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_CommandFind
jpayne@69: #define INCLUDED_CommandFind
jpayne@69: 
jpayne@69: #include "Command.h"
jpayne@69: #include "Sketch.h"
jpayne@69: #include <string.h>
jpayne@69: #include <queue>
jpayne@69: 
jpayne@69: namespace mash {
jpayne@69: 
jpayne@69: class CommandFind : public Command
jpayne@69: {
jpayne@69: public:
jpayne@69:     
jpayne@69:     struct FindInput
jpayne@69:     {
jpayne@69:         FindInput
jpayne@69:         (
jpayne@69:             const Sketch & sketchNew,
jpayne@69:             const char * seqIdNew,
jpayne@69:             const char * seqNew,
jpayne@69:             uint32_t lengthNew,
jpayne@69:             float thresholdNew,
jpayne@69:             int bestNew,
jpayne@69:             bool selfMatchesNew
jpayne@69:         ) :
jpayne@69:         sketch(sketchNew),
jpayne@69:         length(lengthNew),
jpayne@69:         threshold(thresholdNew),
jpayne@69:         seqId(seqIdNew),
jpayne@69:         best(bestNew),
jpayne@69:         selfMatches(selfMatchesNew)
jpayne@69:         {
jpayne@69:             seq = new char[strlen(seqNew) + 1];
jpayne@69:             strcpy(seq, seqNew);
jpayne@69:         }
jpayne@69:         
jpayne@69:         ~FindInput()
jpayne@69:         {
jpayne@69:             delete [] seq;
jpayne@69:         }
jpayne@69:         
jpayne@69:         const Sketch & sketch;
jpayne@69:         std::string seqId;
jpayne@69:         char * seq;
jpayne@69:         uint32_t length;
jpayne@69:         float threshold;
jpayne@69:         int best;
jpayne@69:         bool selfMatches;
jpayne@69:     };
jpayne@69:     
jpayne@69:     struct FindOutput
jpayne@69:     {
jpayne@69:         struct Hit
jpayne@69:         {
jpayne@69:             Hit(uint32_t refNew, uint32_t startNew, uint32_t endNew, bool minusStrandNew, float scoreNew)
jpayne@69:                 :
jpayne@69:                 ref(refNew),
jpayne@69:                 start(startNew),
jpayne@69:                 end(endNew),
jpayne@69:                 minusStrand(minusStrandNew),
jpayne@69:                 score(scoreNew)
jpayne@69:                 {}
jpayne@69:             
jpayne@69:             unsigned int ref;
jpayne@69:             unsigned int start;
jpayne@69:             unsigned int end;
jpayne@69:             bool minusStrand;
jpayne@69:             float score;
jpayne@69:         };
jpayne@69:         
jpayne@69:         std::string seqId;
jpayne@69:         std::priority_queue<Hit> hits;
jpayne@69:     };
jpayne@69:     
jpayne@69:     CommandFind();
jpayne@69:     
jpayne@69:     int run() const; // override
jpayne@69:     
jpayne@69: private:
jpayne@69:     
jpayne@69:     void writeOutput(const Sketch & sketch, FindOutput * output) const;
jpayne@69: };
jpayne@69: 
jpayne@69: CommandFind::FindOutput * find(CommandFind::FindInput * data);
jpayne@69: void findPerStrand(const CommandFind::FindInput * input, CommandFind::FindOutput * output, bool minusStrand);
jpayne@69: bool operator<(const CommandFind::FindOutput::Hit & a, const CommandFind::FindOutput::Hit & b);
jpayne@69: 
jpayne@69: } // namespace mash
jpayne@69: 
jpayne@69: #endif