1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2012 University of Bonn. All rights reserved.
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5 | *
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6 | *
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7 | * This file is part of MoleCuilder.
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8 | *
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9 | * MoleCuilder is free software: you can redistribute it and/or modify
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10 | * it under the terms of the GNU General Public License as published by
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11 | * the Free Software Foundation, either version 2 of the License, or
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12 | * (at your option) any later version.
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13 | *
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14 | * MoleCuilder is distributed in the hope that it will be useful,
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15 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 | * GNU General Public License for more details.
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18 | *
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19 | * You should have received a copy of the GNU General Public License
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20 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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21 | */
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22 |
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23 | /*
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24 | * AtomIdSet.cpp
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25 | *
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26 | * Created on: Feb 21, 2012
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27 | * Author: heber
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28 | */
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29 |
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30 |
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31 | // include config.h
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32 | #ifdef HAVE_CONFIG_H
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33 | #include <config.h>
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34 | #endif
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35 |
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36 | //#include "CodePatterns/MemDebug.hpp"
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37 |
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38 | #include "AtomIdSet.hpp"
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39 |
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40 | #include <boost/foreach.hpp>
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41 |
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42 | #include "Atom/atom.hpp"
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43 | #include "Descriptors/AtomIdDescriptor.hpp"
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44 | #include "Fragmentation/KeySet.hpp"
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45 | #include "World.hpp"
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46 |
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47 | atom * FromIdToAtom::operator()(atomId_t id) const {
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48 | return World::getInstance().getAtom(AtomById(id));
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49 | }
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50 |
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51 | const atom * FromIdToConstAtom::operator()(atomId_t id) const {
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52 | return const_cast<const World &>(World::getInstance()).getAtom(AtomById(id));
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53 | }
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54 |
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55 | /** Constructor for class AtomIdSet.
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56 | *
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57 | * @param _atoms atoms to put into this set
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58 | */
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59 | AtomIdSet::AtomIdSet(const atomIdSet &_atoms) :
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60 | atoms(_atoms)
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61 | {}
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62 |
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63 | /** Constructor for class AtomIdSet.
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64 | *
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65 | * @param _keyset keyset to put into this set
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66 | */
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67 | AtomIdSet::AtomIdSet(const KeySet &_keyset) :
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68 | atoms(atomIdSet(_keyset.begin(), _keyset.end()))
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69 | {}
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70 |
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71 | /** Constructor for class AtomIdSet.
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72 | *
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73 | * @param _atoms atoms to put into this set
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74 | */
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75 | AtomIdSet::AtomIdSet(const std::vector<atom *> &_atoms)
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76 | {
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77 | BOOST_FOREACH(const atom * _atom, _atoms) {
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78 | insert(_atom->getId());
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79 | }
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80 | }
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81 |
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82 | /** Constructor for class AtomIdSet.
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83 | *
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84 | */
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85 | AtomIdSet::AtomIdSet()
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86 | {}
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87 |
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88 | /** Destructor for class AtomIdSet.
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89 | *
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90 | */
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91 | AtomIdSet::~AtomIdSet()
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92 | {}
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93 |
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94 | /** Returns iterator to first atim via a transform_iterator.
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95 | *
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96 | * @return iterator to first atom in this set
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97 | */
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98 | AtomIdSet::iterator AtomIdSet::begin(){
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99 | return iterator(atoms.begin(), FromIdToAtom());
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100 | }
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101 |
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102 | /** Returns constant iterator to first atim via a transform_iterator.
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103 | *
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104 | * @return const iterator to first atom in this set
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105 | */
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106 | AtomIdSet::const_iterator AtomIdSet::begin() const{
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107 | return const_iterator(atoms.begin(), FromIdToConstAtom());
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108 | }
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109 |
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110 | /** Returns iterator to one beyond last atom via a transform_iterator.
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111 | *
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112 | * @return iterator to one beyond last atom in this set
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113 | */
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114 | AtomIdSet::iterator AtomIdSet::end(){
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115 | return iterator(atoms.end(), FromIdToAtom());
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116 | }
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117 |
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118 | /** Returns constant iterator to one beyond last atom via a transform_iterator.
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119 | *
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120 | * @return const iterator to one beyond last atom in this set
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121 | */
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122 | AtomIdSet::const_iterator AtomIdSet::end() const{
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123 | return const_iterator(atoms.end(), FromIdToConstAtom());
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124 | }
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125 |
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126 | /** Returns true if this set is empty.
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127 | *
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128 | * @return true - set is empty, false - there is at least one atom
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129 | */
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130 | bool AtomIdSet::empty() const
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131 | {
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132 | return (atoms.empty());
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133 | }
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134 |
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135 | /** Returns the number of members of this set.
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136 | *
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137 | * @return number of members in set
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138 | */
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139 | size_t AtomIdSet::size() const
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140 | {
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141 | // set has unique members, hence just return its size
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142 | return atoms.size();
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143 | }
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144 |
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145 | /** Predicate whether given atomic id is contained.
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146 | *
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147 | * @param id id to check
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148 | * @return true - is contained, false - is not
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149 | */
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150 | bool AtomIdSet::contains(const atomId_t &id) const
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151 | {
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152 | return (atoms.find(id) != atoms.end());
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153 | }
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154 |
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155 | /** Predicate whether given atom is contained.
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156 | *
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157 | * @param key atom to check
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158 | * @return true - is contained, false - is not
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159 | */
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160 | bool AtomIdSet::contains(const atom * const key) const
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161 | {
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162 | return contains(key->getId());
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163 | }
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164 |
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165 | /** Returns the iterator to the atom \a *key.
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166 | *
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167 | * @param key atom to find
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168 | * @return iterator to atom if found, to end() - else
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169 | */
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170 | AtomIdSet::const_iterator AtomIdSet::find(const atom * const key) const
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171 | {
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172 | return find(key->getId());
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173 | }
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174 |
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175 | /** Returns the iterator to the atom \a *key.
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176 | *
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177 | * @param id atomic id to find
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178 | * @return iterator to atom if found, to end() - else
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179 | */
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180 | AtomIdSet::const_iterator AtomIdSet::find(const atomId_t &id) const
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181 | {
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182 | return const_iterator(atoms.find(id), FromIdToConstAtom());
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183 | }
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184 |
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185 | /** Inserts a given atom into the set.
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186 | *
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187 | * @param key atom to insert
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188 | * @return pair of iterator and bool that states whether element is already present (true) or not (false)
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189 | */
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190 | std::pair<AtomIdSet::iterator, bool> AtomIdSet::insert(const atom * const key)
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191 | {
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192 | std::pair<atomIdSet::iterator, bool> iter =
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193 | atoms.insert(key->getId());
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194 | std::pair<iterator, bool> retiter (std::make_pair(iterator(iter.first), iter.second));
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195 |
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196 | return retiter;
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197 | }
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198 |
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199 | /** Inserts a given atom into the set.
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200 | *
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201 | * @param id atomic id to insert
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202 | * @return pair of iterator and bool that states whether element is already present (true) or not (false)
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203 | */
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204 | std::pair<AtomIdSet::iterator, bool> AtomIdSet::insert(const atomId_t &id)
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205 | {
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206 | std::pair<atomIdSet::iterator, bool> iter =
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207 | atoms.insert(id);
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208 | std::pair<iterator, bool> retiter (std::make_pair(iterator(iter.first), iter.second));
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209 |
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210 | return retiter;
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211 | }
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212 |
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213 | AtomIdSet::const_iterator AtomIdSet::erase(AtomIdSet::const_iterator &loc)
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214 | {
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215 | const_iterator iter = loc;
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216 | ++iter;
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217 | atom * const _atom = const_cast<atom *>(*loc);
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218 | atoms.erase( _atom->getId() );
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219 | return iter;
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220 | }
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221 |
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222 | /** Erase an atom from the list.
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223 | *
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224 | * @param *key key to atom in list
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225 | * @return iterator to just after removed item (compliant with standard)
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226 | */
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227 | AtomIdSet::const_iterator AtomIdSet::erase(const atom * const key)
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228 | {
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229 | const_iterator iter = const_cast<const AtomIdSet &>(*this).find(key);
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230 | if (iter != const_cast<const AtomIdSet &>(*this).end()){
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231 | ++iter;
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232 | atoms.erase( key->getId() );
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233 | }
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234 | return iter;
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235 | }
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236 |
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237 | /** Erase an atom from the list.
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238 | *
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239 | * @param id atomic id atom in list to erase
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240 | * @return iterator to just after removed item (compliant with standard)
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241 | */
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242 | AtomIdSet::const_iterator AtomIdSet::erase(const atomId_t &id)
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243 | {
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244 | atomIdSet::const_iterator iter = atoms.find(id);
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245 | if (iter != atoms.end()){
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246 | ++iter;
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247 | atoms.erase( id );
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248 | }
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249 | return const_iterator(iter, FromIdToConstAtom());
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250 | }
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