Annotation.h

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

#include <vector>
#include <list>
#include "SeqLoc.h"
#include "GffFeature.h"
#include "AnnotationItem.h"
#include "AnnotationMatrix.h"
#include "AnnotationScore.h"
#include "DnaStr.h"

class RegionPrediction;
class CustomScore;

class Annotation {
public:
  typedef std::pair<AnnotationScore,int> aipair_t;
#if _RUNTIME_DEBUG >= 1
  void scoreExon(int,int) const;
#endif

  Annotation(const string& theSequence, bool forceWholeGeneModel, int cutOff) 
  : _theSeq(theSequence), _posSeq(theSequence,dsu::ePos), _negSeq(theSequence,dsu::eNeg),
    _forceWholeGeneModel(forceWholeGeneModel), _cutOff(cutOff) {} 
  ~Annotation() { }

  //void del() { _matrix.del(); }

  const MatrixItemContents
  getBestStart(const CustomScore&) const;
  
  void insert(const std::vector<RegionPrediction*>&, const CustomScore&);

  
  aipair_t 
    scoreHelp(int end5, int end3, dsu::Strand_t strnd, int mid, const CustomScore& cs) const;
  
  bool forceWholeGeneModel() const { return _forceWholeGeneModel; }

  bool empty() const { return _matrix.empty(); }

  const AnnotationMatrix& getMatrix() const { return _matrix; }

#if 0

  int printOptimalParse(std::ostream&,int,const CustomScore&,const string&) const;
#endif

  void print(std::ostream&,const CustomScore&) const;

  std::list<GffFeature*>*
    getGeneList(int&, const CustomScore&) const;

  /*
   * score a gene list
   */
  void 
    scoreGeneList(std::list<GffFeature*>& flst, const CustomScore& cs) const;

protected:
 AnnotationMatrix _matrix;
 const string& _theSeq;
 const DnaStr _posSeq, _negSeq;

private:
 AnnotationScore score(AnnotationItem*, const AnnotationScore&) const;

 bool _forceWholeGeneModel;

 const int _cutOff;
};

#endif // ANNOTATION_H