DataSetAbstractProduct.h

// Copyright (c) 2003, The Institute for Genomic Research (TIGR), Rockville,
// Maryland, U.S.A.  All rights reserved.
/* Generated by Together */

#ifndef DATASETABSTRACTPRODUCT_H
#define DATASETABSTRACTPRODUCT_H
#include <vector>
#include <list>
#include <pair.h>
#include <assert.h>
#include "Prediction.h"

class DataSetAbstractProduct : public Prediction {
public:
  friend std::ostream& operator<<(std::ostream&, const DataSetAbstractProduct&);
  typedef DataStorageType::iterator iterator;
  typedef DataStorageType::const_iterator const_iterator;
  DataSetAbstractProduct(const SeqLoc&, int, const string&, AnnotationScore); 

  void sort();

  virtual void del_temp() { }

  virtual ~DataSetAbstractProduct();

  virtual void del();

  DataStorageType* makePlaceHolders() const;

  const Prediction* getLast() const;
  iterator begin();

  const_iterator begin() const;

  const_iterator end() const;

  iterator end();

  unsigned size() const;

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

  virtual void print(std::ostream&, const string&) const;

  void insert(Prediction*);
  void sort_insert(Prediction*);

  virtual void add_introns();

  const Prediction* getClosestEnd3Exon(int,int) const;
  int getClosestEnd5(int) const;

  const Prediction* getClosestEnd5Exon(int) const;

  void getRelatedPrediction(int,int,std::list<const Prediction*>&) const;
  void getRelatedPrediction5(int,std::list<const Prediction*>&) const;

  void getRelatedPrediction3(int,std::list<const Prediction*>&) const;

  /* not used right now */
  pair<const Prediction*,const Prediction*>
    getRelatedPredictionInterval(int,int) const;

  pair<const Prediction*,const Prediction*>
    getIntronBoundaries(int,int) const;

  const Prediction* getRelatedPrediction(int) const;

  int getListPos(const Prediction*) const;

protected:
  virtual void add_introns_help();

    /*# DataSetAbstractFactory _dataSetAbstractFactory; */

    /*# AnonDataSet _anonDataSet; */

    DataStorageType lnkSeqLoc;
};

#endif //DATASETABSTRACTPRODUCT_H