BioMultipleEmbl.h

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/***************************************************************************
                          BioMultipleEmbl.h  -  description
                             -------------------
    begin                : Wed Jun 2 2004
    copyright            : (C) 2004 by Helix Team
    email                : parisodhana@helixgenomics.com
 ***************************************************************************/
#ifndef BIOMULTIPLEEMBL_H
#define BIOMULTIPLEEMBL_H

#include <string>
#include <vector>
#include "BioEmbl.h"

using namespace std;

class BioMultipleEmbl
{
friend bool operator >(const BioMultipleEmbl& , const BioMultipleEmbl&);
friend bool operator <(const BioMultipleEmbl& , const BioMultipleEmbl&);
friend bool operator ==(const BioMultipleEmbl& , const BioMultipleEmbl&);
        vector <BioEmbl> multipleEmbl_;
   public :
        BioMultipleEmbl();
        BioMultipleEmbl(const string&);


  long getNumberOfEntries();
  long getNumberOfOccurencesOfGene(const string& );
  long getNumberOfGenomes();

  BioMultipleEmbl getEntriesByGene(const string& );
  BioMultipleEmbl getEntriesByGenomes();
  // to add 
  // BioMultipleEmbl getEntriesByOrganism(const string& );
  // vector <string > getUniqueGenes();
  // vector <string> getUniqueOrganisms(); 


        BioEmbl getEntry(long);
        BioEmbl getEntry(const string& );
        
  bool findDefinition( unsigned long i, const string& );
  bool findLocus( unsigned long i, const string& );
  bool findAccessionNumber(unsigned long i,  const string& );
 // to add 
 // bool findSource (unsigned long i, const string& ); 
  bool findOrganism( unsigned long i, const string& );
  bool findTaxanomy( unsigned long i, const string& );
  bool findKeyword( unsigned long i, const string& );

  void showInMultipleFasta(const string& );
  void showInMultipleFasta(ostream& = cout);
  void showInFasta(int, ostream& = cout);

  friend BioMultipleEmbl operator+= (BioMultipleEmbl& , BioEmbl );
  friend BioMultipleEmbl operator+( BioMultipleEmbl , BioEmbl& );
  friend BioMultipleEmbl operator+( BioEmbl&, BioEmbl&);

  void pushEntry(BioEmbl&);

};

#endif