BioProteinSequenceGlobalAlignment.h

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#ifndef BIOPROTEINSEQUENCEGLOBALALIGNMENT_H
#define BIOPROTEINSEQUENCEGLOBALALIGNMENT_H

#include <string>
#include "BioProteinSequence.h"
#include "BioSwissProt.h"
#include "BioFasta.h"
#include "BioProteinSequenceAlignment.h"

class BioProteinSequenceGlobalAlignment : public BioProteinSequenceAlignment
{
 private:
        void formAccumulationMatrix();

        void backTrack();

        void show(ostream & = cout);
 public:
       BioProteinSequenceGlobalAlignment();
//      ~BioProteinSequenceGlobalAlignment(){};

                BioProteinSequenceGlobalAlignment(BioProteinSequence,BioProteinSequence,string mat="BLOSUM62",int GP=-11,int extn=-9999);
                BioProteinSequenceGlobalAlignment(BioProteinSequence,BioProteinSequence,string,string,int GP=-11,int extn=-9999);
                BioProteinSequenceGlobalAlignment(BioProteinSequence,BioProteinSequence,int MS,int MMS,int GP=-11,int extn=-9999);
                BioProteinSequenceGlobalAlignment(BioProteinSequence,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
                BioProteinSequenceGlobalAlignment(BioProteinSequence,string,string,string,int GP=-11,int extn=-9999);
                BioProteinSequenceGlobalAlignment(BioProteinSequence,string,int MS,int MMS,int GP=-11,int extn=-9999);

    BioProteinSequenceGlobalAlignment(BioSwissProt,BioSwissProt,string mat="BLOSUM62",int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioSwissProt,BioSwissProt,string,string,int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioSwissProt,BioSwissProt,int MS,int MMS,int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioSwissProt,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioSwissProt,string,string,string,int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioSwissProt,string,int MS,int MMS,int GP=-11,int extn=-9999);


    BioProteinSequenceGlobalAlignment(BioFasta,BioFasta,string mat="BLOSUM62",int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioFasta,BioFasta,string,string,int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioFasta,BioFasta,int MS,int MMS,int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioFasta,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioFasta,string,string,string,int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(BioFasta,string,int MS,int MMS,int GP=-11,int extn=-9999);


    BioProteinSequenceGlobalAlignment(string,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
    BioProteinSequenceGlobalAlignment(string,string,string,string,int GP=-11,int extn=-9999);
          BioProteinSequenceGlobalAlignment(string,string,int MS,int MMS,int GP=-11,int extn=-9999);
                
    void showAccumulationMatrix(ostream & = cout);

    void showAlignment(ostream & = cout);

    long getNumberOfIdentities();
    long getNumberOfSimilarities();
    float getIdentity();
    float getScore();

    string getAlignedSequence1();
    string getAlignedSequence2();
        string getConsensusSequence(); //Added on 12.04.2012
};

#endif