jpayne@69: // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
jpayne@69: // all rights reserved. Authored by: Brian Ondov, Todd Treangen,
jpayne@69: // Sergey Koren, and Adam Phillippy
jpayne@69: //
jpayne@69: // See the LICENSE.txt file included with this software for license information.
jpayne@69: 
jpayne@69: #ifndef INCLUDED_CommandContain
jpayne@69: #define INCLUDED_CommandContain
jpayne@69: 
jpayne@69: #include "Command.h"
jpayne@69: #include "Sketch.h"
jpayne@69: 
jpayne@69: namespace mash {
jpayne@69: 
jpayne@69: class CommandContain : public Command
jpayne@69: {
jpayne@69: public:
jpayne@69:     
jpayne@69:     struct ContainInput
jpayne@69:     {
jpayne@69:         ContainInput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew, const Sketch::Parameters & parametersNew)
jpayne@69:             :
jpayne@69:             sketchRef(sketchRefNew),
jpayne@69:             sketchQuery(sketchQueryNew),
jpayne@69:             indexRef(indexRefNew),
jpayne@69:             indexQuery(indexQueryNew),
jpayne@69:             pairCount(pairCountNew),
jpayne@69:             parameters(parametersNew)
jpayne@69:             {}
jpayne@69:         
jpayne@69:         const Sketch & sketchRef;
jpayne@69:         const Sketch & sketchQuery;
jpayne@69: 		
jpayne@69:         uint64_t indexRef;
jpayne@69:         uint64_t indexQuery;
jpayne@69:         uint64_t pairCount;
jpayne@69:         
jpayne@69:         std::string nameRef;
jpayne@69:         const Sketch::Parameters & parameters;
jpayne@69:     };
jpayne@69:     
jpayne@69:     struct ContainOutput
jpayne@69:     {
jpayne@69:         ContainOutput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew)
jpayne@69:             :
jpayne@69:             sketchRef(sketchRefNew),
jpayne@69:             sketchQuery(sketchQueryNew),
jpayne@69:             indexRef(indexRefNew),
jpayne@69:             indexQuery(indexQueryNew),
jpayne@69:             pairCount(pairCountNew)
jpayne@69:         {
jpayne@69:             pairs = new PairOutput[pairCount];
jpayne@69:         }
jpayne@69:         
jpayne@69:         ~ContainOutput()
jpayne@69:         {
jpayne@69:             delete [] pairs;
jpayne@69:         }
jpayne@69:         
jpayne@69:         struct PairOutput
jpayne@69:         {
jpayne@69: 			double score;
jpayne@69: 			double error;
jpayne@69: 		};
jpayne@69:     
jpayne@69:         const Sketch & sketchRef;
jpayne@69:         const Sketch & sketchQuery;
jpayne@69: 		
jpayne@69:         uint64_t indexRef;
jpayne@69:         uint64_t indexQuery;
jpayne@69:         uint64_t pairCount;
jpayne@69:         
jpayne@69:         PairOutput * pairs;
jpayne@69:     };
jpayne@69:     
jpayne@69:     CommandContain();
jpayne@69:     
jpayne@69:     int run() const; // override
jpayne@69:     
jpayne@69: private:
jpayne@69:     
jpayne@69:     void writeOutput(ContainOutput * output, float error) const;
jpayne@69: };
jpayne@69: 
jpayne@69: CommandContain::ContainOutput * contain(CommandContain::ContainInput * data);
jpayne@69: double containSketches(const HashList & hashesSortedRef, const HashList & hashesSortedQuery, double & errorToSet);
jpayne@69: 
jpayne@69: } // namespace mash
jpayne@69: 
jpayne@69: #endif