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) 2010 University of Bonn. All rights reserved.
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5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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6 | */
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7 |
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8 | /*
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9 | * World.cpp
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10 | *
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11 | * Created on: Feb 3, 2010
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12 | * Author: crueger
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13 | */
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14 |
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15 | // include config.h
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16 | #ifdef HAVE_CONFIG_H
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17 | #include <config.h>
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18 | #endif
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19 |
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20 | #include "Helpers/MemDebug.hpp"
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21 |
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22 | #include "World.hpp"
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23 |
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24 | #include <functional>
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25 |
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26 | #include "atom.hpp"
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27 | #include "config.hpp"
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28 | #include "molecule.hpp"
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29 | #include "periodentafel.hpp"
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30 | #include "ThermoStatContainer.hpp"
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31 | #include "Descriptors/AtomDescriptor.hpp"
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32 | #include "Descriptors/AtomDescriptor_impl.hpp"
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33 | #include "Descriptors/MoleculeDescriptor.hpp"
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34 | #include "Descriptors/MoleculeDescriptor_impl.hpp"
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35 | #include "Descriptors/SelectiveIterator_impl.hpp"
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36 | #include "Actions/ActionTraits.hpp"
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37 | #include "Actions/ManipulateAtomsProcess.hpp"
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38 | #include "Helpers/Assert.hpp"
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39 | #include "Box.hpp"
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40 | #include "LinearAlgebra/Matrix.hpp"
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41 | #include "defs.hpp"
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42 |
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43 | #include "Patterns/Singleton_impl.hpp"
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44 | #include "Patterns/ObservedContainer_impl.hpp"
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45 |
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46 | using namespace std;
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47 |
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48 | const unsigned int MAX_POOL_FRAGMENTATION=20;
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49 | const unsigned int MAX_FRAGMENTATION_SKIPS=100;
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50 |
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51 | /******************************* getter and setter ************************/
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52 | periodentafel *&World::getPeriode(){
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53 | return periode;
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54 | }
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55 |
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56 | config *&World::getConfig(){
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57 | return configuration;
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58 | }
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59 |
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60 | // Atoms
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61 |
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62 | atom* World::getAtom(AtomDescriptor descriptor){
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63 | return descriptor.find();
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64 | }
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65 |
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66 | World::AtomComposite World::getAllAtoms(AtomDescriptor descriptor){
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67 | return descriptor.findAll();
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68 | }
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69 |
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70 | World::AtomComposite World::getAllAtoms(){
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71 | return getAllAtoms(AllAtoms());
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72 | }
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73 |
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74 | int World::numAtoms(){
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75 | return atoms.size();
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76 | }
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77 |
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78 | // Molecules
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79 |
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80 | molecule *World::getMolecule(MoleculeDescriptor descriptor){
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81 | return descriptor.find();
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82 | }
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83 |
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84 | std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
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85 | return descriptor.findAll();
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86 | }
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87 |
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88 | std::vector<molecule*> World::getAllMolecules(){
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89 | return getAllMolecules(AllMolecules());
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90 | }
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91 |
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92 | int World::numMolecules(){
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93 | return molecules_deprecated->ListOfMolecules.size();
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94 | }
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95 |
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96 | // system
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97 |
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98 | Box& World::getDomain() {
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99 | return *cell_size;
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100 | }
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101 |
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102 | void World::setDomain(const Matrix &mat){
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103 | OBSERVE;
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104 | *cell_size = mat;
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105 | }
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106 |
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107 | void World::setDomain(double * matrix)
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108 | {
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109 | OBSERVE;
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110 | Matrix M = ReturnFullMatrixforSymmetric(matrix);
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111 | cell_size->setM(M);
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112 | }
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113 |
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114 | std::string World::getDefaultName() {
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115 | return defaultName;
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116 | }
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117 |
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118 | void World::setDefaultName(std::string name)
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119 | {
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120 | OBSERVE;
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121 | defaultName = name;
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122 | };
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123 |
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124 | class ThermoStatContainer * World::getThermostats()
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125 | {
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126 | return Thermostats;
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127 | }
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128 |
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129 |
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130 | int World::getExitFlag() {
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131 | return ExitFlag;
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132 | }
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133 |
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134 | void World::setExitFlag(int flag) {
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135 | if (ExitFlag < flag)
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136 | ExitFlag = flag;
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137 | }
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138 |
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139 | /******************** Methods to change World state *********************/
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140 |
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141 | molecule* World::createMolecule(){
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142 | OBSERVE;
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143 | molecule *mol = NULL;
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144 | mol = NewMolecule();
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145 | moleculeId_t id = getNextMoleculeId();
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146 | ASSERT(!molecules.count(id),"proposed id did not specify an unused ID");
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147 | mol->setId(id);
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148 | // store the molecule by ID
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149 | molecules[mol->getId()] = mol;
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150 | mol->signOn(this);
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151 | return mol;
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152 | }
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153 |
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154 | void World::destroyMolecule(molecule* mol){
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155 | OBSERVE;
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156 | ASSERT(mol,"Molecule that was meant to be destroyed did not exist");
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157 | destroyMolecule(mol->getId());
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158 | }
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159 |
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160 | void World::destroyMolecule(moleculeId_t id){
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161 | OBSERVE;
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162 | molecule *mol = molecules[id];
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163 | ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
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164 | DeleteMolecule(mol);
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165 | molecules.erase(id);
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166 | releaseMoleculeId(id);
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167 | }
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168 |
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169 | atom *World::createAtom(){
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170 | OBSERVE;
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171 | atomId_t id = getNextAtomId();
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172 | ASSERT(!atoms.count(id),"proposed id did not specify an unused ID");
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173 | atom *res = NewAtom(id);
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174 | res->setWorld(this);
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175 | // store the atom by ID
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176 | atoms[res->getId()] = res;
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177 | return res;
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178 | }
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179 |
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180 |
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181 | int World::registerAtom(atom *atom){
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182 | OBSERVE;
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183 | atomId_t id = getNextAtomId();
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184 | atom->setId(id);
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185 | atom->setWorld(this);
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186 | atoms[atom->getId()] = atom;
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187 | return atom->getId();
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188 | }
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189 |
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190 | void World::destroyAtom(atom* atom){
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191 | OBSERVE;
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192 | int id = atom->getId();
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193 | destroyAtom(id);
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194 | }
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195 |
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196 | void World::destroyAtom(atomId_t id) {
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197 | OBSERVE;
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198 | atom *atom = atoms[id];
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199 | ASSERT(atom,"Atom ID that was meant to be destroyed did not exist");
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200 | DeleteAtom(atom);
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201 | atoms.erase(id);
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202 | releaseAtomId(id);
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203 | }
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204 |
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205 | bool World::changeAtomId(atomId_t oldId, atomId_t newId, atom* target){
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206 | OBSERVE;
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207 | // in case this call did not originate from inside the atom, we redirect it,
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208 | // to also let it know that it has changed
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209 | if(!target){
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210 | target = atoms[oldId];
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211 | ASSERT(target,"Atom with that ID not found");
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212 | return target->changeId(newId);
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213 | }
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214 | else{
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215 | if(reserveAtomId(newId)){
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216 | atoms.erase(oldId);
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217 | atoms.insert(pair<atomId_t,atom*>(newId,target));
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218 | return true;
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219 | }
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220 | else{
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221 | return false;
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222 | }
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223 | }
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224 | }
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225 |
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226 | bool World::changeMoleculeId(moleculeId_t oldId, moleculeId_t newId, molecule* target){
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227 | OBSERVE;
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228 | // in case this call did not originate from inside the atom, we redirect it,
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229 | // to also let it know that it has changed
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230 | if(!target){
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231 | target = molecules[oldId];
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232 | ASSERT(target,"Molecule with that ID not found");
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233 | return target->changeId(newId);
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234 | }
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235 | else{
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236 | if(reserveMoleculeId(newId)){
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237 | molecules.erase(oldId);
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238 | molecules.insert(pair<moleculeId_t,molecule*>(newId,target));
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239 | return true;
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240 | }
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241 | else{
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242 | return false;
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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 | ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name,AtomDescriptor descr){
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248 | ActionTraits manipulateTrait(name);
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249 | return new ManipulateAtomsProcess(op, descr,manipulateTrait,false);
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250 | }
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251 |
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252 | ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name){
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253 | return manipulateAtoms(op,name,AllAtoms());
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254 | }
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255 |
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256 | /********************* Internal Change methods for double Callback and Observer mechanism ********/
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257 |
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258 | void World::doManipulate(ManipulateAtomsProcess *proc){
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259 | proc->signOn(this);
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260 | {
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261 | OBSERVE;
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262 | proc->doManipulate(this);
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263 | }
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264 | proc->signOff(this);
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265 | }
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266 | /******************************* IDManagement *****************************/
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267 |
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268 | // Atoms
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269 |
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270 | atomId_t World::getNextAtomId(){
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271 | // try to find an Id in the pool;
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272 | if(!atomIdPool.empty()){
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273 | atomIdPool_t::iterator iter=atomIdPool.begin();
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274 | atomId_t id = iter->first;
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275 | range<atomId_t> newRange = makeRange(id+1,iter->last);
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276 | // we wont use this iterator anymore, so we don't care about invalidating
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277 | atomIdPool.erase(iter);
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278 | if(newRange.first<newRange.last){
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279 | atomIdPool.insert(newRange);
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280 | }
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281 | return id;
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282 | }
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283 | // Nothing in the pool... we are out of luck
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284 | return currAtomId++;
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285 | }
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286 |
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287 | void World::releaseAtomId(atomId_t id){
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288 | atomIdPool.insert(makeRange(id,id+1));
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289 | defragAtomIdPool();
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290 | }
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291 |
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292 | bool World::reserveAtomId(atomId_t id){
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293 | if(id>=currAtomId ){
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294 | range<atomId_t> newRange = makeRange(currAtomId,id);
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295 | if(newRange.first<newRange.last){
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296 | atomIdPool.insert(newRange);
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297 | }
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298 | currAtomId=id+1;
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299 | defragAtomIdPool();
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300 | return true;
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301 | }
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302 | // look for a range that matches the request
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303 | for(atomIdPool_t::iterator iter=atomIdPool.begin();iter!=atomIdPool.end();++iter){
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304 | if(iter->isBefore(id)){
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305 | // we have covered all available ranges... nothing to be found here
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306 | break;
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307 | }
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308 | // no need to check first, since it has to be <=id, since otherwise we would have broken out
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309 | if(!iter->isBeyond(id)){
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310 | // we found a matching range... get the id from this range
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311 |
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312 | // split up this range at the point of id
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313 | range<atomId_t> bottomRange = makeRange(iter->first,id);
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314 | range<atomId_t> topRange = makeRange(id+1,iter->last);
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315 | // remove this range
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316 | atomIdPool.erase(iter);
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317 | if(bottomRange.first<bottomRange.last){
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318 | atomIdPool.insert(bottomRange);
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319 | }
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320 | if(topRange.first<topRange.last){
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321 | atomIdPool.insert(topRange);
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322 | }
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323 | defragAtomIdPool();
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324 | return true;
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325 | }
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326 | }
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327 | // this ID could not be reserved
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328 | return false;
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329 | }
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330 |
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331 | void World::defragAtomIdPool(){
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332 | // check if the situation is bad enough to make defragging neccessary
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333 | if((numAtomDefragSkips<MAX_FRAGMENTATION_SKIPS) &&
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334 | (atomIdPool.size()<lastAtomPoolSize+MAX_POOL_FRAGMENTATION)){
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335 | ++numAtomDefragSkips;
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336 | return;
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337 | }
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338 | for(atomIdPool_t::iterator iter = atomIdPool.begin();iter!=atomIdPool.end();){
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339 | // see if this range is adjacent to the next one
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340 | atomIdPool_t::iterator next = iter;
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341 | next++;
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342 | if(next!=atomIdPool.end() && (next->first==iter->last)){
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343 | // merge the two ranges
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344 | range<atomId_t> newRange = makeRange(iter->first,next->last);
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345 | atomIdPool.erase(iter);
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346 | atomIdPool.erase(next);
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347 | pair<atomIdPool_t::iterator,bool> res = atomIdPool.insert(newRange);
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348 | ASSERT(res.second,"Id-Pool was confused");
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349 | iter=res.first;
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350 | continue;
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351 | }
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352 | ++iter;
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353 | }
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354 | if(!atomIdPool.empty()){
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355 | // check if the last range is at the border
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356 | atomIdPool_t::iterator iter = atomIdPool.end();
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357 | iter--;
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358 | if(iter->last==currAtomId){
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359 | currAtomId=iter->first;
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360 | atomIdPool.erase(iter);
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361 | }
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362 | }
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363 | lastAtomPoolSize=atomIdPool.size();
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364 | numAtomDefragSkips=0;
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365 | }
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366 |
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367 | // Molecules
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368 |
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369 | moleculeId_t World::getNextMoleculeId(){
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370 | // try to find an Id in the pool;
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371 | if(!moleculeIdPool.empty()){
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372 | moleculeIdPool_t::iterator iter=moleculeIdPool.begin();
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373 | moleculeId_t id = iter->first;
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374 | range<moleculeId_t> newRange = makeRange(id+1,iter->last);
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375 | // we wont use this iterator anymore, so we don't care about invalidating
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376 | moleculeIdPool.erase(iter);
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377 | if(newRange.first<newRange.last){
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378 | moleculeIdPool.insert(newRange);
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379 | }
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380 | return id;
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381 | }
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382 | // Nothing in the pool... we are out of luck
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383 | return currMoleculeId++;
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384 | }
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385 |
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386 | void World::releaseMoleculeId(moleculeId_t id){
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387 | moleculeIdPool.insert(makeRange(id,id+1));
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388 | defragMoleculeIdPool();
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389 | }
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390 |
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391 | bool World::reserveMoleculeId(moleculeId_t id){
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392 | if(id>=currMoleculeId ){
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393 | range<moleculeId_t> newRange = makeRange(currMoleculeId,id);
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394 | if(newRange.first<newRange.last){
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395 | moleculeIdPool.insert(newRange);
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396 | }
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397 | currMoleculeId=id+1;
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398 | defragMoleculeIdPool();
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399 | return true;
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400 | }
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401 | // look for a range that matches the request
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402 | for(moleculeIdPool_t::iterator iter=moleculeIdPool.begin();iter!=moleculeIdPool.end();++iter){
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403 | if(iter->isBefore(id)){
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404 | // we have coverd all available ranges... nothing to be found here
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405 | break;
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406 | }
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407 | // no need to check first, since it has to be <=id, since otherwise we would have broken out
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408 | if(!iter->isBeyond(id)){
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409 | // we found a matching range... get the id from this range
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410 |
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411 | // split up this range at the point of id
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412 | range<moleculeId_t> bottomRange = makeRange(iter->first,id);
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413 | range<moleculeId_t> topRange = makeRange(id+1,iter->last);
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414 | // remove this range
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415 | moleculeIdPool.erase(iter);
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416 | if(bottomRange.first<bottomRange.last){
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417 | moleculeIdPool.insert(bottomRange);
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418 | }
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419 | if(topRange.first<topRange.last){
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420 | moleculeIdPool.insert(topRange);
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421 | }
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422 | defragMoleculeIdPool();
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423 | return true;
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424 | }
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425 | }
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426 | // this ID could not be reserved
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427 | return false;
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428 | }
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429 |
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430 | void World::defragMoleculeIdPool(){
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431 | // check if the situation is bad enough to make defragging neccessary
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432 | if((numMoleculeDefragSkips<MAX_FRAGMENTATION_SKIPS) &&
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433 | (moleculeIdPool.size()<lastMoleculePoolSize+MAX_POOL_FRAGMENTATION)){
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434 | ++numMoleculeDefragSkips;
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435 | return;
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436 | }
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437 | for(moleculeIdPool_t::iterator iter = moleculeIdPool.begin();iter!=moleculeIdPool.end();){
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438 | // see if this range is adjacent to the next one
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439 | moleculeIdPool_t::iterator next = iter;
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440 | next++;
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441 | if(next!=moleculeIdPool.end() && (next->first==iter->last)){
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442 | // merge the two ranges
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443 | range<moleculeId_t> newRange = makeRange(iter->first,next->last);
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444 | moleculeIdPool.erase(iter);
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445 | moleculeIdPool.erase(next);
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446 | pair<moleculeIdPool_t::iterator,bool> res = moleculeIdPool.insert(newRange);
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447 | ASSERT(res.second,"Id-Pool was confused");
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448 | iter=res.first;
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449 | continue;
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450 | }
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451 | ++iter;
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452 | }
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453 | if(!moleculeIdPool.empty()){
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454 | // check if the last range is at the border
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455 | moleculeIdPool_t::iterator iter = moleculeIdPool.end();
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456 | iter--;
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457 | if(iter->last==currMoleculeId){
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458 | currMoleculeId=iter->first;
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459 | moleculeIdPool.erase(iter);
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460 | }
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461 | }
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462 | lastMoleculePoolSize=moleculeIdPool.size();
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463 | numMoleculeDefragSkips=0;
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464 | }
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465 |
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466 | /******************************* Iterators ********************************/
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467 |
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468 | // external parts with observers
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469 |
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470 | CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor);
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471 |
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472 | World::AtomIterator
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473 | World::getAtomIter(AtomDescriptor descr){
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474 | return AtomIterator(descr,atoms);
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475 | }
|
---|
476 |
|
---|
477 | World::AtomIterator
|
---|
478 | World::getAtomIter(){
|
---|
479 | return AtomIterator(AllAtoms(),atoms);
|
---|
480 | }
|
---|
481 |
|
---|
482 | World::AtomIterator
|
---|
483 | World::atomEnd(){
|
---|
484 | return AtomIterator(AllAtoms(),atoms,atoms.end());
|
---|
485 | }
|
---|
486 |
|
---|
487 | CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet,MoleculeDescriptor);
|
---|
488 |
|
---|
489 | World::MoleculeIterator
|
---|
490 | World::getMoleculeIter(MoleculeDescriptor descr){
|
---|
491 | return MoleculeIterator(descr,molecules);
|
---|
492 | }
|
---|
493 |
|
---|
494 | World::MoleculeIterator
|
---|
495 | World::getMoleculeIter(){
|
---|
496 | return MoleculeIterator(AllMolecules(),molecules);
|
---|
497 | }
|
---|
498 |
|
---|
499 | World::MoleculeIterator
|
---|
500 | World::moleculeEnd(){
|
---|
501 | return MoleculeIterator(AllMolecules(),molecules,molecules.end());
|
---|
502 | }
|
---|
503 |
|
---|
504 | // Internal parts, without observers
|
---|
505 |
|
---|
506 | // Build the AtomIterator from template
|
---|
507 | CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet::set_t,AtomDescriptor);
|
---|
508 |
|
---|
509 |
|
---|
510 | World::internal_AtomIterator
|
---|
511 | World::getAtomIter_internal(AtomDescriptor descr){
|
---|
512 | return internal_AtomIterator(descr,atoms.getContent());
|
---|
513 | }
|
---|
514 |
|
---|
515 | World::internal_AtomIterator
|
---|
516 | World::atomEnd_internal(){
|
---|
517 | return internal_AtomIterator(AllAtoms(),atoms.getContent(),atoms.end_internal());
|
---|
518 | }
|
---|
519 |
|
---|
520 | // build the MoleculeIterator from template
|
---|
521 | CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet::set_t,MoleculeDescriptor);
|
---|
522 |
|
---|
523 | World::internal_MoleculeIterator World::getMoleculeIter_internal(MoleculeDescriptor descr){
|
---|
524 | return internal_MoleculeIterator(descr,molecules.getContent());
|
---|
525 | }
|
---|
526 |
|
---|
527 | World::internal_MoleculeIterator World::moleculeEnd_internal(){
|
---|
528 | return internal_MoleculeIterator(AllMolecules(),molecules.getContent(),molecules.end_internal());
|
---|
529 | }
|
---|
530 |
|
---|
531 | /************************** Selection of Atoms and molecules ******************/
|
---|
532 |
|
---|
533 | // Atoms
|
---|
534 |
|
---|
535 | void World::clearAtomSelection(){
|
---|
536 | selectedAtoms.clear();
|
---|
537 | }
|
---|
538 |
|
---|
539 | void World::selectAtom(const atom *_atom){
|
---|
540 | // atom * is unchanged in this function, but we do store entity as changeable
|
---|
541 | ASSERT(_atom,"Invalid pointer in selection of atom");
|
---|
542 | selectedAtoms[_atom->getId()]=const_cast<atom *>(_atom);
|
---|
543 | }
|
---|
544 |
|
---|
545 | void World::selectAtom(const atomId_t id){
|
---|
546 | ASSERT(atoms.count(id),"Atom Id selected that was not in the world");
|
---|
547 | selectedAtoms[id]=atoms[id];
|
---|
548 | }
|
---|
549 |
|
---|
550 | void World::selectAllAtoms(AtomDescriptor descr){
|
---|
551 | internal_AtomIterator begin = getAtomIter_internal(descr);
|
---|
552 | internal_AtomIterator end = atomEnd_internal();
|
---|
553 | void (World::*func)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
|
---|
554 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
|
---|
555 | }
|
---|
556 |
|
---|
557 | void World::selectAtomsOfMolecule(const molecule *_mol){
|
---|
558 | ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
|
---|
559 | // need to make it const to get the fast iterators
|
---|
560 | const molecule *mol = _mol;
|
---|
561 | void (World::*func)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
|
---|
562 | for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is select... see above
|
---|
563 | }
|
---|
564 |
|
---|
565 | void World::selectAtomsOfMolecule(const moleculeId_t id){
|
---|
566 | ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
|
---|
567 | selectAtomsOfMolecule(molecules[id]);
|
---|
568 | }
|
---|
569 |
|
---|
570 | void World::unselectAtom(const atom *_atom){
|
---|
571 | ASSERT(_atom,"Invalid pointer in unselection of atom");
|
---|
572 | unselectAtom(_atom->getId());
|
---|
573 | }
|
---|
574 |
|
---|
575 | void World::unselectAtom(const atomId_t id){
|
---|
576 | ASSERT(atoms.count(id),"Atom Id unselected that was not in the world");
|
---|
577 | selectedAtoms.erase(id);
|
---|
578 | }
|
---|
579 |
|
---|
580 | void World::unselectAllAtoms(AtomDescriptor descr){
|
---|
581 | internal_AtomIterator begin = getAtomIter_internal(descr);
|
---|
582 | internal_AtomIterator end = atomEnd_internal();
|
---|
583 | void (World::*func)(const atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
|
---|
584 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
|
---|
585 | }
|
---|
586 |
|
---|
587 | void World::unselectAtomsOfMolecule(const molecule *_mol){
|
---|
588 | ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
|
---|
589 | // need to make it const to get the fast iterators
|
---|
590 | const molecule *mol = _mol;
|
---|
591 | void (World::*func)(const atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
|
---|
592 | for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is unsselect... see above
|
---|
593 | }
|
---|
594 |
|
---|
595 | void World::unselectAtomsOfMolecule(const moleculeId_t id){
|
---|
596 | ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
|
---|
597 | unselectAtomsOfMolecule(molecules[id]);
|
---|
598 | }
|
---|
599 |
|
---|
600 | size_t World::countSelectedAtoms() const {
|
---|
601 | size_t count = 0;
|
---|
602 | for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
|
---|
603 | count++;
|
---|
604 | return count;
|
---|
605 | }
|
---|
606 |
|
---|
607 | bool World::isSelected(const atom *_atom) const {
|
---|
608 | return selectedAtoms.find(_atom->getId()) != selectedAtoms.end();
|
---|
609 | }
|
---|
610 |
|
---|
611 | const std::vector<atom *> World::getSelectedAtoms() const {
|
---|
612 | std::vector<atom *> returnAtoms;
|
---|
613 | returnAtoms.resize(countSelectedAtoms());
|
---|
614 | int count = 0;
|
---|
615 | for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
|
---|
616 | returnAtoms[count++] = iter->second;
|
---|
617 | return returnAtoms;
|
---|
618 | }
|
---|
619 |
|
---|
620 |
|
---|
621 | // Molecules
|
---|
622 |
|
---|
623 | void World::clearMoleculeSelection(){
|
---|
624 | selectedMolecules.clear();
|
---|
625 | }
|
---|
626 |
|
---|
627 | void World::selectMolecule(const molecule *_mol){
|
---|
628 | // molecule * is unchanged in this function, but we do store entity as changeable
|
---|
629 | ASSERT(_mol,"Invalid pointer to molecule in selection");
|
---|
630 | selectedMolecules[_mol->getId()]=const_cast<molecule *>(_mol);
|
---|
631 | }
|
---|
632 |
|
---|
633 | void World::selectMolecule(const moleculeId_t id){
|
---|
634 | ASSERT(molecules.count(id),"Molecule Id selected that was not in the world");
|
---|
635 | selectedMolecules[id]=molecules[id];
|
---|
636 | }
|
---|
637 |
|
---|
638 | void World::selectAllMolecules(MoleculeDescriptor descr){
|
---|
639 | internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
|
---|
640 | internal_MoleculeIterator end = moleculeEnd_internal();
|
---|
641 | void (World::*func)(const molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
|
---|
642 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
|
---|
643 | }
|
---|
644 |
|
---|
645 | void World::selectMoleculeOfAtom(const atom *_atom){
|
---|
646 | ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
|
---|
647 | molecule *mol=_atom->getMolecule();
|
---|
648 | // the atom might not be part of a molecule
|
---|
649 | if(mol){
|
---|
650 | selectMolecule(mol);
|
---|
651 | }
|
---|
652 | }
|
---|
653 |
|
---|
654 | void World::selectMoleculeOfAtom(const atomId_t id){
|
---|
655 | ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
|
---|
656 | selectMoleculeOfAtom(atoms[id]);
|
---|
657 | }
|
---|
658 |
|
---|
659 | void World::unselectMolecule(const molecule *_mol){
|
---|
660 | ASSERT(_mol,"invalid pointer in unselection of molecule");
|
---|
661 | unselectMolecule(_mol->getId());
|
---|
662 | }
|
---|
663 |
|
---|
664 | void World::unselectMolecule(const moleculeId_t id){
|
---|
665 | ASSERT(molecules.count(id),"No such molecule with ID in unselection");
|
---|
666 | selectedMolecules.erase(id);
|
---|
667 | }
|
---|
668 |
|
---|
669 | void World::unselectAllMolecules(MoleculeDescriptor descr){
|
---|
670 | internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
|
---|
671 | internal_MoleculeIterator end = moleculeEnd_internal();
|
---|
672 | void (World::*func)(const molecule*) = &World::unselectMolecule; // needed for type resolution of overloaded function
|
---|
673 | for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
|
---|
674 | }
|
---|
675 |
|
---|
676 | void World::unselectMoleculeOfAtom(const atom *_atom){
|
---|
677 | ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
|
---|
678 | molecule *mol=_atom->getMolecule();
|
---|
679 | // the atom might not be part of a molecule
|
---|
680 | if(mol){
|
---|
681 | unselectMolecule(mol);
|
---|
682 | }
|
---|
683 | }
|
---|
684 |
|
---|
685 | void World::unselectMoleculeOfAtom(const atomId_t id){
|
---|
686 | ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
|
---|
687 | unselectMoleculeOfAtom(atoms[id]);
|
---|
688 | }
|
---|
689 |
|
---|
690 | size_t World::countSelectedMolecules() const {
|
---|
691 | size_t count = 0;
|
---|
692 | for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
|
---|
693 | count++;
|
---|
694 | return count;
|
---|
695 | }
|
---|
696 |
|
---|
697 | bool World::isSelected(const molecule *_mol) const {
|
---|
698 | return selectedMolecules.find(_mol->getId()) != selectedMolecules.end();
|
---|
699 | }
|
---|
700 |
|
---|
701 | const std::vector<molecule *> World::getSelectedMolecules() const {
|
---|
702 | std::vector<molecule *> returnMolecules;
|
---|
703 | returnMolecules.resize(countSelectedMolecules());
|
---|
704 | int count = 0;
|
---|
705 | for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
|
---|
706 | returnMolecules[count++] = iter->second;
|
---|
707 | return returnMolecules;
|
---|
708 | }
|
---|
709 |
|
---|
710 | /******************* Iterators over Selection *****************************/
|
---|
711 | World::AtomSelectionIterator World::beginAtomSelection(){
|
---|
712 | return selectedAtoms.begin();
|
---|
713 | }
|
---|
714 |
|
---|
715 | World::AtomSelectionIterator World::endAtomSelection(){
|
---|
716 | return selectedAtoms.end();
|
---|
717 | }
|
---|
718 |
|
---|
719 |
|
---|
720 | World::MoleculeSelectionIterator World::beginMoleculeSelection(){
|
---|
721 | return selectedMolecules.begin();
|
---|
722 | }
|
---|
723 |
|
---|
724 | World::MoleculeSelectionIterator World::endMoleculeSelection(){
|
---|
725 | return selectedMolecules.end();
|
---|
726 | }
|
---|
727 |
|
---|
728 | /******************************* Singleton Stuff **************************/
|
---|
729 |
|
---|
730 | World::World() :
|
---|
731 | Observable("World"),
|
---|
732 | periode(new periodentafel),
|
---|
733 | configuration(new config),
|
---|
734 | Thermostats(new ThermoStatContainer),
|
---|
735 | ExitFlag(0),
|
---|
736 | atoms(this),
|
---|
737 | selectedAtoms(this),
|
---|
738 | currAtomId(0),
|
---|
739 | lastAtomPoolSize(0),
|
---|
740 | numAtomDefragSkips(0),
|
---|
741 | molecules(this),
|
---|
742 | selectedMolecules(this),
|
---|
743 | currMoleculeId(0),
|
---|
744 | lastMoleculePoolSize(0),
|
---|
745 | numMoleculeDefragSkips(0),
|
---|
746 | molecules_deprecated(new MoleculeListClass(this))
|
---|
747 | {
|
---|
748 | cell_size = new Box;
|
---|
749 | Matrix domain;
|
---|
750 | domain.at(0,0) = 20;
|
---|
751 | domain.at(1,1) = 20;
|
---|
752 | domain.at(2,2) = 20;
|
---|
753 | cell_size->setM(domain);
|
---|
754 | defaultName = "none";
|
---|
755 | molecules_deprecated->signOn(this);
|
---|
756 | }
|
---|
757 |
|
---|
758 | World::~World()
|
---|
759 | {
|
---|
760 | molecules_deprecated->signOff(this);
|
---|
761 | delete cell_size;
|
---|
762 | delete molecules_deprecated;
|
---|
763 | MoleculeSet::iterator molIter;
|
---|
764 | for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
|
---|
765 | DeleteMolecule((*molIter).second);
|
---|
766 | }
|
---|
767 | molecules.clear();
|
---|
768 | AtomSet::iterator atIter;
|
---|
769 | for(atIter=atoms.begin();atIter!=atoms.end();++atIter){
|
---|
770 | DeleteAtom((*atIter).second);
|
---|
771 | }
|
---|
772 | atoms.clear();
|
---|
773 | delete periode;
|
---|
774 | delete configuration;
|
---|
775 | delete Thermostats;
|
---|
776 | }
|
---|
777 |
|
---|
778 | // Explicit instantiation of the singleton mechanism at this point
|
---|
779 |
|
---|
780 | CONSTRUCT_SINGLETON(World)
|
---|
781 |
|
---|
782 | CONSTRUCT_OBSERVEDCONTAINER(World::AtomSTLSet)
|
---|
783 |
|
---|
784 | CONSTRUCT_OBSERVEDCONTAINER(World::MoleculeSTLSet)
|
---|
785 |
|
---|
786 | /******************************* deprecated Legacy Stuff ***********************/
|
---|
787 |
|
---|
788 | MoleculeListClass *&World::getMolecules() {
|
---|
789 | return molecules_deprecated;
|
---|
790 | }
|
---|