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_CommandDistance
jpayne@69: #define INCLUDED_CommandDistance
jpayne@69: 
jpayne@69: #include "Command.h"
jpayne@69: #include "Sketch.h"
jpayne@69: 
jpayne@69: namespace mash {
jpayne@69: 
jpayne@69: class CommandDistance : public Command
jpayne@69: {
jpayne@69: public:
jpayne@69:     
jpayne@69:     struct CompareInput
jpayne@69:     {
jpayne@69:         CompareInput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew, const Sketch::Parameters & parametersNew, double maxDistanceNew, double maxPValueNew)
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:             maxDistance(maxDistanceNew),
jpayne@69:             maxPValue(maxPValueNew)
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:         const Sketch::Parameters & parameters;
jpayne@69:         double maxDistance;
jpayne@69:         double maxPValue;
jpayne@69:     };
jpayne@69:     
jpayne@69:     struct CompareOutput
jpayne@69:     {
jpayne@69:         CompareOutput(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:         ~CompareOutput()
jpayne@69:         {
jpayne@69:             delete [] pairs;
jpayne@69:         }
jpayne@69:         
jpayne@69:         struct PairOutput
jpayne@69:         {
jpayne@69:             uint64_t numer;
jpayne@69:             uint64_t denom;
jpayne@69:             double distance;
jpayne@69:             double pValue;
jpayne@69:             bool pass;
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:     CommandDistance();
jpayne@69:     
jpayne@69:     int run() const; // override
jpayne@69:     
jpayne@69: private:
jpayne@69:     
jpayne@69:     void writeOutput(CompareOutput * output, bool table, bool comment) const;
jpayne@69: };
jpayne@69: 
jpayne@69: CommandDistance::CompareOutput * compare(CommandDistance::CompareInput * input);
jpayne@69: void compareSketches(CommandDistance::CompareOutput::PairOutput * output, const Sketch::Reference & refRef, const Sketch::Reference & refQry, uint64_t sketchSize, int kmerSize, double kmerSpace, double maxDistance, double maxPValue);
jpayne@69: double pValue(uint64_t x, uint64_t lengthRef, uint64_t lengthQuery, double kmerSpace, uint64_t sketchSize);
jpayne@69: 
jpayne@69: } // namespace mash
jpayne@69: 
jpayne@69: #endif