Combine.h

// Copyright (c) 2003, The Institute for Genomic Research (TIGR), Rockville,
// Maryland, U.S.A.  All rights reserved.
#ifndef _COMBINE_H
#define _COMBINE_H

#include "Annotation.h"
#include "InputData.h"

class RegionPrediction;
class CustomScore;

class Combine {
 public:
  Combine(const InputData &, const string&, bool,const CustomScore&, int);

  ~Combine();

  void run();

        
  list<RegionPrediction*>& getOutput() { return _lst; }
  const list<RegionPrediction*>& getOutput() const { return _lst; }
  bool empty() const;
  Annotation& getAnnotation() { return *_annotation; }

 private:
  void getAllRelaventData(int,InputData::const_iterator&,bool);
  void mergeScoreInsert();
  void score(list<RegionPrediction*>&);

 private:

  const InputData& _inData;
  const string& _theSequence;
  Annotation* _annotation;
  const CustomScore* _cstmScr;
  list<RegionPrediction*> _lst;
};

#endif // _COMBINE_H