BioRestrictionMap.h

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#ifndef BIORESTRICTIONMAP_H
#define BIORESTRICTIONMAP_H


#include <iostream>
#include <string>
#include <vector>
#include <map>

#include "BioUtilities.h"
#include "BioDnaSequence.h"
#include "BioRaw.h"
#include "BioFasta.h"
#include "BioRestrictionEnzymeLibrary.h"

using namespace std;

class BioRestrictionMap
{
       friend bool operator >(const BioRestrictionMap& , const BioRestrictionMap&);
       friend bool operator <(const BioRestrictionMap& , const BioRestrictionMap&);
       friend bool operator ==(const BioRestrictionMap& , const BioRestrictionMap&);

  string sequence;
  string sequenceName;
  vector <string> restrictionEnzymeNames, RENAll;
  vector <int> reIndex, reIndexAll; //RESTRICTION ENZYME INDEX
  vector <vector <int> > rePos, resPosAll; // RESTRICTIONS ENZYME POSITIONs
  bool status, all;
  map <string,string> dnaAmb;

  void formRestrictionMap();
  void formRestrictionMapAll();
  void init();
  vector < int > processREs(string REs);
  
  public:

     BioRestrictionMap(); // A default constructor
     BioRestrictionMap(BioDnaSequence dnaSeq, string restrictionEnzymeName);
     BioRestrictionMap(BioFasta obj,string restrictionEnzymeName);
     BioRestrictionMap(BioRaw obj,string restrictionEnzymeName);
    ~BioRestrictionMap(); // destructor
    void setSequence(BioDnaSequence dnaSeq);
    void setSequence(BioFasta obj);
    void setSequence(BioRaw obj);

    void setRestrictionEnzyme(string restrictionEnzymeName);

    void addRestrictionEnzyme(string restrictionEnzymeName);

    int getNumberOfRestrictionEnzymes();
    string getRestrictionEnzyme( int   indexRE );     
    int getRestrictionEnzymeIndex(string REName);

    vector < int > getRestrictedPositions( int indexRE );
    vector < int > getRestrictedPositions( string REs);

// this gives the REMap with all the SET REs for this Object.
// Map showing all the REs available in the DB of BOS.
//Indeces of the REs which should be used for getting the Fragments, if it is ALL then
// it'll displays all the Restricted Fragments for all the REs in the Database

     void showRestrictionMap(ostream & fout = cout);     
     void showRestrictionMap(string REs, ostream & fout = cout);
//     void showRestrictionMap(string REs, BioPostScript ps );
//     void showRestrictionMap(string REs,BioHtml bh);

     void showRestrictionMap(int indexRE, ostream & fout = cout); // the Map of ONLY the Indexed RE set.
//     void showRestrictionMap(int indexRE, BioPostScript ps);
//     void showRestrictionMap(int indexRE, BioHtml bh);



//Indeces of the REs which should be used for getting the Fragments, if it is ALL then
// it'll displays all the Restricted Fragments for all the REs in the Database

     vector <string> getRestrictionEnzymeList(int occurrences);
     vector <string> getRestrictionEnzymeList(string occurrences);

     vector <string> getRestrictedFragments(int indexRE = 0 );
     vector <string> getRestrictedFragments(string REs);
     int getNumberOfRestrictedFragments(int indexRE);
     int getNumberOfRestrictedFragments(string REs);
};

#endif