1 | package de.ugoe.cs.quest.coverage;
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2 |
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3 | import java.security.InvalidParameterException;
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4 | import java.util.Collection;
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5 | import java.util.List;
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6 | import java.util.Map;
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7 |
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8 | import de.ugoe.cs.quest.eventcore.Event;
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9 | import de.ugoe.cs.quest.usageprofiles.IStochasticProcess;
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10 |
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11 | /**
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12 | * <p>
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13 | * This class calculates various types of sequence coverage in relation to a stochastic process.
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14 | * </p>
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15 | *
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16 | * @author Steffen Herbold
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17 | * @version 1.0
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18 | */
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19 | public class CoverageCalculatorProcess {
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20 |
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21 | /**
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22 | * <p>
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23 | * Stochastic process that is the foundation for probabilistic coverages and coverages with
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24 | * reference to all possible sequences.
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25 | * </p>
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26 | */
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27 | private final IStochasticProcess process;
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28 |
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29 | /**
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30 | * <p>
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31 | * Sequences for which the coverage is calculated.
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32 | * </p>
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33 | */
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34 | private Collection<List<Event>> sequences;
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35 |
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36 | /**
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37 | * <p>
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38 | * Length of the subsequences in relation to which the coverage is calculated.
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39 | * </p>
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40 | */
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41 | private final int length;
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42 |
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43 | /**
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44 | * <p>
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45 | * All subsequences of {@link #length} of {@link #sequences}.
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46 | * </p>
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47 | */
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48 | private Collection<List<Event>> containedSubSeqs = null;
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49 |
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50 | /**
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51 | * <p>
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52 | * All subsequences of {@link #length} that can be generated by {@link #process}.
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53 | * </p>
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54 | */
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55 | private Collection<List<Event>> allPossibleSubSeqs = null;
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56 |
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57 | /**
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58 | * <p>
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59 | * The probabilities of all subsequences of {@link #length} according to {@link #process}.
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60 | * </p>
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61 | */
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62 | private Map<List<Event>, Double> subSeqWeights = null;
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63 |
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64 | /**
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65 | * <p>
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66 | * Constructor. Creates a new CoverageCalculatorProcess for a given stochastic process and
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67 | * generated sequences.
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68 | * </p>
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69 | *
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70 | * @param process
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71 | * stochastic process used for coverage calculations; must not be null
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72 | * @param sequences
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73 | * sequences for which the coverage is calculated; must not be null
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74 | * @param length
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75 | * length of the subsequences for which the coverage is analyzed; must be >0
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76 | * @throws InvalidParameterException
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77 | * thrown if process or sequences is null or length less than or equal to 0
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78 | */
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79 | public CoverageCalculatorProcess(IStochasticProcess process,
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80 | Collection<List<Event>> sequences,
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81 | int length)
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82 | {
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83 | if (process == null) {
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84 | throw new InvalidParameterException("process must not be null");
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85 | }
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86 | if (sequences == null) {
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87 | throw new InvalidParameterException("sequences must not be null");
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88 | }
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89 | if (length <= 0) {
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90 | throw new InvalidParameterException("length must be >0; actual value: " + length);
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91 | }
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92 | this.process = process;
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93 | this.sequences = sequences;
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94 | this.length = length;
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95 | }
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96 |
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97 | /**
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98 | * <p>
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99 | * Calculates the percentage of subsequences of length k that occur, including those that cannot
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100 | * be generated by {@link #process}.
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101 | * </p>
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102 | *
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103 | * @return coverage percentage
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104 | */
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105 | public double getCoverageAllNoWeight() {
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106 | if (containedSubSeqs == null) {
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107 | containedSubSeqs = SequenceTools.containedSubSequences(sequences, length);
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108 | }
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109 | return ((double) containedSubSeqs.size()) / SequenceTools.numSequences(process, length);
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110 | }
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111 |
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112 | /**
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113 | * <p>
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114 | * Calculates the percentage of subsequences of length k that occur and can generated by
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115 | * {@link #process}.
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116 | * </p>
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117 | *
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118 | * @return coverage percentage
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119 | */
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120 | public double getCoveragePossibleNoWeight() {
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121 | if (containedSubSeqs == null) {
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122 | containedSubSeqs = SequenceTools.containedSubSequences(sequences, length);
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123 | }
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124 | if (allPossibleSubSeqs == null) {
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125 | allPossibleSubSeqs = process.generateSequences(length);
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126 | }
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127 | return ((double) containedSubSeqs.size()) / allPossibleSubSeqs.size();
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128 | }
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129 |
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130 | /**
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131 | * <p>
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132 | * Calculates the weight of the subsequences that occur with relation to {@link #process}, i.e.,
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133 | * the mass of the subsequence probability covered by the subsequences.
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134 | * </p>
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135 | *
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136 | * @return coverage weight
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137 | */
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138 | public double getCoveragePossibleWeight() {
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139 | if (containedSubSeqs == null) {
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140 | containedSubSeqs = SequenceTools.containedSubSequences(sequences, length);
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141 | }
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142 | if (allPossibleSubSeqs == null) {
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143 | allPossibleSubSeqs = process.generateSequences(length);
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144 | }
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145 | if (subSeqWeights == null) {
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146 | subSeqWeights = SequenceTools.generateWeights(process, allPossibleSubSeqs);
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147 | }
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148 | double weight = 0.0;
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149 | for (List<Event> subSeq : containedSubSeqs) {
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150 | Double curWeight = subSeqWeights.get(subSeq);
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151 | if (curWeight != null) {
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152 | weight += curWeight;
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153 | }
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154 | }
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155 | return weight;
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156 | }
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157 |
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158 | /**
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159 | * <p>
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160 | * Returns the number of covered subsequences of length k.
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161 | * </p>
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162 | *
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163 | * @return number of covered subsequences
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164 | */
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165 | public int getNumCovered() {
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166 | if (containedSubSeqs == null) {
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167 | containedSubSeqs = SequenceTools.containedSubSequences(sequences, length);
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168 | }
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169 | return containedSubSeqs.size();
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170 | }
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171 |
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172 | /**
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173 | * <p>
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174 | * Returns the number of possible subsequences of length k according to the stochastic process.
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175 | * </p>
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176 | *
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177 | * @return number of possible subsequences
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178 | */
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179 | public int getNumPossible() {
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180 | if (allPossibleSubSeqs == null) {
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181 | allPossibleSubSeqs = process.generateSequences(length);
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182 | }
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183 | return allPossibleSubSeqs.size();
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184 | }
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185 |
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186 | /**
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187 | * <p>
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188 | * Sets a new collection of sequences for which the coverage is analyzed.
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189 | * </p>
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190 | *
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191 | * @param newSequences
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192 | * new collection of sequences
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193 | * @throws InvalidParameterException
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194 | * thrown is newSequences is null
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195 | */
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196 | public void setSequences(Collection<List<Event>> newSequences) {
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197 | if (newSequences == null) {
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198 | throw new InvalidParameterException("sequences must not be null");
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199 | }
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200 | this.sequences = newSequences;
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201 | containedSubSeqs = null;
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202 | }
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203 |
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204 | }
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