1 | /*
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2 | * HomologyContainer.hpp
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3 | *
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4 | * Created on: Sep 22, 2012
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5 | * Author: heber
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6 | */
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7 |
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8 | #ifndef HOMOLOGYCONTAINER_HPP_
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9 | #define HOMOLOGYCONTAINER_HPP_
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10 |
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11 |
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12 | // include config.h
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13 | #ifdef HAVE_CONFIG_H
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14 | #include <config.h>
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15 | #endif
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16 |
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17 | #include <boost/serialization/export.hpp>
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18 | #include <boost/serialization/map.hpp>
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19 | #include <boost/serialization/split_member.hpp>
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20 | #include <boost/serialization/vector.hpp>
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21 | #include <boost/serialization/version.hpp>
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22 |
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23 | #include <iosfwd>
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24 | #include <map>
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25 | #include <vector>
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26 |
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27 | #include "CodePatterns/IteratorAdaptors.hpp"
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28 | #include "CodePatterns/Observer/Observable.hpp"
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29 |
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30 | #include "Fragmentation/Homology/HomologyGraph.hpp"
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31 | #include "Fragmentation/Summation/SetValues/Fragment.hpp"
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32 | #include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
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33 |
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34 | class HomologyContainerTest;
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35 |
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36 | /** This class takes all KeySets in a Graph, checks for those that homologues
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37 | * of one another and places them together.
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38 | *
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39 | * This is meant as a storage for key, value pairs, where the key is the KeySet
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40 | * and the value is the energy associated to the fragment this keyset
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41 | * represents.
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42 | * Afterwards this can then be used as training data for a high-dimensional
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43 | * approximation to the Born-Oppenheimer-surface decomposed into lower-
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44 | * dimensional terms in an ANOVA-like fashion.
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45 | *
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46 | */
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47 | class HomologyContainer : public Observable
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48 | {
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49 | //!> grant access to output operator
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50 | friend std::ostream& operator<<(std::ostream &out, const HomologyContainer &container);
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51 | //!> grant unit test access
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52 | friend class HomologyContainerTest;
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53 |
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54 | public:
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55 | /** This structure represents all values associated to a specific homology
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56 | * that we wish to store in this container for later reference.
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57 | */
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58 | struct value_t {
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59 | Fragment fragment;
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60 | double energy;
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61 | bool containsGrids;
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62 | SamplingGrid charge_distribution;
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63 | SamplingGrid potential_distribution;
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64 |
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65 | value_t() :
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66 | energy(0.),
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67 | containsGrids(false)
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68 | {}
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69 |
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70 | bool operator==(const value_t &othervalue) const;
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71 |
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72 | private:
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73 | friend class boost::serialization::access;
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74 | // serialization
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75 | template <typename Archive>
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76 | void serialize(Archive& ar, const unsigned int version)
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77 | {
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78 | ar & fragment;
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79 | ar & energy;
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80 | if (version > 0) {
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81 | ar & containsGrids;
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82 | if (containsGrids) {
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83 | ar & charge_distribution;
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84 | ar & potential_distribution;
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85 | }
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86 | }
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87 | }
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88 | };
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89 |
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90 | public:
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91 | typedef std::multimap< HomologyGraph, value_t> container_t;
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92 | typedef container_t::const_iterator const_iterator;
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93 | typedef MapKeyConstIterator<container_t::const_iterator> const_key_iterator;
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94 | typedef std::pair< const_iterator, const_iterator> range_t;
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95 |
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96 | public:
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97 | /** Default Constructor of class HomologyContainer.
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98 | *
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99 | */
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100 | HomologyContainer();
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101 |
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102 | /** Constructor of class HomologyContainer.
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103 | *
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104 | * @param values values with with to initially fill the container
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105 | */
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106 | HomologyContainer(const container_t &values);
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107 |
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108 | /** Destructor of class HomologyContainer.
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109 | *
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110 | */
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111 | ~HomologyContainer() {}
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112 |
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113 | /** Equality comparator.
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114 | *
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115 | * Sadly, the insertion order of a std::multimap's values is not guaranteed
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116 | * by the standard and boost::serialization does not heed the ordering of
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117 | * the values associated to the same key. Hence, we implement a weaker
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118 | * comparator for this class in order for the unit test to pass as we don't
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119 | * actuallty care about the order of the homologous fragments.
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120 | *
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121 | * @param other instance to compare to
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122 | * @return true - each container contains all elements of the other
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123 | */
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124 | bool operator==(const HomologyContainer &other) const {
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125 | return ((*this >= other) && (other >= *this));
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126 | }
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127 | bool operator!=(const HomologyContainer& other) const {
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128 | return !(*this == other);
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129 | }
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130 |
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131 | /** Greater equal comparator, i.e. subset comparator
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132 | *
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133 | * @param other container to check if it's subset
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134 | * @return true - \a other is a subset of this
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135 | */
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136 | bool operator>=(const HomologyContainer &other) const;
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137 |
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138 | /** Inserter for more graphs along with values.
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139 | *
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140 | * @param values graph and values to insert
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141 | */
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142 | void insert(const container_t &values);
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143 |
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144 | /** Returns iterator range with all contained graphs homologous to the given \a graph.
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145 | *
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146 | * @param graph graph to match
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147 | * @return iterator range with all matches
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148 | */
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149 | range_t getHomologousGraphs(const HomologyGraph &graph) const {
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150 | return container.equal_range(graph);
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151 | }
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152 |
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153 | /** Getter for constant iterator to begin of homologous graph container.
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154 | *
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155 | * @return begin constant iterator
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156 | */
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157 | const_iterator begin() const {
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158 | return container.begin();
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159 | }
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160 |
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161 | /** Getter for constant iterator to past end of homologous graph container.
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162 | *
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163 | * @return past end constant iterator
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164 | */
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165 | const_iterator end() const {
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166 | return container.end();
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167 | }
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168 |
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169 | const_key_iterator key_begin() const
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170 | { return const_key_iterator(container.begin()); }
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171 |
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172 | const_key_iterator key_end() const
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173 | { return const_key_iterator(container.end()); }
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174 |
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175 | const_key_iterator getNextKey(const_key_iterator &iter) const
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176 | { return const_key_iterator(container.upper_bound(*iter)); }
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177 |
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178 | /** Clears all homologies from container.
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179 | *
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180 | */
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181 | void clear();
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182 |
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183 | private:
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184 | //!> multimap containing all homologous graph under same key but each with its value
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185 | container_t container;
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186 |
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187 | private:
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188 | friend class boost::serialization::access;
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189 | // serialization
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190 | template <typename Archive>
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191 | void load(Archive& ar, const unsigned int version)
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192 | {
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193 | OBSERVE;
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194 | ar & container;
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195 | }
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196 | template <typename Archive>
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197 | void save(Archive& ar, const unsigned int version) const
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198 | {
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199 | ar & container;
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200 | }
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201 | BOOST_SERIALIZATION_SPLIT_MEMBER()
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202 | };
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203 |
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204 | /** Output operator for HomologyContainer.
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205 | *
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206 | * \param out output stream
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207 | * \param container container to print
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208 | * \return output stream for concatenation
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209 | */
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210 | std::ostream& operator<<(std::ostream &out, const HomologyContainer &container);
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211 |
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212 | // we need to give this class a unique key for serialization
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213 | BOOST_CLASS_EXPORT_KEY(HomologyContainer)
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214 |
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215 | // version for serialized information associated to HomologyGraph
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216 | BOOST_CLASS_VERSION(HomologyContainer::value_t, 1)
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217 |
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218 | #endif /* HOMOLOGYCONTAINER_HPP_ */
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