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1 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
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2 // all rights reserved. Authored by: Brian Ondov, Todd Treangen,
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3 // Sergey Koren, and Adam Phillippy
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4 //
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5 // See the LICENSE.txt file included with this software for license information.
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6
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7 #ifndef INCLUDED_CommandContain
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8 #define INCLUDED_CommandContain
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9
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10 #include "Command.h"
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11 #include "Sketch.h"
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12
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13 namespace mash {
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14
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15 class CommandContain : public Command
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16 {
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17 public:
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18
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19 struct ContainInput
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20 {
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21 ContainInput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew, const Sketch::Parameters & parametersNew)
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22 :
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23 sketchRef(sketchRefNew),
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24 sketchQuery(sketchQueryNew),
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25 indexRef(indexRefNew),
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26 indexQuery(indexQueryNew),
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27 pairCount(pairCountNew),
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28 parameters(parametersNew)
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29 {}
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30
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31 const Sketch & sketchRef;
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32 const Sketch & sketchQuery;
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33
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34 uint64_t indexRef;
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35 uint64_t indexQuery;
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36 uint64_t pairCount;
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37
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38 std::string nameRef;
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39 const Sketch::Parameters & parameters;
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40 };
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41
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42 struct ContainOutput
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43 {
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44 ContainOutput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew)
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45 :
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46 sketchRef(sketchRefNew),
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47 sketchQuery(sketchQueryNew),
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48 indexRef(indexRefNew),
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49 indexQuery(indexQueryNew),
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50 pairCount(pairCountNew)
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51 {
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52 pairs = new PairOutput[pairCount];
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53 }
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54
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55 ~ContainOutput()
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56 {
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57 delete [] pairs;
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58 }
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59
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60 struct PairOutput
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61 {
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62 double score;
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63 double error;
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64 };
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65
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66 const Sketch & sketchRef;
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67 const Sketch & sketchQuery;
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68
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69 uint64_t indexRef;
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70 uint64_t indexQuery;
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71 uint64_t pairCount;
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72
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73 PairOutput * pairs;
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74 };
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75
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76 CommandContain();
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77
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78 int run() const; // override
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79
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80 private:
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81
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82 void writeOutput(ContainOutput * output, float error) const;
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83 };
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84
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85 CommandContain::ContainOutput * contain(CommandContain::ContainInput * data);
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86 double containSketches(const HashList & hashesSortedRef, const HashList & hashesSortedQuery, double & errorToSet);
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87
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88 } // namespace mash
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89
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90 #endif
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