BioDnaSequenceLocalAlignment.h

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#ifndef BIODNASEQUENCELOCLALIGNMENT_H
#define BIODNASEQUENCELOCALALIGNMENT_H

#include <iostream>
#include <fstream>
#include <string>
#include <sstream>
#include "BioUtilities.h"
#include "BioDnaSequence.h"
#include "BioFasta.h"
#include "BioDnaSequenceAlignment.h"

class BioDnaSequenceLocalAlignment : public BioDnaSequenceAlignment
{
 private:

        int localASP1,localASP2;

        void formAccumulationMatrix();

        void backTrack();

        void show(ostream & = cout);
  
 public:
       BioDnaSequenceLocalAlignment();
                BioDnaSequenceLocalAlignment(BioDnaSequence,BioDnaSequence,string,string MatName,int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioDnaSequence,string,string,string MatName,int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioDnaSequence,BioDnaSequence,string mat="IDENTITY",int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioDnaSequence,string,string mat="IDENTITY",int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioDnaSequence,BioDnaSequence,int MS,int MMS,int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioDnaSequence,string,int MS,int MMS,int GP=-50,int extn=-9999);


                BioDnaSequenceLocalAlignment(BioFasta,BioFasta,string,string MatName,int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioFasta,string,string,string MatName,int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioFasta,BioFasta,string mat="IDENTITY",int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioFasta,string,string mat="IDENTITY",int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioFasta,BioFasta,int MS,int MMS,int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(BioFasta,string,int MS,int MMS,int GP=-50,int extn=-9999);


                BioDnaSequenceLocalAlignment(string,string,string,string,int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(string,string,string mat="IDENTITY",int GP=-50,int extn=-9999);
                BioDnaSequenceLocalAlignment(string,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();
    float getIdentity();
    float getScore();

    string getAlignedSequence1();
    string getAlignedSequence2();


};

#endif