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_CommandTriangle
jpayne@69: #define INCLUDED_CommandTriangle
jpayne@69: 
jpayne@69: #include "Command.h"
jpayne@69: #include "CommandDistance.h"
jpayne@69: #include "Sketch.h"
jpayne@69: 
jpayne@69: namespace mash {
jpayne@69: 
jpayne@69: class CommandTriangle : public Command
jpayne@69: {
jpayne@69: public:
jpayne@69:     
jpayne@69:     struct TriangleInput
jpayne@69:     {
jpayne@69:         TriangleInput(const Sketch & sketchNew, uint64_t indexNew, const Sketch::Parameters & parametersNew, double maxDistanceNew, double maxPValueNew)
jpayne@69:             :
jpayne@69:             sketch(sketchNew),
jpayne@69:             index(indexNew),
jpayne@69:             parameters(parametersNew),
jpayne@69:             maxDistance(maxDistanceNew),
jpayne@69:             maxPValue(maxPValueNew)
jpayne@69:             {}
jpayne@69:         
jpayne@69:         const Sketch & sketch;
jpayne@69:         uint64_t index;
jpayne@69:         const Sketch::Parameters & parameters;
jpayne@69:         double maxDistance;
jpayne@69:         double maxPValue;
jpayne@69:     };
jpayne@69:     
jpayne@69:     struct TriangleOutput
jpayne@69:     {
jpayne@69:         TriangleOutput(const Sketch & sketchNew, uint64_t indexNew)
jpayne@69:             :
jpayne@69:             sketch(sketchNew),
jpayne@69:             index(indexNew)
jpayne@69:         {
jpayne@69:             pairs = new CommandDistance::CompareOutput::PairOutput[index];
jpayne@69:         }
jpayne@69:         
jpayne@69:         ~TriangleOutput()
jpayne@69:         {
jpayne@69:             delete [] pairs;
jpayne@69:         }
jpayne@69:         
jpayne@69:         const Sketch & sketch;
jpayne@69:         uint64_t index;
jpayne@69:         
jpayne@69:         CommandDistance::CompareOutput::PairOutput * pairs;
jpayne@69:     };
jpayne@69:     
jpayne@69:     CommandTriangle();
jpayne@69:     
jpayne@69:     int run() const; // override
jpayne@69:     
jpayne@69: private:
jpayne@69:     
jpayne@69:     double pValueMax;
jpayne@69:     bool comment;
jpayne@69:     
jpayne@69:     void writeOutput(TriangleOutput * output, bool comment, bool edge, double & pValuePeakToSet) const;
jpayne@69: };
jpayne@69: 
jpayne@69: CommandTriangle::TriangleOutput * compare(CommandTriangle::TriangleInput * input);
jpayne@69: 
jpayne@69: } // namespace mash
jpayne@69: 
jpayne@69: #endif