BioProteinSequenceLocalAlignment.h

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#ifndef BIOPROTEINSEQUENCELOCALALIGNMENT_H
#define BIOPROTEINSEQUENCELOCALALIGNMENT_H

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

class BioProteinSequenceLocalAlignment : public BioProteinSequenceAlignment
{
 private:

        int localASP1,localASP2;

        void formAccumulationMatrix();

        void backTrack();

        void show(ostream & = cout);

 public:
       BioProteinSequenceLocalAlignment();
        ~BioProteinSequenceLocalAlignment();

                BioProteinSequenceLocalAlignment(BioProteinSequence,BioProteinSequence,string mat="BLOSUM62",int GP=-50,int extn=-9999);
                BioProteinSequenceLocalAlignment(BioProteinSequence,BioProteinSequence,string,string,int GP=-50,int extn=-9999);
                BioProteinSequenceLocalAlignment(BioProteinSequence,BioProteinSequence,int MS,int MMS,int GP=-50,int extn=-9999);
                BioProteinSequenceLocalAlignment(BioProteinSequence,string,string mat="BLOSUM62",int GP=-50,int extn=-9999);
                BioProteinSequenceLocalAlignment(BioProteinSequence,string,string,string,int GP=-50,int extn=-9999);
                BioProteinSequenceLocalAlignment(BioProteinSequence,string,int MS,int MMS,int GP=-50,int extn=-9999);

    BioProteinSequenceLocalAlignment(BioSwissProt,BioSwissProt,string mat="BLOSUM62",int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioSwissProt,BioSwissProt,string,string,int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioSwissProt,BioSwissProt,int MS,int MMS,int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioSwissProt,string,string mat="BLOSUM62",int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioSwissProt,string,string,string,int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioSwissProt,string,int MS,int MMS,int GP=-50,int extn=-9999);


    BioProteinSequenceLocalAlignment(const BioFasta&,const BioFasta&,const string& mat="BLOSUM62",const int& GP=-50,const int& extn=-9999);
    BioProteinSequenceLocalAlignment(BioFasta,BioFasta,string,string,int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioFasta,BioFasta,int MS,int MMS,int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioFasta,string,string mat="BLOSUM62",int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioFasta,string,string,string,int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(BioFasta,string,int MS,int MMS,int GP=-50,int extn=-9999);


    BioProteinSequenceLocalAlignment(const string&,const string&,const string& mat="BLOSUM62",int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(const string&,const string&,const string&,const string&,int GP=-50,int extn=-9999);
    BioProteinSequenceLocalAlignment(const string&,const string&,int MS,int MMS,int GP=-50,int extn=-9999);
                
    void showAccumulationMatrix(ostream & = cout);
    void showAlignment(ostream & = cout);

    long  getSequence1AlignedPosition();
    long getSequence2AlignedPosition();

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

    string getAlignedSequence1();
    string getAlignedSequence2();
};

#endif