1 | // =============================================================== // |
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2 | // // |
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3 | // File : SEC_structure.cxx // |
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4 | // Purpose : general implementation of classes in SEC_root.hxx // |
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5 | // // |
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6 | // Coded by Ralf Westram (coder@reallysoft.de) in August 2007 // |
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7 | // Institute of Microbiology (Technical University Munich) // |
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8 | // http://www.arb-home.de/ // |
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9 | // // |
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10 | // =============================================================== // |
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11 | |
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12 | #include "SEC_root.hxx" |
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13 | #include "SEC_iter.hxx" |
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14 | |
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15 | using namespace std; |
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16 | |
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17 | // ---------------------- |
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18 | // Constructors |
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19 | |
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20 | SEC_segment::SEC_segment() |
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21 | : alpha(0), |
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22 | center1(Origin), |
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23 | center2(Origin), |
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24 | next_helix_strand(NULp), |
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25 | loop(NULp) |
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26 | {} |
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27 | |
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28 | SEC_helix_strand::SEC_helix_strand() |
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29 | : origin_loop(NULp), |
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30 | other_strand(NULp), |
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31 | helix_info(NULp), |
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32 | next_segment(NULp), |
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33 | fixpoint(Origin), |
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34 | rightAttach(Origin), |
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35 | leftAttach(Origin) |
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36 | {} |
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37 | |
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38 | SEC_loop::SEC_loop(SEC_root *root_) |
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39 | : SEC_base(root_), |
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40 | Circumference(0), |
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41 | center(0, 0), |
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42 | primary_strand(NULp) |
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43 | {} |
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44 | |
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45 | SEC_helix::SEC_helix(SEC_root *root_, SEC_helix_strand *to_root, SEC_helix_strand *from_root) |
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46 | : SEC_base(root_), |
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47 | strand_to_root(to_root), |
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48 | base_length(0) |
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49 | { |
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50 | sec_assert(!to_root->get_helix()); |
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51 | sec_assert(!from_root->get_helix()); |
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52 | sec_assert(!to_root->get_other_strand()); |
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53 | sec_assert(!from_root->get_other_strand()); |
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54 | |
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55 | to_root->set_other_strand(from_root); |
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56 | from_root->set_other_strand(to_root); |
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57 | |
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58 | to_root->set_helix_info(this); |
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59 | from_root->set_helix_info(this); |
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60 | } |
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61 | |
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62 | |
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63 | SEC_root::SEC_root() |
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64 | : root_loop(NULp), |
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65 | cursorAbsPos(-1), |
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66 | xString(NULp), |
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67 | constructing(false), |
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68 | db(NULp), |
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69 | bg_color(NULp), |
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70 | autoscroll(NULp), |
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71 | nailedAbsPos(-1), |
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72 | drawnPositions(NULp), |
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73 | cursor_line(LineVector(Origin, ZeroVector)), |
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74 | show_constraints(SEC_NO_TYPE) |
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75 | { |
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76 | for (int i = 0; i<SEC_GC_DATA_COUNT; ++i) { |
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77 | charRadius[i] = -1.0; |
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78 | bg_linewidth[i] = -1.0; |
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79 | } |
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80 | } |
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81 | |
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82 | void SEC_root::init(SEC_graphic *gfx, AWT_canvas *scr, ED4_plugin_host& Host) { |
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83 | db = new SEC_db_interface(gfx, scr, Host); |
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84 | } |
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85 | |
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86 | // --------------------- |
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87 | // Destructors |
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88 | |
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89 | SEC_region::SEC_region(int start, int end) : |
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90 | sequence_start(start), |
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91 | sequence_end(end), |
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92 | baseCount(-1), |
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93 | abspos_array(NULp) |
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94 | #if defined(ASSERTION_USED) |
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95 | ,abspos_array_size(0) |
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96 | #endif // ASSERTION_USED |
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97 | { |
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98 | sec_assert((start == -1 && end == -1) || start != end); |
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99 | } |
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100 | |
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101 | SEC_region::~SEC_region() { |
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102 | invalidate_base_count(); // frees abspos_array |
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103 | delete [] abspos_array; |
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104 | } |
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105 | |
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106 | SEC_segment::~SEC_segment() { |
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107 | } |
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108 | |
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109 | |
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110 | SEC_helix_strand::~SEC_helix_strand() { |
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111 | if (next_segment) { |
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112 | next_segment->delete_pointer_2(this); |
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113 | } |
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114 | |
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115 | delete helix_info; |
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116 | |
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117 | if (other_strand) { |
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118 | if (other_strand->next_segment) { |
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119 | other_strand->next_segment->delete_pointer_2(other_strand); |
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120 | } |
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121 | other_strand->helix_info = NULp; |
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122 | other_strand->other_strand = NULp; |
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123 | other_strand->next_segment = NULp; |
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124 | delete other_strand; |
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125 | } |
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126 | |
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127 | delete origin_loop; |
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128 | } |
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129 | |
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130 | |
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131 | #define SEG_MAX 20 |
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132 | |
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133 | SEC_loop::~SEC_loop() { |
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134 | if (primary_strand) { |
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135 | sec_assert(get_root()->get_root_loop() != this); |
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136 | |
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137 | // collect all segments in an array |
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138 | SEC_segment *segment[SEG_MAX]; |
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139 | int i = 0; |
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140 | |
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141 | for (SEC_strand_iterator strand(this); strand; ++strand) { |
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142 | SEC_segment *seg = strand->get_next_segment(); |
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143 | if (seg) { |
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144 | sec_assert(i < SEG_MAX); |
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145 | sec_assert(seg->get_loop() == this); |
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146 | |
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147 | segment[i++] = seg; |
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148 | } |
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149 | } |
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150 | |
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151 | set_fixpoint_strand(NULp); // disconnect from loop |
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152 | |
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153 | // delete all strands connected to loop |
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154 | int j; |
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155 | for (j=0; j<i; j++) { |
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156 | SEC_helix_strand *strand = segment[j]->get_next_strand(); |
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157 | if (strand) { |
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158 | sec_assert(strand->get_origin_loop() == this); |
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159 | strand->set_origin_loop(NULp); |
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160 | delete strand; |
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161 | } |
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162 | } |
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163 | // delete all segments connected to loop |
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164 | for (j=0; j<i; j++) delete segment[j]; |
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165 | } |
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166 | } |
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167 | |
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168 | SEC_root::~SEC_root() { |
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169 | delete db; |
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170 | delete autoscroll; |
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171 | |
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172 | delete_root_loop(); |
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173 | |
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174 | free(bg_color); |
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175 | |
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176 | delete_announced_positions(); |
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177 | } |
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178 | |
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179 | // -------------------------- |
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180 | // integrity checks |
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181 | |
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182 | #if defined(CHECK_INTEGRITY) |
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183 | |
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184 | void SEC_region::check_integrity(const SEC_root *root, SEC_CHECK_TYPE what) const { |
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185 | if (what&CHECK_SIZE) { |
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186 | sec_assert(baseCount >= 0); |
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187 | if (baseCount>0) { |
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188 | sec_assert(abspos_array || !root->get_db()->canDisplay()); |
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189 | } |
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190 | } |
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191 | } |
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192 | |
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193 | void SEC_segment::check_integrity(SEC_CHECK_TYPE what) const { |
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194 | if (what&CHECK_STRUCTURE) { |
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195 | sec_assert(next_helix_strand); |
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196 | sec_assert(loop == parent()); |
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197 | } |
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198 | if (what&CHECK_SIZE) { |
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199 | sec_assert(alpha == alpha); |
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200 | sec_assert(alpha != 0); |
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201 | } |
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202 | if (what&CHECK_POSITIONS) { |
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203 | sec_assert(center1.valid()); |
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204 | sec_assert(center2.valid()); |
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205 | } |
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206 | get_region()->check_integrity(get_root(), what); |
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207 | } |
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208 | |
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209 | void SEC_helix_strand::check_integrity(SEC_CHECK_TYPE what) const { |
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210 | if (what&CHECK_STRUCTURE) { |
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211 | sec_assert(other_strand != this); |
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212 | sec_assert(other_strand->other_strand == this); |
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213 | sec_assert(helix_info); |
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214 | sec_assert(helix_info == other_strand->helix_info); |
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215 | sec_assert(parent() == helix_info); |
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216 | } |
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217 | if (what&CHECK_SIZE) { |
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218 | get_region()->get_base_count(); // asserts base count is up-to-date |
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219 | } |
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220 | if (what&CHECK_POSITIONS) { |
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221 | sec_assert(fixpoint.valid()); |
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222 | sec_assert(rightAttach.valid()); |
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223 | sec_assert(leftAttach.valid()); |
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224 | } |
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225 | get_region()->check_integrity(get_root(), what); |
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226 | } |
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227 | |
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228 | void SEC_helix::check_integrity(SEC_CHECK_TYPE what) const { |
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229 | sec_assert(strand_to_root); |
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230 | |
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231 | SEC_helix_strand *other_strand = strand_to_root->get_other_strand(); |
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232 | sec_assert(other_strand); |
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233 | |
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234 | if (what&CHECK_STRUCTURE) { |
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235 | sec_assert(strand_to_root->get_helix() == this); |
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236 | sec_assert(other_strand->get_other_strand() == strand_to_root); |
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237 | sec_assert(get_rel_angle().valid()); |
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238 | sec_assert(parent() == rootsideLoop()); |
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239 | } |
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240 | |
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241 | if (what&CHECK_SIZE) { |
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242 | sec_assert(base_length >= 1); |
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243 | sec_assert(drawnSize() >= 0); |
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244 | } |
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245 | |
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246 | strand_to_root->check_integrity(what); |
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247 | other_strand->check_integrity(what); |
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248 | } |
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249 | |
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250 | void SEC_loop::check_integrity(SEC_CHECK_TYPE what) const { |
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251 | int count = 0; |
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252 | int rootStrands = 0; |
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253 | |
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254 | if (what&CHECK_STRUCTURE) { |
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255 | sec_assert(primary_strand); |
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256 | sec_assert(primary_strand->get_origin_loop() == this); |
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257 | sec_assert(get_rel_angle().valid()); |
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258 | } |
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259 | |
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260 | for (SEC_strand_const_iterator strand(this); strand; ++strand) { |
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261 | if (what&CHECK_STRUCTURE) { |
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262 | sec_assert(this == strand->get_origin_loop()); |
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263 | } |
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264 | |
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265 | const SEC_helix *helix = strand->get_helix(); |
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266 | if (this == helix->rootsideLoop()) { // test outgoing helixes |
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267 | helix->check_integrity(what); |
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268 | } |
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269 | else { |
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270 | rootStrands++; |
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271 | } |
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272 | |
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273 | const SEC_segment *seg = strand->get_next_segment(); |
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274 | |
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275 | if (what&CHECK_STRUCTURE) { |
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276 | sec_assert(this == seg->get_loop()); |
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277 | } |
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278 | seg->check_integrity(what); |
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279 | count++; |
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280 | sec_assert(count<100); // more than 100 segments in one loop! assume error in structure! |
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281 | } |
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282 | |
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283 | if (what&CHECK_STRUCTURE) { |
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284 | if (is_root_loop()) { |
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285 | sec_assert(!rootStrands); |
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286 | sec_assert(primary_strand->pointsToOutside()); |
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287 | sec_assert(!parent()); |
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288 | } |
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289 | else { |
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290 | sec_assert(rootStrands); |
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291 | sec_assert(primary_strand->pointsToRoot()); |
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292 | sec_assert(parent() == get_rootside_helix()); |
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293 | } |
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294 | } |
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295 | |
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296 | if (what&CHECK_SIZE) { |
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297 | sec_assert(Circumference>0); |
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298 | sec_assert(drawnSize()>0); |
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299 | } |
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300 | if (what&CHECK_POSITIONS) { |
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301 | sec_assert(center.valid()); |
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302 | if (is_root_loop()) { |
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303 | sec_assert(isOrigin(center)); |
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304 | } |
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305 | } |
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306 | |
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307 | // now recurse downwards |
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308 | for (SEC_strand_const_iterator strand(this); strand; ++strand) { |
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309 | SEC_loop *outsideLoop = strand->get_helix()->outsideLoop(); |
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310 | if (outsideLoop != this) outsideLoop->check_integrity(what); |
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311 | } |
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312 | } |
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313 | |
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314 | void SEC_root::check_integrity(SEC_CHECK_TYPE what) const { |
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315 | if (root_loop) { |
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316 | sec_assert(!under_construction()); // cannot check integrity, when structure is under construction |
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317 | |
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318 | root_loop->check_integrity(what); |
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319 | |
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320 | // check whether structure is a ring and whether regions are correct |
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321 | |
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322 | const SEC_base_part *start_part = root_loop->get_fixpoint_strand(); |
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323 | const SEC_base_part *part = start_part; |
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324 | const SEC_region *region = part->get_region(); |
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325 | |
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326 | int count = 0; |
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327 | do { |
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328 | const SEC_base_part *next_part = part->next(); |
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329 | const SEC_region *next_region = next_part->get_region(); |
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330 | |
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331 | sec_assert(are_adjacent_regions(region, next_region)); |
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332 | |
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333 | part = next_part; |
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334 | region = next_region; |
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335 | |
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336 | count++; |
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337 | sec_assert(count<10000); // structure does not seem to be a ring |
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338 | } |
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339 | while (part != start_part); |
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340 | } |
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341 | } |
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342 | #endif // CHECK_INTEGRITY |
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343 | |
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344 | // --------------------------------- |
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345 | // unlink strands/segments |
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346 | |
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347 | void SEC_helix_strand::unlink(bool fromOtherStrandAsWell) { |
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348 | // if called with fromOtherStrandAsWell == false, |
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349 | // the strand-pair remains deletable |
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350 | |
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351 | next_segment = NULp; |
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352 | origin_loop = NULp; |
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353 | |
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354 | if (fromOtherStrandAsWell) other_strand = NULp; |
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355 | } |
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356 | |
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357 | void SEC_segment::unlink() { |
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358 | next_helix_strand = NULp; |
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359 | } |
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360 | |
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361 | // ------------------------------ |
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362 | // split/merge segments |
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363 | |
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364 | SEC_helix_strand *SEC_segment::split(size_t start, size_t end, SEC_segment **segment2_ptr) { |
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365 | // split segment into 'segment1 - strand - segment2' |
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366 | // segment2 still points to same loop as 'this' (must be corrected by caller) |
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367 | // strand is a single strand (must be connected by caller) |
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368 | |
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369 | sec_assert(get_region()->contains_seq_position(start)); |
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370 | sec_assert(get_region()->contains_seq_position(end-1)); |
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371 | |
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372 | SEC_helix_strand *strand = new SEC_helix_strand; |
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373 | SEC_segment *segment2 = new SEC_segment; |
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374 | |
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375 | segment2->set_sequence_portion(end, get_region()->get_sequence_end()); |
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376 | strand->set_sequence_portion(start, end); |
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377 | set_sequence_portion(get_region()->get_sequence_start(), start); |
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378 | |
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379 | segment2->set_loop(get_loop()); // set to same loop as this (must be corrected later) |
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380 | strand->set_origin_loop(get_loop()); |
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381 | |
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382 | segment2->set_next_strand(get_next_strand()); |
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383 | set_next_strand(strand); |
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384 | |
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385 | *segment2_ptr = segment2; |
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386 | |
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387 | return strand; |
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388 | } |
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389 | |
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390 | void SEC_segment::mergeWith(SEC_segment *other, SEC_loop *target_loop) { |
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391 | set_sequence_portion(get_region()->get_sequence_start(), |
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392 | other->get_region()->get_sequence_end()); |
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393 | |
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394 | set_next_strand(other->get_next_strand()); |
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395 | set_loop(target_loop); |
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396 | delete other; |
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397 | } |
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398 | |
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399 | // ---------------------- |
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400 | // Reset angles |
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401 | |
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402 | void SEC_loop::reset_angles() { |
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403 | for (SEC_strand_iterator strand(this); strand; ++strand) { |
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404 | if (strand->pointsToOutside()) { |
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405 | Angle abs(center, strand->get_fixpoint()); |
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406 | strand->get_helix()->set_abs_angle(abs); |
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407 | } |
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408 | } |
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409 | set_rel_angle(0); |
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410 | } |
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411 | |
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412 | void SEC_helix::reset_angles() { |
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413 | outsideLoop()->set_rel_angle(0); |
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414 | SEC_loop *rloop = rootsideLoop(); |
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415 | |
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416 | Angle toFix(rloop->get_center(), strandToOutside()->get_fixpoint()); |
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417 | set_abs_angle(toFix); |
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418 | } |
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419 | |
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420 | |
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421 | // --------------- |
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422 | // other |
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423 | |
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424 | size_t SEC_base_part::getNextAbspos() const { |
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425 | // returns the next valid abspos |
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426 | const SEC_region *reg = get_region(); |
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427 | int start = reg->get_sequence_start(); |
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428 | |
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429 | if (start != reg->get_sequence_end()) { |
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430 | return start; |
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431 | } |
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432 | return next()->getNextAbspos(); |
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433 | } |
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434 | |
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435 | |
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436 | SEC_segment *SEC_helix_strand::get_previous_segment() { |
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437 | SEC_segment *segment_before; |
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438 | SEC_helix_strand *strand_pointer = next_segment->get_next_strand(); |
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439 | |
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440 | if (strand_pointer == this) { |
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441 | segment_before = next_segment; // we are in a loop with only one segment |
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442 | } |
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443 | else { |
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444 | while (strand_pointer != this) { |
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445 | segment_before = strand_pointer->get_next_segment(); |
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446 | strand_pointer = segment_before->get_next_strand(); |
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447 | } |
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448 | } |
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449 | return segment_before; |
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450 | } |
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451 | |
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452 | static void findLongestHelix(const BI_helix *helix, size_t& start1, size_t& end1, size_t& start2, size_t& end2) { |
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453 | const char *longestHelixNr = NULp; |
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454 | size_t longestLength = 0; |
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455 | |
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456 | const char *lastHelixNr = NULp; |
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457 | size_t lastHelixLen = 0; |
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458 | for (long pos = helix->first_pair_position(); pos != -1; pos = helix->next_pair_position(pos)) { |
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459 | const char *currHelixNr = helix->helixNr(size_t(pos)); |
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460 | if (currHelixNr != lastHelixNr) { |
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461 | if (lastHelixLen>longestLength) { |
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462 | longestLength = lastHelixLen; |
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463 | longestHelixNr = lastHelixNr; |
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464 | } |
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465 | lastHelixNr = currHelixNr; |
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466 | lastHelixLen = 1; |
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467 | } |
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468 | else { |
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469 | lastHelixLen++; |
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470 | } |
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471 | } |
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472 | |
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473 | if (lastHelixLen>longestLength) longestHelixNr = lastHelixNr; |
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474 | |
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475 | sec_assert(longestHelixNr); |
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476 | start1 = helix->first_position(longestHelixNr); |
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477 | end1 = helix->last_position(longestHelixNr); |
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478 | start2 = helix->opposite_position(end1); |
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479 | end2 = helix->opposite_position(start1); |
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480 | } |
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481 | |
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482 | void SEC_root::create_default_bone() { |
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483 | // create default structure |
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484 | |
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485 | set_under_construction(true); |
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486 | |
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487 | SEC_loop *loop1 = new SEC_loop(this); |
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488 | SEC_loop *loop2 = new SEC_loop(this); |
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489 | |
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490 | set_root_loop(loop1); |
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491 | |
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492 | SEC_segment *segment1 = new SEC_segment; |
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493 | SEC_segment *segment2 = new SEC_segment; |
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494 | |
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495 | segment1->set_loop(loop1); |
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496 | segment2->set_loop(loop2); |
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497 | |
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498 | SEC_helix_strand *strand1 = new SEC_helix_strand; |
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499 | SEC_helix_strand *strand2 = new SEC_helix_strand; |
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500 | |
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501 | loop1->set_fixpoint_strand(strand1); |
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502 | loop2->set_fixpoint_strand(strand2); |
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503 | |
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504 | segment1->set_next_strand(strand1); |
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505 | segment2->set_next_strand(strand2); |
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506 | |
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507 | strand1->set_origin_loop(loop1); |
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508 | strand2->set_origin_loop(loop2); |
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509 | |
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510 | SEC_helix *helix = new SEC_helix(this, strand1, strand2); |
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511 | |
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512 | strand1->set_next_segment(segment1); |
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513 | strand2->set_next_segment(segment2); |
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514 | |
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515 | size_t start1, end1, start2, end2; |
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516 | findLongestHelix(get_helixDef(), start1, end1, start2, end2); |
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517 | |
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518 | strand1->set_sequence_portion(start1, end1+1); segment2->set_sequence_portion(end1+1, start2); |
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519 | strand2->set_sequence_portion(start2, end2+1); segment1->set_sequence_portion(end2+1, start1); |
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520 | |
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521 | root_loop = helix->rootsideLoop(); |
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522 | |
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523 | loop1->set_rel_angle(0); |
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524 | loop2->set_rel_angle(0); |
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525 | helix->set_rel_angle(0); |
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526 | |
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527 | root_loop->mark_angle_absolute(); |
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528 | root_loop->set_center(Origin); |
---|
529 | |
---|
530 | set_under_construction(false); |
---|
531 | |
---|
532 | delete xString; |
---|
533 | xString = NULp; |
---|
534 | generate_x_string(); |
---|
535 | |
---|
536 | relayout(); |
---|
537 | } |
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538 | |
---|