigned long found_helix; |
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68 | unsigned long error_counter; |
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69 | |
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70 | unsigned long map_pos, i, j; |
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71 | float max_cost, helix_cost; |
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72 | unsigned long helix_counter; |
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73 | long compl_pos; |
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74 | unsigned char base1, base2; |
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75 | |
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76 | printf("MASK : calls = %ld joins = %ld last_new = %ld last_joins = %ld\n", |
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77 | calls, joins, last_new, last_joins); |
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78 | |
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79 | max_cost = profile->w_sub_maximum() * context->max_cost_of_sub_percent; |
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80 | |
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81 | /* |
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82 | * Delete expensive Bases |
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83 | */ |
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84 | error_counter = 0; |
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85 | for (i = map->first_base(); i <= map->last_base(); i++) { |
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86 | if (!(map->is_inserted(i)) && |
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87 | profile->w_sub(map->position(i), i) > max_cost) { |
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88 | error_counter++; |
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89 | if (error_counter > context->error_count) |
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90 | map->undefine(i); |
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91 | else { |
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92 | if (error_counter == context->error_count) { |
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93 | for (j = i - error_counter + 1; j <= i; j++) |
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94 | map->undefine(j); |
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95 | } |
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96 | } |
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97 | } else { |
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98 | /* |
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99 | * If error was in helix => delete helix total |
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100 | */ |
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101 | if (error_counter > 0 && |
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102 | profile->is_in_helix(map->position(i - 1), &start_hel, &end_hel)) { |
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103 | for (j = i - 1; map->position(j) >= long(start_hel); j--); |
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104 | for (; map->position(j) <= long(end_hel); j++) |
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105 | map->undefine(j); |
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106 | } |
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107 | error_counter = 0; |
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108 | } |
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109 | } |
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110 | |
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111 | /* |
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112 | * Delete expensive Helizes |
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113 | */ |
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114 | inverse_map = map->inverse_without_inserts(); |
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115 | for (i = inverse_map->first_base(); i <= inverse_map->last_base(); i++) { |
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116 | /* |
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117 | * found a helix |
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118 | */ |
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119 | if (profile->is_in_helix(i, &start_hel, &end_hel)) { |
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120 | if (i != start_hel) |
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121 | ali_fatal_error("Inconsistent positions", |
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122 | "ali_prealigner_mask::delete_expensive()"); |
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123 | compl_pos = profile->complement_position(start_hel); |
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124 | /* |
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125 | * only forward bindings |
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126 | */ |
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127 | if (compl_pos > long(end_hel)) { |
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128 | helix_cost = 0.0; |
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129 | helix_counter = 0; |
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130 | while (i <= end_hel) { |
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131 | /* |
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132 | * is binding ? |
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133 | */ |
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134 | if (compl_pos > 0) { |
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135 | if (!inverse_map->is_undefined(i)) { |
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136 | base1 = (profile->sequence())->base( |
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137 | inverse_map->first_reference_base() + |
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138 | inverse_map->position(i)); |
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139 | } else { |
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140 | base1 = ALI_GAP_CODE; |
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141 | } |
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142 | if (!inverse_map->is_undefined(compl_pos)) { |
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143 | base2 = (profile->sequence())->base( |
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144 | inverse_map->first_reference_base() + |
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145 | inverse_map->position(compl_pos)); |
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146 | } else { |
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147 | base2 = ALI_GAP_CODE; |
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148 | } |
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149 | if (base1 != ALI_GAP_CODE || base2 != ALI_GAP_CODE) { |
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150 | helix_cost += profile->w_bind(i, base1, compl_pos, base2); |
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151 | helix_counter++; |
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152 | } |
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153 | } |
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154 | i++; |
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155 | compl_pos = profile->complement_position(i); |
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156 | } |
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157 | if (helix_counter > 0) helix_cost /= helix_counter; |
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158 | if (helix_cost > context->max_cost_of_helix) { |
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159 | for (j = start_hel; j <= end_hel; j++) { |
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160 | if (!inverse_map->is_undefined(j)) { |
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161 | map->undefine(inverse_map->first_reference_base() + inverse_map->position(j)); |
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162 | } |
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163 | } |
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164 | for (j = profile->complement_position(end_hel); long(j) <= profile->complement_position(start_hel); j++) { |
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165 | if (!inverse_map->is_undefined(j)) { |
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166 | map->undefine(inverse_map->first_reference_base() + inverse_map->position(j)); |
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167 | } |
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168 | } |
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169 | } |
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170 | } |
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171 | i = end_hel; |
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172 | } |
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173 | } |
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174 | delete inverse_map; |
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175 | |
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176 | /* |
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177 | * Check for good parts |
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178 | */ |
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179 | for (map_pos = map->first_base(); map_pos <= map->last_base(); map_pos++) { |
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180 | /* |
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181 | * search next defined segment |
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182 | */ |
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183 | if (!map->is_undefined(map_pos)) { |
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184 | /* |
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185 | * find start and end of segment |
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186 | */ |
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187 | start_seq = map_pos; |
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188 | start_mapped = map->position(map_pos); |
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189 | for (map_pos++; map_pos <= map->last_base() && |
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190 | (!map->is_undefined(map_pos)); map_pos++); |
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191 | end_seq = map_pos - 1; |
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192 | end_mapped = map->position(end_seq); |
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193 | |
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194 | /* |
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195 | * Check segment for helizes |
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196 | */ |
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197 | found_helix = 0; |
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198 | start_ok_flag = 0; |
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199 | for (i = start_seq; i <= end_seq; i++) { |
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200 | if (profile->is_in_helix(map->position(i), &start_hel, &end_hel)) { |
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201 | found_helix++; |
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202 | /* |
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203 | * Helix is inside the segment |
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204 | */ |
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205 | if (start_hel >= start_mapped && end_hel <= end_mapped) { |
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206 | if (start_ok_flag == 0) { |
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207 | start_ok = start_hel; |
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208 | start_ok_flag = 1; |
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209 | } |
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210 | end_ok = end_hel; |
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211 | } |
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212 | } |
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213 | } |
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214 | |
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215 | /* |
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216 | * Found good helizes |
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217 | */ |
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218 | if (start_ok_flag == 1) { |
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219 | for (i = start_seq; map->position(i) < long(start_ok); i++) map->undefine(i); |
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220 | for (i = end_seq; map->position(i) > long(end_ok); i--) map->undefine(i); |
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221 | } else { |
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222 | /* |
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223 | * Found bad helizes |
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224 | */ |
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225 | if (found_helix > 0) { |
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226 | for (i = start_seq; i <= end_seq; i++) |
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227 | map->undefine(i); |
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228 | } |
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229 | /* |
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230 | * Segment without helix |
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231 | */ |
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232 | else { |
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233 | if (end_seq - start_seq + 1 >= (unsigned long)((2 * context->intervall_border) + context->intervall_center)) { |
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234 | for (i = start_seq; i < start_seq + context->intervall_border; i++) map->undefine(i); |
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235 | for (i = end_seq; i > end_seq - context->intervall_border; i--) map->undefine(i); |
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236 | } else { |
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237 | for (i = start_seq; i <= end_seq; i++) map->undefine(i); |
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238 | } |
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239 | } |
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240 | } |
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241 | } |
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242 | } |
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243 | } |
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244 | |
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245 | |
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246 | /***************************************************************************** |
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247 | * |
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248 | * class ALI_PREALIGNER (privat) |
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249 | * |
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250 | *****************************************************************************/ |
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251 | |
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252 | GB_INLINE float ALI_PREALIGNER:: |
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253 | minimum2(float a, float b) |
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254 | { |
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255 | return ((a < b) ? a : b); |
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256 | } |
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257 | |
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258 | GB_INLINE float ALI_PREALIGNER:: |
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259 | minimum3(float a, float b, float c) |
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260 | { |
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261 | return ((a < b) ? ((a < c) ? a : c) : ((b < c) ? b : c)); |
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262 | } |
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263 | |
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264 | |
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265 | GB_INLINE void ALI_PREALIGNER:: |
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266 | calculate_first_column_first_cell( |
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267 | ali_prealigner_cell * akt_cell) |
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268 | { |
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269 | float v1, v2, v3; |
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270 | |
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271 | /*** |
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272 | v1 = profile->w_ins(start_x,start_y) + profile->w_del(start_y,start_y); |
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273 | ***/ |
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274 | v1 = profile->w_ins_multi_cheap(start_x, start_y) + |
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275 | profile->w_sub_multi_gap_cheap(start_y, start_y); |
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276 | v2 = profile->w_sub(start_y, start_x); |
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277 | v3 = v1; |
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278 | |
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279 | akt_cell->d = minimum2(v1, v2); |
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280 | |
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281 | if (akt_cell->d == v1) |
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282 | path_map->set(0, 0, ALI_UP | ALI_LEFT); |
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283 | if (akt_cell->d == v2) |
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284 | path_map->set(0, 0, ALI_DIAG); |
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285 | } |
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286 | |
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287 | GB_INLINE void ALI_PREALIGNER:: |
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288 | calculate_first_column_cell( |
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289 | ali_prealigner_cell * up_cell, ali_prealigner_cell * akt_cell, |
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290 | unsigned long pos_y) |
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291 | { |
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292 | float v1, v2, v3; |
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293 | unsigned long positiony; |
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294 | |
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295 | positiony = start_y + pos_y; |
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296 | |
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297 | /*** |
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298 | v1 = up_cell->d + profile->w_del(positiony,positiony); |
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299 | v2 = profile->w_del_multi_unweighted(start_y, positiony - 1) + |
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300 | profile->w_sub(positiony, start_x); |
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301 | v3 = profile->w_del_multi_unweighted(start_y, positiony) + |
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302 | profile->w_ins(start_x,positiony); |
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303 | ***/ |
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304 | v1 = up_cell->d + profile->w_sub_gap(positiony); |
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305 | v2 = profile->w_sub_multi_gap_cheap(start_y, positiony - 1) + |
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306 | profile->w_sub(positiony, start_x); |
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307 | v3 = profile->w_sub_multi_gap_cheap(start_y, positiony) + |
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308 | profile->w_ins(start_x, positiony); |
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309 | |
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310 | akt_cell->d = minimum3(v1, v2, v3); |
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311 | |
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312 | if (v1 == akt_cell->d) |
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313 | path_map->set(0, pos_y, ALI_UP); |
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314 | if (v2 == akt_cell->d) |
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315 | path_map->set(0, pos_y, ALI_DIAG); |
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316 | if (v3 == akt_cell->d) |
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317 | path_map->set(0, pos_y, ALI_LEFT); |
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318 | } |
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319 | |
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320 | void ALI_PREALIGNER:: |
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321 | calculate_first_column(ali_prealigner_column * akt_column) |
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322 | { |
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323 | unsigned long pos_y; |
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324 | |
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325 | calculate_first_column_first_cell(&(*akt_column->cells)[0]); |
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326 | |
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327 | for (pos_y = 1; pos_y < akt_column->column_length; pos_y++) |
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328 | calculate_first_column_cell(&(*akt_column->cells)[pos_y - 1], |
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329 | &(*akt_column->cells)[pos_y], |
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330 | pos_y); |
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331 | } |
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332 | |
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333 | |
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334 | GB_INLINE void ALI_PREALIGNER:: |
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335 | calculate_first_cell( |
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336 | ali_prealigner_cell * left_cell, ali_prealigner_cell * akt_cell, |
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337 | unsigned long pos_x) |
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338 | { |
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339 | float v1, v2, v3; |
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340 | unsigned long positionx; |
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341 | |
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342 | positionx = start_x + pos_x; |
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343 | |
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344 | /*** |
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345 | v1 = profile->w_ins_multi_unweighted(start_x, positionx) + |
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346 | profile->w_del(start_y,start_y); |
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347 | v2 = profile->w_ins_multi_unweighted(start_x, positionx - 1) + |
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348 | profile->w_sub(start_y, positionx); |
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349 | ***/ |
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350 | v1 = profile->w_ins_multi_cheap(start_x, positionx) + |
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351 | profile->w_sub_gap(start_y); |
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352 | v2 = profile->w_ins_multi_cheap(start_x, positionx - 1) + |
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353 | profile->w_sub(start_y, positionx); |
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354 | v3 = left_cell->d + profile->w_ins(positionx, start_y); |
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355 | |
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356 | akt_cell->d = minimum3(v1, v2, v3); |
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357 | |
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358 | if (v1 == akt_cell->d) |
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359 | path_map->set(pos_x, 0, ALI_UP); |
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360 | if (v2 == akt_cell->d) |
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361 | path_map->set(pos_x, 0, ALI_DIAG); |
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362 | if (v3 == akt_cell->d) |
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363 | path_map->set(pos_x, 0, ALI_LEFT); |
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364 | } |
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365 | |
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366 | GB_INLINE void ALI_PREALIGNER:: |
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367 | calculate_cell( |
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368 | ali_prealigner_cell * diag_cell, ali_prealigner_cell * left_cell, |
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369 | ali_prealigner_cell * up_cell, ali_prealigner_cell * akt_cell, |
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370 | unsigned long pos_x, unsigned long pos_y) |
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371 | { |
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372 | float v1, v2, v3; |
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373 | unsigned long positionx, positiony; |
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374 | |
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375 | positionx = start_x + pos_x; |
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376 | positiony = start_y + pos_y; |
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377 | |
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378 | /*** |
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379 | v1 = up_cell->d + profile->w_del(positiony,positiony); |
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380 | ***/ |
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381 | v1 = up_cell->d + profile->w_sub_gap(positiony); |
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382 | v2 = diag_cell->d + profile->w_sub(positiony, positionx); |
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383 | v3 = left_cell->d + profile->w_ins(positionx, positiony); |
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384 | |
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385 | akt_cell->d = minimum3(v1, v2, v3); |
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386 | |
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387 | if (v1 == akt_cell->d) |
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388 | path_map->set(pos_x, pos_y, ALI_UP); |
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389 | if (v2 == akt_cell->d) |
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390 | path_map->set(pos_x, pos_y, ALI_DIAG); |
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391 | if (v3 == akt_cell->d) |
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392 | path_map->set(pos_x, pos_y, ALI_LEFT); |
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393 | } |
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394 | |
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395 | void ALI_PREALIGNER:: |
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396 | calculate_column( |
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397 | ali_prealigner_column * prev_col, ali_prealigner_column * akt_col, |
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398 | unsigned long pos_x) |
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399 | { |
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400 | unsigned long pos_y; |
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401 | |
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402 | calculate_first_cell(&(*prev_col->cells)[0], &(*akt_col->cells)[0], pos_x); |
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403 | |
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404 | for (pos_y = 1; pos_y < akt_col->column_length; pos_y++) |
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405 | calculate_cell(&(*prev_col->cells)[pos_y - 1], &(*prev_col->cells)[pos_y], |
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406 | &(*akt_col->cells)[pos_y - 1], &(*akt_col->cells)[pos_y], |
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407 | pos_x, pos_y); |
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408 | } |
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409 | |
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410 | GB_INLINE void ALI_PREALIGNER:: |
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411 | calculate_last_column_first_cell( |
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412 | ali_prealigner_cell * left_cell, ali_prealigner_cell * akt_cell, |
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413 | unsigned long pos_x) |
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414 | { |
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415 | float v1, v2, v3; |
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416 | unsigned long positionx; |
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417 | |
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418 | positionx = start_x + pos_x; |
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419 | |
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420 | /*** |
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421 | v1 = profile->w_ins_multi_unweighted(start_x, positionx) + |
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422 | profile->w_del(start_y,start_y); |
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423 | v2 = profile->w_ins_multi_unweighted(start_x, positionx - 1) + |
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424 | profile->w_sub(start_y, positionx); |
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425 | ***/ |
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426 | v1 = profile->w_ins_multi_cheap(start_x, positionx) + |
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427 | profile->w_sub_gap_cheap(start_y); |
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428 | v2 = profile->w_ins_multi_cheap(start_x, positionx - 1) + |
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429 | profile->w_sub(start_y, positionx); |
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430 | v3 = left_cell->d + profile->w_ins(positionx, start_y); |
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431 | |
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432 | akt_cell->d = minimum3(v1, v2, v3); |
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433 | |
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434 | if (v1 == akt_cell->d) |
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435 | path_map->set(pos_x, 0, ALI_UP); |
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436 | if (v2 == akt_cell->d) |
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437 | path_map->set(pos_x, 0, ALI_DIAG); |
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438 | if (v3 == akt_cell->d) |
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439 | path_map->set(pos_x, 0, ALI_LEFT); |
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440 | } |
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441 | |
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442 | GB_INLINE void ALI_PREALIGNER:: |
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443 | calculate_last_column_cell( |
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444 | ali_prealigner_cell * diag_cell, ali_prealigner_cell * left_cell, |
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445 | ali_prealigner_cell * up_cell, ali_prealigner_cell * akt_cell, |
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446 | unsigned long pos_x, unsigned long pos_y) |
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447 | { |
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448 | float v1, v2, v3; |
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449 | unsigned long positionx, positiony; |
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450 | |
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451 | positionx = start_x + pos_x; |
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452 | positiony = start_y + pos_y; |
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453 | |
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454 | /*** |
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455 | v1 = up_cell->d + profile->w_del(positiony,positiony); |
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456 | ***/ |
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457 | v1 = up_cell->d + profile->w_sub_gap_cheap(positiony); |
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458 | v2 = diag_cell->d + profile->w_sub(positiony, positionx); |
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459 | v3 = left_cell->d + profile->w_ins(positionx, positiony); |
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460 | |
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461 | akt_cell->d = minimum3(v1, v2, v3); |
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462 | |
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463 | if (v1 == akt_cell->d) |
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464 | path_map->set(pos_x, pos_y, ALI_UP); |
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465 | if (v2 == akt_cell->d) |
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466 | path_map->set(pos_x, pos_y, ALI_DIAG); |
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467 | if (v3 == akt_cell->d) |
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468 | path_map->set(pos_x, pos_y, ALI_LEFT); |
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469 | } |
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470 | |
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471 | void ALI_PREALIGNER:: |
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472 | calculate_last_column( |
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473 | ali_prealigner_column * prev_col, ali_prealigner_column * akt_col, |
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474 | unsigned long pos_x) |
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475 | { |
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476 | unsigned long pos_y; |
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477 | |
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478 | calculate_last_column_first_cell(&(*prev_col->cells)[0], |
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479 | &(*akt_col->cells)[0], pos_x); |
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480 | |
---|
481 | for (pos_y = 1; pos_y < akt_col->column_length; pos_y++) |
---|
482 | calculate_last_column_cell(&(*prev_col->cells)[pos_y - 1], |
---|
483 | &(*prev_col->cells)[pos_y], |
---|
484 | &(*akt_col->cells)[pos_y - 1], &(*akt_col->cells)[pos_y], |
---|
485 | pos_x, pos_y); |
---|
486 | } |
---|
487 | |
---|
488 | |
---|
489 | void ALI_PREALIGNER:: |
---|
490 | calculate_matrix(void) |
---|
491 | { |
---|
492 | unsigned long pos_x; |
---|
493 | ali_prealigner_column *akt_col, *prev_col, *h_col; |
---|
494 | |
---|
495 | akt_col = new ali_prealigner_column(end_y - start_y + 1); |
---|
496 | prev_col = new ali_prealigner_column(end_y - start_y + 1); |
---|
497 | |
---|
498 | calculate_first_column(prev_col); |
---|
499 | |
---|
500 | for (pos_x = 1; pos_x < end_x - start_x + 1; pos_x++) { |
---|
501 | if (pos_x == end_x - start_x || profile->is_internal_last(pos_x)) |
---|
502 | calculate_last_column(prev_col, akt_col, pos_x); |
---|
503 | else |
---|
504 | calculate_column(prev_col, akt_col, pos_x); |
---|
505 | h_col = akt_col; |
---|
506 | akt_col = prev_col; |
---|
507 | prev_col = h_col; |
---|
508 | } |
---|
509 | |
---|
510 | delete akt_col; |
---|
511 | delete prev_col; |
---|
512 | } |
---|
513 | |
---|
514 | |
---|
515 | #if 0 |
---|
516 | |
---|
517 | int ALI_PREALIGNER:: |
---|
518 | find_multiple_path( |
---|
519 | unsigned long start_x, unsigned long start_y, |
---|
520 | unsigned long *end_x, unsigned long *end_y) |
---|
521 | { |
---|
522 | unsigned char value; |
---|
523 | long x1, y1, x2, y2; |
---|
524 | |
---|
525 | value = path_map->get_value(start_x, start_y); |
---|
526 | |
---|
527 | /* |
---|
528 | * (x1,y1) is moving left, diag, up |
---|
529 | */ |
---|
530 | if (value & ALI_LEFT) { |
---|
531 | x1 = start_x - 1; |
---|
532 | y1 = start_y; |
---|
533 | } else { |
---|
534 | if (value & ALI_DIAG) { |
---|
535 | x1 = start_x - 1; |
---|
536 | y1 = start_y - 1; |
---|
537 | } else { |
---|
538 | *end_x = start_x; |
---|
539 | *end_y = start_y - 1; |
---|
540 | return 1; |
---|
541 | } |
---|
542 | } |
---|
543 | |
---|
544 | /* |
---|
545 | * (x2,y2) is moving up, diag, left |
---|
546 | */ |
---|
547 | if (value & ALI_UP) { |
---|
548 | x2 = start_x; |
---|
549 | y2 = start_y - 1; |
---|
550 | } else { |
---|
551 | if (value & ALI_DIAG) { |
---|
552 | x2 = start_x - 1; |
---|
553 | y2 = start_y - 1; |
---|
554 | } else { |
---|
555 | *end_x = start_x - 1; |
---|
556 | *end_y = start_y; |
---|
557 | return 1; |
---|
558 | } |
---|
559 | } |
---|
560 | |
---|
561 | while (x1 > 0 && x2 > 0 && y1 > 0 && y2 > 0 && |
---|
562 | (x1 != x2 || y1 != y2)) { |
---|
563 | /* |
---|
564 | * move (x2,y2) |
---|
565 | */ |
---|
566 | if (y2 < y1) { |
---|
567 | value = path_map->get_value((unsigned long) x1, (unsigned long) y1); |
---|
568 | if (value & ALI_LEFT) { |
---|
569 | x1--; |
---|
570 | } else { |
---|
571 | if (value & ALI_DIAG) { |
---|
572 | x1--; |
---|
573 | y1--; |
---|
574 | } else { |
---|
575 | y1--; |
---|
576 | } |
---|
577 | } |
---|
578 | } |
---|
579 | /* |
---|
580 | * move (x1,y2) |
---|
581 | */ |
---|
582 | else { |
---|
583 | value = path_map->get_value((unsigned long) x2, (unsigned long) y2); |
---|
584 | if (value & ALI_UP) { |
---|
585 | y2--; |
---|
586 | } else { |
---|
587 | if (value & ALI_DIAG) { |
---|
588 | x2--; |
---|
589 | y2--; |
---|
590 | } else { |
---|
591 | x2--; |
---|
592 | } |
---|
593 | } |
---|
594 | } |
---|
595 | } |
---|
596 | |
---|
597 | if (x1 == x2 && y1 == y2) { |
---|
598 | *end_x = x1; |
---|
599 | *end_y = y1; |
---|
600 | return 1; |
---|
601 | } |
---|
602 | return 0; |
---|
603 | } |
---|
604 | #endif |
---|
605 | |
---|
606 | |
---|
607 | /* |
---|
608 | * Generate a sub_solution by deleting all undefined segments |
---|
609 | */ |
---|
610 | void ALI_PREALIGNER:: |
---|
611 | generate_solution(ALI_MAP * map) |
---|
612 | { |
---|
613 | ALI_MAP *seg_map; |
---|
614 | unsigned long map_pos, map_len; |
---|
615 | unsigned long start_seg, end_seg, pos_seg; |
---|
616 | |
---|
617 | sub_solution = new ALI_SUB_SOLUTION(profile); |
---|
618 | |
---|
619 | map_len = map->last_base() - map->first_base() + 1; |
---|
620 | for (map_pos = map->first_base(); map_pos <= map->last_base(); map_pos++) { |
---|
621 | /* |
---|
622 | * search for segment |
---|
623 | */ |
---|
624 | for (start_seg = map_pos; start_seg <= map->last_base() && |
---|
625 | map->is_undefined(start_seg); start_seg++); |
---|
626 | if (start_seg <= map->last_base()) { |
---|
627 | for (end_seg = start_seg; end_seg <= map->last_base() && |
---|
628 | (!map->is_undefined(end_seg)); end_seg++); |
---|
629 | end_seg--; |
---|
630 | |
---|
631 | seg_map = new ALI_MAP(start_seg, |
---|
632 | end_seg, |
---|
633 | map->position(start_seg), |
---|
634 | map->position(end_seg)); |
---|
635 | /* |
---|
636 | * Copy segment |
---|
637 | */ |
---|
638 | for (pos_seg = start_seg; pos_seg <= end_seg; pos_seg++) { |
---|
639 | if (map->is_inserted(pos_seg)) |
---|
640 | seg_map->set(pos_seg, |
---|
641 | map->position(pos_seg) - map->position(start_seg), 1); |
---|
642 | else |
---|
643 | seg_map->set(pos_seg, |
---|
644 | map->position(pos_seg) - map->position(start_seg), 0); |
---|
645 | } |
---|
646 | |
---|
647 | if (sub_solution->insert(seg_map) != 1) |
---|
648 | ali_fatal_error("Inconsistent solution?", |
---|
649 | "ALI_PREALIGNER::generate_solution()"); |
---|
650 | |
---|
651 | map_pos = end_seg; |
---|
652 | } |
---|
653 | } |
---|
654 | } |
---|
655 | |
---|
656 | /* |
---|
657 | * generate the result mask from an stack of operations |
---|
658 | */ |
---|
659 | void ALI_PREALIGNER:: |
---|
660 | generate_result_mask(ALI_TSTACK < unsigned char >*stack) |
---|
661 | { |
---|
662 | ALI_SEQUENCE *seq; |
---|
663 | float cost_of_bindings; |
---|
664 | ALI_MAP *map; |
---|
665 | unsigned long seq_pos, dest_pos; |
---|
666 | long i; |
---|
667 | |
---|
668 | map = new ALI_MAP(start_x, end_x, start_y, end_y); |
---|
669 | |
---|
670 | seq_pos = start_x; |
---|
671 | dest_pos = 0; |
---|
672 | for (i = (long) stack->akt_size() - 1; i >= 0; i--) { |
---|
673 | switch (stack->get(i)) { |
---|
674 | case ALI_PREALIGNER_INS: |
---|
675 | map->set(seq_pos++, dest_pos, 1); |
---|
676 | break; |
---|
677 | case ALI_PREALIGNER_SUB: |
---|
678 | map->set(seq_pos++, dest_pos++, 0); |
---|
679 | break; |
---|
680 | case ALI_PREALIGNER_DEL: |
---|
681 | dest_pos++; |
---|
682 | break; |
---|
683 | case ALI_PREALIGNER_INS | ALI_PREALIGNER_MULTI_FLAG: |
---|
684 | map->set(seq_pos, dest_pos, 1); |
---|
685 | map->undefine(seq_pos++); |
---|
686 | break; |
---|
687 | case ALI_PREALIGNER_SUB | ALI_PREALIGNER_MULTI_FLAG: |
---|
688 | map->set(seq_pos, dest_pos++, 0); |
---|
689 | map->undefine(seq_pos++); |
---|
690 | break; |
---|
691 | case ALI_PREALIGNER_DEL | ALI_PREALIGNER_MULTI_FLAG: |
---|
692 | dest_pos++; |
---|
693 | break; |
---|
694 | default: |
---|
695 | ali_fatal_error("Unexpected value", |
---|
696 | "ALI_PREALIGNER::generate_result_mask()"); |
---|
697 | } |
---|
698 | } |
---|
699 | |
---|
700 | if (result_mask_counter > 0) |
---|
701 | result_mask_counter--; |
---|
702 | |
---|
703 | seq = map->sequence_without_inserts(profile->sequence()); |
---|
704 | cost_of_bindings = profile->w_binding(map->first_reference_base(), seq); |
---|
705 | delete seq; |
---|
706 | |
---|
707 | /* |
---|
708 | * make the intersection |
---|
709 | */ |
---|
710 | result_mask.insert(map, cost_of_bindings); |
---|
711 | } |
---|
712 | |
---|
713 | /* |
---|
714 | * Fill the stack with rest DELs or INSs |
---|
715 | */ |
---|
716 | void ALI_PREALIGNER:: |
---|
717 | mapper_post(ALI_TSTACK < unsigned char >*stack, |
---|
718 | unsigned long ins_nu, unsigned long del_nu) |
---|
719 | { |
---|
720 | if (ins_nu > 0 && del_nu > 0) |
---|
721 | ali_fatal_error("Unexpected values", |
---|
722 | "ALI_PREALIGNER::mapper_post()"); |
---|
723 | |
---|
724 | if (ins_nu > 0) { |
---|
725 | stack->push(ALI_PREALIGNER_INS, ins_nu); |
---|
726 | generate_result_mask(stack); |
---|
727 | stack->pop(ins_nu); |
---|
728 | } else { |
---|
729 | if (del_nu > 0) { |
---|
730 | stack->push(ALI_PREALIGNER_DEL, del_nu); |
---|
731 | generate_result_mask(stack); |
---|
732 | stack->pop(del_nu); |
---|
733 | } else |
---|
734 | generate_result_mask(stack); |
---|
735 | } |
---|
736 | } |
---|
737 | |
---|
738 | /* |
---|
739 | * Fill the stack with rest DELs or INSs (with MULTI_FLAG) |
---|
740 | */ |
---|
741 | void ALI_PREALIGNER:: |
---|
742 | mapper_post_multi(ALI_TSTACK < unsigned char >*stack, |
---|
743 | unsigned long ins_nu, unsigned long del_nu) |
---|
744 | { |
---|
745 | if (ins_nu > 0 && del_nu > 0) |
---|
746 | ali_fatal_error("Unexpected values", |
---|
747 | "ALI_PREALIGNER::mapper_post_multi()"); |
---|
748 | |
---|
749 | if (ins_nu > 0) { |
---|
750 | stack->push(ALI_PREALIGNER_INS | ALI_PREALIGNER_MULTI_FLAG, ins_nu); |
---|
751 | generate_result_mask(stack); |
---|
752 | stack->pop(ins_nu); |
---|
753 | } else { |
---|
754 | if (del_nu > 0) { |
---|
755 | stack->push(ALI_PREALIGNER_DEL | ALI_PREALIGNER_MULTI_FLAG, del_nu); |
---|
756 | generate_result_mask(stack); |
---|
757 | stack->pop(del_nu); |
---|
758 | } else |
---|
759 | generate_result_mask(stack); |
---|
760 | } |
---|
761 | } |
---|
762 | |
---|
763 | /* |
---|
764 | * generate a stack of operations by taking a random path of the pathmap |
---|
765 | */ |
---|
766 | void ALI_PREALIGNER:: |
---|
767 | mapper_random(ALI_TSTACK < unsigned char >*stack, |
---|
768 | unsigned long pos_x, unsigned long pos_y) |
---|
769 | { |
---|
770 | unsigned long next_x, next_y; |
---|
771 | unsigned long random; |
---|
772 | unsigned char value; |
---|
773 | unsigned long stack_counter = 0; |
---|
774 | |
---|
775 | |
---|
776 | |
---|
777 | next_x = pos_x; |
---|
778 | next_y = pos_y; |
---|
779 | while (next_x <= pos_x && next_y <= pos_y) { |
---|
780 | stack_counter++; |
---|
781 | |
---|
782 | random = GB_random(6); |
---|
783 | |
---|
784 | value = path_map->get_value(next_x, next_y); |
---|
785 | if (value == 0) |
---|
786 | ali_fatal_error("Unexpected value (1)", |
---|
787 | "ALI_PREALIGNER::mapper_random()"); |
---|
788 | |
---|
789 | switch (random) { |
---|
790 | case 0: |
---|
791 | if (value & ALI_UP) { |
---|
792 | stack->push(ALI_PREALIGNER_DEL); |
---|
793 | next_y--; |
---|
794 | } else { |
---|
795 | if (value & ALI_DIAG) { |
---|
796 | stack->push(ALI_PREALIGNER_SUB); |
---|
797 | next_x--; |
---|
798 | next_y--; |
---|
799 | } else { |
---|
800 | stack->push(ALI_PREALIGNER_INS); |
---|
801 | next_x--; |
---|
802 | } |
---|
803 | } |
---|
804 | break; |
---|
805 | case 1: |
---|
806 | if (value & ALI_UP) { |
---|
807 | stack->push(ALI_PREALIGNER_DEL); |
---|
808 | next_y--; |
---|
809 | } else { |
---|
810 | if (value & ALI_LEFT) { |
---|
811 | stack->push(ALI_PREALIGNER_INS); |
---|
812 | next_x--; |
---|
813 | } else { |
---|
814 | stack->push(ALI_PREALIGNER_SUB); |
---|
815 | next_x--; |
---|
816 | next_y--; |
---|
817 | } |
---|
818 | } |
---|
819 | break; |
---|
820 | case 2: |
---|
821 | if (value & ALI_DIAG) { |
---|
822 | stack->push(ALI_PREALIGNER_SUB); |
---|
823 | next_x--; |
---|
824 | next_y--; |
---|
825 | } else { |
---|
826 | if (value & ALI_UP) { |
---|
827 | stack->push(ALI_PREALIGNER_DEL); |
---|
828 | next_y--; |
---|
829 | } else { |
---|
830 | stack->push(ALI_PREALIGNER_INS); |
---|
831 | next_x--; |
---|
832 | } |
---|
833 | } |
---|
834 | break; |
---|
835 | case 3: |
---|
836 | if (value & ALI_DIAG) { |
---|
837 | stack->push(ALI_PREALIGNER_SUB); |
---|
838 | next_x--; |
---|
839 | next_y--; |
---|
840 | } else { |
---|
841 | if (value & ALI_LEFT) { |
---|
842 | stack->push(ALI_PREALIGNER_INS); |
---|
843 | next_x--; |
---|
844 | } else { |
---|
845 | stack->push(ALI_PREALIGNER_DEL); |
---|
846 | next_y--; |
---|
847 | } |
---|
848 | } |
---|
849 | break; |
---|
850 | case 4: |
---|
851 | if (value & ALI_LEFT) { |
---|
852 | stack->push(ALI_PREALIGNER_INS); |
---|
853 | next_x--; |
---|
854 | } else { |
---|
855 | if (value & ALI_UP) { |
---|
856 | stack->push(ALI_PREALIGNER_DEL); |
---|
857 | next_y--; |
---|
858 | } else { |
---|
859 | stack->push(ALI_PREALIGNER_SUB); |
---|
860 | next_x--; |
---|
861 | next_y--; |
---|
862 | } |
---|
863 | } |
---|
864 | break; |
---|
865 | case 5: |
---|
866 | if (value & ALI_LEFT) { |
---|
867 | stack->push(ALI_PREALIGNER_INS); |
---|
868 | next_x--; |
---|
869 | } else { |
---|
870 | if (value & ALI_DIAG) { |
---|
871 | stack->push(ALI_PREALIGNER_SUB); |
---|
872 | next_x--; |
---|
873 | next_y--; |
---|
874 | } else { |
---|
875 | stack->push(ALI_PREALIGNER_DEL); |
---|
876 | next_y--; |
---|
877 | } |
---|
878 | } |
---|
879 | break; |
---|
880 | default: |
---|
881 | ali_fatal_error("Unexpected random value", |
---|
882 | "ALI_PREALIGNER::mapper_random()"); |
---|
883 | } |
---|
884 | } |
---|
885 | |
---|
886 | if (next_x <= pos_x) { |
---|
887 | mapper_post(stack, next_x + 1, 0); |
---|
888 | } else { |
---|
889 | if (next_y <= pos_y) { |
---|
890 | mapper_post(stack, 0, next_y + 1); |
---|
891 | } else { |
---|
892 | mapper_post(stack, 0, 0); |
---|
893 | } |
---|
894 | } |
---|
895 | |
---|
896 | if (stack_counter > 0) |
---|
897 | stack->pop(stack_counter); |
---|
898 | } |
---|
899 | |
---|
900 | /* |
---|
901 | * generate a stack of operations by taking every path |
---|
902 | */ |
---|
903 | void ALI_PREALIGNER:: |
---|
904 | mapper(ALI_TSTACK < unsigned char >*stack, |
---|
905 | unsigned long pos_x, unsigned long pos_y) |
---|
906 | { |
---|
907 | unsigned char value; |
---|
908 | unsigned long stack_counter = 0; |
---|
909 | |
---|
910 | value = path_map->get_value(pos_x, pos_y); |
---|
911 | |
---|
912 | if (pos_x == 0 || pos_y == 0) { |
---|
913 | if (value & ALI_UP) { |
---|
914 | stack->push(ALI_PREALIGNER_DEL); |
---|
915 | if (pos_y == 0) |
---|
916 | mapper_post(stack, pos_x + 1, 0); |
---|
917 | else |
---|
918 | mapper(stack, pos_x, pos_y - 1); |
---|
919 | stack->pop(); |
---|
920 | } |
---|
921 | if (value & ALI_DIAG) { |
---|
922 | stack->push(ALI_PREALIGNER_SUB); |
---|
923 | if (pos_y > 0) { |
---|
924 | mapper_post(stack, 0, pos_y); |
---|
925 | } else { |
---|
926 | if (pos_x > 0) { |
---|
927 | mapper_post(stack, pos_x, 0); |
---|
928 | } else { |
---|
929 | mapper_post(stack, 0, 0); |
---|
930 | } |
---|
931 | } |
---|
932 | stack->pop(); |
---|
933 | } |
---|
934 | if (value & ALI_LEFT) { |
---|
935 | stack->push(ALI_PREALIGNER_INS); |
---|
936 | if (pos_x == 0) |
---|
937 | mapper_post(stack, 0, pos_y + 1); |
---|
938 | else |
---|
939 | mapper(stack, pos_x - 1, pos_y); |
---|
940 | stack->pop(); |
---|
941 | } |
---|
942 | return; |
---|
943 | } |
---|
944 | /* |
---|
945 | * follow an unique path |
---|
946 | */ |
---|
947 | while (value == ALI_UP || value == ALI_DIAG || value == ALI_LEFT) { |
---|
948 | stack_counter++; |
---|
949 | switch (value) { |
---|
950 | case ALI_UP: |
---|
951 | stack->push(ALI_PREALIGNER_DEL); |
---|
952 | pos_y--; |
---|
953 | break; |
---|
954 | case ALI_DIAG: |
---|
955 | stack->push(ALI_PREALIGNER_SUB); |
---|
956 | pos_x--; |
---|
957 | pos_y--; |
---|
958 | break; |
---|
959 | case ALI_LEFT: |
---|
960 | stack->push(ALI_PREALIGNER_INS); |
---|
961 | pos_x--; |
---|
962 | break; |
---|
963 | } |
---|
964 | |
---|
965 | value = path_map->get_value(pos_x, pos_y); |
---|
966 | |
---|
967 | if (pos_x == 0 || pos_y == 0) { |
---|
968 | if (value & ALI_UP) { |
---|
969 | stack->push(ALI_PREALIGNER_DEL); |
---|
970 | if (pos_y == 0) |
---|
971 | mapper_post(stack, pos_x + 1, 0); |
---|
972 | else |
---|
973 | mapper(stack, pos_x, pos_y - 1); |
---|
974 | stack->pop(); |
---|
975 | } |
---|
976 | if (value & ALI_DIAG) { |
---|
977 | stack->push(ALI_PREALIGNER_SUB); |
---|
978 | if (pos_y > 0) { |
---|
979 | mapper_post(stack, 0, pos_y); |
---|
980 | } else { |
---|
981 | if (pos_x > 0) { |
---|
982 | mapper_post(stack, pos_x, 0); |
---|
983 | } else { |
---|
984 | mapper_post(stack, 0, 0); |
---|
985 | } |
---|
986 | } |
---|
987 | stack->pop(); |
---|
988 | } |
---|
989 | if (value & ALI_LEFT) { |
---|
990 | stack->push(ALI_PREALIGNER_INS); |
---|
991 | if (pos_x == 0) |
---|
992 | mapper_post(stack, 0, pos_y + 1); |
---|
993 | else |
---|
994 | mapper(stack, pos_x - 1, pos_y); |
---|
995 | stack->pop(); |
---|
996 | } |
---|
997 | if (stack_counter > 0) |
---|
998 | stack->pop(stack_counter); |
---|
999 | |
---|
1000 | return; |
---|
1001 | } |
---|
1002 | } |
---|
1003 | |
---|
1004 | if (value & ALI_UP) { |
---|
1005 | stack->push(ALI_PREALIGNER_DEL); |
---|
1006 | mapper(stack, pos_x, pos_y - 1); |
---|
1007 | stack->pop(); |
---|
1008 | } |
---|
1009 | if (value & ALI_DIAG) { |
---|
1010 | stack->push(ALI_PREALIGNER_SUB); |
---|
1011 | mapper(stack, pos_x - 1, pos_y - 1); |
---|
1012 | stack->pop(); |
---|
1013 | } |
---|
1014 | if (value & ALI_LEFT) { |
---|
1015 | stack->push(ALI_PREALIGNER_INS); |
---|
1016 | mapper(stack, pos_x - 1, pos_y); |
---|
1017 | stack->pop(); |
---|
1018 | } |
---|
1019 | if (stack_counter > 0) |
---|
1020 | stack->pop(stack_counter); |
---|
1021 | } |
---|
1022 | |
---|
1023 | #if 0 |
---|
1024 | |
---|
1025 | void ALI_PREALIGNER:: |
---|
1026 | quick_mapper(ALI_TSTACK < unsigned char >*stack, |
---|
1027 | unsigned long pos_x, unsigned long pos_y) |
---|
1028 | { |
---|
1029 | unsigned long end_x, end_y; |
---|
1030 | unsigned char value; |
---|
1031 | |
---|
1032 | |
---|
1033 | value = path_map->get_value(pos_x, pos_y); |
---|
1034 | |
---|
1035 | while (pos_x > 0 && pos_y > 0) { |
---|
1036 | if (value == ALI_UP || value == ALI_DIAG || value == ALI_LEFT) { |
---|
1037 | switch (value) { |
---|
1038 | case ALI_UP: |
---|
1039 | stack->push(ALI_PREALIGNER_DEL); |
---|
1040 | pos_y--; |
---|
1041 | break; |
---|
1042 | case ALI_DIAG: |
---|
1043 | stack->push(ALI_PREALIGNER_SUB); |
---|
1044 | pos_x--; |
---|
1045 | pos_y--; |
---|
1046 | break; |
---|
1047 | case ALI_LEFT: |
---|
1048 | stack->push(ALI_PREALIGNER_INS); |
---|
1049 | pos_x--; |
---|
1050 | break; |
---|
1051 | } |
---|
1052 | value = path_map->get_value(pos_x, pos_y); |
---|
1053 | } else { |
---|
1054 | if (find_multiple_path(pos_x, pos_y, &end_x, &end_y) == 0) |
---|
1055 | end_x = end_y = 0; |
---|
1056 | while (pos_x != end_x || pos_y != end_y) { |
---|
1057 | if (value & ALI_UP) { |
---|
1058 | stack->push(ALI_PREALIGNER_DEL | ALI_PREALIGNER_MULTI_FLAG); |
---|
1059 | pos_y--; |
---|
1060 | } else { |
---|
1061 | if (value & ALI_DIAG) { |
---|
1062 | stack->push(ALI_PREALIGNER_SUB | ALI_PREALIGNER_MULTI_FLAG); |
---|
1063 | pos_x--; |
---|
1064 | pos_y--; |
---|
1065 | } else { |
---|
1066 | stack->push(ALI_PREALIGNER_INS | ALI_PREALIGNER_MULTI_FLAG); |
---|
1067 | pos_x--; |
---|
1068 | } |
---|
1069 | } |
---|
1070 | value = path_map->get_value(pos_x, pos_y); |
---|
1071 | } |
---|
1072 | } |
---|
1073 | } |
---|
1074 | |
---|
1075 | if (pos_x == 0) { |
---|
1076 | while (pos_y > 0 && value == ALI_UP) { |
---|
1077 | stack->push(ALI_PREALIGNER_DEL); |
---|
1078 | pos_y--; |
---|
1079 | value = path_map->get_value(pos_x, pos_y); |
---|
1080 | } |
---|
1081 | switch (value) { |
---|
1082 | case ALI_UP: |
---|
1083 | stack->push(ALI_PREALIGNER_DEL); |
---|
1084 | mapper_post(stack, pos_x, pos_y); |
---|
1085 | break; |
---|
1086 | case ALI_DIAG: |
---|
1087 | stack->push(ALI_PREALIGNER_SUB); |
---|
1088 | mapper_post(stack, pos_x, pos_y); |
---|
1089 | break; |
---|
1090 | case ALI_LEFT: |
---|
1091 | stack->push(ALI_PREALIGNER_INS); |
---|
1092 | mapper_post(stack, pos_x, pos_y); |
---|
1093 | break; |
---|
1094 | default: |
---|
1095 | stack->push(ALI_PREALIGNER_SUB | ALI_PREALIGNER_MULTI_FLAG); |
---|
1096 | mapper_post_multi(stack, pos_x, pos_y); |
---|
1097 | } |
---|
1098 | } else { |
---|
1099 | while (pos_x > 0 && value == ALI_LEFT) { |
---|
1100 | stack->push(ALI_PREALIGNER_INS); |
---|
1101 | pos_x--; |
---|
1102 | value = path_map->get_value(pos_x, pos_y); |
---|
1103 | } |
---|
1104 | switch (value) { |
---|
1105 | case ALI_UP: |
---|
1106 | stack->push(ALI_PREALIGNER_DEL); |
---|
1107 | mapper_post(stack, pos_x, pos_y); |
---|
1108 | break; |
---|
1109 | case ALI_DIAG: |
---|
1110 | stack->push(ALI_PREALIGNER_SUB); |
---|
1111 | mapper_post(stack, pos_x, pos_y); |
---|
1112 | break; |
---|
1113 | case ALI_LEFT: |
---|
1114 | stack->push(ALI_PREALIGNER_INS); |
---|
1115 | mapper_post(stack, pos_x, pos_y); |
---|
1116 | break; |
---|
1117 | default: |
---|
1118 | stack->push(ALI_PREALIGNER_SUB | ALI_PREALIGNER_MULTI_FLAG); |
---|
1119 | mapper_post_multi(stack, pos_x, pos_y); |
---|
1120 | } |
---|
1121 | } |
---|
1122 | } |
---|
1123 | |
---|
1124 | #endif |
---|
1125 | |
---|
1126 | /* |
---|
1127 | * make the result map from the path matrix |
---|
1128 | */ |
---|
1129 | void ALI_PREALIGNER:: |
---|
1130 | make_map(void) |
---|
1131 | { |
---|
1132 | unsigned long number_of_sol; |
---|
1133 | ALI_TSTACK < unsigned char >*stack; |
---|
1134 | |
---|
1135 | stack = new ALI_TSTACK < unsigned char >(end_x - start_x + end_y - start_y + 3); |
---|
1136 | if (stack == 0) ali_fatal_error("Out of memory"); |
---|
1137 | |
---|
1138 | number_of_sol = number_of_solutions(); |
---|
1139 | printf("%lu solutions generated\n", number_of_sol); |
---|
1140 | |
---|
1141 | if (number_of_sol == 0 || number_of_sol > result_mask_counter) { |
---|
1142 | ali_message("Starting random mapping"); |
---|
1143 | do { |
---|
1144 | mapper_random(stack, end_x - start_x, end_y - start_y); |
---|
1145 | } while (result_mask_counter > 0); |
---|
1146 | } else { |
---|
1147 | ali_message("Starting systematic mapping"); |
---|
1148 | mapper(stack, end_x - start_x, end_y - start_y); |
---|
1149 | } |
---|
1150 | |
---|
1151 | delete stack; |
---|
1152 | |
---|
1153 | ali_message("Mapping finished"); |
---|
1154 | } |
---|
1155 | |
---|
1156 | #if 0 |
---|
1157 | |
---|
1158 | void ALI_PREALIGNER:: |
---|
1159 | make_quick_map(void) |
---|
1160 | { |
---|
1161 | ALI_TSTACK < unsigned char >*stack; |
---|
1162 | |
---|
1163 | ali_message("Starting quick mapping"); |
---|
1164 | |
---|
1165 | stack = new ALI_TSTACK < unsigned char >(end_x - start_x + end_y - start_y + 3); |
---|
1166 | if (stack == 0) |
---|
1167 | ali_fatal_error("Out of memory"); |
---|
1168 | |
---|
1169 | quick_mapper(stack, end_x - start_x, end_y - start_y); |
---|
1170 | |
---|
1171 | delete stack; |
---|
1172 | |
---|
1173 | ali_message("Quick mapping finished"); |
---|
1174 | } |
---|
1175 | |
---|
1176 | #endif |
---|
1177 | |
---|
1178 | /* |
---|
1179 | * generate an approximation of a complete solution |
---|
1180 | */ |
---|
1181 | void ALI_PREALIGNER:: |
---|
1182 | generate_approximation(ALI_SUB_SOLUTION * work_sol) |
---|
1183 | { |
---|
1184 | ALI_MAP *map; |
---|
1185 | ALI_SEQUENCE *seq; |
---|
1186 | char *ins_marker; |
---|
1187 | float binding_costs; |
---|
1188 | |
---|
1189 | map = work_sol->make_one_map(); |
---|
1190 | if (map == 0) |
---|
1191 | ali_fatal_error("Can't make one map", |
---|
1192 | "ALI_PREALIGNER::generate_approximation()"); |
---|
1193 | |
---|
1194 | seq = map->sequence_without_inserts(profile->sequence()); |
---|
1195 | binding_costs = profile->w_binding(map->first_base(), seq); |
---|
1196 | delete seq; |
---|
1197 | |
---|
1198 | ins_marker = map->insert_marker(); |
---|
1199 | |
---|
1200 | result_approx.insert(map, ins_marker, binding_costs); |
---|
1201 | // delete ins_marker; @@@ |
---|
1202 | // delete map; @@@ |
---|
1203 | } |
---|
1204 | |
---|
1205 | /* |
---|
1206 | * combine subsolutions for an approximation |
---|
1207 | */ |
---|
1208 | void ALI_PREALIGNER:: |
---|
1209 | mapper_approximation(unsigned long area_no, |
---|
1210 | ALI_TARRAY < ALI_TLIST < ALI_MAP * >*>*map_lists, |
---|
1211 | ALI_SUB_SOLUTION * work_sol) |
---|
1212 | { |
---|
1213 | ALI_TLIST < ALI_MAP * >*map_list; |
---|
1214 | ALI_MAP *map; |
---|
1215 | |
---|
1216 | /* |
---|
1217 | * stop mapping at last area |
---|
1218 | */ |
---|
1219 | if (area_no > map_lists->size()) |
---|
1220 | return; |
---|
1221 | |
---|
1222 | if (area_no == map_lists->size()) { |
---|
1223 | generate_approximation(work_sol); |
---|
1224 | return; |
---|
1225 | } |
---|
1226 | /* |
---|
1227 | * map area number 'area_no' |
---|
1228 | */ |
---|
1229 | map_list = map_lists->get(area_no); |
---|
1230 | if (map_list->is_empty()) |
---|
1231 | ali_fatal_error("Found empty list", |
---|
1232 | "ALI_PREALIGNER::mapper_approximation()"); |
---|
1233 | |
---|
1234 | /* |
---|
1235 | * combine all possibilities |
---|
1236 | */ |
---|
1237 | map = map_list->first(); |
---|
1238 | do { |
---|
1239 | if (!work_sol->insert(map)) |
---|
1240 | ali_fatal_error("Can't insert map", |
---|
1241 | "ALI_PREALIGNER::mapper_approximation()"); |
---|
1242 | |
---|
1243 | mapper_approximation(area_no + 1, map_lists, work_sol); |
---|
1244 | |
---|
1245 | if (!work_sol->delete_map(map)) |
---|
1246 | ali_fatal_error("Can't delete map", |
---|
1247 | "ALI_PREALIGNER::mapper_approximation()"); |
---|
1248 | |
---|
1249 | if (map_list->is_next()) |
---|
1250 | map = map_list->next(); |
---|
1251 | else |
---|
1252 | map = 0; |
---|
1253 | } while (map != 0); |
---|
1254 | } |
---|
1255 | |
---|
1256 | /* |
---|
1257 | * Make an approximation by aligning the undefined sections |
---|
1258 | */ |
---|
1259 | void ALI_PREALIGNER:: |
---|
1260 | make_approximation(ALI_PREALIGNER_CONTEXT * context) |
---|
1261 | { |
---|
1262 | ALI_SUB_SOLUTION *work_solution; |
---|
1263 | ALI_ALIGNER_CONTEXT aligner_context; |
---|
1264 | ALI_TARRAY < ALI_TLIST < ALI_MAP * >*>*map_lists; |
---|
1265 | ALI_ALIGNER *aligner; |
---|
1266 | unsigned long area_number; |
---|
1267 | unsigned long start_seq, end_seq, start_ref, end_ref; |
---|
1268 | |
---|
1269 | ali_message("Align free areas"); |
---|
1270 | |
---|
1271 | work_solution = new ALI_SUB_SOLUTION(sub_solution); |
---|
1272 | |
---|
1273 | aligner_context.max_number_of_maps = context->max_number_of_maps_aligner; |
---|
1274 | |
---|
1275 | area_number = sub_solution->number_of_free_areas(); |
---|
1276 | printf("number of areas = %ld (Maximal %ld solutions)\n", area_number, |
---|
1277 | aligner_context.max_number_of_maps); |
---|
1278 | |
---|
1279 | map_lists = new ALI_TARRAY < ALI_TLIST < ALI_MAP * >*>(area_number); |
---|
1280 | |
---|
1281 | /* |
---|
1282 | * generate Solutions for all free areas |
---|
1283 | */ |
---|
1284 | area_number = 0; |
---|
1285 | while (sub_solution->free_area(&start_seq, &end_seq, &start_ref, &end_ref, |
---|
1286 | area_number)) { |
---|
1287 | printf("aligning area %ld (%ld,%ld) - (%ld,%ld)\n", |
---|
1288 | area_number, start_seq, end_seq, start_ref, end_ref); |
---|
1289 | |
---|
1290 | aligner = new ALI_ALIGNER(&aligner_context, profile, |
---|
1291 | start_seq, end_seq, start_ref, end_ref); |
---|
1292 | map_lists->set(area_number, aligner->solutions()); |
---|
1293 | |
---|
1294 | printf("%d solutions generated\n", |
---|
1295 | map_lists->get(area_number)->cardinality()); |
---|
1296 | |
---|
1297 | delete aligner; |
---|
1298 | area_number++; |
---|
1299 | } |
---|
1300 | |
---|
1301 | /* |
---|
1302 | * combine and evaluate the solutions |
---|
1303 | */ |
---|
1304 | mapper_approximation(0, map_lists, work_solution); |
---|
1305 | |
---|
1306 | delete work_solution; |
---|
1307 | // delete map_lists; // @@@ |
---|
1308 | |
---|
1309 | ali_message("Free areas aligned"); |
---|
1310 | } |
---|
1311 | |
---|
1312 | |
---|
1313 | /* |
---|
1314 | * approximate the number of solutions in the pathmap |
---|
1315 | */ |
---|
1316 | unsigned long ALI_PREALIGNER:: |
---|
1317 | number_of_solutions(void) |
---|
1318 | { |
---|
1319 | #define INFINIT 1000000 |
---|
1320 | #define ADD(a,b) if (a>=INFINIT || b>=INFINIT) {a = INFINIT;} else {a += b;} |
---|
1321 | |
---|
1322 | unsigned long pos_x, pos_y, col_length; |
---|
1323 | unsigned long number; |
---|
1324 | unsigned char value; |
---|
1325 | unsigned long *column1, *column2, *elem_akt_col, *elem_left_col; |
---|
1326 | |
---|
1327 | col_length = end_y - start_y + 1; |
---|
1328 | column1 = (unsigned long *) CALLOC((unsigned int) col_length, |
---|
1329 | sizeof(unsigned long)); |
---|
1330 | column2 = (unsigned long *) CALLOC((unsigned int) col_length, |
---|
1331 | sizeof(unsigned long)); |
---|
1332 | if (column1 == 0 || column2 == 0) |
---|
1333 | ali_fatal_error("Out of memory"); |
---|
1334 | |
---|
1335 | ali_message("Start: Checking number of solutions"); |
---|
1336 | |
---|
1337 | if (end_x - (start_x & 0x01)) { |
---|
1338 | elem_akt_col = column1 + col_length - 1; |
---|
1339 | elem_left_col = column2 + col_length - 1; |
---|
1340 | } else { |
---|
1341 | elem_akt_col = column2 + col_length - 1; |
---|
1342 | elem_left_col = column1 + col_length - 1; |
---|
1343 | } |
---|
1344 | |
---|
1345 | number = 0; |
---|
1346 | *elem_akt_col = 1; |
---|
1347 | for (pos_x = end_x - start_x; pos_x > 0;) { |
---|
1348 | *(elem_left_col) = 0; |
---|
1349 | for (pos_y = end_y - start_y; pos_y > 0; pos_y--) { |
---|
1350 | *(elem_left_col - 1) = 0; |
---|
1351 | value = path_map->get_value(pos_x, pos_y); |
---|
1352 | if (value & ALI_UP) { |
---|
1353 | /* *(elem_akt_col - 1) += *elem_akt_col; */ |
---|
1354 | ADD(*(elem_akt_col - 1), *elem_akt_col); |
---|
1355 | } |
---|
1356 | if (value & ALI_DIAG) { |
---|
1357 | /* *(elem_left_col - 1) += *elem_akt_col; */ |
---|
1358 | ADD(*(elem_left_col - 1), *elem_akt_col); |
---|
1359 | } |
---|
1360 | if (value & ALI_LEFT) { |
---|
1361 | /* *(elem_left_col) += *elem_akt_col; */ |
---|
1362 | ADD(*(elem_left_col), *elem_akt_col); |
---|
1363 | } |
---|
1364 | elem_akt_col--; |
---|
1365 | elem_left_col--; |
---|
1366 | } |
---|
1367 | value = path_map->get_value(pos_x, 0); |
---|
1368 | if (value & ALI_UP) { |
---|
1369 | /* number += *elem_akt_col; */ |
---|
1370 | ADD(number, *elem_akt_col); |
---|
1371 | } |
---|
1372 | if (value & ALI_DIAG) { |
---|
1373 | /* number += *elem_akt_col; */ |
---|
1374 | ADD(number, *elem_akt_col); |
---|
1375 | } |
---|
1376 | if (value & ALI_LEFT) { |
---|
1377 | /* *(elem_left_col) += *elem_akt_col; */ |
---|
1378 | ADD(*(elem_left_col), *elem_akt_col); |
---|
1379 | } |
---|
1380 | pos_x--; |
---|
1381 | /* |
---|
1382 | * toggle the columns |
---|
1383 | */ |
---|
1384 | if (pos_x & 0x01) { |
---|
1385 | elem_akt_col = column1 + col_length - 1; |
---|
1386 | elem_left_col = column2 + col_length - 1; |
---|
1387 | } else { |
---|
1388 | elem_akt_col = column2 + col_length - 1; |
---|
1389 | elem_left_col = column1 + col_length - 1; |
---|
1390 | } |
---|
1391 | } |
---|
1392 | |
---|
1393 | for (pos_y = end_y - start_y; pos_y > 0; pos_y--) { |
---|
1394 | value = path_map->get_value(0, pos_y); |
---|
1395 | if (value & ALI_UP) { |
---|
1396 | /* *(elem_akt_col - 1) += *elem_akt_col; */ |
---|
1397 | ADD(*(elem_akt_col - 1), *elem_akt_col); |
---|
1398 | } |
---|
1399 | if (value & ALI_DIAG) { |
---|
1400 | /* number += *elem_akt_col; */ |
---|
1401 | ADD(number, *elem_akt_col); |
---|
1402 | } |
---|
1403 | if (value & ALI_LEFT) { |
---|
1404 | /* number += *elem_akt_col; */ |
---|
1405 | ADD(number, *elem_akt_col); |
---|
1406 | } |
---|
1407 | elem_akt_col--; |
---|
1408 | } |
---|
1409 | |
---|
1410 | /* number += *elem_akt_col; */ |
---|
1411 | ADD(number, *elem_akt_col); |
---|
1412 | |
---|
1413 | ali_message("End: Checking number of solutions"); |
---|
1414 | |
---|
1415 | free((char *) column1); |
---|
1416 | free((char *) column2); |
---|
1417 | |
---|
1418 | return number; |
---|
1419 | } |
---|
1420 | |
---|
1421 | |
---|
1422 | /***************************************************************************** |
---|
1423 | * |
---|
1424 | * class ALI_PREALIGNER (public) |
---|
1425 | * |
---|
1426 | *****************************************************************************/ |
---|
1427 | |
---|
1428 | ALI_PREALIGNER::ALI_PREALIGNER(ALI_PREALIGNER_CONTEXT * context, |
---|
1429 | ALI_PROFILE * prof, |
---|
1430 | unsigned long sx, unsigned long ex, |
---|
1431 | unsigned long sy, unsigned long ey) |
---|
1432 | { |
---|
1433 | profile = prof; |
---|
1434 | |
---|
1435 | start_x = sx; |
---|
1436 | end_x = ex; |
---|
1437 | start_y = sy; |
---|
1438 | end_y = ey; |
---|
1439 | |
---|
1440 | result_mask_counter = context->max_number_of_maps; |
---|
1441 | |
---|
1442 | ali_message("Prealigning"); |
---|
1443 | |
---|
1444 | path_map = new ALI_PATHMAP(end_x - start_x + 1, end_y - start_y + 1); |
---|
1445 | |
---|
1446 | calculate_matrix(); |
---|
1447 | |
---|
1448 | make_map(); |
---|
1449 | |
---|
1450 | result_mask.delete_expensive(context, profile); |
---|
1451 | delete path_map; |
---|
1452 | |
---|
1453 | generate_solution(result_mask.map); |
---|
1454 | |
---|
1455 | make_approximation(context); |
---|
1456 | |
---|
1457 | ali_message("Prealigning finished"); |
---|
1458 | } |
---|