AnnotationMatrix.h

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

#include <string>
#include <list>
#include "AnnotationScore.h"
//#include "OutputModel.h"

class SeqLoc;
class AnnotationItem;
class DnaStr;
class UnitScore;
class Compare;
class CustomScore;

using std::list;

class AnnotationMatrix {
 public:
  typedef list<AnnotationItem*>::iterator iterator;
  typedef list<AnnotationItem*>::const_iterator const_iterator;

  AnnotationMatrix();
  ~AnnotationMatrix();

  void del();
  //trace_back_idx initTraceBack(const CustomScore&, const string&,int,bool,bool = false) const; 
  void insert(AnnotationItem*);

  iterator begin();
  iterator end();
  
  unsigned size() const { return _data.size(); }

  const_iterator begin() const;
  const_iterator end() const;

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

 protected:
  list<AnnotationItem*> _data;

 private:
  const Compare* _cmp; 
  /*# AnnotationItem lnkAnnotationItem; */
};

#endif // ANNOTATIONMATRIX_H