AnnotationItem.h

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

#include "AnnotationScore.h"
#include "RegionPrediction.h"
#include "MatrixItemContents.h"
#include "AnnotationMatrix.h"
#include "localtypedef.h"
#include <pair.h>
#include <vector>

class DnaStr;
class CustomScore;

class AnnotationItem {
 public:
  typedef pair<const AnnotationItem*,AnnotationScore> apair_t; 
  typedef pair<int,apair_t> bpair_t;
  typedef pair<dsu::Strand_t,int> strnd_frm_t;
  struct tback {
    tback() : _item(NULL) { }
    tback(const AnnotationItem* i, strnd_frm_t strf, dsu::side_t sd, int type) : _item(i),
         _strf(strf.first,strf.second), _side(sd), _type(type) { }
    int get_type() const { return _type; }
    const AnnotationItem* _item;
    strnd_frm_t _strf;
    dsu::side_t _side;
    int _type;
  };
public:
  AnnotationItem(const std::vector<RegionPrediction*>&,const DnaStr&, const DnaStr&);
  ~AnnotationItem() { }

  // Accessors
  pair<AnnotationScore,MatrixItemContents>
    endScore(const CustomScore&,const AnnotationScore&,bool) const;
  int getEnd5AdjForStop(int model, dsu::Strand_t strnd) const;
  int getEnd3AdjForStop(int model, dsu::Strand_t strnd) const;
  dsu::Strand_t getStrnd() const { return _strnd; }
  int getEnd5() const { return _seq.getEnd5(); }
  int getEnd3() const { return _seq.getEnd3(); }
  int length() const { return _seq.length(); }
  const RegionPrediction& getRegionPrediction() const { return _seq; }
  const DnaStr& getSeq(dsu::Strand_t strnd) const 
    { assert(strnd != dsu::eEither); return strnd==dsu::ePos? _posSeq : _negSeq; }

  tback
  getPred(int,dsu::Strand_t,dsu::side_t,int) const;

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

  // Mutators
  void dpUpdate(const AnnotationItem&, std::vector<scr_pr>&,bool);
  void dpUpdate(std::vector<scr_pr>&, bool, bool);
  AnnotationScore computeNonCodingScore() const;

  void
  update(const MatrixIdx&,const MatrixIdx&, const int, const AnnotationScore&, const AnnotationItem& ); 
  void
  update(const MatrixIdx&,const MatrixIdx&, const int, const AnnotationScore&); 

  static bool 
  checkOrf(const AnnotationItem*, const MatrixIdx&,int,int,const DnaStr&);

  pair<int,dsu::Strand_t>
    getPrevExonType(const MatrixIdx&) const;

  const MatrixItemContents& getBest(const MatrixIdx&) const;
  
  const RegionPrediction* getLeft() const { return _left; }
  const RegionPrediction* getRght() const { return _rght; }

private:
  MatrixItemContents& getBest(const MatrixIdx&);

  void
    dpUpdate(const AnnotationItem& litem, dsu::Strand_t lstrnd,
             std::vector<scr_pr>& inv_scores,
             bool isContig, dsu::Strand_t rstrnd) ;

  void
  updateScore(const AnnotationItem&, bool, std::vector<scr_pr>& inv_scores, int frame,dsu::Strand_t);

  void setStrnd(dsu::Strand_t strnd) { _strnd = strnd; }
  
private:
  RegionPrediction& _seq;
  const DnaStr& _posSeq, _negSeq;
  dsu::Strand_t _strnd;
  std::vector<MatrixItemContents> _best;
  const RegionPrediction* _left;
  const RegionPrediction* _rght;
};

#endif //ANNOTATIONITEM_H